Enzymes catalyze diverse chemical transformations and offer a sustainable approach to both breaking and making chemical bonds. However, finding an enzyme capable of performing a specific chemical reaction remains a challenge. We developed a new framework, Enzyme-toolkit (Enzyme-tk), that integrates 23 open-source tools to enable the discovery of enzymes that have activity toward a specific target reaction. Additionally, we introduce two new methods to facilitate enzyme discovery: (1) Func-e, an ML tool that searches large databases for enzymes that potentially catalyze a specific chemical transformation and (2) Oligopoolio, a gene assembly approach that reduces the cost of accessing protein sequences and thus the barrier to their experimental validation. We applied Enzyme-tk to find enzymes for chemical degradation of two man-made pollutants, di-(2-ethylhexyl) phthalate (DEHP) and triphenyl phosphate (TPP). We demonstrate that new, previously unannotated enzymes with favorable characteristics, such as high thermostability, can be identified using Enzyme-tk for reactions that are dissimilar to the training set.
", "author_list": "Mora, Ariane and Reisenbauer, Julia C., el al." }, { "title": "k-spaces: Mixtures of Gaussian latent variable models", "type": "monograph", "publication_date": "2025-11-28", "publisher": "bioRxiv", "doi": "10.1101/2025.11.24.690254", "cite_using_url": "https://authors.library.caltech.edu/records/z6bgb-cy537", "abstract": "Principal component analysis (PCA) and\n k\n -means clustering are two seemingly different methods for dimension reduction and clustering, respectively, but can be understood as special cases of inference in a Gaussian latent variable model framework. We leverage this insight to develop a probabilistic framework and methods for simultaneous dimension reduction, clustering, and latent space learning that are efficient and interpretable, and that can replace current ad hoc combinations of PCA and clustering. The algorithm,\n k\n -spaces, has broad applicability, which we demonstrate in several distinct genomic settings. In particular, we show how\n k\n -spaces can be used to model gene expression in quantitative hybridization chain reaction (qHCR) images, for inference in epigenomics, and for dimension reduction of single-cell RNA-sequencing data.", "author_list": "Markarian, Nicholas and Engelhardt, Barbara E., el al." }, { "title": "Evolutionary basis of intermale sexual behavior by multiple pheromone switches in Drosophila", "type": "monograph", "publication_date": "2025-11-14", "publisher": "Caltech Library", "doi": "10.7907/xfn4f-11y86", "cite_using_url": "https://authors.library.caltech.edu/records/xfn4f-11y86", "abstract": "We have identified a Drosophila species which exhibits spontaneous and robust intermale sexual behavior. D. santomea males distinguish conspecific sexes but court both vigorously and seldom attack. Elevated intermale courtship stems from at least three evolutionarily derived pheromonal changes. In males, the sexually monomorphic cuticular pheromone 7-tricosene promotes rather than inhibits courtship and the courtship-inhibiting olfactory pheromone cVA is reduced 84-92% compared to close relatives. The third switch is in D. santomea females, where cVA suppresses rather than promotes sexual receptivity. Female cVA aversion and male cVA reduction may have co-evolved to maintain efficient intraspecific mating but prevent hybridization with the sympatric sibling species D. yakuba. High intermale courtship and low cVA also co-occur and appear selectively derived in a distant monomorphic species D. persimilis, implying pheromonal and social behavioral convergence. Changes in pheromone valence and levels may therefore explain the recent evolutionary emergence of intermale sexual behavior in Drosophila.
", "author_list": "Ouadah, Youcef and Naragon, Thomas H., el al." }, { "title": "A Blueprint for a Joint Meteorology and Atmospheric Composition Program", "type": "monograph", "publication_date": "2025-11-07", "publisher": "W. M. Keck Institute of Space Studies (KISS), California Institute of Technology", "doi": "10.26206/sk7nw-4ej15", "cite_using_url": "https://authors.library.caltech.edu/records/sk7nw-4ej15", "abstract": "For greenhouse gas (GHG) observations to more effectively inform climate management strategies, we must be able to better identify the timing, location, and magnitude of surface emissions and removals. Making atmospheric composition data actionable requires improved traceability to surface fluxes. For this, we need better observation of the vertical distribution of trace gases and better modeling of vertical atmospheric mixing. Uncertainty in vertical transport and mixing has been especially problematic because of two factors: (1) long tracer lifetimes can lead to accumulation of vertical mixing errors over time and space, and (2) covariance of vertical mixing with surface fluxes confounds attribution of trace gas data to surface fluxes. These problems are exacerbated by the presence of clouds and wind shear, which can obscure the origin of trace gases.
\nA new generation of models and space-based GHG and wind remote sensing techniques is emerging. These tools show promise for observing and simulating the small scales at which vertical mixing occurs, with near-global coverage. Spaceborne GHG missions will continue to close spatial and temporal sampling gaps, increasingly target collocated species (CO2, CH4, CO, NOx), and vertical gradients (via multi-spectral lidar and spectrometers) for improved sectoral attribution of carbon emissions and removals. Wind missions leveraging passive and active techniques to track the motion of cloud and trace gas spatial features, cloud liquid and ice hydrometeors (radar and lidar), and air/particulates (lidar) are improving our ability to track vertical and horizontal motion within and around clouds. High-resolution numerical weather prediction and climate models and machine learning-driven forecasting that resolve deep convection and permit shallow convection are improving the statistics of vertical mixing at regional scales. The combination of wind and GHG observations with high-resolution models will strengthen our knowledge of GHG mixing, connecting surface exchange to atmospheric abundances.
\nTo provide scientific guidance on how to bring these modeling and observing tools together for more accurate GHG and air quality climate data, the Earth science community needs to move beyond single instrument teams to tackle integrated science challenges. We recommend the development and coordination of a joint meteorology and atmospheric composition program, whose goal is to vastly improve GHG source and sink quantification while simultaneously advancing our understanding of vertical atmospheric mixing.
\nWe envision a three-tiered model-observation integration approach to reduce uncertainty in vertical mixing based on existing and future observations:
\n· Diagnosis–Comparing models to observations to identify process uncertainty,
\n· Optimization–Assimilation of observations into models to optimize parameters and state, and
\n· Prediction–Forward and inverse simulation using calibrated model ensembles.
\nA key component of this approach is the development of testbeds to inform vertical mixing, building on coordinated programs such as the European Union-led Carbon Atmospheric Tracer Research to Improve Numerics and Evaluation (CATRINE) project. These recommendations are supported by the National Academies Earth Science Decadal Survey Midterm findings to expand collaboration opportunities, and to more actively engage the modeling communities.
", "author_list": "Whelan, Mary and Parazoo, Nick, el al." }, { "title": "NOBLE \u2013 Neural Operator with Biologically-informed Latent Embeddings to Capture Experimental Variability in Biological Neuron Models", "type": "monograph", "publication_date": "2025-10-27", "publisher": "arXiv", "doi": "10.48550/arxiv.2506.04536", "issn": "2331-8422", "cite_using_url": "https://authors.library.caltech.edu/records/qgkme-1yq67", "publication": "arXiv", "pages": "2506.04536", "abstract": "Characterizing the cellular properties of neurons is fundamental to understanding their function in the brain. In this quest, the generation of bio-realistic models is central towards integrating multimodal cellular data sets and establishing causal relationships. However, current modeling approaches remain constrained by the limited availability and intrinsic variability of experimental neuronal data. The deterministic formalism of bio-realistic models currently precludes accounting for the natural variability observed experimentally. While deep learning is becoming increasingly relevant in this space, it fails to capture the full biophysical complexity of neurons, their nonlinear voltage dynamics, and variability. To address these shortcomings, we introduce NOBLE, a neural operator framework that learns a mapping from a continuous frequency-modulated embedding of interpretable neuron features to the somatic voltage response induced by current injection. Trained on synthetic data generated from bio-realistic neuron models, NOBLE predicts distributions of neural dynamics accounting for the intrinsic experimental variability. Unlike conventional bio-realistic neuron models, interpolating within the embedding space offers models whose dynamics are consistent with experimentally observed responses. NOBLE enables the efficient generation of synthetic neurons that closely resemble experimental data and exhibit trial-to-trial variability, offering a 4200× speedup over the numerical solver. NOBLE is the first scaled-up deep learning framework that validates its generalization with real experimental data. To this end, NOBLE captures fundamental neural properties in a unique and emergent manner that opens the door to a better understanding of cellular composition and computations, neuromorphic architectures, large-scale brain circuits, and general neuroAI applications.
", "author_list": "Ghafourpour, Luca and Duruisseaux, Valentin, el al." }, { "title": "The Exospace Weather Frontier", "type": "monograph", "publication_date": "2025-10-23", "publisher": "W. M. Keck Institute of Space Studies (KISS), California Institute of Technology", "doi": "10.26206/gmhk5-amp17", "cite_using_url": "https://authors.library.caltech.edu/records/gmhk5-amp17", "abstract": "Space weather is among the most powerful and least understood forces shaping planetary atmospheres.
\nWe observe its effects directly on Solar System bodies through atmospheric escape, chemical disruption,
\ncometary tails, and auroral displays. Yet for exoplanets, we lack the tools and data to robustly assess
\nhow space weather influences their evolution, habitability, and potential biosignatures. Even the past
\nspace weather of the Solar System is shrouded in unknowns.
\nThe Sun emits a constant outflow of charged particles embedded in magnetic fields, known as the
\nsolar wind. The fast-moving particles in the winds of the Sun and stars can erode planetary atmospheres
\nover time, stripping away volatiles essential for climate and life. Potentially even more disruptive are
\nexplosive events, such as flares and coronal mass ejections (CMEs), which hurl vast amounts of energy
\nand particles into space. Collectively, these phenomena define the space weather environment, and for
\nour Sun, they are continuously tracked by a fleet of dedicated spacecraft.
\nDecades of observations reveal that space weather is not unique to the Sun, but is ubiquitous
\namong stars. Many stars exhibit “exospace weather” through flaring activity, sometimes by orders of
\nmagnitude more intense than anything seen from the Sun. These stars must then also host stellar winds
\nand many likely produce CMEs.
\nThe study of exospace weather sits at the intersection of heliophysics, planetary science, astro-
\nphysics, and astrobiology. Observing space weather in exoplanetary systems, in combination with
\nthe beautifully resolved, in-situ context of our own system, is necessary to illuminate how stars and
\nplanets evolve, interact with their environments, and shape the conditions for life. Doing so will benefit
\nheliophysics, planetary science, astrophysics, and astrobiology alike.
\nThe time has come to establish exospace weather as a new pillar of exoplanet and stellar research,
\none that bridges stellar physics, planetary evolution, and the search for life beyond Earth. The science
\ngaps are clear, and many of the tools to close them already exist or can be developed. What is needed
\nnow are coordinated, interdisciplinary research efforts.
", "author_list": "Loyd, R. O. Parke and Shkolnik, Evgenya L., el al." }, { "title": "Standardized Space Telescopes for the Future of Scientific Discovery", "type": "monograph", "publication_date": "2025-10-16", "publisher": "W. M. Keck Institute of Space Studies (KISS), California Institute of Technology", "doi": "10.26206/rv06k-mqx02", "cite_using_url": "https://authors.library.caltech.edu/records/rv06k-mqx02", "abstract": "Transformative science and exploration require broader access to space telescopes
\nWe have identified a Drosophila species in which males exhibit spontaneous, elaborate, and robust intermale sexual behavior. Males of D. santomea, a West African island endemic, distinguish conspecific sexes but court males and females promiscuously and seldom attack. Elevated intermale courtship derives from at least three changes in two separate pheromone systems. In males, the sexually monomorphic cuticular pheromone 7-tricosene promotes rather than inhibits courtship and the courtship-inhibiting olfactory pheromone cVA is reduced 84-92% compared to close relatives, including the sibling species D. yakuba. The third change is surprisingly in D. santomea females, where cVA suppresses rather than promotes sexual receptivity. The female cVA switch and male cVA reduction may have co-evolved to maintain efficient intraspecific mating in D. santomea but prevent sympatric hybridization with D. yakuba, or to reduce intraspecific aggression. We find that high intermale courtship and low cVA also co-occur and appear selectively derived in a distant monomorphic species D. persimilis, implying pheromonal and behavioral convergence in the two recently speciated taxa. The data suggest that sequential changes in the behavioral valence and levels of pheromones explain the recent evolutionary emergence of intermale sexual behavior in Drosophila.
", "author_list": "Ouadah, Youcef and Naragon, Thomas H., el al." }, { "title": "Astronomical Optical Interferometry from the Lunar Surface", "type": "monograph", "publication_date": "2025-10-06", "publisher": "W. M. Keck Institute of Space Studies (KISS), California Institute of Technology", "doi": "10.26206/z655j-jqm38", "cite_using_url": "https://authors.library.caltech.edu/records/z655j-jqm38", "abstract": "The lunar surface is a compelling location for large, distributed optical facilities, with signif-
\nicant advantages over orbital facilities for high spatial resolution astrophysics. The serious
\ndevelopment of mission concepts is timely because of the confluence of multiple compelling
\nfactors. Lunar access technology is maturing rapidly, in the form of both US-based crewed and
\nuncrewed landers, as well as international efforts (Figure 1.1a). Associated with this has been
\na definitive maturation of astronomical optical interferometry technologies at Earth-based fa-
\ncilities over the past three decades, enabling exquisitely sharp views on the universe previously
\nunattainable, though limited at present by the Earth’s atmosphere (Figure 1.1b). Importantly,
\nthe increasing knowledge and experience base about lunar surface operations indicates it is
\nnot just suitable, but highly attractive for lunar telescope arrays.
\n• Unprecedented Imaging Potential: Combining mature terrestrial optical interferometry
\nwith emerging lunar surface technologies could enable optical imaging with far greater
\nresolution and sensitivity than current space or ground-based systems.
\n• Leveraging Existing NASA Funding: NASA Astrophysics and Planetary Science pro-
\ngrams could fund lunar interferometry missions through existing competitive processes,
\nevaluated alongside orbital missions.
\n• Small-Scale Demonstration Opportunity: A near-term, small mission—such as an
\nAstrophysics Pioneers onboard a Commercial Lunar Payload System (CLPS) lander—
\ncould demonstrate the feasibility and value of lunar-based interferometry.
\n• Medium-Class Mission for Advanced Techniques: A competitively selected medium-
\nclass mission (e.g., via Small Explorer or Medium Explorer missions) could enable
\nprecision interferometric methods like astrometry and nulling, supporting goals such as
\nexoplanet reconnaissance.
\n• Large-Scale Mission for Breakthrough Science: A Probe- or Flagship-class mission on
\nthe Moon could deliver unprecedented sub-milliarcsecond imaging across UV to MIR
\nwavelengths, leveraging future lunar infrastructure for transformative astrophysics.
", "author_list": "van Belle, Gerard T. and Shaklan, Stuart B., el al." }, { "title": "The Next-Generation Ground-Based Planetary Radar", "type": "monograph", "publication_date": "2025-09-18", "publisher": "W. M. Keck Institute of Space Studies (KISS), California Institute of Technology", "doi": "10.26206/2jvv7-zjc89", "cite_using_url": "https://authors.library.caltech.edu/records/2jvv7-zjc89", "abstract": "Planetary radar observations have a laudable history of “firsts” including determining the astronomical unit with
\nthe precision sufficient for interplanetary navigation, water ice distribution at the Moon’s south pole, water ice
\nindications in the permanently shadowed regions at Mercury’s poles, determining Venus’ rotation state, polar ice
\nand anomalous surface features on Mars, indications that the asteroid (16) Psyche is an exposed metallic core of
\na planetoid, establishing the icy nature of the Jovian satellites, and the initial characterizations of Titan’s surface.
\nIn many cases, these discoveries made by planetary radar systems have motivated missions and mission radar
\ninstruments.
\nThis W. M. Keck Institute of Space Studies study was intended to identify the compelling science and potential
\ntechnical developments required for a next-generation, ground-based planetary radar. As new discoveries have
\noccurred since the first generation of planetary radar observations, our understanding of the Solar System has
\nimproved, and new questions have emerged. One of the study’s motivations was to identify what discoveries might be
\nenabled or how a next-generation planetary radar might address fundamental questions.
\nThe study found that there are three compelling science drivers for a next-generation planetary radar—Venus,
\nnear-Earth asteroids, and the icy moons (“ocean worlds”) of the outer Solar System.
\nFor Venus (“Earth’s evil twin”), long-term measurements of surface geology obtained with a planetary radar
\nwould provide context within which to interpret measurements from a suite of spacecraft planned to explore that
\nplanet over the next decade or more.
\nFor near-Earth asteroids, an improved characterization of the population (or populations) would result from the
\nincrease in both the quantity of near-Earth asteroids that could be tracked and the quality of the data obtained. A
\nplanetary radar would provide precise orbit determinations for planning future spacecraft missions and assessing
\nplanetary defense hazards.
\nFor the outer Solar System, much like for Venus, observations of icy moons/“ocean worlds” over unparalleled
\ndurations could be obtained, even enabling investigations of seasonal changes. Multiple additional science cases
\nwould be enabled, including potentially the tracking of interstellar objects, thereby bridging the fields of Planetary
\nScience and Astrophysics.A second motivation for this study was the two major ground-based planetary radar facilities were approaching
\ntheir half-century anniversaries in 2023, with the Arecibo Observatory planning to celebrate its 60th anniversary of
\noperations and NASA’s Deep Space Network planning to celebrate the 50th anniversary of the start of construction of
\nits Deep Space Station-14 (DSS-14) antenna, which hosts the Goldstone Solar System Radar (GSSR). Notably, and
\nunfortunately, between the two workshops held as part of this study, the Arecibo Observatory collapsed.
\nThis study found that a next-generation, ground-based planetary radar could be implemented as an antenna array,
\nanalogous to those already used in multiple radio astronomy facilities, which would provide greater resilience than a
\nmonolithic antenna.
\nMuch of the technology for such a planetary radar array is maturing. A planetary radar array could be implemented
\nwith solid-state transmitters at each antenna, leveraging considerable commercial investments in solid-state technology
\nand offering the promise of (much) more reliable performance than the traditional vacuum-tube klystrons. Solid-state
\ntransmitters have been prototyped and, in one case, deployed for spacecraft telecommunications.
\nConsiderable promise exists to develop automation and new algorithms, even within existing systems, for both
\nscheduling observations and processing planetary radar data.
\nFollowing this study, two more specific concept studies were conducted: “Cross-Disciplinary Deep Space Radar
\nNeeds Study” and “A Ground-Based Planetary Radar Array”. Both reached similar conclusions: an array of 15-25
\nm diameter antennas equipped with 50-80 kW transmitters would be technically feasible and could address all
\ncompelling science cases identified in this report. A planetary radar array might even be capable of undertaking a
\nsurvey designed to find near-Earth asteroids, a capability not currently available.
", "author_list": "Lazio, Joseph and de Kleer, Katherine R., el al." }, { "title": "Very Heavy Banjo Strings", "type": "monograph", "publication_date": "2025-09-12", "publisher": "Caltech Library", "doi": "10.7907/nhhat-rs354", "cite_using_url": "https://authors.library.caltech.edu/records/nhhat-rs354", "abstract": "Basic string physics is simple. Rather, this is a reminder that, for the price of a
new set of strings, one can create a different instrument. In particular, for a given
scale length, the tension can be maintained with heavier strings by tuning lower. An
extreme case is illustrated here: replace original light gauge strings with Gold Tone’s
“baritone” strings, which are their choice for their “Missing Link” banjo. On the
particular instrument used for this demo, tuning about an octave low preserves the
original total string tension. That puts the instrument in the league of the baritone
and cello banjos. This is a case of where a difference in degree becomes a difference in kind.
Single-cell mRNA sequencing is an essential technology for transcriptional profiling of cells and tissues. To compare transcriptomes among samples, it is cost-effective to multiplex their processing. Multiplexing is done by barcoding cDNA copies of transcripts from each sample, then combining them into a single library. We performed multiplex sequencing of human peripheral blood mononuclear cells (PBMCs) under three different experimental conditions: resting, treated with T cell activator, and treated with TNF-a. We generated libraries using two split-pool barcode ligation methods: Parse and a new in-house split-pool method, SWIFT-seq, developed by the Guttman group. PBMCs were fixed and permeabilized using a Parse kit for the Parse and SWIFT1 libraries. In a second experiment, we fixed and permeabilized cells using
a new in-house protocol and processed samples using SWIFT-seq to generate the SWIFT2 library. We also processed live cells using the Multiseq method for 10X Genomics-based sequencing, in which cells are indexed with lipid-linked barcodes, to generate the 10X library. These libraries encompass all major PBMC cell types, but myeloid cells were overrepresented in Parse and SWIFT1, probably due to the use of the Parse kit for fixation and permeabilization. Analysis of transcriptomes defined by these libraries shows that all sequencing and analysis methods generate remarkably similar biological conclusions. The Spearman rank correlation coefficients for comparisons of marker gene expression among all methods are >0.7 for all major PBMC cell types in resting and activated populations. The same gene programs are
implicated by the four methods as being involved in transitions from resting to activated states. Our results show that 10X, Parse, and SWIFT-seq methods can be used interchangeably for multiplex sequencing of PBMCs. We estimate that the per cell cost of analysis with SWIFT-seq, which uses reagents purchased individually from suppliers, is about one-third of that for the other methods.
The advancement of automation technologies has helped to enable a surge in large-scale screening efforts across fields such as molecular biology, protein biochemistry, cell biology, and structural biology. In the context of this “omics”-driven research, there is a need to generate automation platforms that are more flexible and less expensive, so that they can be utilized for basic research conducted by small groups. A key challenge in automation lies in developing methods that can replicate fine motor techniques that are normally performed manually by researchers at the bench. We are engaged in a large-scale project to map interactions among human cell-surface and secreted proteins and assess their effects on cells. This project involves production of a library of more than 2000 recombinant His-tagged fusion proteins secreted from transfected Expi293 cells. To execute such a project with a small group at an academic institution required construction of an affordable automated system that could also be used by other investigators. This led us to develop a high-throughput, 96-well format automation platform for end-to-end protein production. The workflow includes transformation of E. coli, plasmid DNA preparation, transient transfection, protein purification, desalting and buffer exchange, protein quantification, and normalization of protein concentrations, resulting in assayready proteins. The system is built around an in-house engineered modular robotic platform that integrates liquid handling with a suite of interchangeable ‘plug-and-play’ mobile enclosed device modules. Housed within a BSL-2 sterile environment, the platform enables flexible, fully automated workflows and can be readily customized for diverse user-defined protocols.
", "author_list": "Vasnarungruengkul, Pavee and Anaya, Michael A., el al." }, { "title": "A multiplex extracellular interactome screening method employing high-avidity nanoparticles", "type": "monograph", "publication_date": "2025-07-09", "publisher": "California Institute of Technology", "doi": "10.7907/vwj5q-cgh20", "cite_using_url": "https://authors.library.caltech.edu/records/vwj5q-cgh20", "abstract": "Metazoan cells signal to each other via direct contact between cell surface proteins (CSPs) and by interactions of CSP receptors with secreted ligands. CSP extracellular domain (ECD) interactions control organ development and physiology and are perturbed in disease states. However, because they cannot be accurately assessed using standard high-throughput screening techniques, they are underrepresented in protein interaction databases. Many ECD interactions are of low affinity, and their detection in vitro requires taking advantage of avidity effects, typically by multimerization of fusion proteins. Assays that test only one or a few interactions in each binding reaction are inadequate for global interactome screening. Here we describe a new multiplex method that uses purified dimeric ECD fusion proteins coupled to 60-mer nanoparticles as soluble prey, and the same dimers coupled to spectrally distinguishable fluorescent microspheres (beads) as bait. We add one prey to a mixture of up to 500 baits in a single well, then use a Luminex FLEXMAP 3D (FM3D) instrument to read out bait identity and prey binding. The FM3D measures the fluorescent dye ratio for each bead and simultaneously determines the amount of epitope-tagged prey bound to that bead. We use the method, denoted as the Multiplex Interactome Assay (MPIA), to analyze a proof-of-concept (PoC) set of 41 CSPs and secreted protens that is derived from larger collections examined in two interactome screens that used
ELISA-based binding assays. By analyzing interactions among PoC proteins, we compared the MPIA with earlier screening methods. The MPIA has a dynamic range that is at least 30-fold greater than ELISA-based assays and appears to be more sensitive. By coupling the MPIA to an automated protein production and purification platform, we hope to be able to conduct a screen for interactions among thousands of human CSPs and secreted ligands.
Chitin is a major structural component of arthropod exoskeletons, and an important carbon and nitrogen source in marine environments. In anoxic sediments, its degradation generates chitooligosaccharides and N-acetylglucosamine (GlcNAc), which are fermented into smaller organic molecules and oxidized anaerobically using soluble electron acceptors or insoluble ones such as metal oxides. To date, many aspects of chitin degradation in deep-sea anoxic sediments have been overlooked, including the potential coupling of insoluble chitin degradation to metal oxide reduction, the involvement of extracellular electron transfer (EET), and the spatial organization of the microorganisms involved. Using anoxic deep-sea sediments recovered from a whale fall site, we developed an innovative workflow based on electrochemical reactors, to characterize chitin degradation in these environments. Sediment samples enriched on poorly crystalline iron oxides, and subsequently transferred into an electrochemical reactor poised at +0.22 V vs SHE, showed active anodic current production when supplied with chitin, which increased 2-fold when amended with GlcNAc. Chitin reactors were dominated byVallitalea(Firmicutes),Spirochaetota,GammaproteobacteriaandDesulfobacterota. Exoenzyme activity assays, metabolite profiling, and continued anodic current production confirmed ongoing chitin degradation linked to EET. We observed metabolic associations between chitin degraders and secondary consumers usingin situimaging (16S rRNA gene FISH coupled with BONCAT and nanoSIMS). These microbial partners, within the electrode-attached community, required close proximity to the poised electrode (≤ 10 µm) to remain metabolically active. Supporting these observations, cultured isolates ofVallitaleasp. andTrichloromonassp. recovered from the whale fall site exhibited chitin degradation and electrochemical activity, respectively. When co-cultured in an bioelectrochemical reactor, the acetate produced byVallitaleasp. during chitin degradation fueledTrichloromonassp., which facilitated EET, hereby demonstrating that syntrophic interactions are used to couple anoxic chitin degradation to EET in deep-sea sediments. These findings exemplify the interspecies interactions and resource optimization occurring in hard-to-reach and largely unknown deep-sea ecosystems.
", "author_list": "Jangir, Yamini and Guo, Yongzhao, el al." }, { "title": "The Ambiguous Genetic Code of Methanogenic Archaea that Grow on Methylamines", "type": "monograph", "publication_date": "2025-06-14", "publisher": "Cold Spring Harbor Laboratory Press", "doi": "10.1101/2025.06.11.659114", "cite_using_url": "https://authors.library.caltech.edu/records/1qy57-1g892", "abstract": "Natural genetic code expansion is a phenomenon wherein an additional amino acid is encoded by a stop codon. These non-standard amino acids are beneficial as they facilitate novel biochemical reactions. However, code expansion leads to ambiguity at the recoded stop codon, which can either be read through or terminated. Pyrrolysine (Pyl) is encoded by the amber codon (TAG/UAG) and is widespread in archaea, where it is required for methylamine-mediated methanogenesis, an environmentally important metabolism. Mechanisms to conditionally suppress the amber stop codon for Pyl installation during protein synthesis have not been identified. Using the model methanogen,Methanosarcina acetivorans,we demonstrate that Pyl-encoding archaea maintain an ambiguous genetic code wherein UAG encodes dual meaning as stop and Pyl. Our data suggest that expression of Pyl biosynthesis and incorporation genes is tuned to the cellular demand for Pyl, which allows these archaea to navigate ambiguous stop decoding in response to environmental cues.
", "author_list": "Shalvarjian, Katie E. and Chadwick, Grayson L., el al." }, { "title": "The Boundary Layer Dispersion and Footprint Model: A fast numerical solver of the Eulerian steady-state advection-diffusion equation", "type": "monograph", "publication_date": "2025-06-10", "publisher": "European Geosciences Union", "doi": "10.5194/egusphere-2025-2415", "cite_using_url": "https://authors.library.caltech.edu/records/2c53k-35564", "abstract": "Understanding how greenhouse gases and pollutants move through the atmosphere is essential for predicting and mitigating their effects. We present a novel atmospheric dispersion and footprint model: the Boundary Layer Dispersion and Footprint Model (BLDFM), which solves the three-dimensional steady-state advection-diffusion equation in Eulerian form using a numerical approach based on the Fourier method, the linear shooting method and the exponential integrator method. In contrast to analytical Gaussian plume or stochastic Lagrangian models, this novel numerical approach proves beneficial as it does not rely on any asymptotic assumptions or estimates. Furthermore, it is fully modular, allowing for the use of a variety of turbulence closure models in its implementation or direct usage of measured or simulated wind profiles. The model is designed to be flexible and can be used for a wide range of applications, including climate impact studies, industrial emissions monitoring and spatial flux attribution. We validate the model using an analytical test case. The numerical results show excellent agreement with the analytical solution. We also compare the model with the well-established Kormann and Meixner (Boundary-Layer Meteorology, 2001) footprint model (FKM) which is based on the analytical Gaussian plume. The results show overall good agreement but some differences in the fetch of the footprints, which are attributed to the neglect of streamwise turbulent mixing – being one of the aforementioned asymptotic assumptions – in the FKM model. Our results demonstrate the potential of the BLDFM model as a useful tool for atmospheric scientists, biogeochemists, ecologists, and engineers.
", "author_list": "Schlutow, Mark and Chew, Ray, el al." }, { "title": "A DNA part library for reliable engineering of the emerging model nematode symbiotic bacterium Xenorhabdus griffiniae HGB2511", "type": "monograph", "publication_date": "2025-06-09", "publisher": "BioRxiv", "doi": "10.1101/2025.06.09.658710", "cite_using_url": "https://authors.library.caltech.edu/records/gyf3c-y6p16", "abstract": "Xenorhabdus griffiniae is a bacterium that lives inside the intestine of the entomopathogenic nematode Steinernema hermaphroditum and partners with the nematode to infect and kill insect larvae in soil. The construction of gene circuits, like reporters, in X. griffiniae would provide tools to study and better understand the symbiotic relationship it has with its host. However, because X. griffiniae is not a model organism, information about gene circuit construction in X. griffiniae is limited. We develop and characterize a DNA part library similar to the CIDAR MoClo extension library for E. coli to allow more efficient construction of genetic circuits in X. griffiniae. TurboRFP expressing strains with different constitutive Anderson promoters and different ribosome binding sites (RBS) were constructed to quantify promoter and RBS strengths in X. griffiniae. Furthermore, two fluorescent proteins sfGFP and sfYFP, as well as the bioluminescent luxCDABE operon were added to the part library and successfully expressed in X. griffiniae. We then used the characterized parts to build and characterize IPTG inducible constructs.
", "author_list": "Larsson, Elin M. and Wang, Olivia Y., el al." }, { "title": "KISS Symposium: Capturing an Opportunity at Apophis", "type": "monograph", "publication_date": "2025-06-04", "publisher": "W. M. Keck Institute of Space Studies (KISS), California Institute of Technology", "doi": "10.26206/m8mtp-68715", "cite_using_url": "https://authors.library.caltech.edu/records/m8mtp-68715", "abstract": "We held our two-day symposium “Capturing an Opportunity at Apophis” on July 31 and August 1, 2024. We organized the Symposium at Caltech and JPL to solicit feedback on a mission under development by Caltech, in collaboration with JPL, to rendezvous with Apophis before and escort it through its close Earth flyby in 2029.
\nWe engaged a focused group of 26 individuals from academia and NASA in the discussions (see participant list). Our participants brought a broad range of expertise, including representation from both planetary science and engineering disciplines. Most participants were based in the US, except for two international participants.
\nWe structured the Symposium as a mix of activities, including keynote talks, breakout sessions with fewer than ten individuals where we discussed predefined topics in detail, lightning talks, and group discussions.
\nOverall, the Caltech mission concept received very positive feedback from our group, and we recommend the following next steps:
\n• Develop a public communications strategy concerning the Apophis close approach
\n• Facilitate and participate in an Apophis session at LPSC
\n• Prepare a publication summarizing Apophis modeling and data
\n• Refine the Caltech mission science case
\n• Conduct trade studies to evaluate minor changes to the mission concept (radar geometry and frequency, adding more instruments)
\n• Coordinate timelines and objectives with other Apophis missions
\n• Ensure modelers, mission teams, and observational astronomers have open lines of communication, promptly sharing new data and predictions to inform mission planning and maximize science return.
\nMany of these follow-on activities are underway.
", "author_list": "Andrade, Jos\u00e9 E. and Raymond, Carol, el al." }, { "title": "Asymmetric Total Synthesis of (\u2013)-Crotonine G and (\u2013)-Crotonolide D", "type": "monograph", "publication_date": "2025-05-08", "publisher": "American Chemical Society (ACS)", "doi": "10.26434/chemrxiv-2025-zh07z", "cite_using_url": "https://authors.library.caltech.edu/records/gtrx1-ayw31", "abstract": "The first enantioselective total syntheses of crotonine G and crotonolide D are disclosed. The synthetic approach employs a SmI2 mediated ketyl radical cyclization to form the highly congested quaternary carbon at the center of these complex molecules. Following the furan introduction, the core structure of the natural product is con-structed via oxidative olefin cleavage to install the unusual C-19 and C-20 oxidation. Finally, palladium catalyzed carbonylation, furan oxidation and acid mediated condensation/epimerization completes the synthesis.", "author_list": "Yu, Hao and Hatano, Yutaro, el al." }, { "title": "Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation", "type": "monograph", "publication_date": "2025-04-24", "publisher": "bioRxiv", "doi": "10.1101/2025.04.21.649844", "cite_using_url": "https://authors.library.caltech.edu/records/x92f3-gfy20", "abstract": "Mapping the impact of genomic variation on gene expression facilitates an understanding of the molecular basis of complex phenotypic traits and disease predisposition. Mouse models provide a controlled and reproducible framework for capturing the breadth of genomic variation observed in different genotypes across a wide variety of tissues. As part of the IGVF consortium's effort to catalog the effects of genetic variation, we uniformly characterized the transcriptomes of eight tissues from each mouse founder strain used to derive the Collaborative Cross strains, comprising five classical laboratory inbred strains and three wild-derived inbred strains. We sequenced samples from four male and four female replicates per tissue using single-nucleus RNA-seq to generate an \"8-cube\" dataset of 5.2 million nuclei across 106 cell types and cell states. As expected, the overall extent of transcriptome variation correlates positively with genetic divergence across the strains with the greatest differential between PWK/PhJ and CAST/EiJ. At the individual tissue level, heart and brain are relatively more similar across strains compared with gonads, adrenal, skeletal muscle, kidney, and liver. Further analyses revealed substantial strain variation, often concentrated in a few cell types as well as cell-state signatures that especially reflect strain-associated immune and metabolic trait differences. The founder 8-cube dataset provides rich transcriptome variation signatures to help explain strain-specific phenotypic traits and disease states, as illustrated by examples in tissue-resident immune cells, muscle degeneration, kidney sex differences, and the hypothalamicpituitary-adrenal axis. This data further provides a systematic foundation for the analysis of these tissues in the founder strains as well as the Collaborative Cross.", "author_list": "Rebboah, Elisabeth and Weber, Ryan, el al." }, { "title": "Exploring non-invasive sexing of early chick embryos in intact eggs using Laser Speckle Contrast Imaging (LSCI) and Deep Neural Network (DNN)", "type": "monograph", "publication_date": "2025-04-23", "publisher": "BioRxiv", "doi": "10.1101/2025.04.17.649355", "cite_using_url": "https://authors.library.caltech.edu/records/ta6s7-wkk12", "abstract": "The ability to image blood flow in early-stage avian embryos has significant applications in developmental biology, drug and vaccine testing, as well as determining sex differentiation. In this project, we used our recently developed laser speckle contrast imaging (LSCI) system to non-invasively image extraembryonic blood vessels and used these images to attempt early sex identification of chick embryos. Specifically, we captured images of blood vessels from 1,251 living chicken embryos between day three and day four of incubation. We then applied deep neural network (DNN) models to evaluate whether it is possible to differentiate sex based on vascular patterns. Using ResNetBiT and YOLOv5 models, our results indicate that sex differentiation from extraembryonic blood vessel images was not achievable with sufficiently high accuracy or statistical significance for practical use. Specifically, ResNetBiT had a five-fold cross-validated average accuracy of 59%±5% (fold-wise p-value, p ≤ 0.3) at day 3 and 61%±3% (fold-wise, p ≤ 0.04) at day 4. YOLOv5 had a five-fold cross-validated average accuracy of 55%±3% (fold-wise, p ≤ 0.3) at day 3 and 53%±3% (fold-wise, p ≤ 0.5) at day 4. Our findings suggest that using vascular pattern imaging alone is inconclusive for reliable early sex identification in chicken embryos.
", "author_list": "Mahler, Simon and Arora, Anika, el al." }, { "title": "SynGAP forms biocondensates at sub-micromolar concentrations and recruits PSD95 and receptor oligomers, functioning as a key initiator of PSD formation", "type": "monograph", "publication_date": "2025-04-23", "publisher": "bioRxiv", "doi": "10.1101/2025.04.22.649955", "cite_using_url": "https://authors.library.caltech.edu/records/hsm44-xme33", "abstract": "A key issue in neuronal circuit regulation is how synapse formation is initiated. Synapse formation could start when one or more synaptic scaffold proteins that can initiate synapse formation reach certain threshold concentrations in the dendritic shaft, which might lead to their oligomerization or even liquid-liquid phase separation (LLPS). By combining in vitro reconstitution of purified proteins with live-cell single-molecule and confocal imaging, we demonstrated that SynGAP alone forms assemblies of nanoscale clusters containing several to several tens of molecules at 10-nM order concentrations and micron-scale LLPS hydrogel-like condensates at submicromolar concentrations. The trimers of SynGAP’s intrinsically disordered region (IDR) induced by its coiled-coil domain are responsible for SynGAP condensation. CaMKII-mediated phosphorylation moderately suppresses SynGAP condensation, and also increases condensate liquidity. While PSD95 fails to form assemblies under these conditions, it is recruited to SynGAP condensates by specifically binding to the PDZ-binding motif of SynGAP. SynGAP[PSD95] condensates selectively immobilize postsynaptic transmembrane proteins, Neuroligin1 and AMPAR-TARP2 complexes, in a manner dependent on their oligomerization state, indicating cooperative recruitment dynamics among SynGAP, PSD95, and transmembrane components, which might mimic initial PSD assembly. These findings suggest that SynGAP may act as a primary nucleator of postsynaptic density assembly, challenging the PSD95-centered models.
", "author_list": "Acharya, Saahil and Tsunoyama, Taka A., el al." }, { "title": "VARS-fUSI: Variable Sampling for Fast and Efficient Functional Ultrasound Imaging using Neural Operators", "type": "monograph", "publication_date": "2025-04-23", "publisher": "arXiv", "doi": "10.1101/2025.04.16.649237", "cite_using_url": "https://authors.library.caltech.edu/records/drbq7-emv23", "abstract": "Functional ultrasound imaging (fUSI) is a promising neuroimaging method that infers neural activity by detecting cerebral blood volume changes. It offers high sensitivity and spatial resolution relative to fMRI and is an epidural alternative to electrophysiology for medical and neuroscience applications, including brain-computer interfaces. However, current fUSI methods require hundreds of compounded images and ultrasound pulse emissions, leading to high computational costs, memory demands, and potential probe heating. We propose VARiable Sampling fUSI (VARS-fUSI), the first deep learning fUSI method to allow for different sampling durations and rates during training and inference by using neural operators. VARS-fUSI reconstructs high-quality fUSI images using 10 − 15% of the time or sampling rate needed per image while preserving decodable behavior-correlated signals. Additionally, VARS-fUSI offers efficient finetuning for generalization to new animals and humans. Demonstrated across mouse, monkey, and human data, VARS-fUSI achieves state-of-the-art performance, enhancing imaging efficiency by significantly reducing storage and processing needs.
", "author_list": "Tolooshams, Bahareh and Lin, Lydia, el al." } ]