[ { "id": "authors:8b5yj-sjn05", "collection": "authors", "collection_id": "8b5yj-sjn05", "cite_using_url": "https://authors.library.caltech.edu/records/8b5yj-sjn05", "type": "monograph", "title": "Synthetic dosage-compensating miRNA circuits allow precision gene therapy for Rett syndrome", "author": [ { "family_name": "Flynn", "given_name": "Michael James", "orcid": "0009-0003-1186-957X", "clpid": "Flynn-Michael-James" }, { "family_name": "Mayfield", "given_name": "Acacia M.", "orcid": "0000-0001-7308-6480", "clpid": "Mayfield-Acacia-M" }, { "family_name": "Du", "given_name": "Rongrong", "orcid": "0009-0003-4942-3020", "clpid": "Du-Rongrong" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "abstract": "

A longstanding challenge in gene therapy is expressing a dosage-sensitive gene within a tight therapeutic window. For example, loss of MECP2 function causes Rett syndrome, while its duplication causes MECP2 duplication syndrome. Viral gene delivery methods generate variable numbers of gene copies in individual cells, creating a need for gene dosage-invariant expression systems. Here, we introduce a compact miRNA-based, incoherent feed-forward loop circuit that achieves precise control of Mecp2 expression in cells and brains, and improves outcomes in an AAV-based mouse model of Rett syndrome gene therapy. Single molecule analysis of endogenous and ectopic Mecp2 mRNA revealed precise, sustained expression across a broad range of gene dosages. Delivered systemically in a brain-targeting AAV capsid, the circuit strongly suppressed Rett behavioral symptoms for over 24 weeks, outperforming an unregulated gene therapy. These results demonstrate that synthetic miRNA-based regulatory circuits can enable precise in vivo expression to improve the safety and efficacy of gene therapy.

", "doi": "10.1101/2024.03.13.584179", "pmcid": "PMC10980028", "issn": "2692-8205", "publisher": "Cold Spring Harbor", "publication": "bioRxiv", "publication_date": "2024-03-14", "pages": "2024.03.13.584179" }, { "id": "authors:wkxf4-kts14", "collection": "authors", "collection_id": "wkxf4-kts14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182503000.37", "type": "monograph", "title": "Dysregulated mammalian estrus cycle rescued by timed activation of VIP neurons in the circadian pacemaker and late afternoon light exposure", "author": [ { "family_name": "Kahan", "given_name": "Anat", "orcid": "0000-0002-4799-3017", "clpid": "Kahan-Anat" }, { "family_name": "Coughlin", "given_name": "Gerard M.", "orcid": "0000-0003-0644-4721", "clpid": "Coughlin-Gerard-M" }, { "family_name": "Borsos", "given_name": "Mate", "orcid": "0000-0002-2801-8910", "clpid": "Borsos-M\u00e1t\u00e9" }, { "family_name": "Brunton", "given_name": "Bingni W.", "orcid": "0000-0002-4831-3466", "clpid": "Brunton-Bingni-W" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Jet lag and shift work disrupt the menstrual cycle and decrease fertility. The circadian pacemaker, the suprachiasmatic nucleus (SCN), is known to modulate ovulation, but the mechanism is unclear. Here we explore this connection by tracking the dynamics of vasoactive intestinal peptide (VIP)-expressing neurons in the SCN in freely-behaving mice. We show that SCNVIPactivity is time-of-day- and sex-dependent, and estrous-state-dependent in late afternoon, gating downstream activation of GnRH neurons. Afternoon light, as well as specific activation of SCNVIPneurons, rescues estrous cycle regularity and egg release in animals in altered light conditions, emphasizing the role of SCNVIPneurons as a time-dependent light-responsive switch. Our results reveal the dynamic mechanism by which SCNVIPneurons mediate light responses to regulate estrous states and demonstrate light-induced fertility rescue.One Sentence SummaryModulating and recording the activity of suprachiasmatic VIP neurons in freely behaving mice reveals their regulation of fertility by mediating the response to late afternoon light.", "doi": "10.1101/2023.01.14.524075", "publication_date": "2023-01-18" }, { "id": "authors:kckqd-x5j42", "collection": "authors", "collection_id": "kckqd-x5j42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182523000.38", "type": "monograph", "title": "Fast, accurate ranking of engineered proteins by receptor binding propensity using structural modeling", "author": [ { "family_name": "Ding", "given_name": "Xiaozhe", "orcid": "0000-0002-0267-0791", "clpid": "Ding-Xiaozhe-Z" }, { "family_name": "Chen", "given_name": "Xinhong", "orcid": "0000-0003-0408-0813", "clpid": "Chen-Xinhong" }, { "family_name": "Sullivan", "given_name": "Erin E.", "clpid": "Sullivan-Erin-E" }, { "family_name": "Shay", "given_name": "Timothy F.", "orcid": "0000-0001-6591-3271", "clpid": "Shay-Timothy-F" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Deep learning-based methods for protein structure prediction have achieved unprecedented accuracy. However, the power of these tools to guide the engineering of protein-based therapeutics remains limited due to a gap between the ability to predict the structures of candidate proteins and the ability to assess which of those proteins are most likely to bind to a target receptor. Here we bridge this gap by introducing Automated Pairwise Peptide-Receptor AnalysIs for Screening Engineered proteins (APPRAISE), a method for predicting the receptor binding propensity of engineered proteins. After generating models of engineered proteins competing for binding to a target using an established structure-prediction tool such as AlphaFold2-multimer or ESMFold, APPRAISE performs a rapid (under 1 CPU second per model) scoring analysis that takes into account biophysical and geometrical constraints. As a proof-of-concept, we demonstrate that APPRAISE can accurately classify receptor-dependent vs. receptor-independent engineered adeno-associated viral vectors, as well as diverse classes of engineered proteins such as miniproteins targeting the SARS-CoV-2 spike protein, nanobodies targeting a G-protein-coupled receptor, and peptides that specifically bind to transferrin receptor and PD-L1. With its high accuracy, interpretability, and generalizability, APPRAISE has the potential to expand the utility of current structural prediction and accelerate protein engineering for biomedical applications.", "doi": "10.1101/2023.01.11.523680", "publication_date": "2023-01-15" }, { "id": "authors:whg22-arb12", "collection": "authors", "collection_id": "whg22-arb12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182564000.42", "type": "monograph", "title": "Primate-conserved Carbonic Anhydrase IV and murine-restricted Ly6c1 are new targets for crossing the blood-brain barrier", "author": [ { "family_name": "Shay", "given_name": "Timothy F.", "orcid": "0000-0001-6591-3271", "clpid": "Shay-Timothy-F" }, { "family_name": "Sullivan", "given_name": "Erin E.", "clpid": "Sullivan-Erin-E" }, { "family_name": "Ding", "given_name": "Xiaozhe", "orcid": "0000-0002-0267-0791", "clpid": "Ding-Xiaozhe-Z" }, { "family_name": "Chen", "given_name": "Xinhong", "orcid": "0000-0003-0408-0813", "clpid": "Chen-Xinhong" }, { "family_name": "Ravindra Kumar", "given_name": "Sripriya", "orcid": "0000-0001-6033-7631", "clpid": "Ravindra-Kumar-Sripriya" }, { "family_name": "Goertsen", "given_name": "David", "orcid": "0000-0001-7138-1697", "clpid": "Goertsen-David" }, { "family_name": "Brown", "given_name": "David", "orcid": "0000-0002-9757-1744", "clpid": "Brown-David" }, { "family_name": "Vielmetter", "given_name": "Jost", "orcid": "0000-0002-4314-7163", "clpid": "Vielmetter-Jost" }, { "family_name": "Borsos", "given_name": "Mate", "orcid": "0000-0002-2801-8910", "clpid": "Borsos-M\u00e1t\u00e9" }, { "family_name": "Lam", "given_name": "Annie W.", "clpid": "Lam-Annie-W" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "The blood-brain barrier (BBB) presents a major challenge to delivering large molecules to study and treat the central nervous system (CNS). This is due in part to the scarcity of effective targets for BBB crossing, the identification of which is the crucial first step of drug development. Here, we leveraged a panel of adeno-associated viruses (AAVs) previously identified through directed evolution for improved BBB transport to reverse engineer protein targets for enhanced BBB crossing. We identify both murine-restricted Ly6c1 and primate-conserved carbonic anhydrase IV (Car4; CA4) as novel receptors for crossing the BBB. We demonstrate how these receptors can unlock new experimental and computational target-focused engineering strategies by creating the enhanced Ly6c1-binding vector AAV-PHP.eC and by applying AlphaFold2-enabled in silico methods to rank capsids against identified receptors and generate capsid-receptor binding models. Here, with Car4, we add a completely new receptor to the very short list currently available for crossing the BBB in humans and, with Ly6c1, we validate a pipeline for receptor-targeted engineering. The identification of Car4/CA4 and structural insights from computational modeling provide new paths toward human brain-penetrant chemicals (drugs) and biologicals (including gene delivery).", "doi": "10.1101/2023.01.12.523632", "publication_date": "2023-01-14" }, { "id": "authors:1r6x5-xdh78", "collection": "authors", "collection_id": "1r6x5-xdh78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182562000.41", "type": "monograph", "title": "Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates", "author": [ { "family_name": "Chen", "given_name": "Xinhong", "orcid": "0000-0003-0408-0813", "clpid": "Chen-Xinhong" }, { "family_name": "Wolfe", "given_name": "Damien A.", "orcid": "0000-0003-3005-6788", "clpid": "Wolfe-Damien-A" }, { "family_name": "Sivadasan Bindu", "given_name": "Dhanesh", "clpid": "Bindu-Dhanesh-Sivadasan" }, { "family_name": "Zhang", "given_name": "Mengying", "orcid": "0000-0003-0674-9437", "clpid": "Zhang-Mengying" }, { "family_name": "Taskin", "given_name": "Naz", "orcid": "0009-0003-2417-8428", "clpid": "Taskin-Naz" }, { "family_name": "Goertsen", "given_name": "David", "orcid": "0000-0001-7138-1697", "clpid": "Goertsen-David" }, { "family_name": "Shay", "given_name": "Timothy F.", "orcid": "0000-0001-6591-3271", "clpid": "Shay-Timothy-F" }, { "family_name": "Sullivan", "given_name": "Erin E.", "orcid": "0000-0002-1724-6520", "clpid": "Sullivan-Erin-E" }, { "family_name": "Huang", "given_name": "Sheng-Fu", "orcid": "0000-0002-6409-5470", "clpid": "Huang-Sheng-Fu" }, { "family_name": "Ravindra Kumar", "given_name": "Sripriya", "orcid": "0000-0001-6033-7631", "clpid": "Ravindra-Kumar-Sripriya" }, { "family_name": "Arokiaraj", "given_name": "Cynthia M.", "orcid": "0000-0003-3201-9868", "clpid": "Arokiaraj-Cynthia-M" }, { "family_name": "Plattner", "given_name": "Viktor M.", "orcid": "0000-0002-0740-2905", "clpid": "Plattner-Viktor-M" }, { "family_name": "Campos", "given_name": "Lillian J.", "orcid": "0000-0003-0839-0288", "clpid": "Campos-Lillian-J" }, { "family_name": "Mich", "given_name": "John", "orcid": "0000-0002-1626-1139", "clpid": "Mich-John-K" }, { "family_name": "Monet", "given_name": "Deja", "clpid": "Monet-Deja" }, { "family_name": "Ngo", "given_name": "Victoria", "orcid": "0000-0001-9973-8379", "clpid": "Ngo-Victoria" }, { "family_name": "Ding", "given_name": "Xiaozhe", "orcid": "0000-0002-0267-0791", "clpid": "Ding-Xiaozhe-Z" }, { "family_name": "Omstead", "given_name": "Victoria", "orcid": "0000-0002-3796-970X", "clpid": "Omstead-Victoria" }, { "family_name": "Weed", "given_name": "Natalie", "orcid": "0000-0003-0891-0327", "clpid": "Weed-Natalie" }, { "family_name": "Bishaw", "given_name": "Yeme", "clpid": "Bishaw-Yeme" }, { "family_name": "Gore", "given_name": "Bryan", "orcid": "0000-0003-1721-4235", "clpid": "Gore-Bryan-B" }, { "family_name": "Lein", "given_name": "Ed S.", "orcid": "0000-0001-9012-6552", "clpid": "Lein-Ed-S" }, { "family_name": "Akrami", "given_name": "Athena", "orcid": "0000-0001-5711-0903", "clpid": "Akrami-Athena" }, { "family_name": "Miller", "given_name": "Cory", "orcid": "0000-0001-8345-2720", "clpid": "Miller-Cory-T" }, { "family_name": "Levi", "given_name": "Boaz P.", "orcid": "0000-0002-8346-872X", "clpid": "Levi-Boaz-P" }, { "family_name": "Keller", "given_name": "Annika", "orcid": "0000-0003-1466-3633", "clpid": "Keller-Annika" }, { "family_name": "Ting", "given_name": "Jonathan T.", "orcid": "0000-0001-8266-0392", "clpid": "Ting-Jonathan-T" }, { "family_name": "Fox", "given_name": "Andrew S.", "orcid": "0000-0003-0695-3323", "clpid": "Fox-Andrew-S" }, { "family_name": "Eroglu", "given_name": "Cagla", "orcid": "0000-0002-7204-0218", "clpid": "Eroglu-Cagla" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Delivering genes to and across the brain vasculature efficiently and specifically across species remains a critical challenge for addressing neurological diseases. We have evolved adeno-associated virus (AAV9) capsids into vectors that transduce brain endothelial cells specifically and efficiently following systemic administration in wild-type mice with diverse genetic backgrounds and rats. These AAVs also exhibit superior transduction of the CNS across non-human primates (marmosets and rhesus macaques), andex vivohuman brain slices although the endothelial tropism is not conserved across species. The capsid modifications translate from AAV9 to other serotypes such as AAV1 and AAV-DJ, enabling serotype switching for sequential AAV administration in mice. We demonstrate that the endothelial specific mouse capsids can be used to genetically engineer the blood-brain barrier by transforming the mouse brain vasculature into a functional biofactory. Vasculature-secreted Hevin (a synaptogenic protein) rescued synaptic deficits in a mouse model.", "doi": "10.1101/2023.01.12.523844", "publication_date": "2023-01-14" }, { "id": "authors:6vtvn-09279", "collection": "authors", "collection_id": "6vtvn-09279", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220706-965670000", "type": "monograph", "title": "A prebiotic diet modulates microglial states and motor deficits in \u03b1-synuclein overexpressing mice", "author": [ { "family_name": "Abdel-Haq", "given_name": "Reem", "orcid": "0000-0002-7418-5736", "clpid": "Abdel-Haq-Reem" }, { "family_name": "Schlachetzki", "given_name": "Johannes C. M.", "orcid": "0000-0002-7801-9743", "clpid": "Schlachetzki-Johannes-C-M" }, { "family_name": "Boktor", "given_name": "Joseph C.", "orcid": "0000-0003-2456-1913", "clpid": "Boktor-Joseph-C" }, { "family_name": "Cantu-Jungles", "given_name": "Thaisa M.", "orcid": "0000-0001-8928-9717", "clpid": "Cantu-Jungles-Thaisa-M" }, { "family_name": "Thron", "given_name": "Taren", "orcid": "0000-0001-9577-2617", "clpid": "Thron-Taren-M" }, { "family_name": "Zhang", "given_name": "Mengying", "clpid": "Zhang-Mengying" }, { "family_name": "Bostick", "given_name": "John W.", "orcid": "0000-0001-8925-2447", "clpid": "Bostick-John-W" }, { "family_name": "Khazaei", "given_name": "Tahmineh", "orcid": "0000-0002-4743-2383", "clpid": "Khazaei-Tahmineh" }, { "family_name": "Chilakala", "given_name": "Sujatha", "orcid": "0000-0003-1581-3381", "clpid": "Chilakala-Sujatha" }, { "family_name": "Morais", "given_name": "Livia H.", "orcid": "0000-0002-5738-2658", "clpid": "Morais-Livia-H" }, { "family_name": "Humphrey", "given_name": "Greg", "clpid": "Humphrey-Gregory" }, { "family_name": "Keshavarzian", "given_name": "Ali", "orcid": "0000-0002-7969-3369", "clpid": "Keshavarzian-Ali" }, { "family_name": "Katz", "given_name": "Jonathan E.", "clpid": "Katz-Jonathan-E" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Knight", "given_name": "Rob", "orcid": "0000-0002-0975-9019", "clpid": "Knight-Rob" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Hamaker", "given_name": "Bruce R.", "orcid": "0000-0001-6591-942X", "clpid": "Hamaker-Bruce-R" }, { "family_name": "Glass", "given_name": "Christopher K.", "orcid": "0000-0003-4344-3592", "clpid": "Glass-Christopher-K" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "orcid": "0000-0003-2713-1513", "clpid": "Mazmanian-S-K" } ], "abstract": "Parkinson's disease (PD) is a movement disorder characterized by neuroinflammation, \u03b1-synuclein pathology, and neurodegeneration. Most cases of PD are non-hereditary, suggesting a strong role for environmental factors, and it has been speculated that disease may originate in peripheral tissues such as the gastrointestinal (GI) tract before affecting the brain. The gut microbiome is altered in PD and may impact motor and GI symptoms as indicated by animal studies, though mechanisms of gut-brain interactions remain incompletely defined. Intestinal bacteria ferment dietary fibers into short-chain fatty acids, with fecal levels of these molecules differing between PD and healthy controls and in mouse models. Among other effects, dietary microbial metabolites can modulate activation of microglia, brain-resident immune cells implicated in PD. We therefore investigated whether a fiber-rich diet influences microglial function in \u03b1-synuclein overexpressing (ASO) mice, a preclinical model with PD-like symptoms and pathology. Feeding a prebiotic high-fiber diet attenuates motor deficits and reduces \u03b1-synuclein aggregation in the substantia nigra of mice. Concomitantly, the gut microbiome of ASO mice adopts a profile correlated with health upon prebiotic treatment, which also reduces microglial activation. Single-cell RNA-seq analysis of microglia from the substantia nigra and striatum uncovers increased pro-inflammatory signaling and reduced homeostatic responses in ASO mice compared to wild-type counterparts on standard diets. However, prebiotic feeding reverses pathogenic microglial states in ASO mice and promotes expansion of protective disease-associated macrophage (DAM) subsets of microglia. Notably, depletion of microglia using a CSF1R inhibitor eliminates the beneficial effects of prebiotics by restoring motor deficits to ASO mice despite feeding a prebiotic diet. These studies uncover a novel microglia-dependent interaction between diet and motor symptoms in mice, findings that may have implications for neuroinflammation and PD.", "doi": "10.1101/2022.06.27.497828", "publication_date": "2022-07-01" }, { "id": "authors:b1t08-32n15", "collection": "authors", "collection_id": "b1t08-32n15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220111-302458000", "type": "monograph", "title": "Intravenous gene transfer throughout the brain of infant Old World primates using AAV", "author": [ { "family_name": "Chuapoco", "given_name": "Miguel R.", "orcid": "0000-0001-5397-996X", "clpid": "Chuapoco-Miguel-R" }, { "family_name": "Flytzanis", "given_name": "Nicholas C.", "orcid": "0000-0002-7921-9392", "clpid": "Flytzanis-Nicholas-C" }, { "family_name": "Goeden", "given_name": "Nick", "clpid": "Goeden-Nick" }, { "family_name": "Octeau", "given_name": "J. Christopher", "clpid": "Octeau-J-Christopher" }, { "family_name": "Roxas", "given_name": "Kristina M.", "clpid": "Roxas-Kristina-M" }, { "family_name": "Chan", "given_name": "Ken Y.", "orcid": "0000-0002-8853-5186", "clpid": "Chan-Ken-Y" }, { "family_name": "Scherrer", "given_name": "Jon", "clpid": "Scherrer-Jon" }, { "family_name": "Winchester", "given_name": "Janet", "clpid": "Winchester-Janet" }, { "family_name": "Blackburn", "given_name": "Roy J.", "clpid": "Blackburn-Roy-J" }, { "family_name": "Campos", "given_name": "Lillian J.", "clpid": "Campos-Lillian-J" }, { "family_name": "Arokiaraj", "given_name": "Cynthia M.", "orcid": "0000-0003-3201-9868", "clpid": "Arokiaraj-Cynthia-M" }, { "family_name": "Miles", "given_name": "Timothy F.", "orcid": "0000-0001-6591-3271", "clpid": "Miles-T-F" }, { "family_name": "Jang", "given_name": "Min J.", "orcid": "0000-0002-1536-7177", "clpid": "Jang-Min-J" }, { "family_name": "Vendemiatti", "given_name": "Julia", "orcid": "0000-0002-6547-9601", "clpid": "Vendemiatti-Julia" }, { "family_name": "Deverman", "given_name": "Benjamin E.", "orcid": "0000-0002-6223-9303", "clpid": "Deverman-Benjamin-E" }, { "family_name": "Pickel", "given_name": "James", "orcid": "0000-0002-3617-3072", "clpid": "Pickel-James" }, { "family_name": "Fox", "given_name": "Andrew S.", "clpid": "Fox-Andrew-S" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Adeno-associated viruses (AAVs) can enable robust and safe gene delivery to the mammalian central nervous system (CNS). While the scientific community has developed numerous neurotropic AAV variants for systemic gene-transfer to the rodent brain, there are few AAVs that efficiently access the CNS of higher order primates. We describe here AAV.CAP-Mac, an engineered AAV variant that enables systemic, brain-wide gene delivery in infants of two Old World primate species--the rhesus macaque (Macaca mulatta) and the green monkey (Chlorocebus sabaeus). We identified CAP-Mac using a multi-species selection strategy, initially screening our library in the adult common marmoset (Callithrix jacchus) and narrowing our pool of test-variants for another round of selection in infant macaques. In individual characterization, CAP-Mac robustly transduces human neurons in vitro and Old World primate neurons in vivo, where it targets all lobes of cortex, the cerebellum, and multiple subcortical regions of disease relevance. We use CAP-Mac for Brainbow-like multicolor labeling of macaque neurons throughout the brain, enabling morphological reconstruction of both medium spiny neurons and cortical pyramidal cells. Because of its broad distribution throughout the brain and high neuronal efficiency in infant Old World primates compared to AAV9, CAP-Mac shows promise for researchers and clinicians alike to unlock novel, noninvasive access to the brain for efficient gene transfer.", "doi": "10.1101/2022.01.08.475342", "publication_date": "2022-01-09" }, { "id": "authors:51hdx-8kz34", "collection": "authors", "collection_id": "51hdx-8kz34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220104-249193900", "type": "monograph", "title": "Multi-Wavelength Analytical Ultracentrifugation of Biopolymer Mixtures and Interactions", "author": [ { "family_name": "Henrickson", "given_name": "Amy", "clpid": "Henrickson-Amy" }, { "family_name": "Gorbet", "given_name": "Gary E.", "clpid": "Gorbet-Gary-E" }, { "family_name": "Savelyev", "given_name": "Alexey", "clpid": "Savelyev-Alexey" }, { "family_name": "Kim", "given_name": "Minji", "clpid": "Kim-Minji" }, { "family_name": "Schultz", "given_name": "Sarah K.", "clpid": "Schultz-Sarah-K" }, { "family_name": "Ding", "given_name": "Xiaozhe", "orcid": "0000-0002-0267-0791", "clpid": "Ding-Xiaozhe-Z" }, { "family_name": "Hargreaves", "given_name": "Jason", "clpid": "Hargreaves-Jason" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Kothe", "given_name": "Ute", "orcid": "0000-0002-2744-7334", "clpid": "Kothe-Ute" }, { "family_name": "Demeler", "given_name": "Borries", "orcid": "0000-0002-2414-9518", "clpid": "Demeler-Borries" } ], "abstract": "Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recent development made possible by new analytical ultracentrifuge optical systems. MW-AUC is suitable for a wide range of applications and biopolymer systems and is poised to become an essential tool to characterize macromolecular interactions. It adds an orthogonal spectral dimension to the traditional hydrodynamic characterization by exploiting unique chromophores in analyte mixtures that may or may not interact. Here we illustrate the utility of MW-AUC for representative classes of challenging biopolymer systems, including interactions between mixtures of different sized proteins with small molecules, mixtures of loaded and empty viral AAV capsids contaminated with free DNA, and mixtures of different proteins, where some have identical hydrodynamic properties, all of which are difficult to resolve with traditional AUC methods. We explain the improvement in resolution and information content obtained by this technique compared to traditional single- or dual-wavelength approaches. We discuss experimental design considerations and limitations of the method, and address the advantages and disadvantages of the two MW optical systems available today, and the differences in data analysis strategies between the two systems.", "doi": "10.1101/2021.12.29.474408", "publication_date": "2021-12-30" }, { "id": "authors:ehr13-wbx82", "collection": "authors", "collection_id": "ehr13-wbx82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210414-072514678", "type": "monograph", "title": "Neuronal Activation of the Gastrointestinal Tract Shapes the Gut Environment in Mice", "author": [ { "family_name": "Yoo", "given_name": "Bryan B.", "orcid": "0000-0003-1450-2696", "clpid": "Yoo-Bryan-B" }, { "family_name": "Griffiths", "given_name": "Jessica A", "orcid": "0000-0002-5586-1567", "clpid": "Griffiths-Jessica-A" }, { "family_name": "Thuy-Boun", "given_name": "Peter", "orcid": "0000-0003-3285-4273", "clpid": "Thuy-Boun-Peter" }, { "family_name": "Cantu", "given_name": "Victor", "clpid": "Cantu-Victor" }, { "family_name": "Weldon", "given_name": "Kelly", "orcid": "0000-0003-1064-8153", "clpid": "Weldon-Kelly" }, { "family_name": "Challis", "given_name": "Collin", "orcid": "0000-0003-4716-6086", "clpid": "Challis-Collin" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-M-J" }, { "family_name": "Chan", "given_name": "Ken Y.", "orcid": "0000-0002-8853-5186", "clpid": "Chan-Ken-Y" }, { "family_name": "Thron", "given_name": "Taren M.", "orcid": "0000-0001-9577-2617", "clpid": "Thron-Taren-M" }, { "family_name": "Sharon", "given_name": "Gil", "orcid": "0000-0002-4605-9943", "clpid": "Sharon-Gil" }, { "family_name": "Moradian", "given_name": "Annie", "orcid": "0000-0002-0407-2031", "clpid": "Moradian-Annie" }, { "family_name": "Humphrey", "given_name": "Gregory", "clpid": "Humphrey-Gregory" }, { "family_name": "Zhu", "given_name": "Qiyun", "clpid": "Zhu-Qiyun" }, { "family_name": "Shaffer", "given_name": "Justin", "orcid": "0000-0002-9371-6336", "clpid": "Shaffer-Justin" }, { "family_name": "Wolan", "given_name": "Dennis W.", "orcid": "0000-0001-9879-8353", "clpid": "Wolan-Dennis-W" }, { "family_name": "Dorrestein", "given_name": "Pieter C.", "orcid": "0000-0002-3003-1030", "clpid": "Dorrestein-Pieter-C" }, { "family_name": "Knight", "given_name": "Rob", "orcid": "0000-0002-0975-9019", "clpid": "Knight-Rob" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "orcid": "0000-0003-2713-1513", "clpid": "Mazmanian-S-K" } ], "abstract": "The enteric nervous system (ENS) coordinates responses that shape the intestinal milieu, and participates in bi-directional communication with various organs including the brain. Tools to study, and knowledge of, ENS development and function lag behind brain research. Herein, we deploy recombinant adeno-associated viral (rAAV) vectors with enhanced tropism for the gut to map and activate gut associated neurons in mice with spatial and temporal resolution. rAAV-mediated fluorescent labelling coupled with whole-tissue clearing methods in the small intestine and colon reveal novel neuronal architectures in the gut of mice. Viral delivery of genetically-encoded calcium indicators enable in vivo measurement of ENS activity. Further, we employed chemogentics to specifically activate gut neurons that express choline acetyltransferase (ChAT\u207a) or tyrosine hydroxylase (TH\u207a). Targeted activation of ChAT\u207a or TH\u207a neuronal populations associated with the gastrointestinal (GI) tract alters the intestinal transcriptome, mouse and microbial proteomes, metagenome, and fecal metabolome. We reveal previously unknown and broad roles for enteric neurons in modulating GI physiology, mucosal immunity, and microbiome structure, and provide evidence for novel functions by the ENS such as regulating fungal colonization and shaping of bile acid profiles in the gut. These advanced experimental tools and rich datasets with multi-parameter characterization of the gut ecosystem may facilitate expanded understanding and study of the ENS.", "doi": "10.1101/2021.04.12.439539", "publication_date": "2021-04-13" }, { "id": "authors:j28da-nn862", "collection": "authors", "collection_id": "j28da-nn862", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200626-103613335", "type": "monograph", "title": "Broad gene expression throughout the mouse and marmoset brain after intravenous delivery of engineered AAV capsids", "author": [ { "family_name": "Flytzanis", "given_name": "Nicholas C.", "orcid": "0000-0002-7921-9392", "clpid": "Flytzanis-N-C" }, { "family_name": "Goeden", "given_name": "Nick", "clpid": "Goeden-N" }, { "family_name": "Goertsen", "given_name": "David", "orcid": "0000-0001-7138-1697", "clpid": "Goertsen-D" }, { "family_name": "Cummins", "given_name": "Alexander", "clpid": "Cummins-A" }, { "family_name": "Pickel", "given_name": "James", "orcid": "0000-0002-3617-3072", "clpid": "Pickel-James" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Genetic intervention is increasingly explored as a therapeutic option for debilitating disorders of the central nervous system. The safety and efficacy of gene therapies relies upon expressing a transgene in affected cells while minimizing off-target expression. To achieve organ/cell-type specific targeting after intravenous delivery of viral vectors, we employed a Cre-transgenic-based screening platform for fast and efficient capsid selection, paired with sequential engineering of multiple surface-exposed loops. We identified capsid variants that are enriched in the brain and detargeted from the liver in mice. The improved enrichment in the brain extends to non-human primates, enabling robust, non-invasive gene delivery to the marmoset brain following IV administration. Importantly, the capsids identified display non-overlapping cell-type tropisms within the brain, with one exhibiting high specificity to neurons. The ability to cross the blood\u2013brain barrier with cell-type specificity in rodents and non-human primates enables new avenues for basic research and potential therapeutic interventions unattainable with naturally occurring serotypes.", "doi": "10.1101/2020.06.16.152975", "publication_date": "2020-06-17" }, { "id": "authors:arewf-cc196", "collection": "authors", "collection_id": "arewf-cc196", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190220-101926873", "type": "monograph", "title": "Epigenetic landscape and AAV targeting of human neocortical cell classes", "author": [ { "family_name": "Mich", "given_name": "John K.", "clpid": "Mich-J-K" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Myriad cell types comprise the human neocortex, but their roles in normal brain function and disease are largely unknown because few tools exist. To find enhancer elements useful for cell type-specific genetic tools, we examined chromatin accessibility in >2,800 high-quality single human neocortical nuclei. Accessible elements frequently are conserved in mouse (34%), often overlap with hypomethylated sites (27%), and connect cell types with neurological diseases via trait-associated SNPs. Directly testing these elements in viral vectors demonstrates functional enhancer activity with cell type specificity predicted by their chromatin accessibility patterns. In summary we present a catalog of human cell class-specific epigenetic elements, and utilize them for new species-agnostic cell type-specific viral genetic tools, which will illuminate human neuron function and drive gene therapy applications.", "doi": "10.1101/555318", "publication_date": "2019-02-19" } ]