Advances in cellular immunotherapy promise new treatments for conditions such as cancer, autoimmune disease, and heart disease. While engineered cells have the ability to recognize clinically relevant signals, traffic to disease sites and interface with the host immune system, their activity must be tightly controlled to minimize undesirable effects in healthy tissues. One approach to obtaining specificity is to activate the cells spatially using externally applied energy, such as ultrasound-delivered heating. To facilitate such control, we designed and characterized a genetic circuit that enables stable transcriptional activation of macrophages after a brief thermal stimulus, resulting in the expression of reporters or secretion of the cytokine IL-12. We demonstrate that in vivo activation of a mouse macrophage cell line containing this bioswitch results in spatially localized gene expression for at least 14 days after ultrasound heating. This thermal bioswitch provides a precise control element for cell-therapeutic agents.
", "doi": "10.1021/acssynbio.5c00395", "pmcid": "PMC12645579", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2025-11-21", "series_number": "11", "volume": "14", "issue": "11", "pages": "4304-4313" }, { "id": "authors:j8478-j3615", "collection": "authors", "collection_id": "j8478-j3615", "cite_using_url": "https://authors.library.caltech.edu/records/j8478-j3615", "type": "article", "title": "Sono-uncaging for Spatiotemporal Control of Chemical Reactivity", "author": [ { "family_name": "Schrunk", "given_name": "Erik", "orcid": "0009-0003-2002-7411", "clpid": "Schrunk-Erik" }, { "family_name": "Lee", "given_name": "Sunho", "orcid": "0009-0008-9871-7929", "clpid": "Lee-Sunho" }, { "family_name": "Dutka", "given_name": "Przemys\u0142aw", "orcid": "0000-0003-3819-1618", "clpid": "Dutka-Przemys\u0142aw" }, { "family_name": "Wu", "given_name": "Di", "orcid": "0000-0002-6848-668X", "clpid": "Wu-Di" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Photo-uncaging\u2500the use of light to reveal the active part of a chemical compound by photolysis of a protecting group\u2500has long been used to study and actuate biochemical processes. However, light scattering limits the applications of photo-uncaging in opaque specimens or tissues. Here, we introduce sono-uncaging, a process in which a chemical functional group becomes exposed upon the application of ultrasound, which can be applied and focused in optically opaque materials. We engineered gas vesicles (GVs), air-filled protein nanostructures sensitive to ultrasound, to contain cysteines on their concealed inner surface, hypothesizing that the application of ultrasound would collapse the GV shell and reveal the cysteines. The resulting SonoCage construct reacted with monobromobimane (mBBr), a fluorogenic, thiol-reactive molecule, only after treatment with ultrasound, establishing the sono-uncaging proof of concept. We then demonstrated the spatial patterning capability of sono-uncaging by embedding the SonoCages in an mBBr-containing hydrogel and creating fluorescent patterns with phased array ultrasound. This patterning could be accomplished using a diagnostic imaging transducer with mild ultrasound conditions. This work establishes sono-uncaging as a method for spatiotemporal control over chemical reactivity using widely available ultrasound technology.", "doi": "10.1021/jacs.5c09181", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2025-10-01", "series_number": "39", "volume": "147", "issue": "39", "pages": "35422-35430" }, { "id": "authors:bzwzt-bxs70", "collection": "authors", "collection_id": "bzwzt-bxs70", "cite_using_url": "https://authors.library.caltech.edu/records/bzwzt-bxs70", "type": "article", "title": "Probiotic acoustic biosensors for noninvasive imaging of gut inflammation", "author": [ { "family_name": "Buss", "given_name": "Marjorie T.", "orcid": "0000-0002-4266-9197", "clpid": "Buss-Marjorie-T" }, { "family_name": "Zhu", "given_name": "Lian", "orcid": "0000-0001-8043-2038", "clpid": "Zhu-Lian" }, { "family_name": "Kwon", "given_name": "Jamie H.", "clpid": "Kwon-Jaime-H" }, { "family_name": "Tabor", "given_name": "Jeffrey J.", "orcid": "0000-0001-7316-0361", "clpid": "Tabor-Jeffrey-J" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Inflammatory bowel diseases (IBD) affect millions of people globally, result in severe symptoms, and are difficult to diagnose and monitor – often necessitating the use of invasive and costly methods such as colonoscopies or endoscopies. Engineered gut bacteria offer a promising alternative due to their ability to persist in the gastrointestinal (GI) tract and sense and respond to specific environmental signals. However, probiotics that have previously been engineered to report on inflammatory and other disease biomarkers in the Gl tract rely on fluorescent or bioluminescent reporters, whose signals cannot be resolved in situ due to the poor penetration of light in tissue, or on colorimetric reporters which rely on plating feces. To overcome this limitation, we introduce probiotic biosensors that can be imaged in situ using ultrasound – a widely available, inexpensive imaging modality providing sub-mm spatial resolution deep inside the body. These biosensors are based on the clinically approved probiotic bacterium E. coli Nissle, which we engineered to transiently colonize the GI tract, sense inflammatory biomarkers, and respond by expressing air-filled sound-scattering protein nanostructures called gas vesicles. After optimizing biomolecular signaling circuits to respond sensitively to the biomarkers thiosulfate and tetrathionate and produce strong and stable ultrasound contrast, we validated our living biosensors in vivo by noninvasively imaging antibiotic-induced inflammation in mice. By connecting cell-based diagnostic agents to ultrasound, these probiotic biosensors will potentially make it easier and cheaper to diagnose and monitor IBD or other GI conditions.
", "doi": "10.1038/s41467-025-62569-1", "pmcid": "PMC12379287", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2025-08-25", "series_number": "1", "volume": "16", "issue": "1", "pages": "7931" }, { "id": "authors:86jw7-7g669", "collection": "authors", "collection_id": "86jw7-7g669", "cite_using_url": "https://authors.library.caltech.edu/records/86jw7-7g669", "type": "article", "title": "Amplitude-Modulated Singular Value Decomposition for Ultrafast Ultrasound Imaging of Gas Vesicles", "author": [ { "family_name": "Zhang", "given_name": "Ge", "orcid": "0009-0008-1617-5602" }, { "family_name": "Vert", "given_name": "Mathis" }, { "family_name": "Nouhoum", "given_name": "Mohamed" }, { "family_name": "Rivera", "given_name": "Esteban" }, { "family_name": "Haidour", "given_name": "Nabil" }, { "family_name": "Jimenez", "given_name": "Anatole" }, { "family_name": "Deffieux", "given_name": "Thomas" }, { "family_name": "Barral", "given_name": "Simon" }, { "family_name": "Hersen", "given_name": "Pascal", "orcid": "0000-0003-2379-4280" }, { "family_name": "Pezet", "given_name": "Sophie" }, { "family_name": "Rabut", "given_name": "Claire", "orcid": "0000-0002-4571-1215", "clpid": "Rabut-Claire" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Tanter", "given_name": "Mickael", "orcid": "0000-0001-7739-8051" } ], "abstract": "Ultrasound imaging holds significant promise for the observation of molecular and cellular phenomena through the utilization of acoustic contrast agents and acoustic reporter genes. Optimizing imaging methodologies for enhanced detection represents an imperative advancement in this field. Most advanced techniques relying on amplitude modulation schemes such as cross amplitude modulation (xAM) and ultrafast amplitude modulation (uAM) combined with Hadamard encoded multiplane wave transmissions have shown efficacy in capturing the acoustic signals of gas vesicles (GVs). Nonetheless, uAM sequence requires odd- or even-element transmissions leading to imprecise amplitude modulation emitting scheme, and the complex multiplane wave transmission scheme inherently yields overlong pulse durations. xAM sequence is limited in terms of field of view and imaging depth. To overcome these limitations, we introduce an innovative ultrafast imaging sequence called amplitude-modulated singular value decomposition (SVD) processing. Our method demonstrates a contrast imaging sensitivity comparable to the current gold-standard xAM and uAM, while requiring 4.8 times fewer pulse transmissions. With a similar number of transmit pulses, amplitude-modulated SVD outperforms xAM and uAM in terms of an improvement in signal-to-background ratio of +4.78 ±0.35 dB and +8.29 ±3.52 dB, respectively. Furthermore, the method exhibits superior robustness across a wide range of acoustic pressures and enables high-contrast imaging in ex vivo and in vivo settings. Furthermore, amplitude-modulated SVD is envisioned to be applicable for the detection of slow moving microbubbles in ultrasound localization microscopy (ULM).
", "doi": "10.1109/tmi.2025.3565023", "issn": "0278-0062", "publisher": "IEEE", "publication": "IEEE Transactions on Medical Imaging", "publication_date": "2025-08", "series_number": "8", "volume": "44", "issue": "8", "pages": "3490-3501" }, { "id": "authors:m5t7p-7v471", "collection": "authors", "collection_id": "m5t7p-7v471", "cite_using_url": "https://authors.library.caltech.edu/records/m5t7p-7v471", "type": "article", "title": "In Vivo Cytosolic Delivery of Biomolecules into Neurons for Super\u2010Resolution Imaging and Genome Modification", "author": [ { "family_name": "Ge", "given_name": "Xiaoqian" }, { "family_name": "Wekselblatt", "given_name": "Joseph B.", "orcid": "0000-0002-0915-313X", "clpid": "Wekselblatt-Joseph-B" }, { "family_name": "Elmore", "given_name": "Scott" }, { "family_name": "Wang", "given_name": "Bo", "orcid": "0000-0002-1310-869X", "clpid": "Wang-Bo" }, { "family_name": "Wang", "given_name": "Tongtong", "clpid": "Wang-Tongtong" }, { "family_name": "Dai", "given_name": "Renjinming" }, { "family_name": "Zhang", "given_name": "Tingting" }, { "family_name": "Dave", "given_name": "Harsh" }, { "family_name": "Ghaderi", "given_name": "Mohammadaref" }, { "family_name": "Anilkumar", "given_name": "Athul Raj" }, { "family_name": "Wang", "given_name": "Bill" }, { "family_name": "Sirsi", "given_name": "Shashank R." }, { "family_name": "Ahn", "given_name": "Jung\u2010Mo" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Oka", "given_name": "Yuki", "orcid": "0000-0003-2686-0677", "clpid": "Oka-Yuki" }, { "family_name": "Lois", "given_name": "Carlos", "orcid": "0000-0002-7305-2317", "clpid": "Lois-Carlos" }, { "family_name": "Qin", "given_name": "Zhenpeng", "orcid": "0000-0003-3406-3045" } ], "abstract": "Efficient delivery of biomolecules into neurons has significant impacts on therapeutic applications in the central nervous system (CNS) and fundamental neuroscience research. Existing viral and non-viral delivery methods often suffer from inefficient intracellular access due to the endocytic pathway. Here, a neuron-targeting and direct cytosolic delivery platform is discovered by using a 15-amino-acid peptide, termed the N1 peptide, which enables neuron-specific targeting and cytosolic delivery of functional biomolecules. The N1 peptide initially binds hyaluronan in the extracellular matrix and subsequently passes the membrane of neurons without being trapped into endosome. This mechanism facilitates the efficient delivery of cell-impermeable and photo-stable fluorescent dye for super-resolution imaging of dendritic spines, and functional proteins, such as Cre recombinase, for site-specific genome modification. Importantly, the N1 peptide exhibits robust neuronal specificity across diverse species, including mice, rats, tree shrews, and zebra finches. Its targeting capability is further demonstrated through various administration routes, including intraparenchymal, intrathecal, and intravenous (i.v.) injections after blood-brain barrier (BBB) opening with focused ultrasound (FUS). These findings establish the N1 peptide as a versatile and functional platform with significant potential for bioimaging and advanced therapeutic applications.
", "doi": "10.1002/advs.202501033", "pmcid": "PMC12224921", "issn": "2198-3844", "publisher": "Wiley", "publication": "Advanced Science", "publication_date": "2025-07-03", "series_number": "25", "volume": "12", "issue": "25", "pages": "2501033" }, { "id": "authors:cd6hm-s7c12", "collection": "authors", "collection_id": "cd6hm-s7c12", "cite_using_url": "https://authors.library.caltech.edu/records/cd6hm-s7c12", "type": "article", "title": "The Binding Affinities of Serum Proteins to Nanoparticles", "author": [ { "family_name": "Stordy", "given_name": "Benjamin P.", "orcid": "0000-0002-1096-3287" }, { "family_name": "Sepahi", "given_name": "Zahra" }, { "family_name": "Patr\u00f3n", "given_name": "Gabriel D.", "orcid": "0000-0001-5241-1416" }, { "family_name": "Yang", "given_name": "Wei" }, { "family_name": "Goodson", "given_name": "Alexander D.", "orcid": "0000-0002-5301-3695" }, { "family_name": "Blackadar", "given_name": "Colin", "orcid": "0000-0002-3847-3693" }, { "family_name": "Tavares", "given_name": "Anthony J." }, { "family_name": "Lin", "given_name": "Guanyou" }, { "family_name": "Malekjahani", "given_name": "Ayden" }, { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Ravichandran", "given_name": "Rashmi" }, { "family_name": "Hicks", "given_name": "Derrick R." }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Zhang", "given_name": "Miqin" }, { "family_name": "King", "given_name": "Neil P.", "orcid": "0000-0002-2978-4692" }, { "family_name": "Baker", "given_name": "David" }, { "family_name": "Ricardez-Sandoval", "given_name": "Luis A.", "orcid": "0000-0001-9867-6778" }, { "family_name": "Chan", "given_name": "Warren C. W.", "orcid": "0000-0001-5435-4785" } ], "abstract": "Nanoparticles can be coated with targeting ligands to deliver medical agents to specific cells. Serum protein adsorption affects the binding of nanoparticles to target cells. We hypothesized that serum proteins and target receptors compete for binding to nanoparticles. We tested the serum protein binding affinity of 251 nanoparticle designs. Here, we discovered that the binding affinities of serum proteins and receptors to a nanoparticle determine whether it can bind to target cells. We developed and validated a quantitative metric, the binding ratio, to identify nanoparticle designs that can bind to targets in serum with 90% sensitivity and 88% specificity. Using the binding ratio as a numerical guideline for nanoparticle design enabled us to improve the efficiency of nanoparticle binding to target cellular receptors.
", "doi": "10.1021/jacs.5c02576", "pmcid": "PMC12661649", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2025-06-18", "series_number": "24", "volume": "147", "issue": "24", "pages": "20475-20492" }, { "id": "authors:d160t-54k35", "collection": "authors", "collection_id": "d160t-54k35", "cite_using_url": "https://authors.library.caltech.edu/records/d160t-54k35", "type": "article", "title": "Acoustic percolation switches enable targeted drug delivery controlled by diagnostic ultrasound", "author": [ { "family_name": "Abundo", "given_name": "Maria Paulene", "orcid": "0000-0002-5122-6937", "clpid": "Abundo-Maria-Paulene" }, { "family_name": "Tifrea", "given_name": "Anna T.", "orcid": "0000-0002-5429-3131", "clpid": "Tifrea-Anna-T" }, { "family_name": "Buss", "given_name": "Marjorie T.", "orcid": "0000-0002-4266-9197", "clpid": "Buss-Marjorie-T" }, { "family_name": "Barturen-Larrea", "given_name": "Pierina", "orcid": "0000-0002-6076-5801", "clpid": "Barturen-Larrea-Pierina" }, { "family_name": "Jin", "given_name": "Zhiyang", "orcid": "0000-0002-4411-6991", "clpid": "Jin-Zhiyang" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Delivering biomedicines to specific sites of disease using remote-controlled devices is a long-standing vision in biomedical research. However, most existing externally triggered delivery systems are based on complex micromachines that are controlled with electromagnetic waves and require custom external instrumentation. Here, we present a drug delivery platform based on a simple protein-containing hydrogel that can be both imaged and triggered to release drugs at specific locations using widely available diagnostic ultrasound devices. This technology is based on the addition of air-filled protein nanostructures called gas vesicles (GVs) to hydrogel delivery vehicles. While intact, GVs sterically block the release of drug payloads and allow the vehicle to be imaged with ultrasound. An increase in ultrasound pressure causes the collapse of GVs within the delivery vehicles at the desired anatomical location, instantly creating percolation channels in the hydrogel, massively increasing diffusivity, and leading to rapid drug release. Unlike previous ultrasound-actuated delivery approaches, both the imaging and release are performed using a simple diagnostic ultrasound probe ubiquitously available in clinical settings. We implement this concept by quantifying ultrasound-controlled drug diffusion and release in vitro and demonstrating image-guided protein delivery in vivo in the gastrointestinal (GI) tract following oral administration. We further validate this technology by using it to deliver anti-inflammatory antibodies to effectively treat a rat model of colitis. Targeted acoustic percolation switches (TAPS) open a conduit for local, image-guided drug delivery with a simple formulation and commonplace ultrasound equipment.
", "doi": "10.1073/pnas.2423078122", "pmcid": "PMC12107142", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2025-05-20", "series_number": "20", "volume": "122", "issue": "20", "pages": "e2423078122" }, { "id": "authors:60nwz-7bb48", "collection": "authors", "collection_id": "60nwz-7bb48", "cite_using_url": "https://authors.library.caltech.edu/records/60nwz-7bb48", "type": "article", "title": "Achieving single cell acoustic localisation with deactivation super resolution", "author": [ { "family_name": "Smith", "given_name": "Cameron A. B.", "clpid": "Smith-Cameron-A-B" }, { "family_name": "Duan", "given_name": "Mengtong", "orcid": "0000-0002-1601-8876", "clpid": "Duan-Mengtong-Tom" }, { "family_name": "Yan", "given_name": "Jipeng" }, { "family_name": "Taylor", "given_name": "Laura" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Tang", "given_name": "Meng-Xing" } ], "abstract": "Photo-activated localization microscopy (PALM) has been a game-changer, breaking the diffraction limit in spatial resolution. This study presents the Deactivation Super Resolution (DSR) method, which utilises the deactivation of genetically encodable contrast agents, enabling us to super-resolve and pinpoint individual cells with ultrasound as they navigate through structures which cannot be resolved by conventional B-Mode imaging. DSR takes advantage of Gas Vesicles (GVs), which are air-filled sub-micron particles that have been expressed in genetically engineered bacterial and mammalian cells to produce acoustic contrast. Our experimental results show that DSR can distinguish sub-wavelength microstructures that standard B-mode ultrasound images fail to resolve by super-localising individual mammalian cells. This study provides a proof of concept for the potential of DSR to serve as a super-resolution ultrasound technique for individual cell localisation, opening new horizons in the field.
", "doi": "10.1038/s44384-025-00008-7", "issn": "3005-141X", "publisher": "Nature Publishing Group", "publication": "npj Acoustics", "publication_date": "2025-04-24", "series_number": "1", "volume": "1", "issue": "1", "pages": "5" }, { "id": "authors:46jcm-4zq19", "collection": "authors", "collection_id": "46jcm-4zq19", "cite_using_url": "https://authors.library.caltech.edu/records/46jcm-4zq19", "type": "article", "title": "Nonlinear sound-sheet microscopy: Imaging opaque organs at the capillary and cellular scale", "author": [ { "family_name": "Heiles", "given_name": "Baptiste", "orcid": "0000-0001-9254-1741" }, { "family_name": "Nelissen", "given_name": "Flora", "orcid": "0009-0004-5478-8283" }, { "family_name": "Waasdorp", "given_name": "Rick", "orcid": "0000-0002-9476-6538" }, { "family_name": "Terwiel", "given_name": "Dion", "orcid": "0000-0001-9899-6341" }, { "family_name": "Park", "given_name": "Byung Min", "orcid": "0000-0001-6965-3630" }, { "family_name": "Ibarra", "given_name": "Eleonora Munoz", "orcid": "0000-0002-9135-5944" }, { "family_name": "Matalliotakis", "given_name": "Agisilaos" }, { "family_name": "Ara", "given_name": "Tarannum", "orcid": "0009-0003-6302-515X" }, { "family_name": "Barturen-Larrea", "given_name": "Pierina", "orcid": "0000-0001-8409-7986", "clpid": "Barturen-Larrea-Pierina" }, { "family_name": "Duan", "given_name": "Mengtong", "orcid": "0000-0002-1601-8876", "clpid": "Duan-Mengtong" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Gazzola", "given_name": "Valeria", "orcid": "0000-0003-0324-0619" }, { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406" } ], "abstract": "Light-sheet fluorescence microscopy has revolutionized biology by visualizing dynamic cellular processes in three dimensions. However, light scattering in thick tissue and photobleaching of fluorescent reporters limit this method to studying thin or translucent specimens. In this study, we applied nondiffractive ultrasound beams in conjunction with a cross-amplitude modulation sequence and nonlinear acoustic reporters to enable fast and volumetric imaging of targeted biological functions. We reported volumetric imaging of tumor gene expression at the cubic centimeter scale using genetically encoded gas vesicles and localization microscopy of cerebral capillary networks using intravascular microbubble contrast agents. Nonlinear sound-sheet microscopy provides a ~64× acceleration in imaging speed, ~35× increase in imaged volume, and ~4× increase in classical imaging resolution compared with the state of the art in biomolecular ultrasound.
", "doi": "10.1126/science.ads1325", "pmcid": "PMC12661648", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2025-04-04", "series_number": "6742", "volume": "388", "issue": "6742", "pages": "eads1325" }, { "id": "authors:6fx9y-j4k93", "collection": "authors", "collection_id": "6fx9y-j4k93", "cite_using_url": "https://authors.library.caltech.edu/records/6fx9y-j4k93", "type": "article", "title": "Harmonic imaging for nonlinear detection of acoustic biomolecules", "author": [ { "family_name": "Nayak", "given_name": "Rohit", "orcid": "0000-0002-4353-6951", "clpid": "Nayak-Rohit" }, { "family_name": "Duan", "given_name": "Mengtong", "orcid": "0000-0002-1601-8876", "clpid": "Duan-Mengtong" }, { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Jin", "given_name": "Zhiyang", "orcid": "0000-0002-4411-6991", "clpid": "Jin-Zhiyang" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Gas vesicles (GVs) based on acoustic reporter genes have emerged as potent contrast agents for cellular and molecular ultrasound imaging. These air-filled, genetically encoded protein nanostructures can be expressed in a variety of cell types in vivo to visualize cell location and activity or injected systemically to label and monitor tissue function. Distinguishing GV signal from tissue deep inside intact organisms requires imaging approaches such as amplitude modulation (AM) or collapse-based pulse sequences. However, these approaches have limitations either in sensitivity or require the destruction of GVs, restricting the imaging of dynamic cellular processes. To address these limitations, we developed harmonic imaging to enhance the sensitivity of nondestructive GV imaging. We hypothesized that harmonic imaging, integrated with AM, could significantly elevate GV detection sensitivity by leveraging the nonlinear acoustic response of GVs. We tested this hypothesis by imaging tissue-mimicking phantoms embedded with purified GVs, mammalian cells genetically modified to express GVs, and mice liver in vivo post-systemic infusion of GVs. Our findings reveal that harmonic cross-propagating wave AM (HxAM) imaging markedly surpasses traditional xAM in isolating GVs' nonlinear acoustic signature, demonstrating significant (p\u2009<\u20090.05) enhancements in imaging performance. HxAM imaging improves detection of GV producing cells up to three folds in vitro, enhances in vivo imaging performance by over 10\u2009dB, while extending imaging depth by up to 20%. Investigation into the backscattered spectra further elucidates the advantages of harmonic imaging. These advancements bolster ultrasound's capability in molecular and cellular imaging, underscoring the potential of harmonic signals to improve GV detection.", "doi": "10.1063/5.0214306", "issn": "2473-2877", "publisher": "American Institute of Physics", "publication": "APL Bioengineering", "publication_date": "2024-12", "series_number": "4", "volume": "8", "issue": "4", "pages": "046110" }, { "id": "authors:3gkmd-rqq82", "collection": "authors", "collection_id": "3gkmd-rqq82", "cite_using_url": "https://authors.library.caltech.edu/records/3gkmd-rqq82", "type": "article", "title": "Imaging-guided bioresorbable acoustic hydrogel microrobots", "author": [ { "family_name": "Han", "given_name": "Hong", "orcid": "0000-0002-2852-8662", "clpid": "Han-Hong" }, { "family_name": "Ma", "given_name": "Xiaotian", "orcid": "0009-0000-8357-9916", "clpid": "Ma-Xiaotian" }, { "family_name": "Deng", "given_name": "Weiting", "orcid": "0000-0003-0984-8027", "clpid": "Deng-Weiting" }, { "family_name": "Zhang", "given_name": "Junhang", "orcid": "0000-0002-7847-3102" }, { "family_name": "Tang", "given_name": "Songsong", "orcid": "0000-0003-4699-6563", "clpid": "Tang-Songsong" }, { "family_name": "Pak", "given_name": "On Shun", "orcid": "0000-0003-1510-7049" }, { "family_name": "Zhu", "given_name": "Lailai", "orcid": "0000-0002-3443-0709" }, { "family_name": "Criado-Hidalgo", "given_name": "Ernesto", "orcid": "0000-0001-9086-9129", "clpid": "Criado-Hidalgo-Ernesto" }, { "family_name": "Gong", "given_name": "Chen", "orcid": "0000-0002-6262-704X" }, { "family_name": "Karshalev", "given_name": "Emil", "orcid": "0000-0001-7802-6153", "clpid": "Karshalev-Emil" }, { "family_name": "Yoo", "given_name": "Jounghyun", "orcid": "0000-0003-4253-2382" }, { "family_name": "You", "given_name": "Ming", "clpid": "You-Ming" }, { "family_name": "Liu", "given_name": "Ann", "orcid": "0000-0002-0908-3506", "clpid": "Liu-Ann" }, { "family_name": "Wang", "given_name": "Canran", "orcid": "0000-0003-3297-9041", "clpid": "Wang-Canran" }, { "family_name": "Shen", "given_name": "Hao K.", "orcid": "0000-0003-2687-0736", "clpid": "Shen-Hao-K" }, { "family_name": "Patel", "given_name": "Payal N.", "clpid": "Patel-Payal-N" }, { "family_name": "Hays", "given_name": "Claire L.", "orcid": "0009-0006-9312-9816", "clpid": "Hays-Claire-L" }, { "family_name": "Gunnarson", "given_name": "Peter J.", "orcid": "0000-0002-4437-5379", "clpid": "Gunnarson-Peter-J" }, { "family_name": "Li", "given_name": "Lei", "orcid": "0000-0001-6164-2646", "clpid": "Li-Lei" }, { "family_name": "Zhang", "given_name": "Yang", "orcid": "0000-0002-4533-4325", "clpid": "Zhang-Yang" }, { "family_name": "Dabiri", "given_name": "John Oluseun", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" }, { "family_name": "Wang", "given_name": "Lihong V.", "orcid": "0000-0001-9783-4383", "clpid": "Wang-Lihong-V" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Wu", "given_name": "Di", "orcid": "0000-0002-6848-668X", "clpid": "Wu-Di" }, { "family_name": "Zhou", "given_name": "Qifa", "orcid": "0000-0003-1527-3020" }, { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" }, { "family_name": "Gao", "given_name": "Wei", "orcid": "0000-0002-8503-4562", "clpid": "Gao-Wei" } ], "abstract": "Micro- and nanorobots excel in navigating the intricate and often inaccessible areas of the human body, offering immense potential for applications such as disease diagnosis, precision drug delivery, detoxification, and minimally invasive surgery. Despite their promise, practical deployment faces hurdles, including achieving stable propulsion in complex in vivo biological environments, real-time imaging and localization through deep tissue, and precise remote control for targeted therapy and ensuring high therapeutic efficacy. To overcome these obstacles, we introduce a hydrogel-based, imaging-guided, bioresorbable acoustic microrobot (BAM) designed to navigate the human body with high stability. Constructed using two-photon polymerization, a BAM comprises magnetic nanoparticles and therapeutic agents integrated into its hydrogel matrix for precision control and drug delivery. The microrobot features an optimized surface chemistry with a hydrophobic inner layer to substantially enhance microbubble retention in biofluids with multiday functionality and a hydrophilic outer layer to minimize aggregation and promote timely degradation. The dual-opening bubble-trapping cavity design enables a BAM to maintain consistent and efficient acoustic propulsion across a range of biological fluids. Under focused ultrasound stimulation, the entrapped microbubbles oscillate and enhance the contrast for real-time ultrasound imaging, facilitating precise tracking and control of BAM movement through wireless magnetic navigation. Moreover, the hydrolysis-driven biodegradability of BAMs ensures its safe dissolution after treatment, posing no risk of long-term residual harm. Thorough in vitro and in vivo experimental evidence demonstrates the promising capabilities of BAMs in biomedical applications. This approach shows promise for advancing minimally invasive medical interventions and targeted therapeutic delivery.", "doi": "10.1126/scirobotics.adp3593", "issn": "2470-9476", "publisher": "American Association for the Advancement of Science", "publication": "Science Robotics", "publication_date": "2024-12", "series_number": "97", "volume": "9", "issue": "97" }, { "id": "authors:g6zm8-meg23", "collection": "authors", "collection_id": "g6zm8-meg23", "cite_using_url": "https://authors.library.caltech.edu/records/g6zm8-meg23", "type": "article", "title": "A 14.8- \u03bc W Power and < 10 \u03bc T \u1d63\u2098\u209b Noise 3-D AC Magnetic Sensor in CMOS for Biomedical Applications", "author": [ { "family_name": "Sharma", "given_name": "Saransh", "orcid": "0000-0002-5052-4932", "clpid": "Sharma-Saransh" }, { "family_name": "Melton", "given_name": "Hayward", "clpid": "Melton-Hayward-J" }, { "family_name": "Edmonds", "given_name": "Liliana B.", "orcid": "0000-0002-2068-3334" }, { "family_name": "Addington", "given_name": "Olivia", "clpid": "Addington-Olivia" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Emami", "given_name": "Azita", "orcid": "0000-0002-6945-9958", "clpid": "Emami-A" } ], "abstract": "Magnetic sensors are used extensively in applications related to automotives, navigation, medical electronics, and consumer products. Hall sensors are commonly used due to their compatibility with the standard CMOS process but suffer from poor 3-D sensitivity and consume high power. Here, we present the first-of-its-kind 3-D ac magnetic sensor in the CMOS process with high-resolution and ultralow-power operation. The sensor is comprised of three orthogonal and highly dense metal coils ( X , Y , and Z ) implemented in the 65-nm node, which generate a voltage in response to ac magnetic fields by electromagnetic induction. The X and Y sensor coils are realized in the vertical plane of the CMOS chip by using interconnect vias as part of the coil structure, while the Z sensor is realized in the horizontal plane. The induced voltage by the three coils is processed by a low-noise instrumentation amplifier (IA), sharp bandpass filter (BPF), programmable gain amplifier (PGA), differential peak detect and hold circuit, 12-bit successive approximation register (SAR) analog-to-digital converter (ADC), and serializer. The entire circuitry consumes only 14.8 μ W to yield μ T-level resolution. The sensor is successfully demonstrated for 3-D localization and tracking of catheters with 500- μ m mean accuracy in a surgical operation room (OR), which shows significant potential toward clinical translation.
", "doi": "10.1109/jssc.2024.3482268", "issn": "0018-9200", "publisher": "IEEE", "publication": "IEEE Journal of Solid-State Circuits", "publication_date": "2024-10-31", "pages": "1-12" }, { "id": "authors:09eq8-exa47", "collection": "authors", "collection_id": "09eq8-exa47", "cite_using_url": "https://authors.library.caltech.edu/records/09eq8-exa47", "type": "article", "title": "Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening", "author": [ { "family_name": "Hurt", "given_name": "Robert C.", "orcid": "0000-0002-4347-6901", "clpid": "Hurt-Robert-C" }, { "family_name": "Jin", "given_name": "Zhiyang", "orcid": "0000-0002-4411-6991", "clpid": "Jin-Zhiyang" }, { "family_name": "Soufi", "given_name": "Mohamed", "orcid": "0009-0000-3447-2178", "clpid": "Soufi-Mohamed" }, { "family_name": "Wong", "given_name": "Katie K.", "orcid": "0000-0002-9662-1113", "clpid": "Wong-Katie-K" }, { "family_name": "Sawyer", "given_name": "Daniel P.", "orcid": "0000-0003-2926-191X", "clpid": "Sawyer-Daniel-P" }, { "family_name": "Shen", "given_name": "Hao K.", "orcid": "0000-0003-2687-0736", "clpid": "Shen-Hao-K" }, { "family_name": "Dutka", "given_name": "Przemys\u0142aw" }, { "family_name": "Deshpande", "given_name": "Ramya", "clpid": "Deshpande-Ramya" }, { "family_name": "Zhang", "given_name": "Ruby", "orcid": "0009-0001-4410-945X", "clpid": "Zhang-Ruby" }, { "family_name": "Mittelstein", "given_name": "David R.", "orcid": "0000-0001-8747-0483", "clpid": "Mittelstein-David-R" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "A major challenge in the fields of biological imaging and synthetic biology is noninvasively visualizing the functions of natural and engineered cells inside opaque samples such as living animals. One promising technology that addresses this limitation is ultrasound (US), with its penetration depth of several cm and spatial resolution on the order of 100 μm. Within the past decade, reporter genes for US have been introduced and engineered to link cellular functions to US signals via heterologous expression in commensal bacteria and mammalian cells. These acoustic reporter genes (ARGs) represent a novel class of genetically encoded US contrast agent, and are based on air-filled protein nanostructures called gas vesicles (GVs). Just as the discovery of fluorescent proteins was followed by the improvement and diversification of their optical properties through directed evolution, here we describe the evolution of GVs as acoustic reporters. To accomplish this task, we establish high-throughput, semiautomated acoustic screening of ARGs in bacterial cultures and use it to screen mutant libraries for variants with increased nonlinear US scattering. Starting with scanning site saturation libraries for two homologues of the primary GV structural protein, GvpA/B, two rounds of evolution resulted in GV variants with 5- and 14-fold stronger acoustic signals than the parent proteins. We anticipate that this and similar approaches will help high-throughput protein engineering play as large a role in the development of acoustic biomolecules as it has for their fluorescent counterparts.
\nHere, we present a method for expressing multiple open reading frames (ORFs) from single transcripts using the leaky scanning model of translation initiation. In this approach termed “stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes” (SEMPER), adjacent ORFs are translated from a single mRNA at tunable ratios determined by their order in the sequence and the strength of their translation initiation sites. We validate this approach by expressing up to three fluorescent proteins from one plasmid in two different cell lines. We then use it to encode a stoichiometrically tuned polycistronic construct encoding gas vesicle acoustic reporter genes that enables efficient formation of the multi-protein complex while minimizing cellular toxicity. We also demonstrate that SEMPER enables polycistronic expression of recombinant monoclonal antibodies from plasmid DNA and of two fluorescent proteins from single mRNAs made through in vitro transcription. Finally, we provide a probabilistic model to elucidate the mechanisms underlying SEMPER. A record of this paper’s transparent peer review process is included in the supplemental information.
\nTargeted gene delivery to the brain is a critical tool for neuroscience research and has significant potential to treat human disease. However, the site-specific delivery of common gene vectors such as adeno-associated viruses (AAVs) is typically performed via invasive injections, which limit its applicable scope of research and clinical applications. Alternatively, focused ultrasound blood-brain-barrier opening (FUS-BBBO), performed noninvasively, enables the site-specific entry of AAVs into the brain from systemic circulation. However, when used in conjunction with natural AAV serotypes, this approach has limited transduction efficiency and results in substantial undesirable transduction of peripheral organs. Here, we use high throughput in vivo selection to engineer new AAV vectors specifically designed for local neuronal transduction at the site of FUS-BBBO. The resulting vectors substantially enhance ultrasound-targeted gene delivery and neuronal tropism while reducing peripheral transduction, providing a more than ten-fold improvement in targeting specificity in two tested mouse strains. In addition to enhancing the only known approach to noninvasively target gene delivery to specific brain regions, these results establish the ability of AAV vectors to be evolved for specific physical delivery mechanisms.
\nPrecise neurostimulation can revolutionize therapies for neurological disorders. Electrode-based stimulation devices face challenges in achieving precise and consistent targeting due to the immune response and the limited penetration of electrical fields. Ultrasound can aid in energy propagation, but transcranial ultrasound stimulation in the deep brain has limited spatial resolution caused by bone and tissue scattering. Here, we report an implantable piezoelectric ultrasound stimulator (ImPULS) that generates an ultrasonic focal pressure of 100 kPa to modulate the activity of neurons. ImPULS is a fully-encapsulated, flexible piezoelectric micromachined ultrasound transducer that incorporates a biocompatible piezoceramic, potassium sodium niobate [(K,Na)NbO3]. The absence of electrochemically active elements poses a new strategy for achieving long-term stability. We demonstrated that ImPULS can i) excite neurons in a mouse hippocampal slice ex vivo, ii) activate cells in the hippocampus of an anesthetized mouse to induce expression of activity-dependent gene c-Fos, and iii) stimulate dopaminergic neurons in the substantia nigra pars compacta to elicit time-locked modulation of nigrostriatal dopamine release. This work introduces a non-genetic ultrasound platform for spatially-localized neural stimulation and exploration of basic functions in the deep brain.
\nGas vesicles (GVs) are proteinaceous nanostructures that, along with virus-like particles, encapsulins, nanocages, and other macromolecular assemblies, are being developed for potential biomedical applications. To facilitate such development, it would be valuable to characterize these nanostructures’ subcellular assembly and localization. However, traditional fluorescent protein fusions are not tolerated by GVs’ primary constituent protein, making optical microscopy a challenge. Here, we introduce a method for fluorescently visualizing intracellular GVs using the bioorthogonal label FlAsH, which becomes fluorescent upon reaction with the six-amino acid tetracysteine (TC) tag. We engineered the GV subunit protein, GvpA, to display the TC tag and showed that GVs bearing TC-tagged GvpA can be successfully assembled and fluorescently visualized in HEK 293T cells. Importantly, this was achieved by replacing only a fraction of GvpA with the tagged version. We used fluorescence images of the tagged GVs to study the GV size and distance distributions within these cells. This bioorthogonal and fractional labeling approach will enable research to provide a greater understanding of GVs and could be adapted to similar proteinaceous nanostructures.
\nNanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography is challenging due to the size and stability constraints of conventional bubble-based agents. Here bicones, truly tiny acoustic contrast agents based on gas vesicles (GVs), a unique class of air-filled protein nanostructures naturally produced in buoyant microbes, are described. It is shown that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.
\nMeasuring cellular and tissue mechanics inside intact living organisms is essential for interrogating the roles of force in physiological and disease processes. Current agents for studying the mechanobiology of intact, living organisms are limited by poor light penetration and material stability. Magnetomotive ultrasound is an emerging modality for real-time in vivo imaging of tissue mechanics. Nonetheless, it has poor sensitivity and spatiotemporal resolution. Here we describe magneto-gas vesicles (MGVs), protein nanostructures based on gas vesicles and magnetic nanoparticles that produce differential ultrasound signals in response to varying mechanical properties of surrounding tissues. These hybrid nanomaterials significantly improve signal strength and detection sensitivity. Furthermore, MGVs enable non-invasive, long-term and quantitative measurements of mechanical properties within three-dimensional tissues and in vivo fibrosis models. Using MGVs as novel contrast agents, we demonstrate their potential for non-invasive imaging of tissue elasticity, offering insights into mechanobiology and its application to disease diagnosis and treatment.
", "doi": "10.1038/s41563-023-01688-w", "pmcid": "PMC10837075", "issn": "1476-1122", "publisher": "Nature Publishing Group", "publication": "Nature Materials", "publication_date": "2024-02", "series_number": "2", "volume": "23", "issue": "2", "pages": "290-300" }, { "id": "authors:zk9sx-n6991", "collection": "authors", "collection_id": "zk9sx-n6991", "cite_using_url": "https://authors.library.caltech.edu/records/zk9sx-n6991", "type": "article", "title": "Effects of focused ultrasound in a \"clean\" mouse model of ultrasonic neuromodulation", "author": [ { "family_name": "Guo", "given_name": "Hongsun", "orcid": "0000-0002-6086-6506", "clpid": "Guo-Hongsun" }, { "family_name": "Salahshoor", "given_name": "Hossein", "orcid": "0000-0002-7264-7650", "clpid": "Salahshoor-Hossein" }, { "family_name": "Wu", "given_name": "Di", "clpid": "Wu-Di" }, { "family_name": "Yoo", "given_name": "Sangjin", "orcid": "0000-0002-0449-4242", "clpid": "Yoo-Sangjin" }, { "family_name": "Sato", "given_name": "Tomokazu", "orcid": "0000-0002-7337-8157", "clpid": "Sato-Tomokazu" }, { "family_name": "Tsao", "given_name": "Doris Y.", "clpid": "Tsao-D-Y" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Recent studies on ultrasonic neuromodulation (UNM) in rodents have shown that focused ultrasound (FUS) can activate peripheral auditory pathways, leading to off-target and brain-wide excitation, which obscures the direct activation of the target area by FUS. To address this issue, we developed a new mouse model, the double transgenic Pou4f3^(+/DTR) \u00d7 Thy1-GCaMP6s, which allows for inducible deafening using diphtheria toxin and minimizes off-target effects of UNM while allowing effects on neural activity to be visualized with fluorescent calcium imaging. Using this model, we found that the auditory confounds caused by FUS can be significantly reduced or eliminated within a certain pressure range. At higher pressures, FUS can result in focal fluorescence dips at the target, elicit non-auditory sensory confounds, and damage tissue, leading to spreading depolarization. Under the acoustic conditions we tested, we did not observe direct calcium responses in the mouse cortex. Our findings provide a cleaner animal model for UNM and sonogenetics research, establish a parameter range within which off-target effects are confidently avoided, and reveal the non-auditory side effects of higher-pressure stimulation.
", "doi": "10.1016/j.isci.2023.108372", "pmcid": "PMC10690554", "issn": "2589-0042", "publisher": "Cell Press", "publication": "iScience", "publication_date": "2023-12-15", "series_number": "12", "volume": "26", "issue": "12", "pages": "108372" }, { "id": "authors:7w289-s1c34", "collection": "authors", "collection_id": "7w289-s1c34", "cite_using_url": "https://authors.library.caltech.edu/records/7w289-s1c34", "type": "article", "title": "Gas Vesicle\u2013Blood Interactions Enhance Ultrasound Imaging Contrast", "author": [ { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Ko", "given_name": "Jeong Hoon", "orcid": "0000-0003-2000-3789", "clpid": "Ko-Jeong-Hoon" }, { "family_name": "Stordy", "given_name": "Benjamin", "orcid": "0000-0002-1096-3287", "clpid": "Stordy-Benjamin" }, { "family_name": "Zhang", "given_name": "Yuwei", "clpid": "Zhang-Yuwei" }, { "family_name": "Didden", "given_name": "Tighe F.", "clpid": "Didden-Tighe-F" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Swift", "given_name": "Margaret B.", "orcid": "0000-0001-9610-0687", "clpid": "Swift-Margaret-B" }, { "family_name": "Chan", "given_name": "Warren C. W.", "orcid": "0000-0001-5435-4785", "clpid": "Chan-Warren-C-W" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Gas vesicles (GVs) are genetically encoded, air-filled protein nanostructures of broad interest for biomedical research and clinical applications, acting as imaging and therapeutic agents for ultrasound, magnetic resonance, and optical techniques. However, the biomedical applications of GVs as systemically injectable nanomaterials have been hindered by a lack of understanding of GVs' interactions with blood components, which can significantly impact in vivo behavior. Here, we investigate the dynamics of GVs in the bloodstream using a combination of ultrasound and optical imaging, surface functionalization, flow cytometry, and mass spectrometry. We find that erythrocytes and serum proteins bind to GVs and shape their acoustic response, circulation time, and immunogenicity. We show that by modifying the GV surface we can alter these interactions and thereby modify GVs' in vivo performance. These results provide critical insights for the development of GVs as agents for nanomedicine.
", "doi": "10.1021/acs.nanolett.3c02780", "pmcid": "PMC10722532", "issn": "1530-6984", "publisher": "American Chemical Society", "publication": "Nano Letters", "publication_date": "2023-12-13", "series_number": "33", "volume": "23", "issue": "33", "pages": "10748-10757" }, { "id": "authors:dbcm4-62w58", "collection": "authors", "collection_id": "dbcm4-62w58", "cite_using_url": "https://authors.library.caltech.edu/records/dbcm4-62w58", "type": "article", "title": "Using ultrasound to 3D-print materials", "author": [ { "family_name": "Yao", "given_name": "Yuxing", "orcid": "0000-0003-0337-6372", "clpid": "Yao-Yuxing" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Additive manufacturing is an emerging technology that involves the progressive assembly of spatially patterned material, and it is reshaping materials fabrication. This process is becoming widely adopted for products ranging from architectural prototypes to consumer footwear (1). However, most existing methods to produce three-dimensional (3D) shapes require a raster-scanning printer (2\u20134) or use patterned light (5, 6) to induce material formation, which limits manufacturing to physically or optically accessible conditions. In principle, ultrasound could be used to print within centimeter-scale volumes of optically opaque media at a spatial resolution of ~100 \u03bcm. This strategy could even work inside the body. On page 1148 of this issue, Kuang et al. (7) present an ultrasoundbased volumetric printing method, showcasing fast and precise printing capabilities, and demonstrate its use for noninvasive biomaterial printing inside living tissue ex vivo.
", "doi": "10.1126/science.adl5887", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2023-12-08", "series_number": "6675", "volume": "382", "issue": "6675", "pages": "1126" }, { "id": "authors:9jqh1-w6t02", "collection": "authors", "collection_id": "9jqh1-w6t02", "cite_using_url": "https://authors.library.caltech.edu/records/9jqh1-w6t02", "type": "article", "title": "Decoding motor plans using a closed-loop ultrasonic brain\u2013machine interface", "author": [ { "family_name": "Griggs", "given_name": "Whitney S.", "orcid": "0000-0003-2941-6803", "clpid": "Griggs-Whitney-S" }, { "family_name": "Norman", "given_name": "Sumner L.", "orcid": "0000-0001-9945-697X", "clpid": "Norman-Sumner-L" }, { "family_name": "Deffieux", "given_name": "Thomas", "orcid": "0000-0001-9114-2028", "clpid": "Deffieux-Thomas" }, { "family_name": "Segura", "given_name": "Florian", "clpid": "Segura-Florian" }, { "family_name": "Osmanski", "given_name": "Bruno-F\u00e9lix", "orcid": "0000-0003-1198-5303", "clpid": "Osmanski-Bruno-F\u00e9lix" }, { "family_name": "Chau", "given_name": "Geeling", "clpid": "Chau-Geeling" }, { "family_name": "Christopoulos", "given_name": "Vasileios", "orcid": "0000-0002-0541-8700", "clpid": "Christopoulos-Vasileios" }, { "family_name": "Liu", "given_name": "Charles", "orcid": "0000-0001-6423-8577", "clpid": "Liu-Charles-Y" }, { "family_name": "Tanter", "given_name": "Mickael", "orcid": "0000-0001-7739-8051", "clpid": "Tanter-Mickael" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Andersen", "given_name": "Richard A.", "orcid": "0000-0002-7947-0472", "clpid": "Andersen-R-A" } ], "abstract": "Brain\u2013machine interfaces (BMIs) enable people living with chronic paralysis to control computers, robots and more with nothing but thought. Existing BMIs have trade-offs across invasiveness, performance, spatial coverage and spatiotemporal resolution. Functional ultrasound (fUS) neuroimaging is an emerging technology that balances these attributes and may complement existing BMI recording technologies. In this study, we use fUS to demonstrate a successful implementation of a closed-loop ultrasonic BMI. We streamed fUS data from the posterior parietal cortex of two rhesus macaque monkeys while they performed eye and hand movements. After training, the monkeys controlled up to eight movement directions using the BMI. We also developed a method for pretraining the BMI using data from previous sessions. This enabled immediate control on subsequent days, even those that occurred months apart, without requiring extensive recalibration. These findings establish the feasibility of ultrasonic BMIs, paving the way for a new class of less-invasive (epidural) interfaces that generalize across extended time periods and promise to restore function to people with neurological impairments.
", "doi": "10.1038/s41593-023-01500-7", "issn": "1097-6256", "publisher": "Nature Publishing Group", "publication": "Nature Neuroscience", "publication_date": "2023-11-30" }, { "id": "authors:6b26e-8v344", "collection": "authors", "collection_id": "6b26e-8v344", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221128-494241100.5", "type": "article", "title": "Geometric effects in gas vesicle buckling under ultrasound", "author": [ { "family_name": "Salahshoor", "given_name": "Hossein", "orcid": "0000-0002-7264-7650", "clpid": "Salahshoor-Hossein" }, { "family_name": "Yao", "given_name": "Yuxing", "orcid": "0000-0003-0337-6372", "clpid": "Yao-Yuxing" }, { "family_name": "Dutka", "given_name": "Przemys\u0142aw", "orcid": "0000-0003-3819-1618", "clpid": "Dutka-Przemys\u0142aw" }, { "family_name": "Nystr\u00f6m", "given_name": "Nivin N.", "orcid": "0000-0001-6288-6060", "clpid": "Nystr\u00f6m-Nivin-N" }, { "family_name": "Jin", "given_name": "Zhiyang", "orcid": "0000-0002-4411-6991", "clpid": "Jin-Zhiyang" }, { "family_name": "Min", "given_name": "Ellen", "clpid": "Min-Ellen" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" }, { "family_name": "Ortiz", "given_name": "Michael", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Acoustic reporter genes based on gas vesicles (GVs) have enabled the use of ultrasound to noninvasively visualize cellular function in vivo. The specific detection of GV signals relative to background acoustic scattering in tissues is facilitated by nonlinear ultrasound imaging techniques taking advantage of the sonomechanical buckling of GVs. However, the effect of geometry on the buckling behavior of GVs under exposure to ultrasound has not been studied. To understand such geometric effects, we developed computational models of GVs of various lengths and diameters and used finite element simulations to predict their threshold buckling pressures and postbuckling deformations. We demonstrated that the GV diameter has an inverse cubic relation to the threshold buckling pressure, whereas length has no substantial effect. To complement these simulations, we experimentally probed the effect of geometry on the mechanical properties of GVs and the corresponding nonlinear ultrasound signals. The results of these experiments corroborate our computational predictions. This study provides fundamental insights into how geometry affects the sonomechanical properties of GVs, which, in turn, can inform further engineering of these nanostructures for high-contrast, nonlinear ultrasound imaging.", "doi": "10.1016/j.bpj.2022.09.004", "pmcid": "PMC9674984", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2023-11-01", "series_number": "21", "volume": "121", "issue": "21", "pages": "4221-4228" }, { "id": "authors:r9ppf-j2b23", "collection": "authors", "collection_id": "r9ppf-j2b23", "cite_using_url": "https://authors.library.caltech.edu/records/r9ppf-j2b23", "type": "article", "title": "Living Material with Temperature\u2010Dependent Light Absorption", "author": [ { "family_name": "Xiong", "given_name": "Lealia L.", "orcid": "0000-0001-7636-5936", "clpid": "Xiong-Lealia-L" }, { "family_name": "Garrett", "given_name": "Michael A.", "clpid": "Garrett-Michael-A" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Engineered living materials (ELMs) exhibit desirable characteristics of the living component, including growth and repair, and responsiveness to external stimuli. Escherichia coli (E. coli) are a promising constituent of ELMs because they are very tractable to genetic engineering, produce heterologous proteins readily, and grow exponentially. However, seasonal variation in ambient temperature presents a challenge in deploying ELMs outside of a laboratory environment because E. coli growth rate is impaired both below and above 37 \u00b0C. Here, a genetic circuit is developed that controls the expression of a light\u2010absorptive chromophore in response to changes in temperature. It is demonstrated that at temperatures below 36 \u00b0C, the engineered E. coli increase in pigmentation, causing an increase in sample temperature and growth rate above non\u2010pigmented counterparts in a model planar ELM. On the other hand, at above 36 \u00b0C, they decrease in pigmentation, protecting the growth compared to bacteria with temperature\u2010independent high pigmentation. Integrating the temperature\u2010responsive circuit into an ELM has the potential to improve living material performance by optimizing growth and protein production in the face of seasonal temperature changes.
", "doi": "10.1002/advs.202301730", "pmcid": "PMC10602556", "issn": "2198-3844", "publisher": "Wiley", "publication": "Advanced Science", "publication_date": "2023-10-26", "series_number": "30", "volume": "10", "issue": "30", "pages": "2301730" }, { "id": "authors:qd23d-g4r92", "collection": "authors", "collection_id": "qd23d-g4r92", "cite_using_url": "https://authors.library.caltech.edu/records/qd23d-g4r92", "type": "article", "title": "Remote control of mechanochemical reactions under physiological conditions using biocompatible focused ultrasound", "author": [ { "family_name": "Yao", "given_name": "Yuxing", "orcid": "0000-0003-0337-6372", "clpid": "Yao-Yuxing" }, { "family_name": "McFadden", "given_name": "Molly E.", "orcid": "0000-0003-3174-6385", "clpid": "McFadden-Molly-E" }, { "family_name": "Luo", "given_name": "Stella M.", "orcid": "0000-0003-4003-7468", "clpid": "Luo-Stella-M" }, { "family_name": "Barber", "given_name": "Ross W.", "clpid": "Barber-Ross-W" }, { "family_name": "Kang", "given_name": "Elin", "clpid": "Kang-Elin" }, { "family_name": "Bar-Zion", "given_name": "Avinoam", "orcid": "0000-0002-7564-9467", "clpid": "Bar-Zion-Avinoam" }, { "family_name": "Smith", "given_name": "Cameron A. B.", "clpid": "Smith-Cameron-A-B" }, { "family_name": "Jin", "given_name": "Zhiyang", "orcid": "0000-0002-4411-6991", "clpid": "Jin-Zhiyang" }, { "family_name": "Legendre", "given_name": "Mark", "orcid": "0009-0008-5910-1574", "clpid": "Legendre-Mark" }, { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Torres", "given_name": "Andrea", "clpid": "Torres-Andrea" }, { "family_name": "Hamza", "given_name": "Tiba", "orcid": "0000-0003-1555-9555", "clpid": "Hamza-Tiba" }, { "family_name": "Edwards", "given_name": "Chelsea E. R.", "orcid": "0000-0003-1540-7594", "clpid": "Edwards-Chelsea-E-R" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Robb", "given_name": "Maxwell J.", "orcid": "0000-0002-0528-9857", "clpid": "Robb-M-J" } ], "abstract": "External control of chemical reactions in biological settings with spatial and temporal precision is a grand challenge for noninvasive diagnostic and therapeutic applications. While light is a conventional stimulus for remote chemical activation, its penetration is severely attenuated in tissues, which limits biological applicability. On the other hand, ultrasound is a biocompatible remote energy source that is highly penetrant and offers a wide range of functional tunability. Coupling ultrasound to the activation of specific chemical reactions under physiological conditions, however, remains a challenge. Here, we describe a synergistic platform that couples the selective mechanochemical activation of mechanophore-functionalized polymers with biocompatible focused ultrasound (FUS) by leveraging pressure-sensitive gas vesicles (GVs) as acousto-mechanical transducers. The power of this approach is illustrated through the mechanically triggered release of covalently bound fluorogenic and therapeutic cargo molecules from polymers containing a masked 2-furylcarbinol mechanophore. Molecular release occurs selectively in the presence of GVs upon exposure to FUS under physiological conditions. These results showcase the viability of this system for enabling remote control of specific mechanochemical reactions with spatiotemporal precision in biologically relevant settings and demonstrate the translational potential of polymer mechanochemistry.", "doi": "10.1073/pnas.2309822120", "pmcid": "PMC10523651", "issn": "0027-8424", "publisher": "Proceedings of the National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2023-09-26", "series_number": "39", "volume": "120", "issue": "39", "pages": "e2309822120" }, { "id": "authors:1z29n-2tq07", "collection": "authors", "collection_id": "1z29n-2tq07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230317-826078000.2", "type": "article", "title": "Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria", "author": [ { "family_name": "Hurt", "given_name": "Robert C.", "orcid": "0000-0002-4347-6901", "clpid": "Hurt-Robert-C" }, { "family_name": "Buss", "given_name": "Marjorie T.", "orcid": "0000-0002-4266-9197", "clpid": "Buss-Marjorie-T" }, { "family_name": "Duan", "given_name": "Mengtong", "orcid": "0000-0002-1601-8876", "clpid": "Duan-Mengtong" }, { "family_name": "Wong", "given_name": "Katie", "clpid": "Wong-Katie" }, { "family_name": "You", "given_name": "Mei Yi", "clpid": "You-Mei-Yi" }, { "family_name": "Sawyer", "given_name": "Daniel P.", "orcid": "0000-0003-2926-191X", "clpid": "Sawyer-Daniel-P" }, { "family_name": "Swift", "given_name": "Margaret B.", "orcid": "0000-0001-9610-0687", "clpid": "Swift-Margaret-B" }, { "family_name": "Dutka", "given_name": "Przemys\u0142aw", "orcid": "0000-0003-3819-1618", "clpid": "Dutka-Przemys\u0142aw" }, { "family_name": "Barturen-Larrea", "given_name": "Pierina", "orcid": "0000-0002-6076-5801", "clpid": "Barturen-Larrea-Pierina" }, { "family_name": "Mittelstein", "given_name": "David R.", "orcid": "0000-0001-8747-0483", "clpid": "Mittelstein-David-R" }, { "family_name": "Jin", "given_name": "Zhiyang", "orcid": "0000-0002-4411-6991", "clpid": "Jin-Zhiyang" }, { "family_name": "Abedi", "given_name": "Mohamad H.", "orcid": "0000-0001-9717-6288", "clpid": "Abedi-Mohamad-H" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Deshpande", "given_name": "Ramya", "clpid": "Deshpande-Ramya" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Ultrasound allows imaging at a much greater depth than optical methods, but existing genetically encoded acoustic reporters for in vivo cellular imaging have been limited by poor sensitivity, specificity and in vivo expression. Here we describe two acoustic reporter genes (ARGs)\u2014one for use in bacteria and one for use in mammalian cells\u2014identified through a phylogenetic screen of candidate gas vesicle gene clusters from diverse bacteria and archaea that provide stronger ultrasound contrast, produce non-linear signals distinguishable from background tissue and have stable long-term expression. Compared to their first-generation counterparts, these improved bacterial and mammalian ARGs produce 9-fold and 38-fold stronger non-linear contrast, respectively. Using these new ARGs, we non-invasively imaged in situ tumor colonization and gene expression in tumor-homing therapeutic bacteria, tracked the progression of tumor gene expression and growth in a mouse model of breast cancer, and performed gene-expression-guided needle biopsies of a genetically mosaic tumor, demonstrating non-invasive access to dynamic biological processes at centimeter depth.", "doi": "10.1038/s41587-022-01581-y", "pmcid": "PMC10344784", "issn": "1087-0156", "publisher": "Nature Publishing Group", "publication": "Nature Biotechnology", "publication_date": "2023-07", "series_number": "7", "volume": "41", "issue": "7", "pages": "919-931" }, { "id": "authors:me61v-mhy57", "collection": "authors", "collection_id": "me61v-mhy57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-257245000.39", "type": "article", "title": "Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET", "author": [ { "family_name": "Dutka", "given_name": "Przemys\u0142aw", "orcid": "0000-0003-3819-1618", "clpid": "Dutka-Przemys\u0142aw" }, { "family_name": "Metskas", "given_name": "Lauren Ann", "orcid": "0000-0002-8073-6960", "clpid": "Metskas-Lauren-Ann" }, { "family_name": "Hurt", "given_name": "Robert C.", "orcid": "0000-0002-4347-6901", "clpid": "Hurt-Robert-C" }, { "family_name": "Salahshoor", "given_name": "Hossein", "orcid": "0000-0002-7264-7650", "clpid": "Salahshoor-Hossein" }, { "family_name": "Wang", "given_name": "Ting-Yu", "clpid": "Wang-Ting-Yu" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Chou", "given_name": "Tsui-Fen", "orcid": "0000-0003-2410-2186", "clpid": "Chou-Tsui-Fen" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a \u03b2 sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.", "doi": "10.1016/j.str.2023.03.011", "pmcid": "PMC10185304", "issn": "0969-2126", "publisher": "Cell Press", "publication": "Structure", "publication_date": "2023-05-04", "series_number": "5", "volume": "31", "issue": "5", "pages": "518-528" }, { "id": "authors:jmq2h-hma72", "collection": "authors", "collection_id": "jmq2h-hma72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230420-711199500.13", "type": "article", "title": "Auditory Mondrian masks the airborne-auditory artifact of focused ultrasound stimulation in humans", "author": [ { "family_name": "Liang", "given_name": "William", "clpid": "Liang-William" }, { "family_name": "Guo", "given_name": "Hongsun", "clpid": "Guo-Hongsun" }, { "family_name": "Mittelstein", "given_name": "David R.", "orcid": "0000-0001-8747-0483", "clpid": "Mittelstein-David-R" }, { "family_name": "Shapiro", "given_name": "Mikhail G..", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Shimojo", "given_name": "Shinsuke", "orcid": "0000-0002-1290-5232", "clpid": "Shimojo-S" }, { "family_name": "Shehata", "given_name": "Mohammad", "orcid": "0000-0003-1710-3009", "clpid": "Shehata-Mohammad" } ], "abstract": "Low-intensity Focused Ultrasound Stimulation (FUS) can modulate neural activity in cortical, subcortical, and deep brain regions, achieving millimeter precision through transcranial ultrasound stimulation (TUS) and can affect behavior [1,2]. However, there is concern that FUS may induce an auditory effect, cortically activating the subject's auditory sensation, thus confounding behavioral and electrophysiological responses during TUS research [[3], [4], [5], [6], [7]]. Several studies have mitigated this auditory artifact through ramping [8] or audio masking [5,6], but prior research has had two main limitations. First, previous studies addressed a limited range of the total FUS parameter space: fundamental frequency (f0), pulse repetition frequency (PRF), duty cycle (DC), sonication duration (SD), and intensity (I) [1,7,[9], [10], [11]]. Second, as these studies used direct stimulation of subjects, they did not distinguish between airborne or tissue conduction effects [[5], [6], [7]]. Here, we evaluate the airborne auditory artifact over a range of FUS parameters through sonographic characterization, the human subject's response to recorded audio clips, and a two-interval forced choice (2IFC) task to test the effectiveness of three mask types: square [5,6], pulsed sine, and random multitone. The multitone random mask, or Auditory Mondrian, is inspired by the visual Mondrian used in the continuous flash suppression to mask visual targets [12].\n\nWe recruited 228 healthy participants for the three online auditory psychophysical experiments (See Supplementary Methods for details). In experiment 1, participants performed a detection task in which they were asked whether they detected a distinct sound while listening to audio recordings of FUS sham and stimulation trials. In experiments 2 and 3, participants performed a two-interval forced choice (2IFC) task in which they chose which interval of a pair contained the FUS stimulation embedded in an auditory mask. Audio clips from the microphone were used without volume (loudness) manipulation and confirmed by experimenters to match the sound produced from the FUS setup.\n\nIn an artificial environment, we found that the ultrasound transducer is a primary source of airborne auditory artifacts (Fig. S1 A and B). Short-time Fourier transforms (STFT) of the audio recordings of FUS revealed clear frequency bands at the PRF and harmonics, along with additional frequency bands in the human hearing range that did not fit with the corresponding PRF (Fig. 1 A). These additional frequency bands were consistent at approximately 8 and 12 kHz throughout all PRF and even seen with continuous wave US bursts (Fig. 1 A, yellow arrows) and appeared regardless of the coupling method or the cone and arm setup (Fig. 1 B). The electrical spectrum density showed no peaks at the human frequency range, so it likely did not contribute to the auditory artifact. Based on the above acoustic analyses, we concluded that the ultrasound transducer is a source of airborne auditory artifacts.", "doi": "10.1016/j.brs.2023.03.002", "pmcid": "PMC10314733", "issn": "1935-861X", "publisher": "Elsevier", "publication": "Brain Stimulation", "publication_date": "2023-03", "series_number": "2", "volume": "16", "issue": "2", "pages": "604-606" }, { "id": "authors:n3gje-t4y22", "collection": "authors", "collection_id": "n3gje-t4y22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230214-651108000.1", "type": "article", "title": "Location-aware ingestible microdevices for wireless monitoring of gastrointestinal dynamics", "author": [ { "family_name": "Sharma", "given_name": "Saransh", "orcid": "0000-0002-5052-4932", "clpid": "Sharma-Saransh" }, { "family_name": "Ramadi", "given_name": "Khalil B.", "clpid": "Ramadi-Khalil-B" }, { "family_name": "Poole", "given_name": "Nikhil H.", "clpid": "Poole-Nikhil-H" }, { "family_name": "Srinivasan", "given_name": "Shriya S.", "orcid": "0000-0002-2508-1324", "clpid": "Srinivasan-Shriya-S" }, { "family_name": "Ishida", "given_name": "Keiko", "orcid": "0000-0003-0894-296X", "clpid": "Ishida-Keiko" }, { "family_name": "Kuosmanen", "given_name": "Johannes", "clpid": "Kuosmanen-Johannes" }, { "family_name": "Jenkins", "given_name": "Josh", "orcid": "0000-0001-7698-9888", "clpid": "Jenkins-Joshua" }, { "family_name": "Aghlmand", "given_name": "Fatemeh", "orcid": "0000-0002-5103-9314", "clpid": "Aghlmand-Fatemeh" }, { "family_name": "Swift", "given_name": "Margaret B.", "orcid": "0000-0001-9610-0687", "clpid": "Swift-Margaret-B" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Traverso", "given_name": "Giovanni", "orcid": "0000-0001-7851-4077", "clpid": "Traverso-Giovanni" }, { "family_name": "Emami", "given_name": "Azita", "orcid": "0000-0002-6945-9958", "clpid": "Emami-A" } ], "abstract": "Localization and tracking of ingestible microdevices in the gastrointestinal (GI) tract is valuable for the diagnosis and treatment of GI disorders. Such systems require a large field-of-view of tracking, high spatiotemporal resolution, wirelessly operated microdevices and a non-obstructive field generator that is safe to use in practical settings. However, the capabilities of current systems remain limited. Here, we report three dimensional (3D) localization and tracking of wireless ingestible microdevices in the GI tract of large animals in real time and with millimetre-scale resolution. This is achieved by generating 3D magnetic field gradients in the GI field-of-view using high-efficiency planar electromagnetic coils that encode each spatial point with a distinct magnetic field magnitude. The field magnitude is measured and transmitted by the miniaturized, low-power and wireless microdevices to decode their location as they travel through the GI tract. This system could be useful for quantitative assessment of the GI transit-time, precision targeting of therapeutic interventions and minimally invasive procedures.", "doi": "10.1038/s41928-023-00916-0", "pmcid": "PMC10516531", "issn": "2520-1131", "publisher": "Nature Publishing Group", "publication": "Nature Electronics", "publication_date": "2023-03", "series_number": "3", "volume": "6", "issue": "3", "pages": "242-256" }, { "id": "authors:q0yqt-d4b86", "collection": "authors", "collection_id": "q0yqt-d4b86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230223-575177000.2", "type": "article", "title": "Biomolecular actuators for genetically selective acoustic manipulation of cells", "author": [ { "family_name": "Wu", "given_name": "Di", "orcid": "0000-0002-6848-668X", "clpid": "Wu-Di" }, { "family_name": "Baresch", "given_name": "Diego", "orcid": "0000-0002-8491-8542", "clpid": "Baresch-Diego" }, { "family_name": "Cook", "given_name": "Colin", "orcid": "0000-0002-6283-5105", "clpid": "Cook-Colin-A" }, { "family_name": "Ma", "given_name": "Zhichao", "orcid": "0000-0003-1288-6745", "clpid": "Ma-Zhichao" }, { "family_name": "Duan", "given_name": "Mengtong", "orcid": "0000-0002-1601-8876", "clpid": "Duan-Mengtong" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Abundo", "given_name": "Maria P.", "orcid": "0000-0002-5122-6937", "clpid": "Abundo-Maria-P" }, { "family_name": "Lee", "given_name": "Justin", "orcid": "0000-0002-3657-4386", "clpid": "Lee-Justin" }, { "family_name": "Shivaei", "given_name": "Shirin", "orcid": "0000-0002-6894-3289", "clpid": "Shivaei-Shirin" }, { "family_name": "Mittelstein", "given_name": "David R.", "orcid": "0000-0001-8747-0483", "clpid": "Mittelstein-David-R" }, { "family_name": "Qiu", "given_name": "Tian", "orcid": "0000-0003-0932-5605", "clpid": "Qiu-Tian" }, { "family_name": "Fischer", "given_name": "Peer", "orcid": "0000-0002-8600-5958", "clpid": "Fischer-Peer" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "The ability to physically manipulate specific cells is critical for the fields of biomedicine, synthetic biology, and living materials. Ultrasound has the ability to manipulate cells with high spatiotemporal precision via acoustic radiation force (ARF). However, because most cells have similar acoustic properties, this capability is disconnected from cellular genetic programs. Here, we show that gas vesicles (GVs)\u2014a unique class of gas-filled protein nanostructures\u2014can serve as genetically encodable actuators for selective acoustic manipulation. Because of their lower density and higher compressibility relative to water, GVs experience strong ARF with opposite polarity to most other materials. When expressed inside cells, GVs invert the cells' acoustic contrast and amplify the magnitude of their ARF, allowing the cells to be selectively manipulated with sound waves based on their genotype. GVs provide a direct link between gene expression and acoustomechanical actuation, opening a paradigm for selective cellular control in a broad range of contexts.", "doi": "10.1126/sciadv.add9186", "pmcid": "PMC9946353", "issn": "2375-2548", "publisher": "American Association for the Advancement of Science", "publication": "Science Advances", "publication_date": "2023-02-22", "series_number": "8", "volume": "9", "issue": "8", "pages": "Art. No. eadd9186" }, { "id": "authors:8g0f4-w3x21", "collection": "authors", "collection_id": "8g0f4-w3x21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221213-185576500.5", "type": "article", "title": "Modular stimuli-responsive hydrogel sealants for early gastrointestinal leak detection and containment", "author": [ { "family_name": "Anthis", "given_name": "Alexandre H. C.", "clpid": "Anthis-Alexandre-H-C" }, { "family_name": "Abundo", "given_name": "Maria Paulene", "orcid": "0000-0002-5122-6937", "clpid": "Abundo-Maria-Paulene" }, { "family_name": "Neuer", "given_name": "Anna L.", "orcid": "0000-0002-5762-4709", "clpid": "Neuer-Anna-L" }, { "family_name": "Tsolaki", "given_name": "Elena", "orcid": "0000-0003-1436-7834", "clpid": "Tsolaki-Elena" }, { "family_name": "Rosendorf", "given_name": "Jachym", "orcid": "0000-0003-2125-0685", "clpid": "Rosendorf-Jachym" }, { "family_name": "Rduch", "given_name": "Thomas", "orcid": "0000-0002-7486-5002", "clpid": "Rduch-Thomas" }, { "family_name": "Starsich", "given_name": "Fabian H. L.", "orcid": "0000-0003-0724-764X", "clpid": "Starsich-Fabian-H-L" }, { "family_name": "Weisse", "given_name": "Bernhard", "orcid": "0000-0002-5267-5777", "clpid": "Weisse-Bernhard" }, { "family_name": "Liska", "given_name": "Vaclav", "orcid": "0000-0002-7755-3856", "clpid": "Liska-Vaclav" }, { "family_name": "Schlegel", "given_name": "Andrea A.", "orcid": "0000-0002-9385-9847", "clpid": "Schlegel-Andrea-A" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Herrmann", "given_name": "Inge K.", "orcid": "0000-0002-3018-6796", "clpid": "Herrmann-Inge-K" } ], "abstract": "Millions of patients every year undergo gastrointestinal surgery. While often lifesaving, sutured and stapled reconnections leak in around 10% of cases. Currently, surgeons rely on the monitoring of surrogate markers and clinical symptoms, which often lack sensitivity and specificity, hence only offering late-stage detection of fully developed leaks. Here, we present a holistic solution in the form of a modular, intelligent suture support sealant patch capable of containing and detecting leaks early. The pH and/or enzyme-responsive triggerable sensing elements can be read out by point-of-need ultrasound imaging. We demonstrate reliable detection of the breaching of sutures, in as little as 3\u2009hours in intestinal leak scenarios and 15\u2009minutes in gastric leak conditions. This technology paves the way for next-generation suture support materials that seal and offer disambiguation in cases of anastomotic leaks based on point-of-need monitoring, without reliance on complex electronics or bulky (bio)electronic implantables.", "doi": "10.1038/s41467-022-34272-y", "pmcid": "PMC9701692", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2022-11-27", "volume": "13", "pages": "Art. No. 7311" }, { "id": "authors:0m0cw-8nh28", "collection": "authors", "collection_id": "0m0cw-8nh28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220720-917501000", "type": "article", "title": "Tunable Temperature-Sensitive Transcriptional Activation Based on Lambda Repressor", "author": [ { "family_name": "Xiong", "given_name": "Lealia L.", "orcid": "0000-0001-7636-5936", "clpid": "Xiong-Lealia-L" }, { "family_name": "Garrett", "given_name": "Michael A.", "clpid": "Garrett-Michael-A" }, { "family_name": "Buss", "given_name": "Marjorie T.", "orcid": "0000-0002-4266-9197", "clpid": "Buss-Marjorie-T" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Temperature is a versatile input signal for the control of engineered cellular functions. Sharp induction of gene expression with heat has been established using bacteria- and phage-derived temperature-sensitive transcriptional repressors with tunable switching temperatures. However, few temperature-sensitive transcriptional activators have been reported that enable direct gene induction with cooling. Such activators would expand the application space for temperature control. In this technical note, we show that temperature-dependent versions of the Lambda phage repressor CI can serve as tunable cold-actuated transactivators. Natively, CI serves as both a repressor and activator of transcription. Previously, thermolabile mutants of CI, known as the TcI family, were used to repress the cognate promoters PR and PL. We hypothesized that TcI mutants can also serve as temperature-sensitive activators of transcription at CI's natural PRM promoter, creating cold-inducible operons with a tunable response to temperature. Indeed, we demonstrate temperature-responsive activation by two variants of TcI with set points at 35.5 and 38.5 \u00b0C in E. coli. In addition, we show that TcI can serve as both an activator and a repressor of different genes in the same genetic circuit, leading to opposite thermal responses. Transcriptional activation by TcI expands the toolbox for control of cellular function using globally or locally applied thermal inputs.", "doi": "10.1021/acssynbio.2c00093", "pmcid": "PMC9295150", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2022-07-15", "series_number": "7", "volume": "11", "issue": "7", "pages": "2518-2522" }, { "id": "authors:57tt8-6m581", "collection": "authors", "collection_id": "57tt8-6m581", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210419-174632997", "type": "article", "title": "Ultrasound-controllable engineered bacteria for cancer immunotherapy", "author": [ { "family_name": "Abedi", "given_name": "Mohamad H.", "orcid": "0000-0001-9717-6288", "clpid": "Abedi-Mohamad-H" }, { "family_name": "Yao", "given_name": "Michael S.", "orcid": "0000-0002-7008-6028", "clpid": "Yao-Michael-S" }, { "family_name": "Mittelstein", "given_name": "David R.", "orcid": "0000-0001-8747-0483", "clpid": "Mittelstein-David-R" }, { "family_name": "Bar-Zion", "given_name": "Avinoam", "orcid": "0000-0002-7564-9467", "clpid": "Bar-Zion-Avinoam" }, { "family_name": "Swift", "given_name": "Margaret B.", "orcid": "0000-0001-9610-0687", "clpid": "Swift-Margaret-B" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Barturen-Larrea", "given_name": "Pierina", "orcid": "0000-0002-6076-5801", "clpid": "Barturen-Larrea-Pierina" }, { "family_name": "Buss", "given_name": "Marjorie T.", "orcid": "0000-0002-4266-9197", "clpid": "Buss-Marjorie-T" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Rapid advances in synthetic biology are driving the development of genetically engineered microbes as therapeutic agents for a multitude of human diseases, including cancer. The immunosuppressive microenvironment of solid tumors, in particular, creates a favorable niche for systemically administered bacteria to engraft and release therapeutic payloads. However, such payloads can be harmful if released outside the tumor in healthy tissues where the bacteria also engraft in smaller numbers. To address this limitation, we engineer therapeutic bacteria to be controlled by focused ultrasound, a form of energy that can be applied noninvasively to specific anatomical sites such as solid tumors. This control is provided by a temperature-actuated genetic state switch that produces lasting therapeutic output in response to briefly applied focused ultrasound hyperthermia. Using a combination of rational design and high-throughput screening we optimize the switching circuits of engineered cells and connect their activity to the release of immune checkpoint inhibitors. In a clinically relevant cancer model, ultrasound-activated therapeutic microbes successfully turn on in situ and induce a marked suppression of tumor growth. This technology provides a critical tool for the spatiotemporal targeting of potent bacterial therapeutics in a variety of biological and clinical scenarios.", "doi": "10.1038/s41467-022-29065-2", "pmcid": "PMC8948203", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2022-03-24", "volume": "13", "pages": "Art. No. 1585" }, { "id": "authors:cafan-6as93", "collection": "authors", "collection_id": "cafan-6as93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220214-859281700", "type": "article", "title": "A gut-derived metabolite alters brain activity and anxiety behaviour in mice", "author": [ { "family_name": "Needham", "given_name": "Brittany D.", "orcid": "0000-0002-0280-1886", "clpid": "Needham-Brittany-D" }, { "family_name": "Funabashi", "given_name": "Masanori", "clpid": "Funabashi-Masanori" }, { "family_name": "Adame", "given_name": "Mark D.", "clpid": "Adame-Mark-D" }, { "family_name": "Wang", "given_name": "Zhuo", "clpid": "Wang-Zhuo" }, { "family_name": "Boktor", "given_name": "Joseph C.", "orcid": "0000-0003-2456-1913", "clpid": "Boktor-Joseph-C" }, { "family_name": "Haney", "given_name": "Jillian", "orcid": "0000-0001-5847-9892", "clpid": "Haney-Jillian" }, { "family_name": "Wu", "given_name": "Wei-Li", "orcid": "0000-0003-2610-1881", "clpid": "Wu-Wei-Li" }, { "family_name": "Rabut", "given_name": "Claire", "orcid": "0000-0002-4571-1215", "clpid": "Rabut-Claire" }, { "family_name": "Ladinsky", "given_name": "Mark S.", "orcid": "0000-0002-1036-3513", "clpid": "Ladinsky-M-S" }, { "family_name": "Hwang", "given_name": "Son-Jong", "orcid": "0000-0002-3210-466X", "clpid": "Hwang-Son-Jong" }, { "family_name": "Guo", "given_name": "Yumei", "clpid": "Guo-Yumei" }, { "family_name": "Zhu", "given_name": "Qiyun", "orcid": "0000-0002-3568-6271", "clpid": "Zhu-Qiyun" }, { "family_name": "Griffiths", "given_name": "Jessica A.", "orcid": "0000-0002-5586-1567", "clpid": "Griffiths-Jessica-A" }, { "family_name": "Knight", "given_name": "Rob", "orcid": "0000-0002-0975-9019", "clpid": "Knight-Rob" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Geschwind", "given_name": "Daniel H.", "orcid": "0000-0003-2896-3450", "clpid": "Geschwind-Daniel-H" }, { "family_name": "Holschneider", "given_name": "Daniel P.", "orcid": "0000-0002-4297-8280", "clpid": "Holschneider-Daniel-P" }, { "family_name": "Fischbach", "given_name": "Michael A.", "orcid": "0000-0003-3079-8247", "clpid": "Fischbach-Michael-A" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "orcid": "0000-0003-2713-1513", "clpid": "Mazmanian-S-K" } ], "abstract": "Integration of sensory and molecular inputs from the environment shapes animal behaviour. A major site of exposure to environmental molecules is the gastrointestinal tract, in which dietary components are chemically transformed by the microbiota and gut-derived metabolites are disseminated to all organs, including the brain. In mice, the gut microbiota impacts behaviour, modulates neurotransmitter production in the gut and brain, and influences brain development and myelination patterns. The mechanisms that mediate the gut\u2013brain interactions remain poorly defined, although they broadly involve humoral or neuronal connections. We previously reported that the levels of the microbial metabolite 4-ethylphenyl sulfate (4EPS) were increased in a mouse model of atypical neurodevelopment. Here we identified biosynthetic genes from the gut microbiome that mediate the conversion of dietary tyrosine to 4-ethylphenol (4EP), and bioengineered gut bacteria to selectively produce 4EPS in mice. 4EPS entered the brain and was associated with changes in region-specific activity and functional connectivity. Gene expression signatures revealed altered oligodendrocyte function in the brain, and 4EPS impaired oligodendrocyte maturation in mice and decreased oligodendrocyte\u2013neuron interactions in ex vivo brain cultures. Mice colonized with 4EP-producing bacteria exhibited reduced myelination of neuronal axons. Altered myelination dynamics in the brain have been associated with behavioural outcomes. Accordingly, we observed that mice exposed to 4EPS displayed anxiety-like behaviours, and pharmacological treatments that promote oligodendrocyte differentiation prevented the behavioural effects of 4EPS. These findings reveal that a gut-derived molecule influences complex behaviours in mice through effects on oligodendrocyte function and myelin patterning in the brain.", "doi": "10.1038/s41586-022-04396-8", "pmcid": "PMC9170029", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2022-02-24", "series_number": "7899", "volume": "602", "issue": "7899", "pages": "647-653" }, { "id": "authors:72vgc-kv512", "collection": "authors", "collection_id": "72vgc-kv512", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200526-071834189", "type": "article", "title": "Focused ultrasound excites cortical neurons via mechanosensitive calcium accumulation and ion channel amplification", "author": [ { "family_name": "Yoo", "given_name": "Sangjin", "orcid": "0000-0002-0449-4242", "clpid": "Yoo-Sangjin" }, { "family_name": "Mittelstein", "given_name": "David R.", "orcid": "0000-0001-8747-0483", "clpid": "Mittelstein-D-R" }, { "family_name": "Hurt", "given_name": "Robert C.", "orcid": "0000-0002-4347-6901", "clpid": "Hurt-Robert-C" }, { "family_name": "Lacroix", "given_name": "Jerome", "orcid": "0000-0001-5687-0652", "clpid": "Lacroix-Jerome" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Ultrasonic neuromodulation has the unique potential to provide non-invasive control of neural activity in deep brain regions with high spatial precision and without chemical or genetic modification. However, the biomolecular and cellular mechanisms by which focused ultrasound excites mammalian neurons have remained unclear, posing significant challenges for the use of this technology in research and potential clinical applications. Here, we show that focused ultrasound excites primary murine cortical neurons in culture through a primarily mechanical mechanism mediated by specific calcium-selective mechanosensitive ion channels. The activation of these channels results in a gradual build-up of calcium, which is amplified by calcium- and voltage-gated channels, generating a burst firing response. Cavitation, temperature changes, large-scale deformation, and synaptic transmission are not required for this excitation to occur. Pharmacological and genetic inhibition of specific ion channels leads to reduced responses to ultrasound, while over-expressing these channels results in stronger ultrasonic stimulation. These findings provide a mechanistic explanation for the effect of ultrasound on neurons to facilitate the further development of ultrasonic neuromodulation and sonogenetics as tools for neuroscience research.", "doi": "10.1038/s41467-022-28040-1", "pmcid": "PMC8789820", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2022-01-25", "volume": "13", "pages": "Art. No. 493" }, { "id": "authors:q7vbx-5eb89", "collection": "authors", "collection_id": "q7vbx-5eb89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210929-163841106", "type": "article", "title": "Mechanics of ultrasonic neuromodulation in a mouse subject", "author": [ { "family_name": "Salahshoor", "given_name": "Hossein", "orcid": "0000-0002-7264-7650", "clpid": "Salahshoor-Hossein" }, { "family_name": "Guo", "given_name": "Hongsun", "clpid": "Guo-Hongsun" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Ortiz", "given_name": "Michael", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" } ], "abstract": "Ultrasound neuromodulation (UNM), where a region in the brain is targeted by focused ultrasound (FUS), which, in turn, causes excitation or inhibition of neural activity, has recently received considerable attention as a promising tool for neuroscience. Despite its great potential, several aspects of UNM are still unknown. An important question pertains to the off-target sensory effects of UNM and their dependence on stimulation frequency. To understand these effects, we have developed a finite-element model of a mouse, including elasticity and viscoelasticity, and used it to interrogate the response of mouse models to focused ultrasound (FUS). We find that, while some degree of focusing and magnification of the signal is achieved within the brain, the induced pressure-wave pattern is complex and delocalized. In addition, we find that the brain is largely insulated, or 'cloaked', from shear waves by the cranium and that the shear waves are largely carried away from the skull by the vertebral column, which acts as a waveguide. We find that, as expected, this waveguide mechanism is strongly frequency dependent, which may contribute to the frequency dependence of UNM effects. Our calculations further suggest that off-target skin locations experience displacements and stresses at levels that, while greatly attenuated from the source, could nevertheless induce sensory responses in the subject.", "doi": "10.1016/j.eml.2021.101539", "pmcid": "PMC10760995", "issn": "2352-4316", "publisher": "Elsevier", "publication": "Extreme Mechanics Letters", "publication_date": "2022-01", "volume": "50", "pages": "101539" }, { "id": "authors:dbnnj-v1v69", "collection": "authors", "collection_id": "dbnnj-v1v69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190429-085425670", "type": "article", "title": "Acoustically triggered mechanotherapy using genetically encoded gas vesicles", "author": [ { "family_name": "Bar-Zion", "given_name": "Avinoam", "orcid": "0000-0002-7564-9467", "clpid": "Bar-Zion-Avinoam" }, { "family_name": "Nourmahnad", "given_name": "Atousa", "orcid": "0000-0001-5208-0020", "clpid": "Nourmahnad-Atousa" }, { "family_name": "Mittelstein", "given_name": "David R.", "orcid": "0000-0001-8747-0483", "clpid": "Mittelstein-David-R" }, { "family_name": "Shivaei", "given_name": "Shirin", "orcid": "0000-0002-6894-3289", "clpid": "Shivaei-Shirin" }, { "family_name": "Yoo", "given_name": "Sangjin", "orcid": "0000-0002-0449-4242", "clpid": "Yoo-Sangjin" }, { "family_name": "Buss", "given_name": "Marjorie T.", "orcid": "0000-0002-4266-9197", "clpid": "Buss-Marjorie-T" }, { "family_name": "Hurt", "given_name": "Robert C.", "orcid": "0000-0002-4347-6901", "clpid": "Hurt-Robert-C" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Abedi", "given_name": "Mohamad H.", "orcid": "0000-0001-9717-6288", "clpid": "Abedi-Mohamad-H" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Swift", "given_name": "Margaret B.", "orcid": "0000-0001-9610-0687", "clpid": "Swift-Margaret-B" }, { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Recent advances in molecular engineering and synthetic biology provide biomolecular and cell-based therapies with a high degree of molecular specificity, but limited spatiotemporal control. Here we show that biomolecules and cells can be engineered to deliver potent mechanical effects at specific locations inside the body through ultrasound-induced inertial cavitation. This capability is enabled by gas vesicles, a unique class of genetically encodable air-filled protein nanostructures. We show that low-frequency ultrasound can convert these biomolecules into micrometre-scale cavitating bubbles, unleashing strong local mechanical effects. This enables engineered gas vesicles to serve as remotely actuated cell-killing and tissue-disrupting agents, and allows genetically engineered cells to lyse, release molecular payloads and produce local mechanical damage on command. We demonstrate the capabilities of biomolecular inertial cavitation in vitro, in cellulo and in vivo, including in a mouse model of tumour-homing probiotic therapy.", "doi": "10.1038/s41565-021-00971-8", "issn": "1748-3387", "publisher": "Nature Publishing Group", "publication": "Nature Nanotechnology", "publication_date": "2021-12", "series_number": "12", "volume": "16", "issue": "12", "pages": "1403-1412" }, { "id": "authors:1ka0f-tfw77", "collection": "authors", "collection_id": "1ka0f-tfw77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210409-105849791", "type": "article", "title": "Wireless 3D Surgical Navigation and Tracking System With 100\u03bcm Accuracy Using Magnetic-Field Gradient-Based Localization", "author": [ { "family_name": "Sharma", "given_name": "Saransh", "orcid": "0000-0002-5052-4932", "clpid": "Sharma-Saransh" }, { "family_name": "Telikicherla", "given_name": "Aditya", "clpid": "Telikicherla-Aditya" }, { "family_name": "Ding", "given_name": "Grace", "orcid": "0000-0002-0484-3385", "clpid": "Ding-Grace" }, { "family_name": "Aghlmand", "given_name": "Fatemeh", "orcid": "0000-0002-5103-9314", "clpid": "Aghlmand-Fatemeh" }, { "family_name": "Talkhooncheh", "given_name": "Arian Hashemi", "orcid": "0000-0001-8946-5047", "clpid": "Talkhooncheh-Arian-Hashemi" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Emami", "given_name": "Azita", "orcid": "0000-0002-6945-9958", "clpid": "Emami-A" } ], "abstract": "This paper describes a high-resolution 3D navigation and tracking system using magnetic field gradients, that can replace X-Ray fluoroscopy in high-precision surgeries. Monotonically varying magnetic fields in X, Y and Z directions are created in the field-of-view (FOV) to produce magnetic field gradients, which encode each spatial point uniquely. Highly miniaturized, wireless and battery-less devices, capable of measuring their local magnetic field, are designed to sense the gradient field. One such device can be attached to an implant inside the body and another to a surgical tool, such that both can simultaneously measure and communicate the magnetic field at their respective locations to an external receiver. The relative location of the two devices on a real-time display can enable precise surgical navigation without using X-Rays. A prototype device is designed consisting of a micro-chip fabricated in 65nm CMOS technology, a 3D magnetic sensor and an inductor-coil. Planar electromagnetic coils are designed for creating the 3D magnetic field gradients in a 20 \u00d7 20 \u00d7 10cm\u00b3 of scalable FOV. Unambiguous and orientation-independent spatial encoding is achieved by: (i) using the gradient in the total field magnitude instead of only the Z-component; and (ii) using a combination of the gradient fields to correct for the non-linearity and non-monotonicity in X and Y gradients. The resultant X and Y FOV yield \u226590% utilization of their respective coil-span. The system is tested in vitro to demonstrate a localization accuracy of <100 \u03bcm in 3D, the highest reported to the best of our knowledge.", "doi": "10.1109/tmi.2021.3071120", "issn": "0278-0062", "publisher": "IEEE", "publication": "IEEE Transactions on Medical Imaging", "publication_date": "2021-08", "series_number": "8", "volume": "40", "issue": "8", "pages": "2066-2079" }, { "id": "authors:84277-csp88", "collection": "authors", "collection_id": "84277-csp88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210601-112517625", "type": "article", "title": "Ultrasensitive ultrasound imaging of gene expression with signal unmixing", "author": [ { "family_name": "Sawyer", "given_name": "Daniel P.", "orcid": "0000-0003-2926-191X", "clpid": "Sawyer-Daniel-P" }, { "family_name": "Bar-Zion", "given_name": "Avinoam", "orcid": "0000-0002-7564-9467", "clpid": "Bar-Zion-Avinoam" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Shivaei", "given_name": "Shirin", "orcid": "0000-0002-6894-3289", "clpid": "Shivaei-Shirin" }, { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Acoustic reporter genes (ARGs) that encode air-filled gas vesicles enable ultrasound-based imaging of gene expression in genetically modified bacteria and mammalian cells, facilitating the study of cellular function in deep tissues. Despite the promise of this technology for biological research and potential clinical applications, the sensitivity with which ARG-expressing cells can be visualized is currently limited. Here we present burst ultrasound reconstructed with signal templates (BURST)\u2014an ARG imaging paradigm that improves the cellular detection limit by more than 1,000-fold compared to conventional methods. BURST takes advantage of the unique temporal signal pattern produced by gas vesicles as they collapse under acoustic pressure above a threshold defined by the ARG. By extracting the unique pattern of this signal from total scattering, BURST boosts the sensitivity of ultrasound to image ARG-expressing cells, as demonstrated in vitro and in vivo in the mouse gastrointestinal tract and liver. Furthermore, in dilute cell suspensions, BURST imaging enables the detection of gene expression in individual bacteria and mammalian cells. The resulting abilities of BURST expand the potential use of ultrasound for non-invasive imaging of cellular functions.", "doi": "10.1038/s41592-021-01229-w", "pmcid": "PMC8363212", "issn": "1548-7091", "publisher": "Nature Publishing Group", "publication": "Nature Methods", "publication_date": "2021-08", "series_number": "8", "volume": "18", "issue": "8", "pages": "945-952" }, { "id": "authors:gbtka-6zy24", "collection": "authors", "collection_id": "gbtka-6zy24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210713-205818850", "type": "article", "title": "Self-assembly of protein superstructures by physical interactions under cytoplasm-like conditions", "author": [ { "family_name": "Yao", "given_name": "Yuxing", "orcid": "0000-0003-0337-6372", "clpid": "Yao-Yuxing" }, { "family_name": "Jin", "given_name": "Zhiyang", "clpid": "Jin-Zhiyang" }, { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "The structure-driven assembly of multimeric protein complexes and the formation of intracellular phase-like protein condensates have been the subject of intense research. However, the assembly of larger superstructures comprising cellular components, such as protein nanoparticles driven by general physical rather than specific biochemical interactions, remains relatively uncharacterized. Here, we use gas vesicles (GVs)\u2014genetically encoded protein nanoparticles that form ordered intracellular clusters\u2014as a model system to study the forces driving multiparticle assembly under cytoplasm-like conditions. Our calculations and experimental results show that the ordered assembly of GVs can be achieved by screening their mutual electrostatic repulsion with electrolytes and creating a crowding force with dissolved macromolecules. The precise balance of these forces results in different packing configurations. Biomacromolecules such as polylysine and DNA are capable of driving GV clustering. These results provide basic insights into how physically driven interactions affect the formation of protein superstructures, offer guidance for manipulating nanoparticle assembly in cellular environments through synthetic biology methods, and inform research on the biotechnology applications of GVs.", "doi": "10.1016/j.bpj.2021.05.007", "pmcid": "PMC8390860", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2021-07-06", "series_number": "13", "volume": "120", "issue": "13", "pages": "2701-2709" }, { "id": "authors:xc1ra-y2z74", "collection": "authors", "collection_id": "xc1ra-y2z74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210524-105548475", "type": "article", "title": "Ultrafast amplitude modulation for molecular and hemodynamic ultrasound imaging", "author": [ { "family_name": "Rabut", "given_name": "Claire", "orcid": "0000-0002-4571-1215", "clpid": "Rabut-Claire" }, { "family_name": "Wu", "given_name": "Di", "orcid": "0000-0002-6848-668X", "clpid": "Wu-Di" }, { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Jin", "given_name": "Zhiyang", "orcid": "0000-0002-4411-6991", "clpid": "Jin-Zhiyang" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Ultrasound is playing an emerging role in molecular and cellular imaging thanks to new micro- and nanoscale contrast agents and reporter genes. Acoustic methods for the selective in vivo detection of these imaging agents are needed to maximize their impact in biology and medicine. Existing ultrasound pulse sequences use the nonlinearity in contrast agents' response to acoustic pressure to distinguish them from mostly linear tissue scattering. However, such pulse sequences typically scan the sample using focused transmissions, resulting in a limited frame rate and restricted field of view. Meanwhile, existing wide-field scanning techniques based on plane wave transmissions suffer from limited sensitivity or nonlinear artifacts. To overcome these limitations, we introduce an ultrafast nonlinear imaging modality combining amplitude-modulated pulses, multiplane wave transmissions, and selective coherent compounding. This technique achieves contrast imaging sensitivity comparable to much slower gold-standard amplitude modulation sequences and enables the acquisition of larger and deeper fields of view, while providing a much faster imaging framerate of 3.2\u2009kHz. Additionally, it enables simultaneous nonlinear and linear image formation and allows concurrent monitoring of phenomena accessible only at ultrafast framerates, such as blood volume variations. We demonstrate the performance of this ultrafast amplitude modulation technique by imaging gas vesicles, an emerging class of genetically encodable biomolecular contrast agents, in several in vitro and in vivo contexts. These demonstrations include the rapid discrimination of moving contrast agents and the real-time monitoring of phagolysosomal function in the mouse liver.", "doi": "10.1063/5.0050807", "pmcid": "PMC8205510", "issn": "0003-6951", "publisher": "American Institute of Physics", "publication": "Applied Physics Letters", "publication_date": "2021-06-14", "series_number": "24", "volume": "118", "issue": "24", "pages": "Art. No. 244102" }, { "id": "authors:va8et-d4k10", "collection": "authors", "collection_id": "va8et-d4k10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200515-085712838", "type": "article", "title": "Single-trial decoding of movement intentions using functional ultrasound neuroimaging", "author": [ { "family_name": "Norman", "given_name": "Sumner L.", "orcid": "0000-0001-9945-697X", "clpid": "Norman-Sumner-L" }, { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Christopoulos", "given_name": "Vasileios N.", "orcid": "0000-0002-0541-8700", "clpid": "Christopoulos-Vasileios-N" }, { "family_name": "Griggs", "given_name": "Whitney S.", "orcid": "0000-0003-2941-6803", "clpid": "Griggs-Whitney-S" }, { "family_name": "Demen\u00e9", "given_name": "Charlie", "orcid": "0000-0002-5329-700X", "clpid": "Demen\u00e9-Charlie" }, { "family_name": "Tanter", "given_name": "Micka\u00ebl", "orcid": "0000-0001-7739-8051", "clpid": "Tanter-Micka\u00ebl" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Andersen", "given_name": "Richard A.", "orcid": "0000-0002-7947-0472", "clpid": "Andersen-R-A" } ], "abstract": "New technologies are key to understanding the dynamic activity of neural circuits and systems in the brain. Here, we show that a minimally invasive approach based on ultrasound can be used to detect the neural correlates of movement planning, including directions and effectors. While non-human primates (NHPs) performed memory-guided movements, we used functional ultrasound (fUS) neuroimaging to record changes in cerebral blood volume with 100 \u03bcm resolution. We recorded from outside the dura above the posterior parietal cortex, a brain area important for spatial perception, multisensory integration, and movement planning. We then used fUS signals from the delay period before movement to decode the animals' intended direction and effector. Single-trial decoding is a prerequisite to brain-machine interfaces, a key application that could benefit from this technology. These results are a critical step in the development of neuro-recording and brain interface tools that are less invasive, high resolution, and scalable.", "doi": "10.1016/j.neuron.2021.03.003", "pmcid": "PMC8105283", "issn": "0896-6273", "publisher": "Cell Press", "publication": "Neuron", "publication_date": "2021-05-05", "series_number": "9", "volume": "109", "issue": "9", "pages": "1554-1566" }, { "id": "authors:bssca-23370", "collection": "authors", "collection_id": "bssca-23370", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210201-105011829", "type": "article", "title": "Genetically encodable materials for non-invasive biological imaging", "author": [ { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Sigmund", "given_name": "Felix", "orcid": "0000-0002-3316-0882", "clpid": "Sigmund-Felix" }, { "family_name": "Westmeyer", "given_name": "Gil Gregor", "orcid": "0000-0001-7224-8919", "clpid": "Westmeyer-Gil-Gregor" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Many questions in basic biology and medicine require the ability to visualize the function of specific cells and molecules inside living organisms. In this context, technologies such as ultrasound, optoacoustics and magnetic resonance provide non-invasive imaging access to deep-tissue regions, as used in many laboratories and clinics to visualize anatomy and physiology. In addition, recent work has enabled these technologies to image the location and function of specific cells and molecules inside the body by coupling the physics of sound waves, nuclear spins and light absorption to unique protein-based materials. These materials, which include air-filled gas vesicles, capsid-like nanocompartments, pigment-producing enzymes and transmembrane transporters, enable new forms of biomolecular and cellular contrast. The ability of these protein-based contrast agents to be genetically encoded and produced by cells creates opportunities for unprecedented in vivo studies of cellular function, while their amenability to genetic engineering enables atomic-level design of their physical, chemical and biological properties.", "doi": "10.1038/s41563-020-00883-3", "issn": "1476-1122", "publisher": "Nature Publishing Group", "publication": "Nature Materials", "publication_date": "2021-05", "series_number": "5", "volume": "20", "issue": "5", "pages": "585-592" }, { "id": "authors:3r2p1-tan16", "collection": "authors", "collection_id": "3r2p1-tan16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210125-082358436", "type": "article", "title": "Measuring gas vesicle dimensions by electron microscopy", "author": [ { "family_name": "Dutka", "given_name": "Przemys\u0142aw", "orcid": "0000-0003-3819-1618", "clpid": "Dutka-Przemys\u0142aw" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Metskas", "given_name": "Lauren Ann", "orcid": "0000-0002-8073-6960", "clpid": "Metskas-Lauren-Ann" }, { "family_name": "Chen", "given_name": "Songye", "orcid": "0000-0001-5407-5049", "clpid": "Chen-Songye" }, { "family_name": "Hurt", "given_name": "Robert C.", "orcid": "0000-0002-4347-6901", "clpid": "Hurt-Robert-C" }, { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Gas vesicles (GVs) are cylindrical or spindle\u2010shaped protein nanostructures filled with air and used for flotation by various cyanobacteria, heterotrophic bacteria, and Archaea. Recently, GVs have gained interest in biotechnology applications due to their ability to serve as imaging agents and actuators for ultrasound, magnetic resonance and several optical techniques. The diameter of GVs is a crucial parameter contributing to their mechanical stability, buoyancy function and evolution in host cells, as well as their properties in imaging applications. Despite its importance, reported diameters for the same types of GV differ depending on the method used for its assessment. Here, we provide an explanation for these discrepancies and utilize electron microscopy (EM) techniques to accurately estimate the diameter of the most commonly studied types of GVs. We show that during air drying on the EM grid, GVs flatten, leading to a ~1.5\u2010fold increase in their apparent diameter. We demonstrate that GVs' diameter can be accurately determined by direct measurements from cryo\u2010EM samples or alternatively indirectly derived from widths of flat collapsed and negatively stained GVs. Our findings help explain the inconsistency in previously reported data and provide accurate methods to measure GVs dimensions.", "doi": "10.1002/pro.4056", "pmcid": "PMC8040859", "issn": "0961-8368", "publisher": "Wiley", "publication": "Protein Science", "publication_date": "2021-05", "series_number": "5", "volume": "30", "issue": "5", "pages": "1081-1086" }, { "id": "authors:cbgry-sfy56", "collection": "authors", "collection_id": "cbgry-sfy56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210505-072449111", "type": "article", "title": "Biomagnetic Materials: Spatial Control of Probiotic Bacteria in the Gastrointestinal Tract Assisted by Magnetic Particles (Adv. Mater. 17/2021)", "author": [ { "family_name": "Buss", "given_name": "Marjorie T.", "orcid": "0000-0002-4266-9197", "clpid": "Buss-Marjorie-T" }, { "family_name": "Ramesh", "given_name": "Pradeep", "clpid": "Ramesh-Pradeep" }, { "family_name": "English", "given_name": "Max Atticus", "clpid": "English-Max-Atticus" }, { "family_name": "Lee\u2010Gosselin", "given_name": "Audrey", "clpid": "Lee\u2010Gosselin-Audrey" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Bacterial agents engineered to diagnose or treat gastrointestinal (GI) diseases have limited ability to colonize specific regions of the GI tract. In article number 2007473, Mikhail G. Shapiro and co\u2010workers show that a composite biomagnetic material comprising microscale magnetic particles and probiotic bacteria can be used, in conjunction with external magnets, to improve the bacterial agents' ability to localize and colonize inside the gut.", "doi": "10.1002/adma.202170134", "issn": "0935-9648", "publisher": "Wiley", "publication": "Advanced Materials", "publication_date": "2021-04-28", "series_number": "17", "volume": "33", "issue": "17", "pages": "Art. No. 2170134" }, { "id": "authors:nbgy3-d7q65", "collection": "authors", "collection_id": "nbgy3-d7q65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210315-102208370", "type": "article", "title": "Spatial Control of Probiotic Bacteria in the Gastrointestinal Tract Assisted by Magnetic Particles", "author": [ { "family_name": "Buss", "given_name": "Marjorie T.", "clpid": "Buss-Marjorie-T" }, { "family_name": "Ramesh", "given_name": "Pradeep", "clpid": "Ramesh-Pradeep" }, { "family_name": "English", "given_name": "Max Atticus", "clpid": "English-Max-Atticus" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Engineered probiotics have the potential to diagnose and treat a variety of gastrointestinal (GI) diseases. However, these exogenous bacterial agents have limited ability to effectively colonize specific regions of the GI tract due to a lack of external control over their localization and persistence. Magnetic fields are well suited to providing such control, since they freely penetrate biological tissues. However, they are difficult to apply with sufficient strength to directly manipulate magnetically labeled cells in deep tissue such as the GI tract. Here, it is demonstrated that a composite biomagnetic material consisting of microscale magnetic particles and probiotic bacteria, when orally administered and combined with an externally applied magnetic field, enables the trapping and retention of probiotic bacteria within the GI tract of mice. This technology improves the ability of these probiotic agents to accumulate at specific locations and stably colonize without antibiotic treatment. By enhancing the ability of GI\u2010targeted probiotics to be at the right place at the right time, cellular localization assisted by magnetic particles (CLAMP) adds external physical control to an important emerging class of microbial theranostics.", "doi": "10.1002/adma.202007473", "issn": "0935-9648", "publisher": "Wiley", "publication": "Advanced Materials", "publication_date": "2021-04-28", "series_number": "17", "volume": "33", "issue": "17", "pages": "Art. No. 2007473" }, { "id": "authors:16gy2-zr896", "collection": "authors", "collection_id": "16gy2-zr896", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191113-111723156", "type": "article", "title": "Genetically Encoded Phase Contrast Agents for Digital Holographic Microscopy", "author": [ { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-A" }, { "family_name": "Bedrossian", "given_name": "Manuel", "clpid": "Bedrossian-Manuel" }, { "family_name": "Lee", "given_name": "Justin", "orcid": "0000-0002-3657-4386", "clpid": "Lee-Justin" }, { "family_name": "Ho", "given_name": "Gabrielle H.", "orcid": "0000-0002-8511-5549", "clpid": "Ho-Gabrielle-H" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Nadeau", "given_name": "Jay L.", "orcid": "0000-0001-5258-0076", "clpid": "Nadeau-J-L" } ], "abstract": "Quantitative phase imaging and digital holographic microscopy have shown great promise for visualizing the motion, structure, and physiology of microorganisms and mammalian cells in three dimensions. However, these imaging techniques currently lack molecular contrast agents analogous to the fluorescent dyes and proteins that have revolutionized fluorescence microscopy. Here we introduce the first genetically encodable phase contrast agents based on gas vesicles. The relatively low index of refraction of the air-filled core of gas vesicles results in optical phase advancement relative to aqueous media, making them a \"positive\" phase contrast agent easily distinguished from organelles, dyes, or microminerals. We demonstrate this capability by identifying and tracking the motion of gas vesicles and gas vesicle-expressing bacteria using digital holographic microscopy, and by imaging the uptake of engineered gas vesicles by mammalian cells. These results give phase imaging a biomolecular contrast agent, expanding the capabilities of this powerful technology for three-dimensional biological imaging.", "doi": "10.1021/acs.nanolett.0c03159", "issn": "1530-6984", "publisher": "American Chemical Society", "publication": "Nano Letters", "publication_date": "2020-11-11", "series_number": "11", "volume": "20", "issue": "11", "pages": "8127-8134" }, { "id": "authors:21m8x-s8281", "collection": "authors", "collection_id": "21m8x-s8281", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201019-101559925", "type": "article", "title": "Ultrasound Technologies for Imaging and Modulating Neural Activity", "author": [ { "family_name": "Rabut", "given_name": "Claire", "clpid": "Rabut-C" }, { "family_name": "Yoo", "given_name": "Sangjin", "orcid": "0000-0002-0449-4242", "clpid": "Yoo-Sangjin" }, { "family_name": "Hurt", "given_name": "Robert C.", "orcid": "0000-0002-4347-6901", "clpid": "Hurt-R-C" }, { "family_name": "Jin", "given_name": "Zhiyang", "orcid": "0000-0002-4411-6991", "clpid": "Jin-Zhiyang" }, { "family_name": "Li", "given_name": "Hongyi", "orcid": "0000-0001-6970-0230", "clpid": "Li-Hongyi" }, { "family_name": "Guo", "given_name": "Hongsun", "clpid": "Guo-Hongsun" }, { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Visualizing and perturbing neural activity on a brain-wide scale in model animals and humans is a major goal of neuroscience technology development. Established electrical and optical techniques typically break down at this scale due to inherent physical limitations. In contrast, ultrasound readily permeates the brain, and in some cases the skull, and interacts with tissue with a fundamental resolution on the order of 100 \u03bcm and 1 ms. This basic ability has motivated major efforts to harness ultrasound as a modality for large-scale brain imaging and modulation. These efforts have resulted in already-useful neuroscience tools, including high-resolution hemodynamic functional imaging, focused ultrasound neuromodulation, and local drug delivery. Furthermore, recent breakthroughs promise to connect ultrasound to neurons at the genetic level for biomolecular imaging and sonogenetic control. In this article, we review the state of the art and ongoing developments in ultrasonic neurotechnology, building from fundamental principles to current utility, open questions, and future potential.", "doi": "10.1016/j.neuron.2020.09.003", "issn": "0896-6273", "publisher": "Cell Press", "publication": "Neuron", "publication_date": "2020-10-14", "series_number": "1", "volume": "108", "issue": "1", "pages": "93-110" }, { "id": "authors:5gfps-pzn07", "collection": "authors", "collection_id": "5gfps-pzn07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200911-133137357", "type": "article", "title": "Biomolecular Ultrasound Imaging of Phagolysosomal Function", "author": [ { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Lee", "given_name": "Justin", "orcid": "0000-0002-3657-4386", "clpid": "Lee-Justin" }, { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Swift", "given_name": "Margaret B.", "orcid": "0000-0001-9610-0687", "clpid": "Swift-Margaret-B" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Phagocytic clearance and lysosomal processing of pathogens and debris are essential functions of the innate immune system. However, the assessment of these functions in vivo is challenging because most nanoscale contrast agents compatible with noninvasive imaging techniques are made from nonbiodegradable synthetic materials that do not undergo regular lysosomal degradation. To overcome this challenge, we describe the use of an all-protein contrast agent to directly visualize and quantify phagocytic and lysosomal activities in vivo by ultrasound imaging. This contrast agent is based on gas vesicles (GVs), a class of air-filled protein nanostructures naturally expressed by buoyant microbes. Using a combination of ultrasound imaging, pharmacology, immunohistology, and live-cell optical microscopy, we show that after intravenous injection, GVs are cleared from circulation by liver-resident macrophages. Once internalized, the GVs undergo lysosomal degradation, resulting in the elimination of their ultrasound contrast. By noninvasively monitoring the temporal dynamics of GV-generated ultrasound signal in circulation and in the liver and fitting them with a pharmacokinetic model, we can quantify the rates of phagocytosis and lysosomal degradation in living animals. We demonstrate the utility of this method by showing how these rates are perturbed in two models of liver dysfunction: phagocyte deficiency and nonalcoholic fatty liver disease. The combination of proteolytically degradable nanoscale contrast agents and quantitative ultrasound imaging thus enables noninvasive functional imaging of cellular degradative processes.", "doi": "10.1021/acsnano.0c05912", "pmcid": "PMC7685203", "issn": "1936-0851", "publisher": "American Chemical Society", "publication": "ACS Nano", "publication_date": "2020-09-22", "series_number": "9", "volume": "14", "issue": "9", "pages": "12210-12221" }, { "id": "authors:yxajs-jh187", "collection": "authors", "collection_id": "yxajs-jh187", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200713-133644814", "type": "article", "title": "Acoustic biosensors for ultrasound imaging of enzyme activity", "author": [ { "family_name": "Lakshmanan", "given_name": "Anupama", "orcid": "0000-0002-6702-837X", "clpid": "Lakshmanan-Anupama" }, { "family_name": "Jin", "given_name": "Zhiyang", "orcid": "0000-0002-4411-6991", "clpid": "Jin-Zhiyang" }, { "family_name": "Nety", "given_name": "Suchita P.", "orcid": "0000-0002-4201-1061", "clpid": "Nety-Suchita-P" }, { "family_name": "Sawyer", "given_name": "Daniel P.", "orcid": "0000-0003-2926-191X", "clpid": "Sawyer-Daniel-P" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Swift", "given_name": "Margaret B.", "orcid": "0000-0001-9610-0687", "clpid": "Swift-Margaret-B" }, { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Visualizing biomolecular and cellular processes inside intact living organisms is a major goal of chemical biology. However, existing molecular biosensors, based primarily on fluorescent emission, have limited utility in this context due to the scattering of light by tissue. In contrast, ultrasound can easily image deep tissue with high spatiotemporal resolution, but lacks the biosensors needed to connect its contrast to the activity of specific biomolecules such as enzymes. To overcome this limitation, we introduce the first genetically encodable acoustic biosensors\u2014molecules that 'light up' in ultrasound imaging in response to protease activity. These biosensors are based on a unique class of air-filled protein nanostructures called gas vesicles, which we engineered to produce nonlinear ultrasound signals in response to the activity of three different protease enzymes. We demonstrate the ability of these biosensors to be imaged in vitro, inside engineered probiotic bacteria, and in vivo in the mouse gastrointestinal tract.", "doi": "10.1038/s41589-020-0591-0", "pmcid": "PMC7713704", "issn": "1552-4450", "publisher": "Nature Publishing Group", "publication": "Nature Chemical Biology", "publication_date": "2020-09", "series_number": "9", "volume": "16", "issue": "9", "pages": "988-996" }, { "id": "authors:mf5w4-kxd98", "collection": "authors", "collection_id": "mf5w4-kxd98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200420-130655482", "type": "article", "title": "Thermal Control of Engineered T-cells", "author": [ { "family_name": "Abedi", "given_name": "Mohamad H.", "orcid": "0000-0001-9717-6288", "clpid": "Abedi-Mohamad-H" }, { "family_name": "Lee", "given_name": "Justin", "orcid": "0000-0002-3657-4386", "clpid": "Lee-Justin" }, { "family_name": "Piraner", "given_name": "Dan I.", "orcid": "0000-0003-3857-9487", "clpid": "Piraner-Dan-I" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Genetically engineered T-cells are being developed to perform a variety of therapeutic functions. However, no robust mechanisms exist to externally control the activity of T-cells at specific locations within the body. Such spatiotemporal control could help mitigate potential off-target toxicity due to incomplete molecular specificity in applications such as T-cell immunotherapy against solid tumors. Temperature is a versatile external control signal that can be delivered to target tissues in vivo using techniques such as focused ultrasound and magnetic hyperthermia. Here, we test the ability of heat shock promoters to mediate thermal actuation of genetic circuits in primary human T-cells in the well-tolerated temperature range of 37\u201342 \u00b0C, and introduce genetic architectures enabling the tuning of the amplitude and duration of thermal activation. We demonstrate the use of these circuits to control the expression of chimeric antigen receptors and cytokines, and the killing of target tumor cells. This technology provides a critical tool to direct the activity of T-cells after they are deployed inside the body.", "doi": "10.1021/acssynbio.0c00238", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2020-08-21", "series_number": "8", "volume": "9", "issue": "8", "pages": "1941-1950" }, { "id": "authors:j38vz-wd018", "collection": "authors", "collection_id": "j38vz-wd018", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190401-103122114", "type": "article", "title": "Genetically Encodable Contrast Agents for Optical Coherence Tomography", "author": [ { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Chou", "given_name": "Li-dek", "clpid": "Chou-Li-dek" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Patel", "given_name": "Amit K.", "clpid": "Patel-Amit-K" }, { "family_name": "Welsbie", "given_name": "Derek S.", "clpid": "Welsbie-Derek-S" }, { "family_name": "Chao", "given_name": "Daniel L.", "clpid": "Chao-Daniel-L" }, { "family_name": "Ramalingam", "given_name": "Tirunelveli", "clpid": "Ramalingam-Tirunelveli" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Optical coherence tomography (OCT) has gained wide adoption in biological research and medical imaging due to its exceptional tissue penetration, 3D imaging speed, and rich contrast. However, OCT plays a relatively small role in molecular and cellular imaging due to the lack of suitable biomolecular contrast agents. In particular, while the green fluorescent protein has provided revolutionary capabilities to fluorescence microscopy by connecting it to cellular functions such as gene expression, no equivalent reporter gene is currently available for OCT. Here, we introduce gas vesicles, a class of naturally evolved gas-filled protein nanostructures, as genetically encodable OCT contrast agents. The differential refractive index of their gas compartments relative to surrounding aqueous tissue and their nanoscale motion enables gas vesicles to be detected by static and dynamic OCT. Furthermore, the OCT contrast of gas vesicles can be selectively erased in situ with ultrasound, allowing unambiguous assignment of their location. In addition, gas vesicle clustering modulates their temporal signal, enabling the design of dynamic biosensors. We demonstrate the use of gas vesicles as reporter genes in bacterial colonies and as purified contrast agents in vivo in the mouse retina. Our results expand the utility of OCT to image a wider variety of cellular and molecular processes.", "doi": "10.1021/acsnano.9b08432", "pmcid": "PMC7685218", "issn": "1936-0851", "publisher": "American Chemical Society", "publication": "ACS Nano", "publication_date": "2020-07-28", "series_number": "7", "volume": "14", "issue": "7", "pages": "7823-7831" }, { "id": "authors:v4qcx-njq83", "collection": "authors", "collection_id": "v4qcx-njq83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200420-131214393", "type": "article", "title": "Transcranial Focused Ultrasound Generates Skull-Conducted Shear Waves: Computational Model and Implications for Neuromodulation", "author": [ { "family_name": "Salahshoor", "given_name": "Hossein", "clpid": "Salahshoor-Hossein" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Ortiz", "given_name": "Michael", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" } ], "abstract": "Focused ultrasound (FUS) is an established technique for non-invasive surgery and has recently attracted considerable attention as a potential method for non-invasive neuromodulation. While the pressure waves in FUS procedures have been extensively studied in this context, the accompanying shear waves are often neglected due to the relatively high shear compliance of soft tissues. However, in bony structures such as the skull, acoustic pressure can also induce significant shear waves that could propagate outside the ultrasound focus. Here, we investigate wave propagation in the human cranium by means of a finite-element model that accounts for the anatomy, elasticity, and viscoelasticity of the skull and brain. We show that, when a region on the scalp is subjected to FUS, the skull acts as a waveguide for shear waves that propagate with a speed close to 1500 m/s, reaching off-target structures such as the cochlea. In particular, when a sharp onset of FUS is introduced in a zone proximal to the intersection of the parietal and temporal cranium, the bone-propagated shear waves reach the inner ear in about 40\u2009\u03bcs, leading to cumulative displacements of about 1\u2009\u03bcm. We further quantify the effect of ramped and sharp application of FUS on the cumulative displacements in the inner ear. Our results help explain the off-target auditory responses observed during neuromodulation experiments and inform the development of mitigation and sham control strategies.", "doi": "10.1063/5.0011837", "pmcid": "PMC7386437", "issn": "0003-6951", "publisher": "American Institute of Physics", "publication": "Applied Physics Letters", "publication_date": "2020-07-20", "series_number": "3", "volume": "117", "issue": "3", "pages": "Art. No. 033702" }, { "id": "authors:hzt0y-7gd52", "collection": "authors", "collection_id": "hzt0y-7gd52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200507-125032304", "type": "article", "title": "Acoustically Targeted Chemogenetics for Noninvasive Control of Neural Circuits", "author": [ { "family_name": "Szablowski", "given_name": "Jerzy", "orcid": "0000-0001-7851-5408", "clpid": "Szablowski-J-O" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-A" }, { "family_name": "Lue", "given_name": "Brian", "clpid": "Lue-Brian" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-D" }, { "family_name": "Shapiro", "given_name": "Mikhail", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Existing treatments for brain disorders aim to modulate the activity of neural circuits, but are either not cell type-specific, lack spatial targeting, or require invasive procedures. Previously, we introduced an approach to modulating neural circuits noninvasively with spatial, cell-type, and temporal specificity called acoustically targeted chemogenetics, or ATAC. We use ultrasound to open the blood brain barrier to transduce neurons at specific locations in the brain with virally-encoded chemogenetic receptors. To show neuronal inhibition expressed inhibitory DREADD (hM4Di) throughout the hippocampus and tested mice in a fear conditioning protocol. The context fear test showed that mice treated with saline froze significantly more than those who had received CNO (p<2E-5, n=7,11) during the training phase.", "doi": "10.1016/j.biopsych.2020.02.263", "issn": "0006-3223", "publisher": "Elsevier", "publication": "Biological Psychiatry", "publication_date": "2020-05-01", "series_number": "9", "volume": "87", "issue": "9", "pages": "S95" }, { "id": "authors:8ary5-0wy57", "collection": "authors", "collection_id": "8ary5-0wy57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190815-094537072", "type": "article", "title": "Acoustic biomolecules enhance hemodynamic functional ultrasound imaging of neural activity", "author": [ { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-D" }, { "family_name": "Payen", "given_name": "Thomas", "clpid": "Payen-T" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-A" }, { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-D" }, { "family_name": "Demen\u00e9", "given_name": "Charlie", "orcid": "0000-0002-5329-700X", "clpid": "Demen\u00e9-C" }, { "family_name": "Tanter", "given_name": "Micka\u00ebl", "orcid": "0000-0001-7739-8051", "clpid": "Tanter-M" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Hemodynamic functional ultrasound imaging (fUS) of neural activity provides a unique combination of spatial coverage, spatiotemporal resolution and compatibility with freely moving animals. However, deep and transcranial monitoring of brain activity and the imaging of dynamics in slow-flowing blood vessels remains challenging. To enhance fUS capabilities, we introduce biomolecular hemodynamic enhancers based on gas vesicles (GVs), genetically encodable ultrasound contrast agents derived from buoyant photosynthetic microorganisms. We show that intravenously infused GVs enhance ultrafast Doppler ultrasound contrast and visually-evoked hemodynamic contrast in transcranial fUS of the mouse brain. This hemodynamic contrast enhancement is smoother than that provided by conventional microbubbles, allowing GVs to more reliably amplify neuroimaging signals.", "doi": "10.1016/j.neuroimage.2019.116467", "pmcid": "PMC6955150", "issn": "1053-8119", "publisher": "Elsevier", "publication": "NeuroImage", "publication_date": "2020-04-01", "volume": "209", "pages": "Art. No. 116467" }, { "id": "authors:nc5aa-k7608", "collection": "authors", "collection_id": "nc5aa-k7608", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191223-114059821", "type": "article", "title": "A dynamical model of oncotripsy by mechanical cell fatigue: selective cancer cell ablation by low-intensity pulsed ultrasound", "author": [ { "family_name": "Schibber", "given_name": "E. F.", "orcid": "0000-0002-6629-297X", "clpid": "Schibber-E-F" }, { "family_name": "Mittelstein", "given_name": "D. R.", "orcid": "0000-0001-8747-0483", "clpid": "Mittelstein-D-R" }, { "family_name": "Gharib", "given_name": "M.", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Shapiro", "given_name": "M. G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Lee", "given_name": "P. P.", "clpid": "Lee-P-P" }, { "family_name": "Ortiz", "given_name": "M.", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" } ], "abstract": "The method of oncotripsy, first proposed in Heyden & Ortiz (Heyden & Ortiz 2016 J. Mech. Phys. Solids 92, 164\u2013175 (doi:10.1016/j.jmps.2016.04.016)), exploits aberrations in the material properties and morphology of cancerous cells in order to ablate them selectively by means of tuned low-intensity pulsed ultrasound. We propose the dynamical model of oncotripsy that follows as an application of cell dynamics, statistical mechanical theory of network elasticity and 'birth\u2013death' kinetics to describe the processes of damage and repair of the cytoskeleton. We also develop a reduced dynamical model that approximates the three-dimensional dynamics of the cell and facilitates parametric studies, including sensitivity analysis and process optimization. We show that the dynamical model predicts\u2014and provides a conceptual basis for understanding\u2014the oncotripsy effect and other trends in the data of Mittelstein et al. (Mittelstein et al. 2019 Appl. Phys. Lett. 116, 013701 (doi:10.1063/1.5128627)), for cells in suspension, including the dependence of cell-death curves on cell and process parameters.", "doi": "10.1098/rspa.2019.0692", "pmcid": "PMC7209139", "issn": "1364-5021", "publisher": "Royal Society of London", "publication": "Proceedings of the Royal Society A: Mathematical, physical, and engineering sciences", "publication_date": "2020-03-31", "series_number": "2236", "volume": "476", "issue": "2236", "pages": "Art. No. 20190692" }, { "id": "authors:0tqzf-em128", "collection": "authors", "collection_id": "0tqzf-em128", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200203-092720672", "type": "article", "title": "Nanoscale Heat Transfer from Magnetic Nanoparticles and Ferritin in an Alternating Magnetic Field", "author": [ { "family_name": "Davis", "given_name": "Hunter C.", "orcid": "0000-0003-1655-692X", "clpid": "Davis-H-C" }, { "family_name": "Kang", "given_name": "Sunghwi", "clpid": "Kang-Sunghwi" }, { "family_name": "Lee", "given_name": "Jae-Hyun", "clpid": "Lee-Jae-Hyun" }, { "family_name": "Shin", "given_name": "Tae-Hyun", "clpid": "Shin-Tae-Hyun" }, { "family_name": "Putterman", "given_name": "Harry", "clpid": "Putterman-H" }, { "family_name": "Cheon", "given_name": "Jinwoo", "clpid": "Cheon-Jinwoo" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Recent suggestions of nanoscale heat confinement on the surface of synthetic and biogenic magnetic nanoparticles during heating by radio frequency-alternating magnetic fields have generated intense interest because of the potential utility of this phenomenon for noninvasive control of biomolecular and cellular function. However, such confinement would represent a significant departure from the classical heat transfer theory. Here, we report an experimental investigation of nanoscale heat confinement on the surface of several types of iron oxide nanoparticles commonly used in biological research, using an all-optical method devoid of the potential artifacts present in previous studies. By simultaneously measuring the fluorescence of distinct thermochromic dyes attached to the particle surface or dissolved in the surrounding fluid during radio frequency magnetic stimulation, we found no measurable difference between the nanoparticle surface temperature and that of the surrounding fluid for three distinct nanoparticle types. Furthermore, the metalloprotein ferritin produced no temperature increase on the protein surface nor in the surrounding fluid. Experiments mimicking the designs of previous studies revealed potential sources of the artifacts. These findings inform the use of magnetic nanoparticle hyperthermia in engineered cellular and molecular systems.", "doi": "10.1016/j.bpj.2020.01.028", "pmcid": "PMC7091488", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2020-03-24", "series_number": "6", "volume": "118", "issue": "6", "pages": "1502-1510" }, { "id": "authors:dyxwb-qgz32", "collection": "authors", "collection_id": "dyxwb-qgz32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200409-084500008", "type": "article", "title": "The Vibration Behavior of Sub-Micrometer Gas Vesicles in Response to Acoustic Excitation Determined via Laser Doppler Vibrometry", "author": [ { "family_name": "Zhang", "given_name": "Shuai", "clpid": "Zhang-Shuai" }, { "family_name": "Huang", "given_name": "An", "clpid": "Huang-An" }, { "family_name": "Bar-Zion", "given_name": "Avinoam", "orcid": "0000-0002-7564-9467", "clpid": "Bar-Zion-A" }, { "family_name": "Wang", "given_name": "Jiaying", "orcid": "0000-0003-2749-8470", "clpid": "Wang-Jiaying" }, { "family_name": "Vazquez Mena", "given_name": "Oscar", "orcid": "0000-0001-9054-5183", "clpid": "Vazquez-Mena-O" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Friend", "given_name": "James", "orcid": "0000-0003-0416-2165", "clpid": "Friend-J" } ], "abstract": "The ability to monitor sub\u2010micrometer gas vesicles' (GVs) vibration behavior to nonlinear buckling and collapse using laser Doppler vibrometry is reported, providing a precise noncontact technique for monitoring the motion of sub\u2010micrometer objects. The fundamental and first harmonic resonance frequencies of the vesicles are found to be 1.024 and 1.710 GHz, respectively. An interparticle resonance is furthermore identified at \u2248300 MHz, inversely dependent upon the agglomerated GV size of around 615 nm. Most importantly, the vesicles amplify and broaden input acoustic signals at far lower frequencies\u2014for example, 7 MHz\u2014associated with medical and industrial applications, and they are found to transition from a linear to nonlinear response at 150 kPa and to collapse at 350 kPa or greater.", "doi": "10.1002/adfm.202000239", "issn": "1616-301X", "publisher": "Wiley", "publication": "Advanced Functional Materials", "publication_date": "2020-03-24", "series_number": "13", "volume": "30", "issue": "13", "pages": "Art. No. 2000239" }, { "id": "authors:tnhgj-me123", "collection": "authors", "collection_id": "tnhgj-me123", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191002-094950438", "type": "article", "title": "Selective Ablation of Cancer Cells with Low Intensity Pulsed Ultrasound", "author": [ { "family_name": "Mittelstein", "given_name": "David R.", "orcid": "0000-0001-8747-0483", "clpid": "Mittelstein-David-R" }, { "family_name": "Ye", "given_name": "Jian", "orcid": "0000-0002-7168-0117", "clpid": "Ye-Jian" }, { "family_name": "Schibber", "given_name": "Erika F.", "orcid": "0000-0002-6629-297X", "clpid": "Schibber-Erika-F" }, { "family_name": "Roychoudhury", "given_name": "Ankita", "clpid": "Roychoudhury-Ankita" }, { "family_name": "Troyas Martinez", "given_name": "Leyre", "orcid": "0000-0003-4512-0666", "clpid": "Troyas-Leyre" }, { "family_name": "Fekrazad", "given_name": "M. Houman", "clpid": "Fekrazad-M-Houmam" }, { "family_name": "Ortiz", "given_name": "Michael", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" }, { "family_name": "Lee", "given_name": "Peter P.", "orcid": "0000-0002-2660-4377", "clpid": "Lee-Peter-P" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" } ], "abstract": "Ultrasound can be focused into deep tissues with millimeter precision to perform noninvasive ablative therapy for diseases such as cancer. In most cases, this ablation uses high intensity ultrasound to deposit nonselective thermal or mechanical energy at the ultrasound focus, damaging both healthy bystander tissue and cancer cells. Here, we describe an alternative low intensity (I_(SPTA) < 5\u2009W/cm\u00b2) pulsed ultrasound approach that leverages the distinct mechanical properties of neoplastic cells to achieve inherent cancer selectivity. We show that ultrasound applied at a frequency of 0.5\u20130.67\u2009MHz and a pulse duration of >20\u2009ms causes selective disruption of a panel of breast, colon, and leukemia cancer cell models in suspension without significantly damaging healthy immune or red blood cells. Mechanistic experiments reveal that the formation of acoustic standing waves and the emergence of cell-seeded cavitation lead to cytoskeletal disruption, expression of apoptotic markers, and cell death. The inherent selectivity of this low intensity pulsed ultrasound approach offers a potentially safer and thus more broadly applicable alternative to nonselective high intensity ultrasound ablation.", "doi": "10.1063/1.5128627", "issn": "0003-6951", "publisher": "American Institute of Physics", "publication": "Applied Physics Letters", "publication_date": "2020-01-06", "series_number": "1", "volume": "116", "issue": "1", "pages": "Art. No. 013701" }, { "id": "authors:xcgh2-3ba36", "collection": "authors", "collection_id": "xcgh2-3ba36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190716-114821416", "type": "article", "title": "Modular Thermal Control of Protein Dimerization", "author": [ { "family_name": "Piraner", "given_name": "Dan I.", "orcid": "0000-0003-3857-9487", "clpid": "Piraner-D-I" }, { "family_name": "Wu", "given_name": "Yan", "clpid": "Wu-Yan" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Protein\u2013protein interactions and protein localization are essential mechanisms of cellular signal transduction. The ability to externally control such interactions using chemical and optogenetic methods has facilitated biological research and provided components for the engineering of cell-based therapies and materials. However, chemical and optical methods are limited in their ability to provide spatiotemporal specificity in light-scattering tissues. To overcome these limitations, we present \"thermomers\", modular protein dimerization domains controlled with temperature\u2014a form of energy that can be delivered to cells both globally and locally in a wide variety of in vitro and in vivo contexts. Thermomers are based on a sharply thermolabile coiled-coil protein, which we engineered to heterodimerize at a tunable transition temperature within the biocompatible range of 37\u201342 \u00b0C. When fused to other proteins, thermomers can reversibly control their association, as demonstrated via membrane localization in mammalian cells. This technology enables remote control of intracellular protein\u2013protein interactions with a form of energy that can be delivered with spatiotemporal precision in a wide range of biological, therapeutic, and living material scenarios.", "doi": "10.1021/acssynbio.9b00275", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2019-10-18", "series_number": "10", "volume": "8", "issue": "10", "pages": "2256-2262" }, { "id": "authors:yqjd4-kgz14", "collection": "authors", "collection_id": "yqjd4-kgz14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190319-072910559", "type": "article", "title": "Ultrasound Imaging of Gene Expression in Mammalian Cells", "author": [ { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-A" }, { "family_name": "Ho", "given_name": "Gabrielle H.", "orcid": "0000-0002-8511-5549", "clpid": "Ho-Gabrielle-H" }, { "family_name": "Sawyer", "given_name": "Daniel P.", "orcid": "0000-0003-2926-191X", "clpid": "Sawyer-D-P" }, { "family_name": "Bourdeau", "given_name": "Raymond W.", "orcid": "0000-0003-2202-1980", "clpid": "Bourdeau-R-W" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "The study of cellular processes occurring inside intact organisms requires methods to visualize cellular functions such as gene expression in deep tissues. Ultrasound is a widely used biomedical technology enabling noninvasive imaging with high spatial and temporal resolution. However, no genetically encoded molecular reporters are available to connect ultrasound contrast to gene expression in mammalian cells. To address this limitation, we introduce mammalian acoustic reporter genes. Starting with a gene cluster derived from bacteria, we engineered a eukaryotic genetic program whose introduction into mammalian cells results in the expression of intracellular air-filled protein nanostructures called gas vesicles, which produce ultrasound contrast. Mammalian acoustic reporter genes allow cells to be visualized at volumetric densities below 0.5% and permit high-resolution imaging of gene expression in living animals.", "doi": "10.1126/science.aax4804", "pmcid": "PMC6860372", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2019-09-27", "series_number": "6460", "volume": "365", "issue": "6460", "pages": "1469-1475" }, { "id": "authors:2a6a9-f4j43", "collection": "authors", "collection_id": "2a6a9-f4j43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190809-160556043", "type": "article", "title": "Achieving Spatial and Molecular Specificity with Ultrasound-Targeted Biomolecular Nanotherapeutics", "author": [ { "family_name": "Szablowski", "given_name": "Jerzy O.", "orcid": "0000-0001-7851-5408", "clpid": "Szablowski-J-O" }, { "family_name": "Bar-Zion", "given_name": "Avinoam", "orcid": "0000-0002-7564-9467", "clpid": "Bar-Zion-A" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "The precise targeting of cells in deep tissues is one of the primary goals of nanomedicine. However, targeting a specific cellular population within an entire organism is challenging due to off-target effects and the need for deep tissue delivery. Focused ultrasound can reduce off-targeted effects by spatially restricting the delivery or action of molecular constructs to specific anatomical sites. Ultrasound can also increase the efficiency of nanotherapeutic delivery into deep tissues by enhancing the permeability of tissue boundaries, promoting convection, or depositing energy to actuate cellular activity. In this review we focus on the interface between biomolecular engineering and focused ultrasound and describe the applications of this intersection in neuroscience, oncology, and synthetic biology. Ultrasound can be used to trigger the transport of therapeutic payloads into a range of tissues, including specific regions of the brain, where it can be targeted with millimeter precision through intact skull. Locally delivered molecular constructs can then control specific cells and molecular pathways within the targeted region. When combined with viral vectors and engineered neural receptors, this technique enables noninvasive control of specific circuits and behaviors. The penetrant energy of ultrasound can also be used to more directly actuate micro- and nanotherapeutic constructs, including microbubbles, vaporizable nanodroplets, and polymeric nanocups, which nucleate cavitation upon ultrasound exposure, leading to local mechanical effects. In addition, it was recently discovered that a unique class of acoustic biomolecules\u2014genetically encodable nanoscale protein structures called gas vesicles\u2014can be acoustically \"detonated\" as sources of inertial cavitation. This enables the targeted disruption of selected cells within the area of insonation by gas vesicles that are engineered to bind cell surface receptors. It also facilitates ultrasound-triggered release of molecular payloads from engineered therapeutic cells heterologously expressing intracellular gas vesicles. Finally, focused ultrasound energy can be used to locally elevate tissue temperature and activate temperature-sensitive proteins and pathways. The elevation of temperature allows noninvasive control of gene expression in vivo in cells engineered to express thermal bioswitches. Overall, the intersection of biomolecular engineering, nanomaterials and focused ultrasound can provide unparalleled specificity in controlling, modulating, and treating physiological processes in deep tissues.", "doi": "10.1021/acs.accounts.9b00277", "issn": "0001-4842", "publisher": "American Chemical Society", "publication": "Accounts of Chemical Research", "publication_date": "2019-09-17", "series_number": "9", "volume": "52", "issue": "9", "pages": "2427-2434" }, { "id": "authors:cj5g1-wmb70", "collection": "authors", "collection_id": "cj5g1-wmb70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180911-131832804", "type": "article", "title": "Protein Nanostructures Produce Self-Adjusting Hyperpolarized Magnetic Resonance Imaging Contrast through Physical Gas Partitioning", "author": [ { "family_name": "Kunth", "given_name": "Martin", "orcid": "0000-0002-9741-9881", "clpid": "Kunth-Martin" }, { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Witte", "given_name": "Christopher", "orcid": "0000-0002-4098-6623", "clpid": "Witte-C" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Schr\u00f6der", "given_name": "Leif", "orcid": "0000-0003-4901-0325", "clpid": "Schr\u00f6der-L" } ], "abstract": "Signal amplification strategies are critical for overcoming the intrinsically poor sensitivity of nuclear magnetic resonance (NMR) reporters in noninvasive molecular detection. A mechanism widely used for signal enhancement is chemical exchange saturation transfer (CEST) of nuclei between a dilute sensing pool and an abundant detection pool. However, the dependence of CEST amplification on the relative size of these spin pools confounds quantitative molecular detection with a larger detection pool typically making saturation transfer less efficient. Here we show that a recently discovered class of genetically encoded nanoscale reporters for ^(129)Xe magnetic resonance overcomes this fundamental limitation through an elastic binding capacity for NMR-active nuclei. This approach pairs high signal amplification from hyperpolarized spins with ideal, self-adjusting saturation transfer behavior as the overall spin ensemble changes in size. These reporters are based on gas vesicles, i.e., microbe-derived, gas-filled protein nanostructures. We show that the xenon fraction that partitions into gas vesicles follows the ideal gas law, allowing the signal transfer under hyperpolarized xenon chemical exchange saturation transfer (Hyper-CEST) imaging to scale linearly with the total xenon ensemble. This conceptually distinct elastic response allows the production of quantitative signal contrast that is robust to variability in the concentration of xenon, enabling virtually unlimited improvement in absolute contrast with increased xenon delivery, and establishing a unique principle of operation for contrast agent development in emerging biochemical and in vivo applications of hyperpolarized NMR and magnetic resonance imaging.", "doi": "10.1021/acsnano.8b04222", "issn": "1936-0851", "publisher": "American Chemical Society", "publication": "ACS Nano", "publication_date": "2018-11-27", "series_number": "11", "volume": "12", "issue": "11", "pages": "10939-10948" }, { "id": "authors:3hpeq-46352", "collection": "authors", "collection_id": "3hpeq-46352", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181004-091624730", "type": "article", "title": "Nonlinear X-Wave Ultrasound Imaging of Acoustic Biomolecules", "author": [ { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Sawyer", "given_name": "Daniel P.", "orcid": "0000-0003-2926-191X", "clpid": "Sawyer-Daniel-P" }, { "family_name": "Renaud", "given_name": "Guillaume", "orcid": "0000-0002-6666-1114", "clpid": "Renaud-Guillaume" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "The basic physics of sound waves enables ultrasound to visualize biological tissues with high spatial and temporal resolution. Recently, this capability was enhanced with the development of acoustic biomolecules\u2014proteins with physical properties enabling them to scatter sound. The expression of these unique air-filled proteins, known as gas vesicles (GVs), in cells allows ultrasound to image cellular functions such as gene expression in vivo, providing ultrasound with its analog of optical fluorescent proteins. Acoustical methods for the in vivo detection of GVs are now required to maximize the impact of this technology in biology and medicine. We previously engineered GVs exhibiting a nonlinear scattering behavior in response to acoustic pressures above 300 kPa and showed that amplitude-modulated (AM) ultrasound pulse sequences that excite both the linear and nonlinear GV scattering regimes were highly effective at distinguishing GVs from linear scatterers like soft biological tissues. Unfortunately, the in vivo specificity of AM ultrasound imaging is systematically compromised by the nonlinearity added by the GVs to propagating waves, resulting in strong image artifacts from linear scatterers downstream of GV inclusions. To address this issue, we present an imaging paradigm, cross-amplitude modulation (xAM), which relies on cross-propagating plane-wave transmissions of finite aperture X waves to achieve quasi-artifact-free in vivo imaging of GVs. The xAM method derives from counterpropagating wave interaction theory, which predicts that, in media exhibiting quadratic elastic nonlinearity like biological tissue, the nonlinear interaction of counterpropagating acoustic waves is inefficient. By transmitting cross-propagating plane waves, we minimize cumulative nonlinear interaction effects due to collinear wave propagation while generating a transient wave-amplitude modulation at the two plane waves' intersection. In both simulations and experiments, we show that residual xAM nonlinearity due to wave propagation decreases as the plane-wave cross-propagation angle increases. We demonstrate in tissue-mimicking phantoms that imaging artifacts distal to GV inclusions decrease as the plane-wave cross-propagation angle opens, nearing complete extinction at angles above 16.5 degrees. Finally, we demonstrate that xAM enables highly specific in vivo imaging of GVs located in the gastrointestinal tract, a target of prime interest for future cellular imaging. These results advance the physical facet of the emerging field of biomolecular ultrasound and are also relevant to synthetic ultrasound contrast agents.", "doi": "10.1103/physrevx.8.041002", "pmcid": "PMC8147876", "issn": "2160-3308", "publisher": "American Physical Society", "publication": "Physical Review X", "publication_date": "2018-10", "series_number": "4", "volume": "8", "issue": "4", "pages": "Art. No. 041002" }, { "id": "authors:jdpbn-eya48", "collection": "authors", "collection_id": "jdpbn-eya48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180813-080049505", "type": "article", "title": "Ultraparamagnetic cells formed through intracellular oxidation and chelation of paramagnetic iron", "author": [ { "family_name": "Ramesh", "given_name": "Pradeep", "clpid": "Ramesh-P" }, { "family_name": "Hwang", "given_name": "Son-Jong", "orcid": "0000-0002-3210-466X", "clpid": "Hwang-Son-Jong" }, { "family_name": "Davis", "given_name": "Hunter C.", "orcid": "0000-0003-1655-692X", "clpid": "Davis-H-C" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-A" }, { "family_name": "Bharadwaj", "given_name": "Vivek", "clpid": "Bharadwaj-V" }, { "family_name": "English", "given_name": "Max A.", "clpid": "English-M-A" }, { "family_name": "Sheng", "given_name": "Jenny", "clpid": "Sheng-Jenny" }, { "family_name": "Iyer", "given_name": "Vasant", "clpid": "Iyer-V" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Making cells magnetic is a long\u2010standing goal of chemical biology, aiming to enable the separation of cells from complex biological samples and their visualization in vivo using magnetic resonance imaging (MRI). Previous efforts towards this goal, focused on engineering cells to biomineralize superparamagnetic or ferromagnetic iron oxides, have been largely unsuccessful due to the stringent required chemical conditions. Here, we introduce an alternative approach to making cells magnetic, focused on biochemically maximizing cellular paramagnetism. We show that a novel genetic construct combining the functions of ferroxidation and iron chelation enables engineered bacterial cells to accumulate iron in \"ultraparamagnetic\" macromolecular complexes, allowing these cells to be trapped with magnetic fields and imaged with MRI in vitro and in vivo. We characterize the properties of these cells and complexes using magnetometry, nuclear magnetic resonance, biochemical assays, and computational modeling to elucidate the unique mechanisms and capabilities of this paramagnetic concept.", "doi": "10.1002/anie.201805042", "issn": "1433-7851", "publisher": "Wiley", "publication": "Angewandte Chemie International Edition", "publication_date": "2018-09-17", "series_number": "38", "volume": "57", "issue": "38", "pages": "12385-12389" }, { "id": "authors:0zg21-zx104", "collection": "authors", "collection_id": "0zg21-zx104", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180322-135005180", "type": "article", "title": "Proteins, air and water: reporter genes for ultrasound and magnetic resonance imaging", "author": [ { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Mukherjee", "given_name": "Arnab", "orcid": "0000-0002-6783-8225", "clpid": "Mukherjee-Arnab" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "A long-standing goal of molecular imaging is to visualize cellular function within the context of living animals, necessitating the development of reporter genes compatible with deeply penetrant imaging modalities such as ultrasound and magnetic resonance imaging (MRI). Until recently, no reporter genes for ultrasound were available, and most genetically encoded reporters for MRI were limited by metal availability or relatively low sensitivity. Here we review how these limitations are being addressed by recently introduced reporter genes based on air-filled and water-transporting biomolecules. We focus on gas-filled protein nanostructures adapted from buoyant microbes, which scatter sound waves, perturb magnetic fields and interact with hyperpolarized nuclei, as well as transmembrane water channels that alter the effective diffusivity of water in tissue.", "doi": "10.1016/j.cbpa.2018.02.011", "pmcid": "PMC6076850", "issn": "1367-5931", "publisher": "Elsevier", "publication": "Current Opinion in Chemical Biology", "publication_date": "2018-08", "volume": "45", "pages": "57-63" }, { "id": "authors:e1v82-9ks43", "collection": "authors", "collection_id": "e1v82-9ks43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180226-134658661", "type": "article", "title": "Recombinantly Expressed Gas Vesicles as Nanoscale Contrast Agents for Ultrasound and Hyperpolarized MRI", "author": [ { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Ho", "given_name": "Gabrielle", "orcid": "0000-0002-8511-5549", "clpid": "Ho-Gabrielle-H" }, { "family_name": "Kunth", "given_name": "Martin", "orcid": "0000-0002-9741-9881", "clpid": "Kunth-Martin" }, { "family_name": "Ling", "given_name": "Bill", "orcid": "0000-0002-1276-7204", "clpid": "Ling-Bill" }, { "family_name": "Lakshmanan", "given_name": "Anupama", "orcid": "0000-0002-6702-837X", "clpid": "Lakshmanan-Anupama" }, { "family_name": "Lu", "given_name": "George", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Bourdeau", "given_name": "Raymond W.", "orcid": "0000-0003-2202-1980", "clpid": "Bourdeau-Raymond-W" }, { "family_name": "Schr\u00f6der", "given_name": "Leif", "orcid": "0000-0003-4901-0325", "clpid": "Schr\u00f6der-Leif" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Ultrasound and hyperpolarized magnetic resonance imaging enable the visualization of biological processes in deep tissues. However, few molecular contrast agents are available to connect these modalities to specific aspects of biological function. We recently discovered that a unique class of gas\u2010filled protein nanostructures known as gas vesicles could serve as nanoscale molecular reporters for these modalities. However, the need to produce these nanostructures via expression in specialized cultures of cyanobacteria or haloarchaea limits their broader adoption by other laboratories and hinders genetic engineering of their properties. Here, we describe recombinant expression and purification of Bacillus megaterium gas vesicles using a common laboratory strain of Escherichia coli, and characterize the physical, acoustic, and magnetic resonance properties of these nanostructures. Recombinantly expressed gas vesicles produce ultrasound and hyperpolarized ^(129)Xe MRI contrast at subnanomolar concentrations, thus validating a simple platform for their production and engineering.", "doi": "10.1002/aic.16138", "pmcid": "PMC6289519", "issn": "0001-1541", "publisher": "Wiley", "publication": "AIChE Journal", "publication_date": "2018-08", "series_number": "8", "volume": "64", "issue": "8", "pages": "2927-2933" }, { "id": "authors:h4pdz-ens95", "collection": "authors", "collection_id": "h4pdz-ens95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180108-133221204", "type": "article", "title": "Acoustically Targeted Chemogenetics for Noninvasive Control of Neural Circuits", "author": [ { "family_name": "Szablowski", "given_name": "Jerzy O.", "orcid": "0000-0001-7851-5408", "clpid": "Szablowski-J-O" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-A" }, { "family_name": "Lue", "given_name": "Brian", "clpid": "Lue-Brian" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-D" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Neurological and psychiatric disorders are often characterized by dysfunctional neural circuits in specific regions of the brain. Existing treatment strategies, including the use of drugs and implantable brain stimulators, aim to modulate the activity of these circuits. However, they are not cell-type-specific, lack spatial targeting or require invasive procedures. Here, we report a cell-type-specific and non-invasive approach based on acoustically targeted chemogenetics that enables the modulation of neural circuits with spatiotemporal specificity. The approach uses ultrasound waves to transiently open the blood\u2013brain barrier and transduce neurons at specific locations in the brain with virally encoded engineered G-protein-coupled receptors. The engineered neurons subsequently respond to systemically administered designer compounds to activate or inhibit their activity. In a mouse model of memory formation, the approach can modify and subsequently activate or inhibit excitatory neurons within the hippocampus, with selective control over individual brain regions. This technology overcomes some of the key limitations associated with conventional brain therapies.", "doi": "10.1038/s41551-018-0258-2", "issn": "2157-846X", "publisher": "Nature Publishing Group", "publication": "Nature Biomedical Engineering", "publication_date": "2018-07", "series_number": "7", "volume": "2", "issue": "7", "pages": "475-484" }, { "id": "authors:w5enq-13s77", "collection": "authors", "collection_id": "w5enq-13s77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180108-132355264", "type": "article", "title": "Ultrasonic Neuromodulation Causes Widespread Cortical Activation via an Indirect Auditory Mechanism", "author": [ { "family_name": "Sato", "given_name": "Tomokazu", "clpid": "Sato-Tomokazu-F" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Tsao", "given_name": "Doris Y.", "orcid": "0000-0003-1083-1919", "clpid": "Tsao-D-Y" } ], "abstract": "Ultrasound has received widespread attention as an emerging technology for targeted, non-invasive neuromodulation based on its ability to evoke electrophysiological and motor responses in animals. However, little is known about the spatiotemporal pattern of ultrasound-induced brain activity that could drive these responses. Here, we address this question by combining focused ultrasound with wide-field optical imaging of calcium signals in transgenic mice. Surprisingly, we find cortical activity patterns consistent with indirect activation of auditory pathways rather than direct neuromodulation at the ultrasound focus. Ultrasound-induced activity is similar to that evoked by audible sound. Furthermore, both ultrasound and audible sound elicit motor responses consistent with a startle reflex, with both responses reduced by chemical deafening. These findings reveal an indirect auditory mechanism for ultrasound-induced cortical activity and movement requiring careful consideration in future development of ultrasonic neuromodulation as a tool in neuroscience research.", "doi": "10.1016/j.neuron.2018.05.009", "pmcid": "PMC8127805", "issn": "0896-6273", "publisher": "Cell Press", "publication": "Neuron", "publication_date": "2018-06-06", "series_number": "5", "volume": "98", "issue": "5", "pages": "1031-1041" }, { "id": "authors:8n2xy-avm68", "collection": "authors", "collection_id": "8n2xy-avm68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180330-152125173", "type": "article", "title": "Biomolecular Ultrasound and Sonogenetics", "author": [ { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Lakshmanan", "given_name": "Anupama", "orcid": "0000-0002-6702-837X", "clpid": "Lakshmanan-Anupama" }, { "family_name": "Abedi", "given_name": "Mohamad H.", "orcid": "0000-0001-9717-6288", "clpid": "Abedi-Mohamad-H" }, { "family_name": "Bar-Zion", "given_name": "Avinoam", "orcid": "0000-0002-7564-9467", "clpid": "Bar-Zion-Avinoam" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Szablowski", "given_name": "Jerzy O.", "orcid": "0000-0001-7851-5408", "clpid": "Szablowski-Jerzy-O" }, { "family_name": "Wu", "given_name": "Di", "orcid": "0000-0002-6848-668X", "clpid": "Wu-Di" }, { "family_name": "Yoo", "given_name": "Sangjin", "orcid": "0000-0002-0449-4242", "clpid": "Yoo-Sangjin" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Visualizing and modulating molecular and cellular processes occurring deep within living organisms is fundamental to our study of basic biology and disease. Currently, the most sophisticated tools available to dynamically monitor and control cellular events rely on light-responsive proteins, which are difficult to use outside of optically transparent model systems, cultured cells, or surgically accessed regions owing to strong scattering of light by biological tissue. In contrast, ultrasound is a widely used medical imaging and therapeutic modality that enables the observation and perturbation of internal anatomy and physiology but has historically had limited ability to monitor and control specific cellular processes. Recent advances are beginning to address this limitation through the development of biomolecular tools that allow ultrasound to connect directly to cellular functions such as gene expression. Driven by the discovery and engineering of new contrast agents, reporter genes, and bioswitches, the nascent field of biomolecular ultrasound carries a wave of exciting opportunities.", "doi": "10.1146/annurev-chembioeng-060817-084034", "pmcid": "PMC6086606", "issn": "1947-5438", "publisher": "Annual Reviews", "publication": "Annual Review of Chemical and Biomolecular Engineering", "publication_date": "2018-06", "volume": "9", "pages": "229-252" }, { "id": "authors:zvm7s-gmr58", "collection": "authors", "collection_id": "zvm7s-gmr58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171215-092640151", "type": "article", "title": "Acoustically modulated magnetic resonance imaging of gas-filled protein nanostructures", "author": [ { "family_name": "Lu", "given_name": "George Jiaozhi", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Szablowski", "given_name": "Jerzy O.", "orcid": "0000-0001-7851-5408", "clpid": "Szablowski-Jerzy-O" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Barnes", "given_name": "Samuel R.", "orcid": "0000-0002-1065-8442", "clpid": "Barnes-Samuel-R" }, { "family_name": "Lakshmanan", "given_name": "Anupama", "orcid": "0000-0002-6702-837X", "clpid": "Lakshmanan-Anupama" }, { "family_name": "Bourdeau", "given_name": "Raymond W.", "orcid": "0000-0003-2202-1980", "clpid": "Bourdeau-Raymond-W" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Non-invasive biological imaging requires materials capable of interacting with deeply penetrant forms of energy such as magnetic fields and sound waves. Here, we show that gas vesicles (GVs), a unique class of gas-filled protein nanostructures with differential magnetic susceptibility relative to water, can produce robust contrast in magnetic resonance imaging (MRI) at sub-nanomolar concentrations, and that this contrast can be inactivated with ultrasound in situ to enable background-free imaging. We demonstrate this capability in vitro, in cells expressing these nanostructures as genetically encoded reporters, and in three model in vivo scenarios. Genetic variants of GVs, differing in their magnetic or mechanical phenotypes, allow multiplexed imaging using parametric MRI and differential acoustic sensitivity. Additionally, clustering-induced changes in MRI contrast enable the design of dynamic molecular sensors. By coupling the complementary physics of MRI and ultrasound, this nanomaterial gives rise to a distinct modality for molecular imaging with unique advantages and capabilities.", "doi": "10.1038/s41563-018-0023-7", "pmcid": "PMC6015773", "issn": "1476-1122", "publisher": "Nature Publishing Group", "publication": "Nature Materials", "publication_date": "2018-05", "series_number": "5", "volume": "17", "issue": "5", "pages": "456-463" }, { "id": "authors:g0zkt-b8f55", "collection": "authors", "collection_id": "g0zkt-b8f55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180411-114459829", "type": "article", "title": "In vivo Biodistribution of Radiolabeled Acoustic Protein Nanostructures", "author": [ { "family_name": "Le Floc'h", "given_name": "Johann", "orcid": "0000-0003-0010-5120", "clpid": "Le-Floc'h-Johann" }, { "family_name": "Zlitni", "given_name": "Aimen", "clpid": "Zlitni-Aimen" }, { "family_name": "Bilton", "given_name": "Holly A.", "clpid": "Bilton-Holly-A" }, { "family_name": "Yin", "given_name": "Melissa", "clpid": "Yin-Melissa" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-A" }, { "family_name": "Janzen", "given_name": "Nancy R.", "clpid": "Janzen-Nancy-R" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Valliant", "given_name": "John F.", "clpid": "Valliant-John-F" }, { "family_name": "Foster", "given_name": "F. Stuart", "clpid": "Foster-F-S" } ], "abstract": "Purpose: Contrast-enhanced ultrasound plays an expanding role in oncology, but its applicability to molecular imaging is hindered by a lack of nanoscale contrast agents that can reach targets outside the vasculature. Gas vesicles (GVs)\u2014a unique class of gas-filled protein nanostructures\u2014have recently been introduced as a promising new class of ultrasound contrast agents that can potentially access the extravascular space and be modified for molecular targeting. The purpose of the present study is to determine the quantitative biodistribution of GVs, which is critical for their development as imaging agents. \n\nProcedures: We use a novel bioorthogonal radiolabeling strategy to prepare technetium-99m-radiolabeled ([99mTc])GVs in high radiochemical purity. We use single photon emission computed tomography (SPECT) and tissue counting to quantitatively assess GV biodistribution in mice. \n\nResults: Twenty minutes following administration to mice, the SPECT biodistribution shows that 84 % of [99mTc]GVs are taken up by the reticuloendothelial system (RES) and 13 % are found in the gall bladder and duodenum. Quantitative tissue counting shows that the uptake (mean \u00b1 SEM % of injected dose/organ) is 0.6 \u00b1 0.2 for the gall bladder, 46.2 \u00b1 3.1 for the liver, 1.91 \u00b1 0.16 for the lungs, and 1.3 \u00b1 0.3 for the spleen. Fluorescence imaging confirmed the presence of GVs in RES. \n\nConclusions: These results provide essential information for the development of GVs as targeted nanoscale imaging agents for ultrasound.", "doi": "10.1007/s11307-017-1122-6", "pmcid": "PMC6110388", "issn": "1536-1632", "publisher": "Springer", "publication": "Molecular Imaging and Biology", "publication_date": "2018-04", "series_number": "2", "volume": "20", "issue": "2", "pages": "230-239" }, { "id": "authors:57q26-hfy77", "collection": "authors", "collection_id": "57q26-hfy77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161205-095517669", "type": "article", "title": "Mapping the microscale origins of magnetic resonance image contrast with subcellular diamond magnetometry", "author": [ { "family_name": "Davis", "given_name": "Hunter C.", "orcid": "0000-0003-1655-692X", "clpid": "Davis-Hunter-C" }, { "family_name": "Ramesh", "given_name": "Pradeep", "clpid": "Ramesh-Pradeep" }, { "family_name": "Bhatnagar", "given_name": "Aadyot", "clpid": "Bhatnagar-Aadyot" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Barry", "given_name": "John F.", "clpid": "Barry-John-F" }, { "family_name": "Glenn", "given_name": "David R.", "clpid": "Glenn-David-R" }, { "family_name": "Walsworth", "given_name": "Ronald L.", "orcid": "0000-0003-0311-4751", "clpid": "Walsworth-Ronald-L" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Magnetic resonance imaging (MRI) is a widely used biomedical imaging modality that derives much of its contrast from microscale magnetic field gradients in biological tissues. However, the connection between these sub-voxel field patterns and MRI contrast has not been studied experimentally. Here, we describe a new method to map subcellular magnetic fields in mammalian cells and tissues using nitrogen vacancy diamond magnetometry and connect these maps to voxel-scale MRI contrast, providing insights for in vivo imaging and contrast agent design.", "doi": "10.1038/s41467-017-02471-7", "pmcid": "PMC5760582", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2018-01-09", "volume": "9", "pages": "Art. No. 131" }, { "id": "authors:wjax0-7pg43", "collection": "authors", "collection_id": "wjax0-7pg43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171102-124711465", "type": "article", "title": "Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts", "author": [ { "family_name": "Bourdeau", "given_name": "Raymond W.", "orcid": "0000-0003-2202-1980", "clpid": "Bourdeau-Raymond-W" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Lakshmanan", "given_name": "Anupama", "orcid": "0000-0002-6702-837X", "clpid": "Lakshmanan-Anupama" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Ravindra Kumar", "given_name": "Sripriya", "orcid": "0000-0001-6033-7631", "clpid": "Ravindra-Kumar-S" }, { "family_name": "Nety", "given_name": "Suchita P.", "orcid": "0000-0002-4201-1061", "clpid": "Nety-Suchita-P" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "The mammalian microbiome has many important roles in health and disease1,2, and genetic engineering is enabling the development of microbial therapeutics and diagnostics3,4,5,6,7. A key determinant of the activity of both natural and engineered microorganisms in vivo is their location within the host organism8,9. However, existing methods for imaging cellular location and function, primarily based on optical reporter genes, have limited deep tissue performance owing to light scattering or require radioactive tracers10,11,12. Here we introduce acoustic reporter genes, which are genetic constructs that allow bacterial gene expression to be visualized in vivo using ultrasound, a widely available inexpensive technique with deep tissue penetration and high spatial resolution13,14,15. These constructs are based on gas vesicles, a unique class of gas-filled protein nanostructures that are expressed primarily in water-dwelling photosynthetic organisms as a means to regulate buoyancy16,17. Heterologous expression of engineered gene clusters encoding gas vesicles allows Escherichia coli and Salmonella typhimurium to be imaged noninvasively at volumetric densities below 0.01% with a resolution of less than 100\u2009\u03bcm. We demonstrate the imaging of engineered cells in vivo in proof-of-concept models of gastrointestinal and tumour localization, and develop acoustically distinct reporters that enable multiplexed imaging of cellular populations. This technology equips microbial cells with a means to be visualized deep inside mammalian hosts, facilitating the study of the mammalian microbiome and the development of diagnostic and therapeutic cellular agents.", "doi": "10.1038/nature25021", "pmcid": "PMC5920530", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2018-01-04", "series_number": "7686", "volume": "553", "issue": "7686", "pages": "86-90" }, { "id": "authors:pryv3-5p232", "collection": "authors", "collection_id": "pryv3-5p232", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180215-134720732", "type": "article", "title": "In Vivo Selection of a Computationally Designed SCHEMA AAV Library Yields a Novel Variant for Infection of Adult Neural Stem Cells in the SVZ", "author": [ { "family_name": "Ojala", "given_name": "David S.", "clpid": "Ojala-D-S" }, { "family_name": "Sun", "given_name": "Sabrina", "clpid": "Sun-Sabrina" }, { "family_name": "Santiago-Ortiz", "given_name": "Jorge L.", "clpid": "Santiago-Ortiz-J-L" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Romero", "given_name": "Philip A.", "orcid": "0000-0002-2586-7263", "clpid": "Romero-P-A" }, { "family_name": "Schaffer", "given_name": "David V.", "clpid": "Schaffer-D-V" } ], "abstract": "Directed evolution continues to expand the capabilities of complex biomolecules for a range of applications, such as adeno-associated virus vectors for gene therapy; however, advances in library design and selection strategies are key to develop variants that overcome barriers to clinical translation. To address this need, we applied structure-guided SCHEMA recombination of the multimeric adeno-associated virus (AAV) capsid to generate a highly diversified chimeric library with minimal structural disruption. A stringent in vivo Cre-dependent selection strategy was implemented to identify variants that transduce adult neural stem cells (NSCs) in the subventricular zone. A novel variant, SCH9, infected 60% of NSCs and mediated 24-fold higher GFP expression and a 12-fold greater transduction volume than AAV9. SCH9 utilizes both galactose and heparan sulfate as cell surface receptors and exhibits increased resistance to neutralizing antibodies. These results establish the SCHEMA library as a valuable tool for directed evolution and SCH9 as an effective gene delivery vector to investigate subventricular NSCs.", "doi": "10.1016/j.ymthe.2017.09.006", "pmcid": "PMC5762983", "issn": "1525-0016", "publisher": "American Society of Gene & Cell Therapy", "publication": "Molecular Therapy", "publication_date": "2018-01-03", "series_number": "1", "volume": "26", "issue": "1", "pages": "304-319" }, { "id": "authors:5wtzv-kb621", "collection": "authors", "collection_id": "5wtzv-kb621", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171113-132039361", "type": "article", "title": "Correspondence: Reply to 'Revisiting the theoretical cell membrane thermal capacitance response'", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Homma", "given_name": "Kazuaki", "clpid": "Homma-Kazuaki" }, { "family_name": "Villarreal", "given_name": "Sebastian", "clpid": "Villarreal-Sebastian" }, { "family_name": "Richter", "given_name": "Claus-Peter", "clpid": "Richter-Claus-Peter" }, { "family_name": "Bezanilla", "given_name": "Francisco", "clpid": "Bezanilla-Francisco" } ], "abstract": "We thank Plaksin, Kimmel, and Shoham for their correspondence regarding our 2012 article on the mechanism of infrared stimulation of excitable cells. In this study, we showed that the heating of cellular water by infrared light leads to an increase in the electrical capacitance of the cell membrane. This time-varying capacitance produces a current leading to membrane depolarization and generation of action potentials. Although our experimental findings were the primary focus of the paper and account for most of its impact to date, we also attempted to provide a theoretical explanation of how the membrane capacitance changes with temperature.", "doi": "10.1038/s41467-017-00436-4", "pmcid": "PMC5681563", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2017-11-10", "volume": "8", "pages": "Art. No. 1432" }, { "id": "authors:ecqwr-7jk02", "collection": "authors", "collection_id": "ecqwr-7jk02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170619-073109351", "type": "article", "title": "Biomolecular MRI reporters: Evolution of new mechanisms", "author": [ { "family_name": "Mukherjee", "given_name": "Arnab", "orcid": "0000-0002-6783-8225", "clpid": "Mukherjee-Arnab" }, { "family_name": "Davis", "given_name": "Hunter C.", "orcid": "0000-0003-1655-692X", "clpid": "Davis-Hunter-C" }, { "family_name": "Ramesh", "given_name": "Pradeep", "clpid": "Ramesh-Pradeep" }, { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Magnetic resonance imaging (MRI) is a powerful technique for observing the function of specific cells and molecules inside living organisms. However, compared to optical microscopy, in which fluorescent protein reporters are available to visualize hundreds of cellular functions ranging from gene expression and chemical signaling to biomechanics, to date relatively few such reporters are available for MRI. Efforts to develop MRI-detectable biomolecules have mainly focused on proteins transporting paramagnetic metals for T_1 and T_2 relaxation enhancement or containing large numbers of exchangeable protons for chemical exchange saturation transfer. While these pioneering developments established several key uses of biomolecular MRI, such as imaging of gene expression and functional biosensing, they also revealed that low molecular sensitivity poses a major challenge for broader adoption in biology and medicine. Recently, new classes of biomolecular reporters have been developed based on alternative contrast mechanisms, including enhancement of spin diffusivity, interactions with hyperpolarized nuclei, and modulation of blood flow. These novel reporters promise to improve sensitivity and enable new forms of multiplexed and functional imaging.", "doi": "10.1016/j.pnmrs.2017.05.002", "pmcid": "PMC5726449", "issn": "0079-6565", "publisher": "Elsevier", "publication": "Progress in Nuclear Magnetic Resonance Spectroscopy", "publication_date": "2017-11", "volume": "102-103", "pages": "32-42" }, { "id": "authors:58f6k-1ep71", "collection": "authors", "collection_id": "58f6k-1ep71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170814-132937862", "type": "article", "title": "Going Deeper: Biomolecular Tools for Acoustic and Magnetic Imaging and Control of Cellular Function", "author": [ { "family_name": "Piraner", "given_name": "Dan I.", "orcid": "0000-0003-3857-9487", "clpid": "Piraner-Dan-I" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Davis", "given_name": "Hunter C.", "orcid": "0000-0003-1655-692X", "clpid": "Davis-Hunter-C" }, { "family_name": "Wu", "given_name": "Di", "orcid": "0000-0002-6848-668X", "clpid": "Wu-Di" }, { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Szablowski", "given_name": "Jerzy O.", "orcid": "0000-0001-7851-5408", "clpid": "Szablowski-Jerzy-O" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Most cellular phenomena of interest to mammalian biology occur within the context of living tissues and organisms. However, today's most advanced tools for observing and manipulating cellular function, based on fluorescent or light-controlled proteins, work best in cultured cells, transparent model species, or small, surgically accessed anatomical regions. Their reach into deep tissues and larger animals is limited by photon scattering. To overcome this limitation, we must design biochemical tools that interface with more penetrant forms of energy. For example, sound waves and magnetic fields easily permeate most biological tissues, allowing the formation of images and delivery of energy for actuation. These capabilities are widely used in clinical techniques such as diagnostic ultrasound, magnetic resonance imaging, focused ultrasound ablation, and magnetic particle hyperthermia. Each of these modalities offers spatial and temporal precision that could be used to study a multitude of cellular processes in vivo. However, connecting these techniques to cellular functions such as gene expression, proliferation, migration, and signaling requires the development of new biochemical tools that can interact with sound waves and magnetic fields as optogenetic tools interact with photons. Here, we discuss the exciting challenges this poses for biomolecular engineering and provide examples of recent advances pointing the way to greater depth in in vivo cell biology.", "doi": "10.1021/acs.biochem.7b00443", "pmcid": "PMC6058970", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2017-10-03", "series_number": "39", "volume": "56", "issue": "39", "pages": "5202-5209" }, { "id": "authors:79ffp-qyg97", "collection": "authors", "collection_id": "79ffp-qyg97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170517-151452626", "type": "article", "title": "Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI", "author": [ { "family_name": "Lakshmanan", "given_name": "Anupama", "orcid": "0000-0002-6702-837X", "clpid": "Lakshmanan-Anupama" }, { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Nety", "given_name": "Suchita P.", "clpid": "Nety-Suchita-P" }, { "family_name": "Kunth", "given_name": "Martin", "orcid": "0000-0002-9741-9881", "clpid": "Kunth-Martin" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Bourdeau", "given_name": "Raymond W.", "orcid": "0000-0003-2202-1980", "clpid": "Bourdeau-Raymond-W" }, { "family_name": "Yin", "given_name": "Melissa", "clpid": "Yin-Melissa" }, { "family_name": "Yan", "given_name": "Judy", "clpid": "Yan-Judy" }, { "family_name": "Witte", "given_name": "Christopher", "orcid": "0000-0002-4098-6623", "clpid": "Witte-Chistopher" }, { "family_name": "Malounda", "given_name": "Dina", "orcid": "0000-0001-7086-9877", "clpid": "Malounda-Dina" }, { "family_name": "Foster", "given_name": "F. Stuart", "clpid": "Foster-F-Stuart" }, { "family_name": "Schr\u00f6der", "given_name": "Leif", "orcid": "0000-0003-4901-0325", "clpid": "Schr\u00f6der-Leif" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Gas vesicles (GVs) are a unique class of gas-filled protein nanostructures that are detectable at subnanomolar concentrations and whose physical properties allow them to serve as highly sensitive imaging agents for ultrasound and MRI. Here we provide a protocol for isolating GVs from native and heterologous host organisms, functionalizing these nanostructures with moieties for targeting and fluorescence, characterizing their biophysical properties and imaging them using ultrasound and MRI. GVs can be isolated from natural cyanobacterial and haloarchaeal host organisms or from Escherichia coli expressing a heterologous GV gene cluster and purified using buoyancy-assisted techniques. They can then be modified by replacing surface-bound proteins with engineered, heterologously expressed variants or through chemical conjugation, resulting in altered mechanical, surface and targeting properties. Pressurized absorbance spectroscopy is used to characterize their mechanical properties, whereas dynamic light scattering (DLS)and transmission electron microscopy (TEM) are used to determine nanoparticle size and morphology, respectively. GVs can then be imaged with ultrasound in vitro and in vivo using pulse sequences optimized for their detection versus background. They can also be imaged with hyperpolarized xenon MRI using chemical exchange saturation transfer between GV-bound and dissolved xenon\u2014a technique currently implemented in vitro. Taking 3\u20138 d to prepare, these genetically encodable nanostructures enable multimodal, noninvasive biological imaging with high sensitivity and potential for molecular targeting.", "doi": "10.1038/nprot.2017.081", "pmcid": "PMC6185898", "issn": "1754-2189", "publisher": "Nature Publishing Group", "publication": "Nature Protocols", "publication_date": "2017-10", "series_number": "10", "volume": "12", "issue": "10", "pages": "2050-2080" }, { "id": "authors:qw6z7-6kk35", "collection": "authors", "collection_id": "qw6z7-6kk35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170731-162137444", "type": "article", "title": "Localization of Microscale Devices In Vivo using Addressable Transmitters Operated as Magnetic Spins", "author": [ { "family_name": "Monge", "given_name": "Manuel", "orcid": "0000-0001-9799-0693", "clpid": "Monge-Manuel" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-A" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Emami", "given_name": "Azita", "orcid": "0000-0002-6945-9958", "clpid": "Emami-A" } ], "abstract": "The function of miniature wireless medical devices, such as capsule endoscopes, biosensors and drug-delivery systems, depends critically on their location inside the body. However, existing electromagnetic, acoustic and imaging-based methods for localizing and communicating with such devices suffer from limitations arising from physical tissue properties or from the performance of the imaging modality. Here, we embody the principles of nuclear magnetic resonance in a silicon integrated-circuit approach for microscale device localization. Analogous to the behaviour of nuclear spins, the engineered miniaturized radio frequency transmitters encode their location in space by shifting their output frequency in proportion to the local magnetic field; applied field gradients thus allow each device to be located precisely from its signal's frequency. The devices are integrated in circuits smaller than 0.7 mm3 and manufactured through a standard complementary-metal-oxide-semiconductor process, and are capable of sub-millimetre localization in vitro and in vivo. The technology is inherently robust to tissue properties, scalable to multiple devices, and suitable for the development of microscale devices to monitor and treat disease.", "doi": "10.1038/s41551-017-0129-2", "issn": "2157-846X", "publisher": "Nature Publishing Group", "publication": "Nature Biomedical Engineering", "publication_date": "2017-09", "series_number": "9", "volume": "1", "issue": "9", "pages": "736-744" }, { "id": "authors:wat3g-vjn71", "collection": "authors", "collection_id": "wat3g-vjn71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170711-140321159", "type": "article", "title": "Characterizing Single Polymeric and Protein Nanoparticles with Surface Plasmon Resonance Imaging Measurements", "author": [ { "family_name": "Maley", "given_name": "Adam M.", "orcid": "0000-0003-1851-984X", "clpid": "Maley-Adam-M" }, { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Corn", "given_name": "Robert M.", "orcid": "0000-0002-4756-2161", "clpid": "Corn-Robert-M" } ], "abstract": "Near-infrared surface plasmon resonance imaging (SPRI) microscopy is used to detect and characterize the adsorption of single polymeric and protein nanoparticles (PPNPs) onto chemically modified gold thin films in real time. The single-nanoparticle SPRI responses, \u0394%R_(NP), from several hundred adsorbed nanoparticles are collected in a single SPRI adsorption measurement. Analysis of \u0394%R_(NP) frequency distribution histograms is used to provide information on the size, material content, and interparticle interactions of the PPNPs. Examples include the measurement of log-normal \u0394%R_(NP) distributions for mixtures of polystyrene nanoparticles, the quantitation of bioaffinity uptake into and aggregation of porous NIPAm-based (N-isopropylacrylamide) hydrogel nanoparticles specifically engineered to bind peptides and proteins, and the characterization of the negative single-nanoparticle SPRI response and log-normal \u0394%R_(NP) distributions obtained for three different types of genetically encoded gas-filled protein nanostructures derived from bacteria.", "doi": "10.1021/acsnano.7b03859", "pmcid": "PMC5531002", "issn": "1936-0851", "publisher": "American Chemical Society", "publication": "ACS Nano", "publication_date": "2017-07-25", "series_number": "7", "volume": "11", "issue": "7", "pages": "7447-7456" }, { "id": "authors:1sm7a-p1n93", "collection": "authors", "collection_id": "1sm7a-p1n93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170227-101317014", "type": "article", "title": "Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging", "author": [ { "family_name": "Gilad", "given_name": "Assaf A.", "clpid": "Gilad-A-A" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.", "doi": "10.1007/s11307-017-1062-1", "pmcid": "PMC6058969", "issn": "1536-1632", "publisher": "Springer", "publication": "Molecular Imaging and Biology", "publication_date": "2017-06", "series_number": "3", "volume": "19", "issue": "3", "pages": "373-378" }, { "id": "authors:70b8p-pfj67", "collection": "authors", "collection_id": "70b8p-pfj67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170621-073438342", "type": "article", "title": "Gas vesicles: Acoustic biomolecules for ultrasound imaging", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Expanding the capabilities of ultrasound for biological and diagnostic imaging requires the development of contrast agents linked to cellular and molecular processes in vivo. In optical imaging this is commonly accomplished using fluorescent biomolecules such as the green fluorescent protein. Analogously, we recently introduced gas vesicles (GVs) as the first acoustic biomolecules for ultrasound. GVs are physically stable gas-filled protein nanostructures (~250 nm) naturally expressed in aquatic photosynthetic microbes as a means to regulate buoyancy. Purified GVs produce robust ultrasound contrast across a range of frequencies at picomolar concentrations, exhibit nonlinear scattering to enable enhanced detection versus background in vivo, and have species-dependent thresholds for pressure-induced collapse to enable multiplexed imaging. Here, I will present our recent progress on understanding the biophysical and acoustic properties of these biomolecular contrast agents, engineering their mechanics and targeting at the genetic level, developing ultrasound pulse sequences to enhance their detection in vivo and expressing them heterologously as acoustic reporter genes. 1. Shapiro, M.G. et al. Nat. Nanotechnol. 9, 311-316 (2014). 2. Cherin, M. et al. U.M.B. (In press). 3. Lakshmanan, A. et al. ACS Nano 10, 7314-7322 (2016). 4. Maresca, D. et al. In revision. 5. Bourdeau, R.W. et al. Submitted. More information at http://shapirolab.caltech.edu.", "doi": "10.1121/1.4988979", "issn": "0001-4966", "publisher": "Acoustical Society of America", "publication": "Journal of the Acoustical Society of America", "publication_date": "2017-06", "series_number": "5", "volume": "141", "issue": "5", "pages": "Art. No. 3953" }, { "id": "authors:gxtxg-18j82", "collection": "authors", "collection_id": "gxtxg-18j82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170313-090300487", "type": "article", "title": "Acoustic Behavior of Halobacterium salinarum Gas Vesicles in the High-Frequency Range: Experiments and Modeling", "author": [ { "family_name": "Cherin", "given_name": "Emmanuel", "clpid": "Cherin-E" }, { "family_name": "Melis", "given_name": "Johan M.", "clpid": "Melis-J-M" }, { "family_name": "Bourdeau", "given_name": "Raymond W.", "orcid": "0000-0003-2202-1980", "clpid": "Bourdeau-R-W" }, { "family_name": "Yin", "given_name": "Melissa", "clpid": "Yin-Melissa" }, { "family_name": "Kochmann", "given_name": "Dennis M.", "orcid": "0000-0002-9112-6615", "clpid": "Kochmann-D-M" }, { "family_name": "Foster", "given_name": "F. Stuart", "clpid": "Foster-F-S" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Gas vesicles (GVs) are a new and unique class of biologically derived ultrasound contrast agents with sub-micron size whose acoustic properties have not been fully elucidated. In this study, we investigated the acoustic collapse pressure and behavior of Halobacterium salinarum gas vesicles at transmit center frequencies ranging from 12.5 to 27.5 MHz. The acoustic collapse pressure was found to be above 550 kPa at all frequencies, nine-fold higher than the critical pressure observed under hydrostatic conditions. We illustrate that gas vesicles behave non-linearly when exposed to ultrasound at incident pressure ranging from 160 kPa to the collapse pressure and generate second harmonic amplitudes of \u22122 to \u22126 dB below the fundamental in media with viscosities ranging from 0.89 to 8 mPa\u00b7s. Simulations performed using a Rayleigh\u2013Plesset-type model accounting for buckling and a dynamic finite-element analysis suggest that buckling is the mechanism behind the generation of harmonics. We found good agreement between the level of second harmonic relative to the fundamental measured at 20 MHz and the Rayleigh\u2013Plesset model predictions. Finite-element simulations extended these findings to a non-spherical geometry, confirmed that the acoustic buckling pressure corresponds to the critical pressure under hydrostatic conditions and support the hypothesis of limited gas flow across the GV shell during the compression phase in the frequency range investigated. From simulations, estimates of GV bandwidth-limited scattering indicate that a single GV has a scattering cross section comparable to that of a red blood cell. These findings will inform the development of GV-based contrast agents and pulse sequences to optimize their detection with ultrasound.", "doi": "10.1016/j.ultrasmedbio.2016.12.020", "pmcid": "PMC5385285", "issn": "0301-5629", "publisher": "Elsevier", "publication": "Ultrasound in Medicine and Biology", "publication_date": "2017-05", "series_number": "5", "volume": "43", "issue": "5", "pages": "1016-1030" }, { "id": "authors:ats7f-skv08", "collection": "authors", "collection_id": "ats7f-skv08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180307-123920544", "type": "article", "title": "What Is the Role of Circuit Design in the Advancement of Synthetic Biology? Part 1", "author": [ { "family_name": "Chen", "given_name": "Yvonne Y.", "clpid": "Chen-Yvonne-Y" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Ruder", "given_name": "Warren", "clpid": "Ruder-W" }, { "family_name": "Ye", "given_name": "Haifeng", "clpid": "Ye-Haifeng" }, { "family_name": "Kiani", "given_name": "Samira", "clpid": "Kiana-Samira" }, { "family_name": "Moon", "given_name": "Tae Seok", "clpid": "Moon-Tae-Seok" }, { "family_name": "Raman", "given_name": "Srivatsan", "clpid": "Raman-Srivatsan" }, { "family_name": "Beisel", "given_name": "Chase", "clpid": "Beisel-C-L" }, { "family_name": "Barnes", "given_name": "Chris", "orcid": "0000-0003-2754-5951", "clpid": "Barnes-C-O" } ], "abstract": "Enabling real-world applications and therapeutics.", "doi": "10.1016/j.cels.2017.04.003", "issn": "2405-4712", "publisher": "Elsevier", "publication": "Cell Systems", "publication_date": "2017-04-26", "series_number": "4", "volume": "4", "issue": "4", "pages": "370-372" }, { "id": "authors:fpz65-n5k62", "collection": "authors", "collection_id": "fpz65-n5k62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170221-114609641", "type": "article", "title": "Nonlinear ultrasound imaging of nanoscale acoustic biomolecules", "author": [ { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Lakshmanan", "given_name": "Anupama", "orcid": "0000-0002-6702-837X", "clpid": "Lakshmanan-Anupama" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Melis", "given_name": "Johan M.", "clpid": "Melis-Johan-M" }, { "family_name": "Ni", "given_name": "Yu-Li", "orcid": "0000-0003-1600-9854", "clpid": "Ni-Yu-Li" }, { "family_name": "Bourdeau", "given_name": "Raymond W.", "orcid": "0000-0003-2202-1980", "clpid": "Bourdeau-Raymond-W" }, { "family_name": "Kochmann", "given_name": "Dennis M.", "orcid": "0000-0002-9112-6615", "clpid": "Kochmann-D-M" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Ultrasound imaging is widely used to probe the mechanical structure of tissues and visualize blood flow. However, the ability of ultrasound to observe specific molecular and cellular signals is limited. Recently, a unique class of gas-filled protein nanostructures called gas vesicles (GVs) was introduced as nanoscale (\u223c250\u2009nm) contrast agents for ultrasound, accompanied by the possibilities of genetic engineering, imaging of targets outside the vasculature and monitoring of cellular signals such as gene expression. These possibilities would be aided by methods to discriminate GV-generated ultrasound signals from anatomical background. Here, we show that the nonlinear response of engineered GVs to acoustic pressure enables selective imaging of these nanostructures using a tailored amplitude modulation strategy. Finite element modeling predicted a strongly nonlinear mechanical deformation and acoustic response to ultrasound in engineered GVs. This response was confirmed with ultrasound measurements in the range of 10 to 25\u2009MHz. An amplitude modulation pulse sequence based on this nonlinear response allows engineered GVs to be distinguished from linear scatterers and other GV types with a contrast ratio greater than 11.5\u2009dB. We demonstrate the effectiveness of this nonlinear imaging strategy in vitro, in cellulo, and in vivo.", "doi": "10.1063/1.4976105", "pmcid": "PMC5315666", "issn": "0003-6951", "publisher": "American Institute of Physics", "publication": "Applied Physics Letters", "publication_date": "2017-02-13", "series_number": "7", "volume": "110", "issue": "7", "pages": "Art. No. 073704" }, { "id": "authors:mmtzc-xvc40", "collection": "authors", "collection_id": "mmtzc-xvc40", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161018-095718409", "type": "article", "title": "NMR Hyperpolarization Techniques of Gases", "author": [ { "family_name": "Barskiy", "given_name": "Danila A.", "clpid": "Barskiy-Danila-A" }, { "family_name": "Coffey", "given_name": "Aaron M", "clpid": "Coffey-Aaron-M" }, { "family_name": "Nikolaou", "given_name": "Panayiotis", "clpid": "Nikolaou-Panayiotis" }, { "family_name": "Mikhaylov", "given_name": "Dmitry M.", "clpid": "Mikhaylov-Dmitry-M" }, { "family_name": "Goodson", "given_name": "Boyd M.", "orcid": "0000-0001-6079-5077", "clpid": "Goodson-Boyd-M" }, { "family_name": "Branca", "given_name": "Rosa T.", "clpid": "Branca-Rosa-T" }, { "family_name": "Lu", "given_name": "George J.", "orcid": "0000-0002-4689-9686", "clpid": "Lu-George-Jiaozhi" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Telkki", "given_name": "Ville-Veikko", "orcid": "0000-0003-0846-6852", "clpid": "Telkki-Ville-Veikko" }, { "family_name": "Zhivonitko", "given_name": "Vladimir V.", "clpid": "Zhivonitko-Vladimir-V" }, { "family_name": "Koptyug", "given_name": "Igor V.", "clpid": "Koptyug-Igor-V" }, { "family_name": "Salnikov", "given_name": "Oleg G.", "clpid": "Salnikov-Oleg-G" }, { "family_name": "Kovtunov", "given_name": "Kirill V.", "clpid": "Kovtunov-Kirill-V" }, { "family_name": "Bukhtiyarov", "given_name": "Valerii I.", "clpid": "Bukhtiyarov-Valerii-I" }, { "family_name": "Rosen", "given_name": "Matthew S.", "clpid": "Rosen-Matthew-S" }, { "family_name": "Barlow", "given_name": "Michael J.", "clpid": "Barlow-Michael-J" }, { "family_name": "Safavi", "given_name": "Shahideh", "clpid": "Safavi-Shahideh" }, { "family_name": "Hall", "given_name": "Ian P.", "clpid": "Hall-Ian-P" }, { "family_name": "Schr\u00f6der", "given_name": "Leif", "orcid": "0000-0003-4901-0325", "clpid": "Schr\u00f6der-Leif" }, { "family_name": "Chekmenev", "given_name": "Eduard Y.", "clpid": "Chekmenev-Eduard-Y" } ], "abstract": "Nuclear spin polarization can be significantly increased through the process of hyperpolarization, leading to an increase in the sensitivity of nuclear magnetic resonance (NMR) experiments by 4-8 orders of magnitude. Hyperpolarized gases, unlike liquids and solids, can be more readily separated and purified from the compounds used to mediate the hyperpolarization processes. These pure hyperpolarized gases enabled many novel MRI applications including the visualization of void spaces, imaging of lung function, and remote detection. Additionally, hyperpolarized gases can be dissolved in liquids and can be used as sensitive molecular probes and reporters. This mini-review covers the fundamentals of the preparation of hyperpolarized gases and focuses on selected applications of interest to biomedicine and materials science.", "doi": "10.1002/chem.201603884", "pmcid": "PMC5462469", "issn": "0947-6539", "publisher": "John Wiley & Sons", "publication": "Chemistry: a European Journal", "publication_date": "2017-01-18", "series_number": "4", "volume": "23", "issue": "4", "pages": "725-751" }, { "id": "authors:2kk27-c6972", "collection": "authors", "collection_id": "2kk27-c6972", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160906-121824624", "type": "article", "title": "Tunable thermal bioswitches for in vivo control of microbial therapeutics", "author": [ { "family_name": "Piraner", "given_name": "Dan I.", "orcid": "0000-0003-3857-9487", "clpid": "Piraner-Dan-I" }, { "family_name": "Abedi", "given_name": "Mohamad H.", "orcid": "0000-0001-9717-6288", "clpid": "Abedi-Mohamad-H" }, { "family_name": "Moser", "given_name": "Brittany A.", "clpid": "Moser-Brittany-A" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Temperature is a unique input signal that could be used by engineered microbial therapeutics to sense and respond to host conditions or spatially targeted external triggers such as focused ultrasound. To enable these possibilities, we present two families of tunable, orthogonal, temperature-dependent transcriptional repressors providing switch-like control of bacterial gene expression at thresholds spanning the biomedically relevant range of 32\u201346\u00b0C. We integrate these molecular bioswitches into thermal logic circuits and demonstrate their utility in three in vivo microbial therapy scenarios, including spatially precise activation using focused ultrasound, modulation of activity in response to a host fever, and self-destruction after fecal elimination to prevent environmental escape. This technology provides a critical capability for coupling endogenous or applied thermal signals to cellular function in basic research, biomedical and industrial applications.", "doi": "10.1038/nchembio.2233", "issn": "1552-4450", "publisher": "Nature Publishing Group", "publication": "Nature Chemical Biology", "publication_date": "2017-01", "series_number": "1", "volume": "13", "issue": "1", "pages": "75-80" }, { "id": "authors:q27k5-1wf62", "collection": "authors", "collection_id": "q27k5-1wf62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161222-161549671", "type": "article", "title": "Non-invasive imaging using reporter genes altering cellular water permeability", "author": [ { "family_name": "Mukherjee", "given_name": "Arnab", "orcid": "0000-0002-6783-8225", "clpid": "Mukherjee-Arnab" }, { "family_name": "Wu", "given_name": "Di", "orcid": "0000-0002-6848-668X", "clpid": "Wu-Di" }, { "family_name": "Davis", "given_name": "Hunter C.", "orcid": "0000-0003-1655-692X", "clpid": "Davis-Hunter-C" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Non-invasive imaging of gene expression in live, optically opaque animals is important for multiple applications, including monitoring of genetic circuits and tracking of cell-based therapeutics. Magnetic resonance imaging (MRI) could enable such monitoring with high spatiotemporal resolution. However, existing MRI reporter genes based on metalloproteins or chemical exchange probes are limited by their reliance on metals or relatively low sensitivity. Here we introduce a new class of MRI reporters based on the human water channel aquaporin 1. We show that aquaporin overexpression produces contrast in diffusion-weighted MRI by increasing tissue water diffusivity without affecting viability. Low aquaporin levels or mixed populations comprising as few as 10% aquaporin-expressing cells are sufficient to produce MRI contrast. We characterize this new contrast mechanism through experiments and simulations, and demonstrate its utility in vivo by imaging gene expression in tumours. Our results establish an alternative class of sensitive, metal-free reporter genes for non-invasive imaging.", "doi": "10.1038/ncomms13891", "pmcid": "PMC5196229", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2016-12-23", "volume": "7", "pages": "Art. No. 13891" }, { "id": "authors:cw7hv-0xq40", "collection": "authors", "collection_id": "cw7hv-0xq40", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160714-134344625", "type": "article", "title": "Molecular Engineering of Acoustic Protein Nanostructures", "author": [ { "family_name": "Lakshmanan", "given_name": "Anupama", "orcid": "0000-0002-6702-837X", "clpid": "Lakshmanan-Anupama" }, { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" }, { "family_name": "Nety", "given_name": "Suchita P.", "orcid": "0000-0002-4201-1061", "clpid": "Nety-Suchita-P" }, { "family_name": "Lee-Gosselin", "given_name": "Audrey", "orcid": "0000-0002-2431-2741", "clpid": "Lee-Gosselin-Audrey" }, { "family_name": "Bourdeau", "given_name": "Raymond W.", "orcid": "0000-0003-2202-1980", "clpid": "Bourdeau-Raymond-W" }, { "family_name": "Maresca", "given_name": "David", "orcid": "0000-0002-4921-6406", "clpid": "Maresca-David" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "Ultrasound is among the most widely used biomedical imaging modalities, but has limited ability to image specific molecular targets due to the lack of suitable nanoscale contrast agents. Gas vesicles\u2014genetically encoded protein nanostructures isolated from buoyant photosynthetic microbes\u2014have recently been identified as nanoscale reporters for ultrasound. Their unique physical properties give gas vesicles significant advantages over conventional microbubble contrast agents, including nanoscale dimensions and inherent physical stability. Furthermore, as a genetically encoded material, gas vesicles present the possibility that the nanoscale mechanical, acoustic, and targeting properties of an imaging agent can be engineered at the level of its constituent proteins. Here, we demonstrate that genetic engineering of gas vesicles results in nanostructures with new mechanical, acoustic, surface, and functional properties to enable harmonic, multiplexed, and multimodal ultrasound imaging as well as cell-specific molecular targeting. These results establish a biomolecular platform for the engineering of acoustic nanomaterials.", "doi": "10.1021/acsnano.6b03364", "pmcid": "PMC6058967", "issn": "1936-0851", "publisher": "American Chemical Society", "publication": "ACS Nano", "publication_date": "2016-08-23", "series_number": "8", "volume": "10", "issue": "8", "pages": "7314-7322" }, { "id": "authors:7673v-0mf89", "collection": "authors", "collection_id": "7673v-0mf89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140308-200856771", "type": "article", "title": "Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Ramirez", "given_name": "R. Matthew", "clpid": "Ramirez-R-M" }, { "family_name": "Sperling", "given_name": "Lindsay J.", "clpid": "Sperling-L-J" }, { "family_name": "Sun", "given_name": "George", "clpid": "Sun-George" }, { "family_name": "Sun", "given_name": "Jinny", "clpid": "Sun-Jinny" }, { "family_name": "Pines", "given_name": "Alexander", "clpid": "Pines-Alexander" }, { "family_name": "Schaffer", "given_name": "David V.", "clpid": "Schaffer-D-V" }, { "family_name": "Bajaj", "given_name": "Vikram S.", "clpid": "Bajaj-Vikram-S" } ], "abstract": "Magnetic resonance imaging (MRI) enables high-resolution non-invasive observation of the anatomy and function of intact organisms. However, previous MRI reporters of key biological processes tied to gene expression have been limited by the inherently low molecular sensitivity of conventional ^1H MRI. This limitation could be overcome through the use of hyperpolarized nuclei, such as in the noble gas xenon, but previous reporters acting on such nuclei have been synthetic. Here, we introduce the first genetically encoded reporters for hyperpolarized ^(129)Xe MRI. These expressible reporters are based on gas vesicles (GVs), gas-binding protein nanostructures expressed by certain buoyant microorganisms. We show that GVs are capable of chemical exchange saturation transfer interactions with xenon, which enables chemically amplified GV detection at picomolar concentrations (a 100- to 10,000-fold improvement over comparable constructs for ^1H MRI). We demonstrate the use of GVs as heterologously expressed indicators of gene expression and chemically targeted exogenous labels in MRI experiments performed on living cells.", "doi": "10.1038/nchem.1934", "issn": "1755-4330", "publisher": "Nature Publishing Group", "publication": "Nature Chemistry", "publication_date": "2014-07", "series_number": "7", "volume": "6", "issue": "7", "pages": "629-634" }, { "id": "authors:4e056-8s911", "collection": "authors", "collection_id": "4e056-8s911", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140423-142811017", "type": "article", "title": "Biogenic gas nanostructures as ultrasonic molecular reporters", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Goodwill", "given_name": "Patrick W.", "clpid": "Goodwill-P-W" }, { "family_name": "Neogy", "given_name": "Arkosnato", "clpid": "Neogy-A" }, { "family_name": "Yin", "given_name": "Melissa", "clpid": "Yin-M" }, { "family_name": "Foster", "given_name": "F. Stuart", "clpid": "Foster-F-S" }, { "family_name": "Schaffer", "given_name": "David V.", "clpid": "Schaffer-D-V" }, { "family_name": "Conolly", "given_name": "Steven M.", "clpid": "Conolly-S-M" } ], "abstract": "Ultrasound is among the most widely used non-invasive imaging modalities in biomedicine, but plays a surprisingly small role in molecular imaging due to a lack of suitable molecular reporters on the nanoscale. Here, we introduce a new class of reporters for ultrasound based on genetically encoded gas nanostructures from microorganisms, including bacteria and archaea. Gas vesicles are gas-filled protein-shelled compartments with typical widths of 45\u2013250 nm and lengths of 100\u2013600 nm that exclude water and are permeable to gas. We show that gas vesicles produce stable ultrasound contrast that is readily detected in vitro and in vivo, that their genetically encoded physical properties enable multiple modes of imaging, and that contrast enhancement through aggregation permits their use as molecular biosensors.", "doi": "10.1038/nnano.2014.32", "pmcid": "PMC4023545", "issn": "1748-3387", "publisher": "Nature Publishing Group", "publication": "Nature Nanotechnology", "publication_date": "2014-04", "series_number": "4", "volume": "9", "issue": "4", "pages": "311-316" }, { "id": "authors:vvkv4-yq016", "collection": "authors", "collection_id": "vvkv4-yq016", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140710-085633858", "type": "article", "title": "Genetically Encoded Gas Nanostructures as Biophyically Tunable Molecular Reporters for MRI and Ultrasound", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "abstract": "The study of cellular and molecular processes occurring deep inside living organisms requires new technologies for non-invasive molecular imaging. In particular, there is a need for \"magnetic\" and \"acoustic\" analogs of the green fluorescent protein (GFP) that can be used to sensitively observe gene expression using magnetic resonance imaging (MRI) and ultrasound. We are developing genetic reporters for both of these modalities based on the unique biophysical properties of genetically encoded gas nanostructures known as gas vesicles (GVs). Expressed by aquatic microorganism as a means to control buoyancy, GVs are hollow protein-shelled nano-compartments that exclude water but are permeable to gas. We have adapted GVs as the first genetically encoded reporters for hyperpolarized MRI - a form of imaging in which nuclei such as the biocompatible noble gas xenon are introduced into tissues in a non-equilibrium state with 10^4 - 10^5 stronger polarization compared to conventional 1H-MRI. Xenon partitioning into GVs enables their detection using chemical exchange saturation transfer at sub-nanomolar reporter concentrations. In parallel, we have shown that GVs can be detected with high frequency ultrasound, their physical properties enabling linear, harmonic and collapse-mode imaging in vitro and in vivo. Furthermore, inter-species differences in the genetically encoded biophysical properties of gas vesicles enable multiplexed imaging with both MRI and ultrasound and provide clues for genetic-level biophysical tuning of these unique nanostructures.", "doi": "10.1016/j.bpj.2013.11.159", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2014-01-28", "series_number": "2", "volume": "106", "issue": "2", "pages": "19A" }, { "id": "authors:78sex-awh37", "collection": "authors", "collection_id": "78sex-awh37", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131125-140948447", "type": "article", "title": "Physical principles for scalable neural recoding", "author": [ { "family_name": "Marblestone", "given_name": "Adam H.", "clpid": "Marblestone-Adam-H" }, { "family_name": "Zamft", "given_name": "Bradley M.", "clpid": "Zamft-Bradley-M" }, { "family_name": "Maguire", "given_name": "Yael G.", "clpid": "Maguire-Yael-G" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Cybulski", "given_name": "Thaddeus R.", "clpid": "Cybulski-Thaddeus-R" }, { "family_name": "Glaser", "given_name": "Joshua I.", "clpid": "Glaser-Joshua-I" }, { "family_name": "Amodei", "given_name": "Dario", "clpid": "Amodei-Dario" }, { "family_name": "Stranges", "given_name": "P. Benjamin", "clpid": "Stranges-P-Benjamin" }, { "family_name": "Kalhor", "given_name": "Reza", "clpid": "Kalhor-Reza" }, { "family_name": "Dalrymple", "given_name": "David A.", "clpid": "Dalrymple-David-A" }, { "family_name": "Seo", "given_name": "Dongjin", "clpid": "Seo-Dongjin" }, { "family_name": "Alon", "given_name": "Elad", "clpid": "Alon-Elad" }, { "family_name": "Maharbiz", "given_name": "Michel M.", "clpid": "Maharbiz-Michel-M" }, { "family_name": "Carmena", "given_name": "Jose M.", "clpid": "Carmena-Jose-M" }, { "family_name": "Rabaey", "given_name": "Jan M.", "clpid": "Rabaey-Jan-M" }, { "family_name": "Boyden", "given_name": "Edward S.", "clpid": "Boyden-Edward-S" }, { "family_name": "Church", "given_name": "George M.", "clpid": "Church-George-M" }, { "family_name": "Kording", "given_name": "Konrad P.", "clpid": "Kording-Konrad-P" } ], "abstract": "Simultaneously measuring the activities of all neurons in a mammalian brain at millisecond resolution is a challenge beyond the limits of existing techniques in neuroscience. Entirely new approaches may be required, motivating an analysis of the fundamental physical constraints on the problem. We outline the physical principles governing brain activity mapping using optical, electrical, magnetic resonance, and molecular modalities of neural recording. Focusing on the mouse brain, we analyze the scalability of each method, concentrating on the limitations imposed by spatiotemporal resolution, energy dissipation, and volume displacement. Based on this analysis, all existing approaches require orders of magnitude improvement in key parameters. Electrical recording is limited by the low multiplexing capacity of electrodes and their lack of intrinsic spatial resolution, optical methods are constrained by the scattering of visible light in brain tissue, magnetic resonance is hindered by the diffusion and relaxation timescales of water protons, and the implementation of molecular recording is complicated by the stochastic kinetics of enzymes. Understanding the physical limits of brain activity mapping may provide insight into opportunities for novel solutions. For example, unconventional methods for delivering electrodes may enable unprecedented numbers of recording sites, embedded optical devices could allow optical detectors to be placed within a few scattering lengths of the measured neurons, and new classes of molecularly engineered sensors might obviate cumbersome hardware architectures. We also study the physics of powering and communicating with microscale devices embedded in brain tissue and find that, while radio-frequency electromagnetic data transmission suffers from a severe power\u2013bandwidth tradeoff, communication via infrared light or ultrasound may allow high data rates due to the possibility of spatial multiplexing. The use of embedded local recording and wireless data transmission would only be viable, however, given major improvements to the power efficiency of microelectronic devices.", "doi": "10.48550/arXiv.1306.5709", "pmcid": "PMC3807567", "issn": "1662-5188", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Computational Neuroscience", "publication_date": "2013-10", "volume": "7", "pages": "Art. No. 137" }, { "id": "authors:m4nfx-rsx65", "collection": "authors", "collection_id": "m4nfx-rsx65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140423-135048974", "type": "article", "title": "Thermal Mechanisms of Millimeter Wave Stimulation of Excitable Cells", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Priest", "given_name": "Michael F.", "clpid": "Priest-M-F" }, { "family_name": "Siegel", "given_name": "Peter H.", "orcid": "0000-0002-2539-4646", "clpid": "Siegel-P-H" }, { "family_name": "Bezanilla", "given_name": "Francisco", "clpid": "Bezanilla-F" } ], "abstract": "Interactions between millimeter waves (MMWs) and biological systems have received increasing attention due to the growing use of MMW radiation in technologies ranging from experimental medical devices to telecommunications and airport security. Studies have shown that MMW exposure alters cellular function, especially in neurons and muscles. However, the biophysical mechanisms underlying such effects are still poorly understood. Due to the high aqueous absorbance of MMW, thermal mechanisms are likely. However, nonthermal mechanisms based on resonance effects have also been postulated. We studied MMW stimulation in a simplified preparation comprising Xenopus laevis oocytes expressing proteins that underlie membrane excitability. Using electrophysiological recordings simultaneously with 60 GHz stimulation, we observed changes in the kinetics and activity levels of voltage-gated potassium and sodium channels and a sodium-potassium pump that are consistent with a thermal mechanism. Furthermore, we showed that MMW stimulation significantly increased the action potential firing rate in oocytes coexpressing voltage-gated sodium and potassium channels, as predicted by thermal terms in the Hodgkin-Huxley model of neurons. Our results suggest that MMW stimulation produces significant thermally mediated effects on excitable cells via basic thermodynamic mechanisms that must be taken into account in the study and use of MMW radiation in biological systems.", "doi": "10.1016/j.bpj.2013.05.014", "pmcid": "PMC3686354", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2013-06-18", "series_number": "12", "volume": "104", "issue": "12", "pages": "2622-2628" }, { "id": "authors:t37gq-68p43", "collection": "authors", "collection_id": "t37gq-68p43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120926-114816752", "type": "article", "title": "Unparalleled Control of Neural Activity Using Orthogonal Pharmacogenetics", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Frazier", "given_name": "Shawnalea J.", "clpid": "Frazier-S-J" }, { "family_name": "Lester", "given_name": "Henry A.", "orcid": "0000-0002-5470-5255", "clpid": "Lester-H-A" } ], "abstract": "Studying the functional architecture of the brain requires technologies to precisely measure and perturb the activity of specific neural cells and circuits in live animals. Substantial progress has been made in recent years to develop and apply such tools. In particular, technologies that provide precise control of activity in genetically defined populations of neurons have enabled the study of causal relationships between and among neural circuit elements and behavioral outputs. Here, we review an important subset of such technologies, in which neurons are genetically engineered to respond to specific chemical ligands that have no interfering pharmacological effect in the central nervous system. A rapidly expanding set of these \"orthogonal pharmacogenetic\" tools provides a unique combination of genetic specificity, functional diversity, spatiotemporal precision, and potential for multiplexing. We review the main classes of orthogonal pharmacogenetic technologies, including neuroreceptors to control neuronal excitability, systems to control gene transcription and translation, and general constructs to control protein\u2013protein interactions, enzymatic function, and protein stability. We describe the key performance characteristics informing the use of these technologies in the brain, and potential directions for improvement and expansion of the orthogonal pharmacogenetics toolkit to enable more sophisticated systems neuroscience.", "doi": "10.1021/cn300053q", "pmcid": "PMC3419455", "issn": "1948-7193", "publisher": "American Chemical Society", "publication": "ACS Chemical Neuroscience", "publication_date": "2012-08-15", "series_number": "8", "volume": "3", "issue": "8", "pages": "619-629" }, { "id": "authors:kmm22-n7586", "collection": "authors", "collection_id": "kmm22-n7586", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140423-134017519", "type": "article", "title": "Infrared light excites cells by changing their electrical capacitance", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Homma", "given_name": "Kazuaki", "clpid": "Homma-Kazuaki" }, { "family_name": "Villarreal", "given_name": "Sebastian", "clpid": "Villarreal-S" }, { "family_name": "Richter", "given_name": "Claus-Peter", "clpid": "Richter-C-P" }, { "family_name": "Bezanilla", "given_name": "Francisco", "clpid": "Bezanilla-F" } ], "abstract": "Optical stimulation has enabled important advances in the study of brain function and other biological processes, and holds promise for medical applications ranging from hearing restoration to cardiac pace making. In particular, pulsed laser stimulation using infrared wavelengths >1.5 \u03bcm has therapeutic potential based on its ability to directly stimulate nerves and muscles without any genetic or chemical pre-treatment. However, the mechanism of infrared stimulation has been a mystery, hindering its path to the clinic. Here we show that infrared light excites cells through a novel, highly general electrostatic mechanism. Infrared pulses are absorbed by water, producing a rapid local increase in temperature. This heating reversibly alters the electrical capacitance of the plasma membrane, depolarizing the target cell. This mechanism is fully reversible and requires only the most basic properties of cell membranes. Our findings underscore the generality of pulsed infrared stimulation and its medical potential.", "doi": "10.1038/ncomms1742", "pmcid": "PMC3316879", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2012-03", "volume": "3", "pages": "Art. No. 736" }, { "id": "authors:pnv70-3vd29", "collection": "authors", "collection_id": "pnv70-3vd29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100326-111303498", "type": "article", "title": "Directed evolution of a magnetic resonance imaging contrast agent for noninvasive imaging of dopamine", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Westmeyer", "given_name": "Gil G.", "clpid": "Westmeyer-G-G" }, { "family_name": "Romero", "given_name": "Philip A.", "orcid": "0000-0002-2586-7263", "clpid": "Romero-P-A" }, { "family_name": "Szablowski", "given_name": "Jerzy O.", "orcid": "0000-0001-7851-5408", "clpid": "Szablowski-J-O" }, { "family_name": "K\u00fcster", "given_name": "Benedict", "clpid": "K\u00fcster-B" }, { "family_name": "Shah", "given_name": "Ameer", "clpid": "Shah-Ameer" }, { "family_name": "Otey", "given_name": "Christopher R.", "clpid": "Otey-C-R" }, { "family_name": "Langer", "given_name": "Robert", "clpid": "Langer-R-M" }, { "family_name": "Arnold", "given_name": "Frances H.", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Jasanoff", "given_name": "Alan", "orcid": "0000-0002-2834-6359", "clpid": "Jasanoff-A" } ], "abstract": "The development of molecular probes that allow in vivo imaging of neural signaling processes with high temporal and spatial resolution remains challenging. Here we applied directed evolution techniques to create magnetic resonance imaging (MRI) contrast agents sensitive to the neurotransmitter dopamine. The sensors were derived from the heme domain of the bacterial cytochrome P450-BM3 (BM3h). Ligand binding to a site near BM3h's paramagnetic heme iron led to a drop in MRI signal enhancement and a shift in optical absorbance. Using an absorbance-based screen, we evolved the specificity of BM3h away from its natural ligand and toward dopamine, producing sensors with dissociation constants for dopamine of 3.3\u20138.9 \u03bcM. These molecules were used to image depolarization-triggered neurotransmitter release from PC12 cells and in the brains of live animals. Our results demonstrate the feasibility of molecular-level functional MRI using neural activity\u2013dependent sensors, and our protein engineering approach can be generalized to create probes for other targets.", "doi": "10.1038/nbt.1609", "pmcid": "PMC3073400", "issn": "1087-0156", "publisher": "Nature Publishing Group", "publication": "Nature Biotechnology", "publication_date": "2010-03", "series_number": "3", "volume": "28", "issue": "3", "pages": "264-270" }, { "id": "authors:3xf3q-a8f51", "collection": "authors", "collection_id": "3xf3q-a8f51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140423-132454335", "type": "article", "title": "Protein Nanoparticles Engineered to Sense Kinase Activity in MRI", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Szablowski", "given_name": "Jerzy O.", "orcid": "0000-0001-7851-5408", "clpid": "Szablowski-J-O" }, { "family_name": "Langer", "given_name": "Robert", "clpid": "Langer-R-M" }, { "family_name": "Jasanoff", "given_name": "Alan", "orcid": "0000-0002-2834-6359", "clpid": "Jasanoff-A" } ], "abstract": "We introduce a family of protein nanoparticles capable of sensing analytes in conjunction with magnetic resonance imaging (MRI). The new sensors are derived from the iron storage protein ferritin (Ft); they are designed and optimized using facile protein engineering methods, and self-assembled in cells harboring specific combinations of DNA coding sequences. As illustration, we show that suitably constructed Ft-based sensors can report activity of the important neural signaling enzyme protein kinase A (PKA). Phosphorylation of the engineered Ft-based nanoparticles by PKA promotes clustering and changes in T_2-weighted MRI signal.", "doi": "10.1021/ja8086938", "pmcid": "PMC2662502", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2009-02-25", "series_number": "7", "volume": "131", "issue": "7", "pages": "2484-2486" }, { "id": "authors:fyenm-0qt03", "collection": "authors", "collection_id": "fyenm-0qt03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140423-130954448", "type": "article", "title": "Dynamic imaging with MRI contrast agents: quantitative considerations", "author": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Atanasijevic", "given_name": "Tatjana", "clpid": "Atanasijevic-T" }, { "family_name": "Faas", "given_name": "Henryk", "clpid": "Faas-H" }, { "family_name": "Westmeyer", "given_name": "Gil G.", "clpid": "Westmeyer-G-G" }, { "family_name": "Jasanoff", "given_name": "Alan", "orcid": "0000-0002-2834-6359", "clpid": "Jasanoff-A" } ], "abstract": "Time-resolved MRI has had enormous impact in cognitive science and may become a significant tool in basic biological research with the application of new molecular imaging agents. In this paper, we examine the temporal characteristics of MRI contrast agents that could be used in dynamic studies. We consider \"smart\" T1 contrast agents, T2 agents based on reversible aggregation of superparamagnetic nanoparticles and sensors that produce changes in saturation transfer effects (chemical exchange saturation transfer, CEST). We discuss response properties of several agents with reference to available experimental data, and we develop a new theoretical model that predicts the response rates and relaxivity changes of aggregation-based sensors. We also perform calculations to define the extent to which constraints on temporal resolution are imposed by the imaging methods themselves. Our analysis confirms that some small T1 agents may be compatible with MRI temporal resolution on the order of 100 ms. Nanoparticle aggregation T2 sensors are applicable at much lower concentrations, but are likely to respond on a single second or slower timescale. CEST agents work at high concentrations and temporal resolutions of 1\u201310 s, limited by a requirement for long presaturation periods in the MRI pulse sequence.", "doi": "10.1016/j.mri.2005.12.033", "issn": "0730-725X", "publisher": "Elsevier", "publication": "Magnetic Resonance Imaging", "publication_date": "2006-05", "series_number": "4", "volume": "24", "issue": "4", "pages": "449-462" } ]