[ { "id": "authors:keb3d-k3567", "collection": "authors", "collection_id": "keb3d-k3567", "cite_using_url": "https://authors.library.caltech.edu/records/keb3d-k3567", "type": "article", "title": "Revealing a coherent cell-state landscape across single-cell datasets with CONCORD", "author": [ { "family_name": "Zhu", "given_name": "Qin", "orcid": "0000-0001-5539-6071" }, { "family_name": "Jiang", "given_name": "Zuzhi", "orcid": "0009-0009-1402-8235" }, { "family_name": "Zuckerman", "given_name": "Binyamin", "orcid": "0000-0002-6216-011X" }, { "family_name": "Weinberger", "given_name": "Leor", "orcid": "0000-0002-9987-6357" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Gartner", "given_name": "Zev J.", "orcid": "0000-0001-7803-1219" } ], "abstract": "

Revealing the underlying cell-state landscape from single-cell data requires overcoming the critical obstacles of batch integration, denoising and dimensionality reduction. Here we present CONCORD, a unified framework that simultaneously addresses these challenges within a single self-supervised model. At its core, CONCORD implements a probabilistic sampling strategy that corrects batch effects through dataset-aware sampling and enhances biological resolution through hard-negative sampling. Using only a minimalist neural network with a single hidden layer and contrastive learning, CONCORD surpasses state-of-the-art performance without relying on deep architectures, auxiliary losses or external supervision. It seamlessly integrates data across batches, technologies and even species to generate high-resolution cell atlases. The resulting latent representations are denoised and biologically meaningful, capturing gene coexpression programs, revealing detailed lineage trajectories and preserving both local geometric relationships and global topological structures. We demonstrate CONCORD's broad applicability across diverse datasets, establishing it as a general-purpose framework for learning unified, high-fidelity representations of cellular identity and dynamics.

", "doi": "10.1038/s41587-025-02950-z", "issn": "1087-0156", "publisher": "Nature Publishing Group", "publication": "Nature Biotechnology", "publication_date": "2026-01-05" }, { "id": "authors:3n4ah-x3781", "collection": "authors", "collection_id": "3n4ah-x3781", "cite_using_url": "https://authors.library.caltech.edu/records/3n4ah-x3781", "type": "article", "title": "Geometry-dependent defect merging induces bifurcated dynamics in active networks", "author": [ { "family_name": "Yang", "given_name": "Fan", "orcid": "0000-0002-2248-2026", "clpid": "Yang-Fan" }, { "family_name": "Liu", "given_name": "Shichen", "clpid": "Liu-Shichen" }, { "family_name": "Wang", "given_name": "Hao", "orcid": "0000-0001-9976-9247", "clpid": "Wang-Hao" }, { "family_name": "Lee", "given_name": "Heun Jin", "orcid": "0009-0002-4615-9271", "clpid": "Lee-Heun-Jin" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Cytoskeletal networks can repair defects to maintain structural integrity. However, the mechanisms and dynamics of defect merging remain poorly understood. Here, we report a geometry-tunable merging mechanism in microtubule-motor networks initiated by active crosslinking. We directly generate defects using a light-controlled microtubule-motor system in O-shaped and V-shaped networks, and observe that the defects can self-close. Combining theory and experiment, we find that the V-shaped networks must overcome internal elastic resistance in order to zip up cracks, giving rise to a bifurcation of dynamics dependent on the initial opening angle of the crack: the crack merges below a critical angle and opens up at larger angles. Simulation of a continuum model reproduces the bifurcation dynamics, revealing the importance of overlapping boundary layers where free motors and microtubules can actively crosslink and thereby merge the defects. We also formulate a simple elastic-rod model that can qualitatively predict the critical angle, which is tunable by the network geometry.", "doi": "10.1103/m8cb-gf1q", "issn": "2643-1564", "publisher": "American Physical Society", "publication": "Physical Review Research", "publication_date": "2025-10-03", "series_number": "4", "volume": "7", "issue": "4", "pages": "L042006" }, { "id": "authors:dkwem-9s246", "collection": "authors", "collection_id": "dkwem-9s246", "cite_using_url": "https://authors.library.caltech.edu/records/dkwem-9s246", "type": "article", "title": "Motor-driven microtubule diffusion in a photobleached dynamical coordinate system", "author": [ { "family_name": "Hirokawa", "given_name": "Soichi", "orcid": "0000-0001-5584-2676", "clpid": "Hirokawa-Soichi" }, { "family_name": "Lee", "given_name": "Heun Jin", "orcid": "0009-0002-4615-9271", "clpid": "Lee-Heun-Jin" }, { "family_name": "Banks", "given_name": "Rachel A.", "orcid": "0000-0003-2028-2925", "clpid": "Banks-Rachel-A" }, { "family_name": "Duarte", "given_name": "Ana I.", "orcid": "0000-0003-3726-3018", "clpid": "Duarte-Ana-I" }, { "family_name": "Najma", "given_name": "Bibi", "clpid": "Najma-Bibi" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "abstract": "

A hallmark feature of active matter systems is the ability of individual elements to interact and organize over length scales exceeding that of the constituent molecular players. However, the nature of internal redistribution that occurs in the bulk of the collective is less clear. Using light-dimerizable kinesin motors to spatially control the formation and contraction of a microtubule network, we deliberately photobleach a grid pattern onto the filament network serving as a transient and dynamic coordinate system to observe the deformation and translation of the remaining fluorescent squares of microtubules. We find that the network contracts at a rate set by motor speed but is accompanied by a diffusive-like spread throughout the bulk of the contracting network with effective diffusion constant two orders of magnitude lower than that for freely diffusing microtubules. We further find that on micron scales, the diffusive timescale is only a factor of ≈3 slower than that of advection regardless of conditions, showing that the global contraction and long-time relaxation from this diffusive behavior are both motor-driven but exhibit local competition within the network bulk.

", "doi": "10.1073/pnas.2417020122", "pmcid": "PMC12184364", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2025-06-17", "series_number": "24", "volume": "122", "issue": "24", "pages": "e2417020122" }, { "id": "authors:6jd2w-a0388", "collection": "authors", "collection_id": "6jd2w-a0388", "cite_using_url": "https://authors.library.caltech.edu/records/6jd2w-a0388", "type": "article", "title": "Identifying perturbations that boost T-cell infiltration into tumours via counterfactual learning of their spatial proteomic profiles", "author": [ { "family_name": "Wang", "given_name": "Zitong Jerry", "orcid": "0000-0001-8008-7318", "clpid": "Wang-Zitong-Jerry" }, { "family_name": "Farooq", "given_name": "Abdullah S.", "clpid": "Farooq-Abdullah-S" }, { "family_name": "Chen", "given_name": "Yu-Jen", "orcid": "0009-0009-0992-8976", "clpid": "Chen-Yu-Jen" }, { "family_name": "Bhargava", "given_name": "Aman", "orcid": "0000-0002-3347-0602", "clpid": "Bhargava-Aman" }, { "family_name": "Xu", "given_name": "Alexander M.", "orcid": "0000-0003-4877-4358" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Cancer progression can be slowed down or halted via the activation of either endogenous or engineered T cells and their infiltration of the tumour microenvironment. Here we describe a deep-learning model that uses large-scale spatial proteomic profiles of tumours to generate minimal tumour perturbations that boost T-cell infiltration. The model integrates a counterfactual optimization strategy for the generation of the perturbations with the prediction of T-cell infiltration as a self-supervised machine learning problem. We applied the model to 368 samples of metastatic melanoma and colorectal cancer assayed using 40-plex imaging mass cytometry, and discovered cohort-dependent combinatorial perturbations (CXCL9, CXCL10, CCL22 and CCL18 for melanoma, and CXCR4, PD-1, PD-L1 and CYR61 for colorectal cancer) that support T-cell infiltration across patient cohorts, as confirmed via in vitro experiments. Leveraging counterfactual-based predictions of spatial omics data may aid the design of cancer therapeutics.", "doi": "10.1038/s41551-025-01357-0", "issn": "2157-846X", "publisher": "Nature Publishing Group", "publication": "Nature Biomedical Engineering", "publication_date": "2025-03-05" }, { "id": "authors:g6ph9-7ec61", "collection": "authors", "collection_id": "g6ph9-7ec61", "cite_using_url": "https://authors.library.caltech.edu/records/g6ph9-7ec61", "type": "article", "title": "Benchmarking protein language models for protein crystallization", "author": [ { "family_name": "Mall", "given_name": "Raghvendra" }, { "family_name": "Kaushik", "given_name": "Rahul" }, { "family_name": "Martinez", "given_name": "Zachary A.", "orcid": "0000-0002-7830-3162", "clpid": "Martinez-Zachary-A" }, { "family_name": "Thomson", "given_name": "Matt W.", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Castiglione", "given_name": "Filippo" } ], "abstract": "

The problem of protein structure determination is usually solved by X-ray crystallography. Several in silico deep learning methods have been developed to overcome the high attrition rate, cost of experiments and extensive trial-and-error settings, for predicting the crystallization propensities of proteins based on their sequences. In this work, we benchmark the power of open protein language models (PLMs) through the TRILL platform, a be-spoke framework democratizing the usage of PLMs for the task of predicting crystallization propensities of proteins. By comparing LightGBM / XGBoost classifiers built on the average embedding representations of proteins learned by different PLMs, such as ESM2, Ankh, ProtT5-XL, ProstT5, xTrimoPGLM, SaProt with the performance of state-of-the-art sequence-based methods like DeepCrystal, ATTCrys and CLPred, we identify the most effective methods for predicting crystallization outcomes. The LightGBM classifiers utilizing embeddings from ESM2 model with 30 and 36 transformer layers and 150 and 3000 million parameters respectively have performance gains by 3- $$5\\%$$ than all compared models for various evaluation metrics, including AUPR (Area Under Precision-Recall Curve), AUC (Area Under the Receiver Operating Characteristic Curve), and F1 on independent test sets. Furthermore, we fine-tune the ProtGPT2 model available via TRILL to generate crystallizable proteins. Starting with 3000 generated proteins and through a step of filtration processes including consensus of all open PLM-based classifiers, sequence identity through CD-HIT, secondary structure compatibility, aggregation screening, homology search and foldability evaluation, we identified a set of 5 novel proteins as potentially crystallizable.

", "doi": "10.1038/s41598-025-86519-5", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2025-01-18", "series_number": "1", "volume": "15", "issue": "1", "pages": "2381" }, { "id": "authors:qkjf6-g0038", "collection": "authors", "collection_id": "qkjf6-g0038", "cite_using_url": "https://authors.library.caltech.edu/records/qkjf6-g0038", "type": "article", "title": "Control of spatio-temporal patterning via cell growth in a multicellular synthetic gene circuit", "author": [ { "family_name": "Santorelli", "given_name": "Marco", "orcid": "0000-0002-9633-7825" }, { "family_name": "Bhamidipati", "given_name": "Pranav S.", "orcid": "0000-0002-6199-6505", "clpid": "Bhamidipati-Pranav-S" }, { "family_name": "Courte", "given_name": "Josquin" }, { "family_name": "Swedlund", "given_name": "Benjamin" }, { "family_name": "Jain", "given_name": "Naisargee", "orcid": "0009-0004-2505-2189" }, { "family_name": "Poon", "given_name": "Kyle" }, { "family_name": "Schildknecht", "given_name": "Dominik", "orcid": "0000-0002-0678-0904", "clpid": "Schildknecht-Dominik" }, { "family_name": "Kavanagh", "given_name": "Andriu" }, { "family_name": "MacKrell", "given_name": "Victoria A." }, { "family_name": "Sondkar", "given_name": "Trusha" }, { "family_name": "Malaguti", "given_name": "Mattias", "orcid": "0000-0003-4392-7183" }, { "family_name": "Quadrato", "given_name": "Giorgia", "orcid": "0000-0003-0717-4874" }, { "family_name": "Lowell", "given_name": "Sally" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Morsut", "given_name": "Leonardo", "orcid": "0000-0001-7049-3478" } ], "abstract": "A major goal in synthetic development is to build gene regulatory circuits that control patterning. In natural development, an interplay between mechanical and chemical communication shapes the dynamics of multicellular gene regulatory circuits. For synthetic circuits, how non-genetic properties of the growth environment impact circuit behavior remains poorly explored. Here, we first describe an occurrence of mechano-chemical coupling in synthetic Notch (synNotch) patterning circuits: high cell density decreases synNotch-gated gene expression in different cellular systems in vitro. We then construct, both in vitro and in silico, a synNotch-based signal propagation circuit whose outcome can be regulated by cell density. Spatial and temporal patterning outcomes of this circuit can be predicted and controlled via modulation of cell proliferation, initial cell density, and/or spatial distribution of cell density. Our work demonstrates that synthetic patterning circuit outcome can be controlled via cellular growth, providing a means for programming multicellular circuit patterning outcomes.", "doi": "10.1038/s41467-024-53078-8", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2024-11-19", "volume": "15", "pages": "9867" }, { "id": "authors:0j638-jx111", "collection": "authors", "collection_id": "0j638-jx111", "cite_using_url": "https://authors.library.caltech.edu/records/0j638-jx111", "type": "article", "title": "Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease", "author": [ { "family_name": "Polonsky", "given_name": "Michal", "orcid": "0000-0003-3871-460X", "clpid": "Polonsky-Michal" }, { "family_name": "Gerhardt", "given_name": "Louisa M. S." }, { "family_name": "Yun", "given_name": "Jina", "clpid": "Yun-Chi-H-Jina" }, { "family_name": "Koppitch", "given_name": "Kari" }, { "family_name": "Col\u00f3n", "given_name": "Katsuya Lex", "orcid": "0000-0002-7347-6128", "clpid": "Col\u00f3n-Katsuya-Lex" }, { "family_name": "Amrhein", "given_name": "Henry", "orcid": "0000-0002-4264-140X", "clpid": "Amrhein-H" }, { "family_name": "Wold", "given_name": "Barbara", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Zheng", "given_name": "Shiwei" }, { "family_name": "Yuan", "given_name": "Guo-Cheng", "orcid": "0000-0002-2283-4714" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Cai", "given_name": "Long", "orcid": "0000-0002-7154-5361", "clpid": "Cai-Long" }, { "family_name": "McMahon", "given_name": "Andrew P.", "orcid": "0000-0002-3779-1729", "clpid": "McMahon-Andrew-P" } ], "abstract": "

Kidney injury disrupts the intricate renal architecture and triggers limited regeneration, together with injury-invoked inflammation and fibrosis. Deciphering the molecular pathways and cellular interactions driving these processes is challenging due to the complex tissue structure. Here, we apply single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics reveals injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predicts Clcf1-Crfl1 in a molecular interplay between persistently injured proximal tubule cells and their neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis identifies cellular microenvironments resembling early tertiary lymphoid structures and associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease.

", "doi": "10.1038/s41467-024-51186-z", "pmcid": "PMC11377535", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2024-09-05", "series_number": "1", "volume": "15", "issue": "1", "pages": "7010" }, { "id": "authors:81t8j-xc538", "collection": "authors", "collection_id": "81t8j-xc538", "cite_using_url": "https://authors.library.caltech.edu/records/81t8j-xc538", "type": "article", "title": "Engineering programmable material-to-cell pathways via synthetic notch receptors to spatially control differentiation in multicellular constructs", "author": [ { "family_name": "Garibyan", "given_name": "Mher", "orcid": "0009-0002-4168-0375", "clpid": "Garibyan-Mher" }, { "family_name": "Hoffman", "given_name": "Tyler", "clpid": "Hoffman-Tyler" }, { "family_name": "Makaske", "given_name": "Thijs", "clpid": "Makaske-Thijs" }, { "family_name": "Do", "given_name": "Stephanie K.", "orcid": "0009-0007-6101-0068", "clpid": "Do-Stephanie-K" }, { "family_name": "Wu", "given_name": "Yifan", "orcid": "0009-0009-0537-5518", "clpid": "Wu-Yifan" }, { "family_name": "Williams", "given_name": "Brian A.", "clpid": "Williams-Brian-A" }, { "family_name": "March", "given_name": "Alexander R.", "orcid": "0000-0001-7495-1739", "clpid": "March-Alexander-R" }, { "family_name": "Cho", "given_name": "Nathan", "clpid": "Cho-Nathan" }, { "family_name": "Pedroncelli", "given_name": "Nicolas", "clpid": "Pedroncelli-Nicolas" }, { "family_name": "Espinosa Lima", "given_name": "Ricardo", "clpid": "Espinosa-Lima-Ricardo" }, { "family_name": "Soto", "given_name": "Jennifer", "clpid": "Soto-Jennifer" }, { "family_name": "Jackson", "given_name": "Brooke", "clpid": "Jackson-Brooke" }, { "family_name": "Santoso", "given_name": "Jeffrey W.", "orcid": "0000-0003-3321-9829", "clpid": "Santoso-Jeffrey-W" }, { "family_name": "Khademhosseini", "given_name": "Ali", "orcid": "0000-0002-2692-1524", "clpid": "Khademhosseini-Ali" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Li", "given_name": "Song", "orcid": "0000-0002-4760-8828", "clpid": "Li-Song" }, { "family_name": "McCain", "given_name": "Megan L.", "orcid": "0000-0003-1908-6783", "clpid": "McCain-Megan-L" }, { "family_name": "Morsut", "given_name": "Leonardo", "orcid": "0000-0001-7049-3478", "clpid": "Morsut-Leonardo" } ], "abstract": "
\n
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Synthetic Notch (synNotch) receptors are genetically encoded, modular synthetic receptors that enable mammalian cells to detect environmental signals and respond by activating user-prescribed transcriptional programs. Although some materials have been modified to present synNotch ligands with coarse spatial control, applications in tissue engineering generally require extracellular matrix (ECM)-derived scaffolds and/or finer spatial positioning of multiple ligands. Thus, we develop here a suite of materials that activate synNotch receptors for generalizable engineering of material-to-cell signaling. We genetically and chemically fuse functional synNotch ligands to ECM proteins and ECM-derived materials. We also generate tissues with microscale precision over four distinct reporter phenotypes by culturing cells with two orthogonal synNotch programs on surfaces microcontact-printed with two synNotch ligands. Finally, we showcase applications in tissue engineering by co-transdifferentiating fibroblasts into skeletal muscle or endothelial cell precursors in user-defined micropatterns. These technologies provide avenues for spatially controlling cellular phenotypes in mammalian tissues.

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", "doi": "10.1038/s41467-024-50126-1", "pmcid": "PMC11246427", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2024-07-13", "volume": "15", "pages": "5891" }, { "id": "authors:bbdk1-vxg07", "collection": "authors", "collection_id": "bbdk1-vxg07", "cite_using_url": "https://authors.library.caltech.edu/records/bbdk1-vxg07", "type": "article", "title": "Patterning and folding of intestinal villi by active mesenchymal dewetting", "author": [ { "family_name": "Huycke", "given_name": "Tyler R.", "orcid": "0000-0001-8328-5061" }, { "family_name": "H\u00e4kkinen", "given_name": "Teemu J.", "orcid": "0000-0003-0130-7314" }, { "family_name": "Miyazaki", "given_name": "Hikaru" }, { "family_name": "Srivastava", "given_name": "Vasudha", "orcid": "0000-0001-8845-9518" }, { "family_name": "Barruet", "given_name": "Emilie" }, { "family_name": "McGinnis", "given_name": "Christopher S.", "orcid": "0000-0001-6923-9341" }, { "family_name": "Kalantari", "given_name": "Ali" }, { "family_name": "Cornwall-Scoones", "given_name": "Jake", "orcid": "0000-0002-7435-486X", "clpid": "Cornwall-Scoones-Jake" }, { "family_name": "Vaka", "given_name": "Dedeepya", "orcid": "0000-0001-7951-5514" }, { "family_name": "Zhu", "given_name": "Qin", "orcid": "0000-0001-5539-6071" }, { "family_name": "Jo", "given_name": "Hyunil", "orcid": "0000-0002-4863-0779" }, { "family_name": "Oria", "given_name": "Roger" }, { "family_name": "Weaver", "given_name": "Valerie M.", "orcid": "0000-0003-4786-6752" }, { "family_name": "DeGrado", "given_name": "William F." }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Garikipati", "given_name": "Krishna" }, { "family_name": "Boffelli", "given_name": "Dario", "orcid": "0000-0003-2529-9056" }, { "family_name": "Klein", "given_name": "Ophir D.", "orcid": "0000-0002-6254-7082" }, { "family_name": "Gartner", "given_name": "Zev J.", "orcid": "0000-0001-7803-1219" } ], "abstract": "

Tissue folds are structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to villi, finger-like protrusions that enable nutrient absorption. However, the molecular and mechanical processes driving villus morphogenesis remain unclear. Here, we identify an active mechanical mechanism that simultaneously patterns and folds the intestinal epithelium to initiate villus formation. At the cellular level, we find that PDGFRA+ subepithelial mesenchymal cells generate myosin II-dependent forces sufficient to produce patterned curvature in neighboring tissue interfaces. This symmetry-breaking process requires altered cell and extracellular matrix interactions that are enabled by matrix metalloproteinase-mediated tissue fluidization. Computational models, together with in vitro and in vivo experiments, revealed that these cellular features manifest at the tissue level as differences in interfacial tensions that promote mesenchymal aggregation and interface bending through a process analogous to the active dewetting of a thin liquid film.

", "doi": "10.1016/j.cell.2024.04.039", "issn": "0092-8674", "publisher": "Cell Press", "publication": "Cell", "publication_date": "2024-06-06", "series_number": "12", "volume": "187", "issue": "12", "pages": "3072-3089.e20" }, { "id": "authors:2ccwa-pwz14", "collection": "authors", "collection_id": "2ccwa-pwz14", "cite_using_url": "https://authors.library.caltech.edu/records/2ccwa-pwz14", "type": "article", "title": "Theoretical limits of energy extraction in active fluids", "author": [ { "family_name": "Shadkhoo", "given_name": "Shahriar", "orcid": "0000-0003-3582-0634", "clpid": "Shadkhoo-Shahriar" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "

Active materials form a class of far-from-equilibrium systems that are driven internally and exhibit self-organization, which can be harnessed to perform mechanical work. Inspired by experiments on synthetic active polymer networks, in this paper we examine limits of work extraction from an active viscoelastic medium by analyzing the transport of a particle. The active viscoelastic material possesses an equilibrium density where the active and passive forces are balanced out. In a one-dimensional system, a gliding activation front (AF), which converts a passive to an active medium, provides active energy at a constant rate, which is injected into the system at one end and propagates to the other. We demonstrate that there exists a maximum velocity of the AF, above which the activated region fails to deliver the transport power. We hypothesize and intuitively argue based on the limit cases that the feasibility and the velocity of transport of the particle can be interpreted in terms of the velocity of an equilibration domain wall of the field, which is set by two parameters: (i) a measure of activity, and (ii) the viscoelastic timescale. The phase diagram is divided into “transport” and “no-transport” sectors, namely, for any pair of the two parameters, there exists a threshold velocity of the AF above which the particle transport becomes impossible. Constructing the phase diagram we find that (1) there are regions of the phase diagram for which the threshold velocity of the AF diverges, and (2) larger viscoelastic timescale makes the transport region more accessible and also increases the transport velocity therein. Furthermore, we find that increasing the velocity of AF, results in larger extracted power but smaller transport coefficient; defined as the ratio of the transport velocity and that of the AF. Our model provides a framework for understanding the energetics of transport phenomena in biology and designing efficient mechanisms of transport in synthetic active materials.

", "doi": "10.1103/physrevresearch.6.023195", "issn": "2643-1564", "publisher": "American Physical Society", "publication": "Physical Review Research", "publication_date": "2024-05", "series_number": "2", "volume": "6", "issue": "2", "pages": "023195" }, { "id": "authors:w9sxn-f7e77", "collection": "authors", "collection_id": "w9sxn-f7e77", "cite_using_url": "https://authors.library.caltech.edu/records/w9sxn-f7e77", "type": "article", "title": "Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice", "author": [ { "family_name": "Vasquez Ayala", "given_name": "Adriana", "orcid": "0000-0001-6917-3581", "clpid": "Vasquez-Ayala-Adriana" }, { "family_name": "Hsu", "given_name": "Chia-Yun", "orcid": "0000-0002-5283-1020", "clpid": "Hsu-Chia-Yun" }, { "family_name": "Oles", "given_name": "Renee E.", "orcid": "0000-0001-5945-0215", "clpid": "Oles-Renee-E" }, { "family_name": "Matsuo", "given_name": "Kazuhiko", "orcid": "0000-0001-5782-5300", "clpid": "Matsuo-Kazuhiko" }, { "family_name": "Loomis", "given_name": "Luke R.", "orcid": "0009-0003-1131-7185", "clpid": "Loomis-Luke-R" }, { "family_name": "Buzun", "given_name": "Ekaterina", "orcid": "0000-0002-1223-1290", "clpid": "Buzun-Ekaterina" }, { "family_name": "Carrillo Terrazas", "given_name": "Marvic", "orcid": "0000-0002-8830-5161", "clpid": "Carrillo-Terrazas-Marvic" }, { "family_name": "Gerner", "given_name": "Romana R.", "orcid": "0000-0003-2377-6509", "clpid": "Gerner-Romana-R" }, { "family_name": "Lu", "given_name": "Hsueh-Han", "orcid": "0000-0002-0832-9607", "clpid": "Lu-Hsueh-Han" }, { "family_name": "Kim", "given_name": "Sohee", "orcid": "0009-0003-0989-5584", "clpid": "Kim-Sohee" }, { "family_name": "Zhang", "given_name": "Ziyue", "orcid": "0009-0002-8996-6049", "clpid": "Zhang-Ziyue" }, { "family_name": "Park", "given_name": "Jong Hwee", "orcid": "0009-0002-6522-7049", "clpid": "Park-Jong-Hwee" }, { "family_name": "Rivaud", "given_name": "Paul", "orcid": "0000-0001-8637-3331", "clpid": "Rivaud-Paul" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Lu", "given_name": "Li-Fan", "orcid": "0000-0002-9727-0036", "clpid": "Lu-Li-Fan" }, { "family_name": "Min", "given_name": "Booki", "orcid": "0000-0002-2151-9413", "clpid": "Min-Booki" }, { "family_name": "Chu", "given_name": "Hiutung", "orcid": "0000-0001-7489-0446", "clpid": "Chu-Hiutung" } ], "abstract": "

Type I interferons (IFNs) exert a broad range of biological effects important in coordinating immune responses, which have classically been studied in the context of pathogen clearance. Yet, whether immunomodulatory bacteria operate through IFN pathways to support intestinal immune tolerance remains elusive. Here, we reveal that the commensal bacterium, Bacteroides fragilis, utilizes canonical antiviral pathways to modulate intestinal dendritic cells (DCs) and regulatory T cell (Treg) responses. Specifically, IFN signaling is required for commensal-induced tolerance as IFNAR1-deficient DCs display blunted IL-10 and IL-27 production in response to B. fragilis. We further establish that IFN-driven IL-27 in DCs is critical in shaping the ensuing Foxp\u00b3\u207a Treg via IL-27R\u03b1 signaling. Consistent with these findings, single-cell RNA sequencing of gut Tregs demonstrated that colonization with B. fragilis promotes a distinct IFN gene signature in Foxp3+ Tregs during intestinal inflammation. Altogether, our findings demonstrate a critical role of commensal-mediated immune tolerance via tonic type I IFN signaling.

", "doi": "10.1084/jem.20230063", "pmcid": "PMC10716256", "issn": "0022-1007", "publisher": "Rockefeller University Press", "publication": "Journal of Experimental Medicine", "publication_date": "2024-01-01", "series_number": "1", "volume": "221", "issue": "1", "pages": "e20230063" }, { "id": "authors:e527q-6pq77", "collection": "authors", "collection_id": "e527q-6pq77", "cite_using_url": "https://authors.library.caltech.edu/records/e527q-6pq77", "type": "article", "title": "Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references", "author": [ { "family_name": "Pool", "given_name": "Allan-Hermann", "orcid": "0000-0002-0811-9861", "clpid": "Pool-Allan-Hermann" }, { "family_name": "Poldsam", "given_name": "Helen", "orcid": "0009-0008-0390-2620", "clpid": "Poldsam-Helen" }, { "family_name": "Chen", "given_name": "Sisi" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Oka", "given_name": "Yuki", "orcid": "0000-0003-2686-0677", "clpid": "Oka-Yuki" } ], "abstract": "

Single-cell RNA-sequencing (scRNA-seq) is an indispensable tool for characterizing cellular diversity and generating hypotheses throughout biology. Droplet-based scRNA-seq datasets often lack expression data for genes that can be detected with other methods. Here we show that the observed sensitivity deficits stem from three sources: (1) poor annotation of 3\u2032 gene ends; (2) issues with intronic read incorporation; and (3) gene overlap-derived read loss. We show that missing gene expression data can be recovered by optimizing the reference transcriptome for scRNA-seq through recovering false intergenic reads, implementing a hybrid pre-mRNA mapping strategy and resolving gene overlaps. We demonstrate, with a diverse collection of mouse and human tissue data, that reference optimization can substantially improve cellular profiling resolution and reveal missing cell types and marker genes. Our findings argue that transcriptomic references need to be optimized for scRNA-seq analysis and warrant a reanalysis of previously published datasets and cell atlases.

", "doi": "10.1038/s41592-023-02003-w", "issn": "1548-7091", "publisher": "Nature Publishing Group", "publication": "Nature Methods", "publication_date": "2023-09-11" }, { "id": "authors:5bqk7-b1e47", "collection": "authors", "collection_id": "5bqk7-b1e47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230602-251540000.11", "type": "article", "title": "Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension", "author": [ { "family_name": "Bao", "given_name": "Min", "orcid": "0000-0003-0992-9388", "clpid": "Bao-Min" }, { "family_name": "Cornwall-Scoones", "given_name": "Jake", "orcid": "0000-0002-7435-486X", "clpid": "Cornwall-Scoones-Jake" }, { "family_name": "Sanchez-Vasquez", "given_name": "Estefania", "orcid": "0000-0002-6585-8548", "clpid": "Sanchez-Vasquez-Estefania" }, { "family_name": "Cox", "given_name": "Andy L.", "clpid": "Cox-Andy-L" }, { "family_name": "Chen", "given_name": "Dong-Yuan", "orcid": "0000-0003-2179-2847", "clpid": "Chen-Dong-Yuan" }, { "family_name": "De Jonghe", "given_name": "Joachim", "orcid": "0000-0003-0584-8265", "clpid": "De-Jonghe-Joachim" }, { "family_name": "Shadkhoo", "given_name": "Shahriar", "orcid": "0000-0003-3582-0634", "clpid": "Shadkhoo-Shahriar" }, { "family_name": "Hollfelder", "given_name": "Florian", "orcid": "0000-0002-1367-6312", "clpid": "Hollfelder-Florian" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Glover", "given_name": "David M.", "orcid": "0000-0003-0956-0103", "clpid": "Glover-D-M" }, { "family_name": "Zernicka-Goetz", "given_name": "Magdalena", "orcid": "0000-0002-7004-2471", "clpid": "Zernicka-Goetz-M" } ], "abstract": "Mammalian embryos sequentially differentiate into trophectoderm and an inner cell mass, the latter of which differentiates into primitive endoderm and epiblast. Trophoblast stem (TS), extraembryonic endoderm (XEN) and embryonic stem (ES) cells derived from these three lineages can self-assemble into synthetic embryos, but the mechanisms remain unknown. Here, we show that a stem cell-specific cadherin code drives synthetic embryogenesis. The XEN cell cadherin code enables XEN cell sorting into a layer below ES cells, recapitulating the sorting of epiblast and primitive endoderm before implantation. The TS cell cadherin code enables TS cell sorting above ES cells, resembling extraembryonic ectoderm clustering above epiblast following implantation. Whereas differential cadherin expression drives initial cell sorting, cortical tension consolidates tissue organization. By optimizing cadherin code expression in different stem cell lines, we tripled the frequency of correctly formed synthetic embryos. Thus, by exploiting cadherin codes from different stages of development, lineage-specific stem cells bypass the preimplantation structure to directly assemble a postimplantation embryo.", "doi": "10.1038/s41556-022-00984-y", "pmcid": "PMC9481465", "issn": "1465-7392", "publisher": "Nature Publishing Group", "publication": "Nature Cell Biology", "publication_date": "2023-09", "series_number": "9", "volume": "24", "issue": "9", "pages": "1341-2349" }, { "id": "authors:k79gc-vkp02", "collection": "authors", "collection_id": "k79gc-vkp02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-344482000.1", "type": "article", "title": "Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types", "author": [ { "family_name": "Winnett", "given_name": "Alexander Viloria", "clpid": "Winnett-Alexander-Viloria" }, { "family_name": "Akana", "given_name": "Reid", "clpid": "Akana-Reid" }, { "family_name": "Shelby", "given_name": "Natasha", "clpid": "Shelby-Natasha" }, { "family_name": "Davich", "given_name": "Hannah", "clpid": "Davich-Hannah" }, { "family_name": "Caldera", "given_name": "Saharai", "clpid": "Caldera-Saharai" }, { "family_name": "Yamada", "given_name": "Taikun", "clpid": "Yamada-Taikun" }, { "family_name": "Reyna", "given_name": "John Raymond B.", "clpid": "Reyna-John-Raymond-B" }, { "family_name": "Romano", "given_name": "Anna E.", "clpid": "Romano-Anne-E" }, { "family_name": "Carter", "given_name": "Alyssa M.", "clpid": "Carter-Alyssa-M" }, { "family_name": "Kim", "given_name": "Mi Kyung", "clpid": "Kim-Mi-Kyung" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Tognazzini", "given_name": "Colten", "clpid": "Tognazzini-Colten" }, { "family_name": "Feaster", "given_name": "Matthew", "clpid": "Feaster-Matthew" }, { "family_name": "Goh", "given_name": "Ying-Ying", "clpid": "Goh-Ying-Ying" }, { "family_name": "Chew", "given_name": "Yap Ching", "clpid": "Chew-Yap-Ching" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "In a recent household transmission study of SARS-CoV-2, we found extreme differences in SARS-CoV-2 viral loads among paired saliva, anterior nares swab (ANS), and oropharyngeal swab specimens collected from the same time point. We hypothesized these differences may hinder low-analytical-sensitivity assays (including antigen rapid diagnostic tests [Ag-RDTs]) by using a single specimen type (e.g., ANS) from reliably detecting infected and infectious individuals. We evaluated daily at-home ANS Ag-RDTs (Quidel QuickVue) in a cross-sectional analysis of 228 individuals and a longitudinal analysis (throughout infection) of 17 individuals enrolled early in the course of infection. Ag-RDT results were compared to reverse transcription-quantitative PCR (RT-qPCR) results and high, presumably infectious viral loads (in each, or any, specimen type). The ANS Ag-RDT correctly detected only 44% of time points from infected individuals on cross-sectional analysis, and this population had an inferred limit of detection of 7.6\u2009\u00d7\u200910\u2076 copies/mL. From the longitudinal cohort, daily Ag-RDT clinical sensitivity was very low (<3%) during the early, preinfectious period of the infection. Further, the Ag-RDT detected \u226463% of presumably infectious time points. The poor observed clinical sensitivity of the Ag-RDT was similar to what was predicted based on quantitative ANS viral loads and the inferred limit of detection of the ANS Ag-RDT being evaluated, indicating high-quality self-sampling. Nasal Ag-RDTs, even when used daily, can miss individuals infected with the Omicron variant and even those presumably infectious. Evaluations of Ag-RDTs for detection of infected or infectious individuals should be compared with a composite (multispecimen) infection status to correctly assess performance.\n\nImportance:\nWe reveal three findings from a longitudinal study of daily nasal antigen rapid diagnostic test (Ag-RDT) evaluated against SARS-CoV-2 viral load quantification in three specimen types (saliva, nasal swab, and throat swab) in participants enrolled at the incidence of infection. First, the evaluated Ag-RDT showed low (44%) clinical sensitivity for detecting infected persons at all infection stages. Second, the Ag-RDT poorly detected (\u226463%) time points that participants had high and presumably infectious viral loads in at least one specimen type. This poor clinical sensitivity to detect infectious individuals is inconsistent with the commonly held view that daily Ag-RDTs have near-perfect detection of infectious individuals. Third, use of a combination nasal-throat specimen type was inferred by viral loads to significantly improve Ag-RDT performance to detect infectious individuals.", "doi": "10.1128/spectrum.01295-23", "pmcid": "PMC10434058", "issn": "2165-0497", "publisher": "American Society for Microbiology", "publication": "Microbiology Spectrum", "publication_date": "2023-07", "series_number": "4", "volume": "11", "issue": "4", "pages": "e01295-23" }, { "id": "authors:n6ej8-0m894", "collection": "authors", "collection_id": "n6ej8-0m894", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-257194000.34", "type": "article", "title": "Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids", "author": [ { "family_name": "Lemma", "given_name": "Linnea M.", "orcid": "0000-0001-8482-4573", "clpid": "Lemma-Linnea-M" }, { "family_name": "Varghese", "given_name": "Minu", "orcid": "0000-0003-4410-0233", "clpid": "Varghese-Minu" }, { "family_name": "Ross", "given_name": "Tyler D.", "orcid": "0000-0002-7872-3992", "clpid": "Ross-Tyler-D" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Baskaran", "given_name": "Aparna", "orcid": "0000-0003-1899-9978", "clpid": "Baskaran-Aparna" }, { "family_name": "Dogic", "given_name": "Zvonimir", "orcid": "0000-0003-0142-1838", "clpid": "Dogic-Zvonimir" } ], "abstract": "Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.", "doi": "10.1093/pnasnexus/pgad130", "pmcid": "PMC10165807", "issn": "2752-6542", "publisher": "Oxford University Press", "publication": "PNAS Nexus", "publication_date": "2023-05", "series_number": "5", "volume": "2", "issue": "5", "pages": "Art. No. pgad130" }, { "id": "authors:8xx2v-fk653", "collection": "authors", "collection_id": "8xx2v-fk653", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230323-759607000.4", "type": "article", "title": "Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods", "author": [ { "family_name": "Winnett", "given_name": "Alexander Viloria", "orcid": "0000-0002-7338-5605", "clpid": "Winnett-Alexander-Viloria" }, { "family_name": "Akana", "given_name": "Reid", "orcid": "0000-0003-4422-587X", "clpid": "Akana-Reid" }, { "family_name": "Shelby", "given_name": "Natasha", "orcid": "0000-0001-9097-3663", "clpid": "Shelby-Natasha" }, { "family_name": "Davich", "given_name": "Hannah", "orcid": "0000-0001-6880-3086", "clpid": "Davich-Hannah" }, { "family_name": "Caldera", "given_name": "Saharai", "orcid": "0000-0001-5057-9186", "clpid": "Caldera-Saharai" }, { "family_name": "Yamada", "given_name": "Taikun", "clpid": "Yamada-Taikun" }, { "family_name": "Reyna", "given_name": "John Raymond B.", "clpid": "Reyna-John-Raymond-B" }, { "family_name": "Romano", "given_name": "Anna E.", "orcid": "0000-0002-7148-0668", "clpid": "Romano-Anne-E" }, { "family_name": "Carter", "given_name": "Alyssa M.", "orcid": "0000-0002-2776-9421", "clpid": "Carter-Alyssa-M" }, { "family_name": "Kim", "given_name": "Mi Kyung", "clpid": "Kim-Mi-Kyung" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Tognazzini", "given_name": "Colten", "orcid": "0000-0002-2754-3588", "clpid": "Tognazzini-Colten" }, { "family_name": "Feaster", "given_name": "Matthew", "orcid": "0000-0001-9966-2845", "clpid": "Feaster-Matthew" }, { "family_name": "Goh", "given_name": "Ying-Ying", "orcid": "0000-0001-5136-7214", "clpid": "Goh-Ying-Ying" }, { "family_name": "Chew", "given_name": "Yap Ching", "orcid": "0000-0002-1686-6541", "clpid": "Chew-Yap-Ching" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "SARS-CoV-2 viral-load measurements from a single-specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus\u2013host interactions. However, measurements from a single-specimen type are implicitly assumed to be representative of other specimen types. We quantified viral-load timecourses from individuals who began daily self-sampling of saliva, anterior-nares (nasal), and oropharyngeal (throat) swabs before or at the incidence of infection with the Omicron variant. Viral loads in different specimen types from the same person at the same timepoint exhibited extreme differences, up to 109 copies/mL. These differences were not due to variation in sample self-collection, which was consistent. For most individuals, longitudinal viral-load timecourses in different specimen types did not correlate. Throat-swab and saliva viral loads began to rise as many as 7 days earlier than nasal-swab viral loads in most individuals, leading to very low clinical sensitivity of nasal swabs during the first days of infection. Individuals frequently exhibited presumably infectious viral loads in one specimen type while viral loads were low or undetectable in other specimen types. Therefore, defining an individual as infectious based on assessment of a single-specimen type underestimates the infectious period, and overestimates the ability of that specimen type to detect infectious individuals. For diagnostic COVID-19 testing, these three single-specimen types have low clinical sensitivity, whereas a combined throat\u2013nasal swab, and assays with high analytical sensitivity, was inferred to have significantly better clinical sensitivity to detect presumed pre-infectious and infectious individuals.", "doi": "10.1093/pnasnexus/pgad033", "pmcid": "PMC10013338", "issn": "2752-6542", "publisher": "Oxford University Press", "publication": "PNAS Nexus", "publication_date": "2023-03", "series_number": "3", "volume": "2", "issue": "3", "pages": "pgad033" }, { "id": "authors:694bn-4vx45", "collection": "authors", "collection_id": "694bn-4vx45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230510-982977000.2", "type": "article", "title": "Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies", "author": [ { "family_name": "Banks", "given_name": "Rachel A.", "orcid": "0000-0003-2028-2925", "clpid": "Banks-Rachel-A" }, { "family_name": "Galstyan", "given_name": "Vahe", "orcid": "0000-0001-7073-9175", "clpid": "Galstyan-Vahe" }, { "family_name": "Lee", "given_name": "Heun Jin", "clpid": "Lee-Heun-Jin" }, { "family_name": "Hirokawa", "given_name": "Soichi", "orcid": "0000-0001-5584-2676", "clpid": "Hirokawa-Soichi" }, { "family_name": "Ierokomos", "given_name": "Athena", "clpid": "Ierokomos-Athena" }, { "family_name": "Ross", "given_name": "Tyler D.", "orcid": "0000-0002-7872-3992", "clpid": "Ross-Tyler-D" }, { "family_name": "Bryant", "given_name": "Zev", "clpid": "Bryant-Zev" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "abstract": "Active matter systems can generate highly ordered structures, avoiding equilibrium through the consumption of energy by individual constituents. How the microscopic parameters that characterize the active agents are translated to the observed mesoscopic properties of the assembly has remained an open question. These active systems are prevalent in living matter; for example, in cells, the cytoskeleton is organized into structures such as the mitotic spindle through the coordinated activity of many motor proteins walking along microtubules. Here, we investigate how the microscopic motor-microtubule interactions affect the coherent structures formed in a reconstituted motor-microtubule system. This question is of deeper evolutionary significance as we suspect motor and microtubule type contribute to the shape and size of resulting structures. We explore key parameters experimentally and theoretically, using a variety of motors with different speeds, processivities, and directionalities. We demonstrate that aster size depends on the motor used to create the aster, and develop a model for the distribution of motors and microtubules in steady-state asters that depends on parameters related to motor speed and processivity. Further, we show that network contraction rates scale linearly with the single-motor speed in quasi-one-dimensional contraction experiments. In all, this theoretical and experimental work helps elucidate how microscopic motor properties are translated to the much larger scale of collective motor-microtubule assemblies.", "doi": "10.7554/elife.79402", "pmcid": "PMC10014072", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2023-02-08", "volume": "12", "pages": "Art. No. e79402" }, { "id": "authors:fy1nv-rgf30", "collection": "authors", "collection_id": "fy1nv-rgf30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230314-846690800.94", "type": "article", "title": "Spin glasses, error correcting codes, and synchronization of human stem cell organoids", "author": [ { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Magnetic spins, pendulum clocks, and fireflies all self-organize into coherent collectives when arranged into groups of spatially coupled and interacting individuals. Ramanathan and colleagues demonstrate that spatial coupling of human stem cell organoids induces coherent progression through developmental transitions, allowing the dissection of molecular circuits underlying human development.", "doi": "10.1016/j.cell.2023.01.006", "issn": "0092-8674", "publisher": "Cell Press", "publication": "Cell", "publication_date": "2023-02-02", "series_number": "3", "volume": "186", "issue": "3", "pages": "461-463" }, { "id": "authors:ndk7v-fhz93", "collection": "authors", "collection_id": "ndk7v-fhz93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221202-906989500.8", "type": "article", "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": "Matthew", "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, although 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": "10.7554/elife.81453", "pmcid": "PMC9668333", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2022-11-08", "volume": "11", "pages": "Art. No. e81453" }, { "id": "authors:am7bp-3g465", "collection": "authors", "collection_id": "am7bp-3g465", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220919-149101800", "type": "article", "title": "Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension", "author": [ { "family_name": "Bao", "given_name": "Min", "orcid": "0000-0003-0992-9388", "clpid": "Bao-Min" }, { "family_name": "Cornwall-Scoones", "given_name": "Jake", "orcid": "0000-0002-7435-486X", "clpid": "Cornwall-Scoones-Jake" }, { "family_name": "Sanchez-Vasquez", "given_name": "Estefania", "orcid": "0000-0002-6585-8548", "clpid": "Sanchez-Vasquez-Estefania" }, { "family_name": "Cox", "given_name": "Andy L.", "clpid": "Cox-Andy-L" }, { "family_name": "Chen", "given_name": "Dong-Yuan", "orcid": "0000-0003-2179-2847", "clpid": "Chen-Dong-Yuan" }, { "family_name": "De Jonghe", "given_name": "Joachim", "orcid": "0000-0003-0584-8265", "clpid": "De-Jonghe-Joachim" }, { "family_name": "Shadkhoo", "given_name": "Shahriar", "orcid": "0000-0003-3582-0634", "clpid": "Shadkhoo-Shahriar" }, { "family_name": "Hollfelder", "given_name": "Florian", "orcid": "0000-0002-1367-6312", "clpid": "Hollfelder-Florian" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Glover", "given_name": "David M.", "orcid": "0000-0003-0956-0103", "clpid": "Glover-D-M" }, { "family_name": "Zernicka-Goetz", "given_name": "Magdalena", "orcid": "0000-0002-7004-2471", "clpid": "Zernicka-Goetz-M" } ], "abstract": "Mammalian embryos sequentially differentiate into trophectoderm and an inner cell mass, the latter of which differentiates into primitive endoderm and epiblast. Trophoblast stem (TS), extraembryonic endoderm (XEN) and embryonic stem (ES) cells derived from these three lineages can self-assemble into synthetic embryos, but the mechanisms remain unknown. Here, we show that a stem cell-specific cadherin code drives synthetic embryogenesis. The XEN cell cadherin code enables XEN cell sorting into a layer below ES cells, recapitulating the sorting of epiblast and primitive endoderm before implantation. The TS cell cadherin code enables TS cell sorting above ES cells, resembling extraembryonic ectoderm clustering above epiblast following implantation. Whereas differential cadherin expression drives initial cell sorting, cortical tension consolidates tissue organization. By optimizing cadherin code expression in different stem cell lines, we tripled the frequency of correctly formed synthetic embryos. Thus, by exploiting cadherin codes from different stages of development, lineage-specific stem cells bypass the preimplantation structure to directly assemble a postimplantation embryo.", "doi": "10.1038/s41556-022-00984-y", "pmcid": "PMC9481465", "issn": "1465-7392", "publisher": "Nature Publishing Group", "publication": "Nature Cell Biology", "publication_date": "2022-09-13", "series_number": "9", "volume": "24", "issue": "9", "pages": "1341-1349" }, { "id": "authors:4hyzx-m8z96", "collection": "authors", "collection_id": "4hyzx-m8z96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220720-918411000", "type": "article", "title": "Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution", "author": [ { "family_name": "Murrow", "given_name": "Lyndsay M.", "clpid": "Murrow-Lyndsay-M" }, { "family_name": "Weber", "given_name": "Robert J.", "clpid": "Weber-Robert-J" }, { "family_name": "Caruso", "given_name": "Joseph A.", "clpid": "Caruso-Joseph-A" }, { "family_name": "McGinnis", "given_name": "Christopher S.", "clpid": "McGinnis-Christopher-S" }, { "family_name": "Phong", "given_name": "Kiet", "clpid": "Phong-Kiet" }, { "family_name": "Gascard", "given_name": "Philippe", "clpid": "Gascard-Philippe" }, { "family_name": "Rabadam", "given_name": "Gabrielle", "clpid": "Rabadam-Gabrielle" }, { "family_name": "Borowsky", "given_name": "Alexander D.", "clpid": "Borowsky-Alexander-D" }, { "family_name": "Desai", "given_name": "Tejal A.", "clpid": "Desai-T-A" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Tlsty", "given_name": "Thea", "clpid": "Tlsty-Thea" }, { "family_name": "Gartner", "given_name": "Zev J.", "clpid": "Gartner-Zev-J" } ], "abstract": "The rise and fall of estrogen and progesterone across menstrual cycles and during pregnancy regulates breast development and modifies cancer risk. How these hormones impact each cell type in the breast remains poorly understood because they act indirectly through paracrine networks. Using single-cell analysis of premenopausal breast tissue, we reveal a network of coordinated transcriptional programs representing the tissue-level response to changing hormone levels. Our computational approach, DECIPHER-seq, leverages person-to-person variability in breast composition and cell state to uncover programs that co-vary across individuals. We use differences in cell-type proportions to infer a subset of programs that arise from direct cell-cell interactions regulated by hormones. Further, we demonstrate that prior pregnancy and obesity modify hormone responsiveness through distinct mechanisms: obesity reduces the proportion of hormone-responsive cells, whereas pregnancy dampens the direct response of these cells to hormones. Together, these results provide a comprehensive map of the cycling human breast.", "doi": "10.1016/j.cels.2022.06.005", "pmcid": "PMC9590200", "issn": "2405-4712", "publisher": "Cell Press", "publication": "Cell Systems", "publication_date": "2022-08-17", "series_number": "8", "volume": "13", "issue": "8", "pages": "644-664.e8" }, { "id": "authors:77z9r-qkg14", "collection": "authors", "collection_id": "77z9r-qkg14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210707-155629727", "type": "article", "title": "Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments", "author": [ { "family_name": "Wang", "given_name": "Zitong Jerry", "orcid": "0000-0001-8008-7318", "clpid": "Wang-Zitong-Jerry" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Cells in natural environments, such as tissue or soil, sense and respond to extracellular ligands with intricately structured and non-monotonic spatial distributions, sculpted by processes such as fluid flow and substrate adhesion. In this work, we show that spatial sensing and navigation can be optimized by adapting the spatial organization of signaling pathways to the spatial structure of the environment. We develop an information-theoretic framework for computing the optimal spatial organization of a sensing system for a given signaling environment. We find that receptor localization previously observed in cells maximizes information acquisition in simulated natural contexts, including tissue and soil. Specifically, information acquisition is maximized when receptors form localized patches at regions of maximal ligand concentration. Receptor localization extends naturally to produce a dynamic protocol for continuously redistributing signaling receptors, which when implemented using simple feedback, boosts cell navigation efficiency by 30-fold.", "doi": "10.1016/j.cels.2022.05.004", "issn": "2405-4712", "publisher": "Cell Press", "publication": "Cell Systems", "publication_date": "2022-07-20", "series_number": "7", "volume": "13", "issue": "7", "pages": "530-546" }, { "id": "authors:n9ncy-s9d66", "collection": "authors", "collection_id": "n9ncy-s9d66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220707-978247000", "type": "article", "title": "Minimal gene set discovery in single-cell mRNA-seq datasets with ActiveSVM", "author": [ { "family_name": "Chen", "given_name": "Xiaoqiao", "orcid": "0000-0003-4685-3466", "clpid": "Chen-Xiaoqiao" }, { "family_name": "Chen", "given_name": "Sisi", "orcid": "0000-0001-9448-9713", "clpid": "Chen-Sisi" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Sequencing costs currently prohibit the application of single-cell mRNA-seq to many biological and clinical analyses. Targeted single-cell mRNA-sequencing reduces sequencing costs by profiling reduced gene sets that capture biological information with a minimal number of genes. Here we introduce an active learning method that identifies minimal but highly informative gene sets that enable the identification of cell types, physiological states and genetic perturbations in single-cell data using a small number of genes. Our active feature selection procedure generates minimal gene sets from single-cell data by employing an active support vector machine (ActiveSVM) classifier. We demonstrate that ActiveSVM feature selection identifies gene sets that enable ~90% cell-type classification accuracy across, for example, cell atlas and disease-characterization datasets. The discovery of small but highly informative gene sets should enable reductions in the number of measurements necessary for application of single-cell mRNA-seq to clinical tests, therapeutic discovery and genetic screens.", "doi": "10.1038/s43588-022-00263-8", "issn": "2662-8457", "publisher": "Nature Publishing Group", "publication": "Nature Computational Science", "publication_date": "2022-06", "series_number": "6", "volume": "2", "issue": "6", "pages": "387-398" }, { "id": "authors:twv8k-e4262", "collection": "authors", "collection_id": "twv8k-e4262", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220422-225704323", "type": "article", "title": "Reconstituting the nonequilibrium biophysics of the LECA cytoskeleton in active matter", "author": [ { "family_name": "Larios", "given_name": "David A.", "clpid": "Larios-David-A" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "The eukaryotic cytoskeleton is a dense network of filaments and motor proteins that enables nearly all cellular force-generating behaviors, including movement, internal transport, and genome segregation through the mitotic spindle. Even though prokaryotes contain homologous force-generating filaments that drive processes like motion and cell division, no motor proteins have been found in bacterial and archaeal genomes. Current models suggest that eukaryotes emerged from the endosymbiosis and coevolution of two prokaryotic organisms; however, bioinformatic reconstructions reveal a LECA (Last Eukaryotic Common Ancestor) with multiple families of filaments and motor proteins. In this project, we aim to explore how the cytoskeleton underwent such a radical functional expansion during eukaryotic evolution, as well as to reconstruct a minimal active matter model of the LECA cytoskeleton. To do so, we built a computational-experimental platform to identify and synthesize cytoskeletal components in vitro and characterize their self-organizing properties with functional assays. As a proof of concept, we generated two synthetic protozoan motors, one of which produces a novel phase with ballistic microtubule motion. With this approach, our future work will expand our platform to a broader range of cytoskeletal components, including prokaryotic filaments. By exploring diverse eukaryotic and hybrid (eukaryote-prokaryote) cytoskeletal systems under multiple physiological conditions, we aim to provide insights into the evolution of eukaryotic active matter.", "doi": "10.1016/j.bpj.2021.11.2744", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2022-02-11", "series_number": "3", "volume": "121", "issue": "3", "pages": "521a" }, { "id": "authors:0fp8r-q9q88", "collection": "authors", "collection_id": "0fp8r-q9q88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220422-296339700", "type": "article", "title": "Measuring energy consumption through space and time in an active matter system of cytoskeletal motors and filaments", "author": [ { "family_name": "Duarte", "given_name": "Ana I.", "clpid": "Duarte-Ana-I" }, { "family_name": "Jin Lee", "given_name": "Heun", "clpid": "Jin-Lee-Heun" }, { "family_name": "Banks", "given_name": "Rachel A.", "orcid": "0000-0003-2028-2925", "clpid": "Banks-Rachel-A" }, { "family_name": "Hirokawa", "given_name": "Soichi", "orcid": "0000-0001-5584-2676", "clpid": "Hirokawa-Soichi" }, { "family_name": "Galstyan", "given_name": "Vahe", "orcid": "0000-0001-7073-9175", "clpid": "Galstyan-Vahe" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "abstract": "Active matter systems consume energy from their environment to form organized, dynamical patterns and structures. These ordered states do not exist in the absence of an energy source. As such, a more general description of energy-driven behavior than is offered by near-equilibrium approaches is required to describe active matter. To gain insight into the energetic cost to form and maintain order, we investigate the assembly of an ordered aster from a disordered, homogeneous mixture of microtubules. This formation occurs due to optogenetically controllable cross-linking of the molecular motors that walk on the microtubules and hydrolyze ATP. Theoretical reaction-diffusion models predict a non-equilibrium ATP distribution resulting from a corresponding motor profile; we test these models via fluorescent readouts of ATP and motor concentrations in both space and time. Comparing the theoretical versus measured ATP profiles provides insight into the dynamics of structure formation and properties of the motors, such as if motors operate cooperatively. Our experiments revealed an ATP depletion gradient that is maximized at the aster core, where the concentration of the motors is highest. This work is a first step in understanding the role of energy consumption through space and time in the formation and maintenance of organization in this active matter system. More broadly, our work provides a case study towards the larger effort of developing generalized theories of non-equilibrium systems.", "doi": "10.1016/j.bpj.2021.11.2745", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2022-02-11", "series_number": "3", "volume": "121", "issue": "3", "pages": "521a-522a" }, { "id": "authors:jbnpr-kv294", "collection": "authors", "collection_id": "jbnpr-kv294", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211221-866382000", "type": "article", "title": "Reinforcement learning reveals fundamental limits on the mixing of active particles", "author": [ { "family_name": "Schildknecht", "given_name": "Dominik", "orcid": "0000-0002-0678-0904", "clpid": "Schildknecht-Dominik" }, { "family_name": "Popova", "given_name": "Anastasia N.", "clpid": "Popova-Anastasia-N" }, { "family_name": "Stellwagen", "given_name": "Jack", "clpid": "Stellwagen-Jack" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "The control of far-from-equilibrium physical systems, including active materials, requires advanced control strategies due to the non-linear dynamics and long-range interactions between particles, preventing explicit solutions to optimal control problems. In such situations, Reinforcement Learning (RL) has emerged as an approach to derive suitable control strategies. However, for active matter systems, it is an important open question how the mathematical structure and the physical properties determine the tractability of RL. In this paper, we demonstrate that RL can only find good mixing strategies for active matter systems that combine attractive and repulsive interactions. Using analytic results from dynamical systems theory, we show that combining both interaction types is indeed necessary for the existence of mixing-inducing hyperbolic dynamics and therefore the ability of RL to find homogeneous mixing strategies. In particular, we show that for drag-dominated translational-invariant particle systems, mixing relies on combined attractive and repulsive interactions. Therefore, our work demonstrates which experimental developments need to be made to make protein-based active matter applicable, and it provides some classification of microscopic interactions based on macroscopic behavior.", "doi": "10.1039/d1sm01400e", "issn": "1744-683X", "publisher": "Royal Society of Chemistry", "publication": "Soft Matter", "publication_date": "2022-01-21", "series_number": "3", "volume": "18", "issue": "3", "pages": "617-625" }, { "id": "authors:zvjg3-dry41", "collection": "authors", "collection_id": "zvjg3-dry41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210629-153450418", "type": "article", "title": "Deep Parallel Characterization of AAV Tropism and AAV-Mediated Transcriptional Changes via Single-Cell RNA Sequencing", "author": [ { "family_name": "Brown", "given_name": "David", "orcid": "0000-0002-9757-1744", "clpid": "Brown-David" }, { "family_name": "Altermatt", "given_name": "Michael", "orcid": "0000-0003-2841-5374", "clpid": "Altermatt-Michael" }, { "family_name": "Dobreva", "given_name": "Tatyana", "orcid": "0000-0002-2625-8873", "clpid": "Dobreva-Tatyana" }, { "family_name": "Chen", "given_name": "Sisi", "orcid": "0000-0001-9448-9713", "clpid": "Chen-Sisi" }, { "family_name": "Wang", "given_name": "Alexander", "orcid": "0000-0001-7375-5445", "clpid": "Wang-Alexander" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Engineered variants of recombinant adeno-associated viruses (rAAVs) are being developed rapidly to meet the need for gene-therapy delivery vehicles with particular cell-type and tissue tropisms. While high-throughput AAV engineering and selection methods have generated numerous variants, subsequent tropism and response characterization have remained low throughput and lack resolution across the many relevant cell and tissue types. To fully leverage the output of these large screening paradigms across multiple targets, we have developed an experimental and computational single-cell RNA sequencing (scRNA-seq) pipeline for in vivo characterization of barcoded rAAV pools at high resolution. Using this platform, we have both corroborated previously reported viral tropisms and discovered unidentified AAV capsid targeting biases. As expected, we observed that the tropism profile of AAV.CAP-B10 in mice was shifted toward neurons and away from astrocytes when compared with AAV-PHP.eB. Transcriptomic analysis revealed that this neuronal bias is due mainly to increased targeting efficiency for glutamatergic neurons, which we confirmed by RNA fluorescence in situ hybridization. We further uncovered cell subtype tropisms of AAV variants in vascular and glial cells, such as low transduction of pericytes and Myoc+ astrocytes. Additionally, we have observed cell-type-specific transitory responses to systemic AAV-PHP.eB administration, such as upregulation of genes involved in p53 signaling in endothelial cells three days post-injection, which return to control levels by day twenty-five. The presented experimental and computational approaches for parallel characterization of AAV tropism will facilitate the advancement of safe and precise gene delivery vehicles, and showcase the power of understanding responses to gene therapies at the single-cell level.", "doi": "10.3389/fimmu.2021.730825", "pmcid": "PMC8574206", "issn": "1664-3224", "publisher": "Frontiers Media", "publication": "Frontiers in Immunology", "publication_date": "2021-10-21", "volume": "12", "pages": "Art. No. 730825" }, { "id": "authors:ks7h3-tf644", "collection": "authors", "collection_id": "ks7h3-tf644", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201110-143708446", "type": "article", "title": "Persistent fluid flows defined by active matter boundaries", "author": [ { "family_name": "Qu", "given_name": "Zijie", "orcid": "0000-0003-1500-3207", "clpid": "Qu-Zijie" }, { "family_name": "Schildknecht", "given_name": "Dominik", "orcid": "0000-0002-0678-0904", "clpid": "Schildknecht-Dominik" }, { "family_name": "Shadkhoo", "given_name": "Shahriar", "orcid": "0000-0003-3582-0634", "clpid": "Shadkhoo-Shahriar" }, { "family_name": "Amaya", "given_name": "Enrique", "clpid": "Amaya-Enrique" }, { "family_name": "Jiang", "given_name": "Jialong", "clpid": "Jiang-Jialong" }, { "family_name": "Lee", "given_name": "Heun Jin", "clpid": "Lee-Heun-Jin" }, { "family_name": "Larios", "given_name": "David", "clpid": "Larios-David" }, { "family_name": "Yang", "given_name": "Fan", "orcid": "0000-0002-2248-2026", "clpid": "Yang-Fan" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Biological systems control ambient fluids through the self-organization of active protein structures, including flagella, cilia, and cytoskeletal networks. Self-organization of protein components enables the control and modulation of fluid flow fields on micron scales, however, the physical principles underlying the organization and control of active-matter-driven fluid flows are poorly understood. Here, we use an optically-controlled active-matter system composed of microtubule filaments and light-switchable kinesin motor proteins to analyze the emergence of persistent flow fields. Using light, we form contractile microtubule networks of varying size and shape, and demonstrate that the geometry of microtubule flux at the corners of contracting microtubule networks predicts the architecture of fluid flow fields across network geometries through a simple point force model. Our work provides a foundation for programming microscopic fluid flows with controllable active matter and could enable the engineering of versatile and dynamic microfluidic devices.", "doi": "10.1038/s42005-021-00703-3", "issn": "2399-3650", "publisher": "Nature Publishing Group", "publication": "Communications Physics", "publication_date": "2021-08-27", "volume": "4", "pages": "Art. No. 198" }, { "id": "authors:j2jhj-wph98", "collection": "authors", "collection_id": "j2jhj-wph98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210726-193944737", "type": "article", "title": "A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions", "author": [ { "family_name": "Desai", "given_name": "Ravi V.", "orcid": "0000-0002-0336-0883", "clpid": "Desai-Ravi-V" }, { "family_name": "Chen", "given_name": "Xinyue", "orcid": "0000-0001-8288-7685", "clpid": "Chen-Xinyue" }, { "family_name": "Martin", "given_name": "Benjamin", "orcid": "0000-0002-9673-2008", "clpid": "Martin-Benjamin" }, { "family_name": "Chaturvedi", "given_name": "Sonali", "orcid": "0000-0002-9175-8110", "clpid": "Chaturvedi-Sonali" }, { "family_name": "Hwang", "given_name": "Dong Woo", "orcid": "0000-0001-5806-067X", "clpid": "Hwang-Dong-Woo" }, { "family_name": "Li", "given_name": "Weihan", "orcid": "0000-0003-4718-1884", "clpid": "Li-Weihan" }, { "family_name": "Yu", "given_name": "Chen", "clpid": "Yu-Chen" }, { "family_name": "Ding", "given_name": "Sheng", "orcid": "0000-0002-7525-2144", "clpid": "Ding-Sheng" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Singer", "given_name": "Robert H.", "clpid": "Singer-Robert-H" }, { "family_name": "Coleman", "given_name": "Robert A.", "clpid": "Coleman-Robert-A" }, { "family_name": "Hansen", "given_name": "Maike M. K.", "orcid": "0000-0001-7998-6631", "clpid": "Hansen-Maike-M-K" }, { "family_name": "Weinberger", "given_name": "Leor S.", "orcid": "0000-0002-9987-6357", "clpid": "Weinberger-Leor-S" } ], "abstract": "Stochastic fluctuations in gene expression (\"noise\") are often considered detrimental, but fluctuations can also be exploited for benefit (e.g., dither). We show here that DNA base excision repair amplifies transcriptional noise to facilitate cellular reprogramming. Specifically, the DNA repair protein Apex1, which recognizes both naturally occurring and unnatural base modifications, amplifies expression noise while homeostatically maintaining mean expression levels. This amplified expression noise originates from shorter-duration, higher-intensity transcriptional bursts generated by Apex1-mediated DNA supercoiling. The remodeling of DNA topology first impedes and then accelerates transcription to maintain mean levels. This mechanism, which we refer to as \"discordant transcription through repair\" (\"DiThR,\" which is pronounced \"dither\"), potentiates cellular reprogramming and differentiation. Our study reveals a potential functional role for transcriptional fluctuations mediated by DNA base modifications in embryonic development and disease.", "doi": "10.1126/science.abc6506", "pmcid": "PMC8667278", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2021-08-20", "series_number": "6557", "volume": "373", "issue": "6557", "pages": "Art. No. eabc6506" }, { "id": "authors:ztte2-h5j24", "collection": "authors", "collection_id": "ztte2-h5j24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200811-074939566", "type": "article", "title": "Phenomenological model of motility by spatiotemporal modulation of active interactions", "author": [ { "family_name": "Schildknecht", "given_name": "Dominik", "orcid": "0000-0002-0678-0904", "clpid": "Schildknecht-Dominik" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Transport at microscopic length scales is essential in biological systems and various technologies, including microfluidics. Recent experiments achieved self-organized transport phenomena in microtubule active matter using light to modulate motor-protein activity in time and space. Here, we introduce a novel phenomenological model to explain such experiments. Our model, based on spatially modulated particle interactions, reveals a possible mechanism for emergent transport phenomena in light-controlled active matter, including motility and contraction. In particular, the model's analytic treatment elucidates the conservation of the center of mass of activated particles as a fundamental mechanism of material transport and demonstrates the necessity of memory for sustained motility. Furthermore, we generalize the model to explain other phenomena, like microtubule aster\u2013aster interactions induced by more complicated activation geometries. Our results demonstrate that the model provides a possible foundation for the phenomenological understanding of light-controlled active matter, and it will enable the design and optimization of transport protocols for active matter devices.", "doi": "10.1088/1367-2630/ac1144", "issn": "1367-2630", "publisher": "IOP", "publication": "New Journal of Physics", "publication_date": "2021-08", "series_number": "8", "volume": "23", "issue": "8", "pages": "Art. No. 083001" }, { "id": "authors:zngyj-6pw88", "collection": "authors", "collection_id": "zngyj-6pw88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210503-102948566", "type": "article", "title": "Identifying Enthalpic Barriers to Entropically-Driven Structural Disruption in Breast Cancers", "author": [ { "family_name": "Srivastava", "given_name": "Vasudha", "clpid": "Srivastava-Vasudha" }, { "family_name": "Hu", "given_name": "Jennifer L.", "clpid": "Hu-Jennifer-L" }, { "family_name": "Garbe", "given_name": "James C.", "clpid": "Garbe-James-C" }, { "family_name": "Stampfer", "given_name": "Martha R.", "clpid": "Stampfer-Martha-R" }, { "family_name": "LaBarge", "given_name": "Mark A.", "clpid": "LaBarge-Mark-A" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Gartner", "given_name": "Zev J.", "clpid": "Gartner-Zev-J" } ], "abstract": "Tissues can span a large structural phase space, but only occupy a small set of configurations as interfacial tension-driven self-organization counters entropically-favored disorganization. Historical self-organization models often do not address structural variability and transitions commonly observed during morphogenesis and disease. In breast cancer, structural breakdown of the bilayered mammary epithelium, comprised of inner luminal (LEP) layer surrounded by an outer myoepithelial (MEP) layer, is directly linked increased patient risk upon invasion. Organotypic cultures of patient-derived human mammary epithelial cells self-organize in vitro, largely driven by differences in favorability of LEP and MEP interface with the extracellular matrix. The observed distribution of organoid structures closely aligns with Boltzmann statistics - a function of the underlying interfacial energies (enthalpy), geometric constraints (entropy), and mechanical fluctuations (activity) of the tissue. We predict that transformations which increase the probability of LEP occupancy in the basal compartment can destabilize tissue structure and promote invasion, consistent with observations in murine organoid models.To test these predictions experimentally, we examined the ability of 15 cancer-associated genetic changes to alter interfacial tensions of LEP and disrupt self-organization in reconstituted human mammary organoids. While most perturbations only minimally impacted self-organization, PIK3CA activation in LEP uniquely reduced their ECM interfacial energy and disrupted tissue structure. Modeling predicts that normalization of PIK3CA-LEP interfacial energy or decreasing overall tissue activity can correct tissue structure, which we confirm experimentally. Consistently, upregulation of basal adhesion (enthalpy) is observed during progression from in situ to invasive human cancers. Additionally changes in tissue composition (entropy) and remodeling (activity) are linked to changes in cancer risk post-pregnancy. Collectively, this statistical mechanical framework presents a new strategy for understanding and targeting cancer progression, emphasizing the importance of structural probability distributions rather than average structures.", "doi": "10.1016/j.bpj.2020.11.1347", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2021-02-12", "series_number": "3", "volume": "120", "issue": "3", "pages": "196A" }, { "id": "authors:teegz-hk924", "collection": "authors", "collection_id": "teegz-hk924", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200212-084819179", "type": "article", "title": "Developmental clock and mechanism of de novo polarization of the mouse embryo", "author": [ { "family_name": "Zhu", "given_name": "Meng", "orcid": "0000-0001-6157-8840", "clpid": "Zhu-Meng" }, { "family_name": "Cornwall-Scoones", "given_name": "Jake", "orcid": "0000-0002-7435-486X", "clpid": "Cornwall-Scoones-Jake" }, { "family_name": "Wang", "given_name": "Peizhe", "clpid": "Wang-Peizhe" }, { "family_name": "Handford", "given_name": "Charlotte E.", "orcid": "0000-0002-5245-8027", "clpid": "Handford-Charlotte-E" }, { "family_name": "Na", "given_name": "Jie", "orcid": "0000-0003-1820-0548", "clpid": "Na-Jie" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Zernicka-Goetz", "given_name": "Magdalena", "orcid": "0000-0002-7004-2471", "clpid": "Zernicka-Goetz-M" } ], "abstract": "Embryo polarization is critical for mouse development; however, neither the regulatory clock nor the molecular trigger that it activates is known. Here, we show that the embryo polarization clock reflects the onset of zygotic genome activation, and we identify three factors required to trigger polarization. Advancing the timing of transcription factor AP-2 gamma (Tfap2c) and TEA domain transcription factor 4 (Tead4) expression in the presence of activated Ras homolog family member A (RhoA) induces precocious polarization as well as subsequent cell fate specification and morphogenesis. Tfap2c and Tead4 induce expression of actin regulators that control the recruitment of apical proteins on the membrane, whereas RhoA regulates their lateral mobility, allowing the emergence of the apical domain. Thus, Tfap2c, Tead4, and RhoA are regulators for the onset of polarization and cell fate segregation in the mouse.", "doi": "10.1126/science.abd2703", "pmcid": "PMC8210885", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2020-12-11", "series_number": "6522", "volume": "370", "issue": "6522", "pages": "Art. No. eabd2703" }, { "id": "authors:c03z0-nfg11", "collection": "authors", "collection_id": "c03z0-nfg11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201130-100709314", "type": "article", "title": "Single cell profiling of capillary blood enables out of clinic human immunity studies", "author": [ { "family_name": "Dobreva", "given_name": "Tatyana", "orcid": "0000-0002-2625-8873", "clpid": "Dobreva-Tatyana" }, { "family_name": "Brown", "given_name": "David", "orcid": "0000-0002-9757-1744", "clpid": "Brown-David" }, { "family_name": "Park", "given_name": "Jong Hwee", "clpid": "Park-Jong-Hwee" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "An individual's immune system is driven by both genetic and environmental factors that vary over time. To better understand the temporal and inter-individual variability of gene expression within distinct immune cell types, we developed a platform that leverages multiplexed single-cell sequencing and out-of-clinic capillary blood extraction to enable simplified, cost-effective profiling of the human immune system across people and time at single-cell resolution. Using the platform, we detect widespread differences in cell type-specific gene expression between subjects that are stable over multiple days.", "doi": "10.1038/s41598-020-77073-3", "pmcid": "PMC7688970", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2020-11-25", "volume": "10", "pages": "Art. No. 20540" }, { "id": "authors:0cqqx-m7s93", "collection": "authors", "collection_id": "0cqqx-m7s93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180927-114224716", "type": "article", "title": "Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign", "author": [ { "family_name": "Chen", "given_name": "Sisi", "orcid": "0000-0001-9448-9713", "clpid": "Chen-Sisi" }, { "family_name": "Rivaud", "given_name": "Paul", "orcid": "0000-0001-8637-3331", "clpid": "Rivaud-Paul" }, { "family_name": "Park", "given_name": "Jong H.", "clpid": "Park-Jong-Hwee" }, { "family_name": "Tsou", "given_name": "Tiffany", "orcid": "0000-0002-5651-2879", "clpid": "Tsou-Tiffany" }, { "family_name": "Charles", "given_name": "Emeric", "clpid": "Charles-Emeric" }, { "family_name": "Haliburton", "given_name": "John R.", "clpid": "Haliburton-John-R" }, { "family_name": "Pichiorri", "given_name": "Flavia", "orcid": "0009-0006-8429-9397", "clpid": "Pichiorri-Flavia" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Single-cell measurement techniques can now probe gene expression in heterogeneous cell populations from the human body across a range of environmental and physiological conditions. However, new mathematical and computational methods are required to represent and analyze gene expression changes that occur in complex mixtures of single cells as they respond to signals, drugs, or disease states. Here, we introduce a mathematical modeling platform, PopAlign, that automatically identifies subpopulations of cells within a heterogeneous mixture, and tracks gene expression and cell abundance changes across subpopulations by constructing and comparing probabilistic models. We apply PopAlign to analyze the impact of 42 different immunomodulatory compounds on a heterogeneous population of donor-derived human immune cells as well as patient-specific disease signatures in multiple myeloma. PopAlign scales to comparisons involving tens to hundreds of samples, enabling large-scale studies of natural and engineered cell populations as they respond to drugs, signals or physiological change.", "doi": "10.1073/pnas.2005990117", "pmcid": "PMC7682438", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2020-11-17", "series_number": "46", "volume": "117", "issue": "46", "pages": "28784-28794" }, { "id": "authors:wrtcf-y5749", "collection": "authors", "collection_id": "wrtcf-y5749", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200929-102516984", "type": "article", "title": "Bimodal function of chromatin remodeler Hmga1 in neural crest induction and Wnt-dependent emigration", "author": [ { "family_name": "Gandhi", "given_name": "Shashank", "orcid": "0000-0002-4081-4338", "clpid": "Gandhi-Shashank" }, { "family_name": "Hutchins", "given_name": "Erica J.", "orcid": "0000-0002-4316-0333", "clpid": "Hutchins-Erica-J" }, { "family_name": "Maruszko", "given_name": "Krystyna", "clpid": "Maruszko-Krystyna" }, { "family_name": "Park", "given_name": "Jong H.", "clpid": "Park-Jong-H" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Bronner", "given_name": "Marianne E.", "orcid": "0000-0003-4274-1862", "clpid": "Bronner-M-E" } ], "abstract": "During gastrulation, neural crest cells are specified at the neural plate border, as characterized by Pax7 expression. Using single-cell RNA sequencing coupled with high resolution in situ hybridization to identify novel transcriptional regulators, we show that chromatin remodeler Hmga1 is highly expressed prior to specification and maintained in migrating chick neural crest cells. Temporally-controlled CRISPR-Cas9-mediated knockouts uncovered two distinct functions of Hmga1 in neural crest development. At the neural plate border, Hmga1 regulates Pax7-dependent neural crest lineage specification. At premigratory stages, a second role manifests where Hmga1 loss reduces cranial crest emigration from the dorsal neural tube independent of Pax7. Interestingly, this is rescued by stabilized \u00df-catenin, thus implicating Hmga1 as a canonical Wnt activator. Together, our results show that Hmga1 functions in a bimodal manner during neural crest development to regulate specification at the neural plate border, and subsequent emigration from the neural tube via canonical Wnt signaling.", "doi": "10.7554/elife.57779", "pmcid": "PMC7591248", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2020-09-23", "series_number": "9", "volume": "2020", "issue": "9", "pages": "Art. No. e57779" }, { "id": "authors:rrtwx-57q24", "collection": "authors", "collection_id": "rrtwx-57q24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200604-075354300", "type": "article", "title": "In-Depth Parallel Profiling of Tissue and Cell-Type Tropism of AAV Variants by Single-Cell RNA Sequencing", "author": [ { "family_name": "Altermatt", "given_name": "Michael", "clpid": "Altermatt-M" }, { "family_name": "Brown", "given_name": "David", "clpid": "Brown-D" }, { "family_name": "Dobreva", "given_name": "Tatyana", "orcid": "0000-0002-2625-8873", "clpid": "Dobreva-T" }, { "family_name": "Jang", "given_name": "Min Jee", "orcid": "0000-0002-1536-7177", "clpid": "Jang-Min-Jee" }, { "family_name": "Coughlin", "given_name": "Gerard M.", "clpid": "Coughlin-G-M" }, { "family_name": "Pool", "given_name": "Allan-Hermann", "orcid": "0000-0002-0811-9861", "clpid": "Pool-A-H" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Adeno-associated viruses (AAVs) are popular gene delivery vehicles and there is a continuing high demand for AAV variants with improved transduction efficiency and specificity. Directed evolution and/or rational design have been used extensively to engineer the capsid of naturally occurring AAVs in order to better customize their properties for research and clinical work. While these engineering approaches are scalable and have generated useful variants, the subsequent transduction profiling of these variants remains either low throughput or lacks resolution across the many relevant cell and tissue types. Single-cell RNA sequencing (scRNA-seq) via droplet-based methods allows in-depth profiling of gene expression of several thousand individual cells. We established a tissue processing and data analysis pipeline that leverages the capabilities of scRNA-seq to achieve simultaneous characterization of AAV variants across multiplexed tissue cell types. To verify our approach, we retro-orbitally co-injected C57Bl/6 mice with PHP.eB (Chan et al., Nat. Neurosci., 2017) and a neuron-biased PHP.eB-evolved variant (Flytzanis*, Goeden* et al., ASGCT, 2019), each packaging a construct expressing different fluorophores. \n\nAfter two weeks of expression we harvested the brain and used one hemisphere for characterization by traditional immunohistochemistry and one hemisphere for characterization by scRNA-seq. Single-cell libraries were prepared with the Chromium Single Cell Kit by 10x Genomics and analyzed with multiplexed Illumina sequencing. As a proof of concept, we compared the two characterization methods by analyzing the infection rate of neurons (NeuN), astrocytes (S100b) or oligodendrocytes (Olig2). For immunohistochemistry, a cell was classified as infected based on expression of fluorophores while in scRNA-seq transduced cells were identified based on the presence of defining viral transcripts. Louvain community detection method (Blondel et al., J. Stat. Mech., 2008) followed by analysis of significantly differentially expressed genes was used to identify cell types in the scRNA-seq data set. Given the differences in RNA and protein abundance and detection thresholds between imaging and sequencing, the two characterization methods detect different absolute numbers of infection rates; however, the cell type transduction biases are consistent among the three different cell types we tested. After verifying our method, we further explored the data set beyond major cell types and discovered previously unnoticed sub-cell type enrichments in, for example, cortical inhibitory neurons. These findings are being confirmed by mapping mRNA expression using in situ hybridization chain reaction. Besides sub-cell type tropism characterization, we are analyzing the transcriptome of infected and non-infected cells in search of mechanistic insights into AAV transduction that could facilitate rational design of recombinant AAVs with disease-relevant cell-type specificity. Our approach will aid the gene therapy field to both characterize more thoroughly existing recombinant AAVs and guide engineering of novel AAV variants.", "doi": "10.1016/j.ymthe.2020.04.019", "issn": "1525-0016", "publisher": "American Society of Gene & Cell Therapy", "publication": "Molecular Therapy", "publication_date": "2020-04-28", "series_number": "4", "volume": "28", "issue": "4", "pages": "399-400" }, { "id": "authors:zk45d-25a12", "collection": "authors", "collection_id": "zk45d-25a12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200604-102237108", "type": "article", "title": "A Computational and Experimental Platform for Detecting Full Transcriptome Cell Type Tropism of Lowly Expressed Barcoded and Pooled AAV Variants via Single-Cell RNA Sequencing", "author": [ { "family_name": "Brown", "given_name": "David", "clpid": "Brown-D" }, { "family_name": "Altermatt", "given_name": "Michael", "clpid": "Altermatt-M" }, { "family_name": "Dobreva", "given_name": "Tatyana", "orcid": "0000-0002-2625-8873", "clpid": "Dobreva-T" }, { "family_name": "Park", "given_name": "Jong H.", "clpid": "Park-Jong-H" }, { "family_name": "Ravindra-Kumar", "given_name": "Sripriya", "orcid": "0000-0001-6033-7631", "clpid": "Ravindra-Kumar-S" }, { "family_name": "Chen", "given_name": "Xinhong", "orcid": "0000-0003-0408-0813", "clpid": "Chen-Xinhong" }, { "family_name": "Coughlin", "given_name": "Gerard M.", "clpid": "Coughlin-G-M" }, { "family_name": "Pool", "given_name": "Allan-Hermann", "orcid": "0000-0002-0811-9861", "clpid": "Pool-A-H" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "abstract": "Despite being one of the primary gene therapy delivery vehicles, adeno-associated viruses (AAVs) are limited in their specificity towards certain cell types implicated in disease. Recombinant AAVs (rAAVs) are addressing these limitations through both capsid engineering and gene regulatory approaches that alter viral tropism or viral expression patterns. Current rAAV targeting, selection, screening, and characterization methods are typically based on single- or few-molecule read-outs, such as promoter and enhancer-driven constructs, mouse lines expressing Cre recombinase under a cell type-specific promoter, or cell type-specific antibodies for imaging. Such methods harbor challenges for parallelizing rAAV characterization, or extending characterization and engineering to complex or previously unknown cell types. The recent advent of single-cell RNA sequencing (scRNAseq) has revealed a rich diversity of cell types and states, many of which are not associated with canonical cell type markers, and can even be defined by multi-gene programs. To aid in the engineering of rAAVs aimed at such complex cell states and aid in the discovery of novel tropisms, we have developed a scRNA-seq AAV screening method, whereby we inspect full transcriptomes of cells transduced with pools of AAV vectors in a single animal. To generate pools of variants that can be differentiated in sequencing, we package variants with either unique transgenes, or the same transgene with unique barcodes incorporated in the polyA region. We then co-inject mice with these pools of variants, wait for expression, and harvest tissue slices for downstream cell dissociation and single-cell sequencing using the Chromium 10X Single Cell Kit. In order to accommodate the low expression rates of virally delivered cargo and the loss of the region of mRNA upstream of the polyA capture site that identifies the capsid variant, we amplify the viral transcripts from the full cDNA library with primers near the differentiating region of the cargo. To characterize variants, we developed a customized computational pipeline that addresses the unique challenges of these datasets: (1) to discern the variant that delivered each transgene read, we demultiplex the amplified viral transgene reads based on their differentiating sequences; (2) to reduce the effects of PCR amplification noise, we convert variant transgene reads into probabilistic estimates of the number of transcripts per cell; and (3) to calculate cell type biases, we automatically identify a cell type hierarchy and compare the distribution of viral transcripts by cell type to a null model of empty droplets. Thus far, our platform has corroborated several expected virus tropism findings from imaging (e.g. for brain vasculature or neuronal preference). To apply this barcoding strategy to even larger pools without individually cloning and producing each variant, and link arbitrary mutations in the capsid genome to the barcode, we have further developed a plasmid that contains both the expressed transgene and the capsid gene, but inverted in orientation, with their 3' ends adjacent. With these barcoding strategies and computational methods, we enable fast identification and characterization of rAAV variant pools with precise disease-relevant tropisms, with the ultimate goal of aiding the gene therapy field in developing precision delivery vehicles.", "doi": "10.1016/j.ymthe.2020.04.019", "issn": "1525-0016", "publisher": "American Society of Gene & Cell Therapy", "publication": "Molecular Therapy", "publication_date": "2020-04-28", "series_number": "4", "volume": "28", "issue": "4", "pages": "80-81" }, { "id": "authors:s9b9v-5r123", "collection": "authors", "collection_id": "s9b9v-5r123", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200210-111806006", "type": "article", "title": "Bridging Kinesin Properties with System-scale Characteristics of Microtubule-Motor Assemblies", "author": [ { "family_name": "Banks", "given_name": "Rachel", "clpid": "Banks-R-A" }, { "family_name": "Lee", "given_name": "Heun Jin", "clpid": "Lee-Heun-Jin" }, { "family_name": "Ross", "given_name": "Tyler", "orcid": "0000-0002-7872-3992", "clpid": "Ross-T-D" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "abstract": "In a dividing cell, multiple subfamilies of kinesin and dynein motors work together to form the mitotic spindle out of microtubule filaments. This complex structure has incited much study into how it is formed and regulated. Knockdown experiments in cells yielded a number of insights, however, the complex environment of the cell prevents a detailed quantitative picture connecting biophysical motor properties to the resulting mesoscopic phenomena. However, in vitro, reconstituted systems of few purified components strip away the other reactions occuring within the cell, creating the opportunity to work from the bottom up. We use an optogenetic system wherein motor interactions are controlled by light to form microtubule structures such as asters. We connect length and speed scales of microtubule structures to motor properties such as speed and processivity by performing experiments with various kinesin motors. With this approach, we develop and test a model explaining how contraction speed varies with network size and motor speed. We also observe how the motors are distributed within microtubule structures and how that varies depending on the motor used. Further, we arrange competition between kinesins that walk towards opposite ends of the microtubules and demonstrate how this competition yields unique structures with properties that depend on both motors. This work is a step towards bridging microscopic motor properties to mesoscopic system-scale characteristics and answering the question of how cooperation between various kinesins can result in the generation of cellular structures.", "doi": "10.1016/j.bpj.2019.11.1081", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2020-02-07", "series_number": "3", "volume": "118", "issue": "3", "pages": "176a-177a" }, { "id": "authors:m07dw-3jq86", "collection": "authors", "collection_id": "m07dw-3jq86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181030-145533155", "type": "article", "title": "Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins", "author": [ { "family_name": "Gehring", "given_name": "Jase", "orcid": "0000-0002-3894-9495", "clpid": "Gehring-J" }, { "family_name": "Park", "given_name": "Jong Hwee", "clpid": "Park-Jong-Hwee" }, { "family_name": "Chen", "given_name": "Sisi", "orcid": "0000-0001-9448-9713", "clpid": "Chen-Sisi" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Pachter", "given_name": "Lior", "orcid": "0000-0002-9164-6231", "clpid": "Pachter-L" } ], "abstract": "We describe a universal sample multiplexing method for single-cell RNA sequencing in which fixed cells are chemically labeled by attaching identifying DNA oligonucleotides to cellular proteins. Analysis of a 96-plex perturbation experiment revealed changes in cell population structure and transcriptional states that cannot be discerned from bulk measurements, establishing an efficient method for surveying cell populations from large experiments or clinical samples with the depth and resolution of single-cell RNA sequencing.", "doi": "10.1038/s41587-019-0372-z", "issn": "1087-0156", "publisher": "Nature Publishing Group", "publication": "Nature Biotechnology", "publication_date": "2020-01", "series_number": "1", "volume": "38", "issue": "1", "pages": "35-38" }, { "id": "authors:kp5yc-avm39", "collection": "authors", "collection_id": "kp5yc-avm39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190102-092232993", "type": "article", "title": "Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries", "author": [ { "family_name": "Ross", "given_name": "Tyler D.", "orcid": "0000-0002-7872-3992", "clpid": "Ross-Tyler-D" }, { "family_name": "Lee", "given_name": "Heun Jin", "clpid": "Lee-Heun-Jin" }, { "family_name": "Qu", "given_name": "Zijie", "orcid": "0000-0003-1500-3207", "clpid": "Qu-Zijie" }, { "family_name": "Banks", "given_name": "Rachel A.", "orcid": "0000-0003-2028-2925", "clpid": "Banks-Rachel-A" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Living systems are capable of locomotion, reconfiguration and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, 'active' molecules that create and manipulate non-equilibrium structures and force fields of up to millimetre length scales. Experimental active-matter systems of biological or synthetic molecules are capable of spontaneously organizing into structures and generating global flows. However, these experimental systems lack the spatiotemporal control found in cells, limiting their utility for studying non-equilibrium phenomena and bioinspired engineering. Here we uncover non-equilibrium phenomena and principles of boundary-mediated control by optically modulating structures and fluid flow in an engineered system of active biomolecules. Our system consists of purified microtubules and light-activatable motor proteins that crosslink and organize the microtubules into distinct structures upon illumination. We develop basic operations\u2014defined as sets of light patterns\u2014to create, move and merge the microtubule structures. By combining these operations, we create microtubule networks that span several hundred micrometres in length and contract at speeds up to an order of magnitude higher than the speed of an individual motor protein. We manipulate these contractile networks to generate and sculpt persistent fluid flows. The principles of boundary-mediated control that we uncover may be used to study emergent cellular structures and forces and to develop programmable active-matter devices.", "doi": "10.1038/s41586-019-1447-1", "pmcid": "PMC6719720", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2019-08-08", "series_number": "7768", "volume": "572", "issue": "7768", "pages": "224-229" }, { "id": "authors:j2fzf-ybw74", "collection": "authors", "collection_id": "j2fzf-ybw74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180910-090801725", "type": "article", "title": "Integrated measurement of intracellular proteins and transcripts in single cells", "author": [ { "family_name": "Xu", "given_name": "Alexander M.", "orcid": "0000-0003-4877-4358", "clpid": "Xu-Alexander-M" }, { "family_name": "Liu", "given_name": "Qianhe", "orcid": "0000-0002-7517-4772", "clpid": "Liu-Qianhe" }, { "family_name": "Takata", "given_name": "Kaitlyn L.", "orcid": "0000-0003-4864-9741", "clpid": "Takata-Kaitlyn-L" }, { "family_name": "Jeoung", "given_name": "Sarah", "clpid": "Jeoung-Sarah" }, { "family_name": "Su", "given_name": "Yapeng", "orcid": "0000-0002-6305-8467", "clpid": "Su-Yapeng" }, { "family_name": "Antoshechkin", "given_name": "Igor", "orcid": "0000-0002-9934-3040", "clpid": "Antoshechkin-I-A" }, { "family_name": "Chen", "given_name": "Sisi", "orcid": "0000-0001-9448-9713", "clpid": "Chen-Sisi" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "abstract": "Biological function arises from the interplay of proteins, transcripts, and metabolites. An ongoing revolution in miniaturization technologies has created tools to analyze any one of these species in single cells, thus resolving the heterogeneity of tissues previously invisible to bulk measurements. An emerging frontier is single cell multi-omics, which is the measurement of multiple classes of analytes from single cells. Here, we combine bead-based transcriptomics with microchip-based proteomics to measure intracellular proteins and transcripts from single cells and defined small numbers of cells. The transcripts and proteins are independently measured by sequencing and fluorescent immunoassays respectively, to preserve their optimal measurement modes, and linked by encoding the physical address locations of the cells into digital sequencing space using spatially patterned DNA barcodes. We resolve cell-type-specific protein and transcript signatures and present a path forward to scaling the platform to high-throughput.", "doi": "10.1039/c8lc00639c", "pmcid": "PMC6752714", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2018-11-07", "series_number": "21", "volume": "18", "issue": "21", "pages": "3251-3262" }, { "id": "authors:2xggp-q6k41", "collection": "authors", "collection_id": "2xggp-q6k41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180212-080247041", "type": "article", "title": "Diffusion as a Ruler: Modeling Kinesin Diffusion as a Length Sensor for Intraflagellar Transport", "author": [ { "family_name": "Hendel", "given_name": "Nathan L.", "clpid": "Hendel-Nathan-L" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Marshall", "given_name": "Wallace F.", "clpid": "Marshall-Wallace-F" } ], "abstract": "An important question in cell biology is whether cells are able to measure size, either whole cell size or organelle size. Perhaps cells have an internal chemical representation of size that can be used to precisely regulate growth, or perhaps size is just an accident that emerges due to constraint of nutrients. The eukaryotic flagellum is an ideal model for studying size sensing and control because its linear geometry makes it essentially one-dimensional, greatly simplifying mathematical modeling. The assembly of flagella is regulated by intraflagellar transport (IFT), in which kinesin motors carry cargo adaptors for flagellar proteins along the flagellum and then deposit them at the tip, lengthening the flagellum. The rate at which IFT motors are recruited to begin transport into the flagellum is anticorrelated with the flagellar length, implying some kind of communication between the base and the tip and possibly indicating that cells contain some mechanism for measuring flagellar length. Although it is possible to imagine many complex scenarios in which additional signaling molecules sense length and carry feedback signals to the cell body to control IFT, might the already-known components of the IFT system be sufficient to allow length dependence of IFT? Here we investigate a model in which the anterograde kinesin motors unbind after cargo delivery, diffuse back to the base, and are subsequently reused to power entry of new IFT trains into the flagellum. By mathematically modeling and simulating such a system, we are able to show that the diffusion time of the motors can in principle be sufficient to serve as a proxy for length measurement. We found that the diffusion model can not only achieve a stable steady-state length without the addition of any other signaling molecules or pathways, but also is able to produce the anticorrelation between length and IFT recruitment rate that has been observed in quantitative imaging studies.", "doi": "10.1016/j.bpj.2017.11.3784", "pmcid": "PMC5985012", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2018-02-06", "series_number": "3", "volume": "114", "issue": "3", "pages": "663-674" }, { "id": "authors:pzdeb-r9f71", "collection": "authors", "collection_id": "pzdeb-r9f71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180523-145718338", "type": "article", "title": "Diffusion as a Ruler: Modeling Kinesin Diffusion as a Lenth Sensor for Intraflagellar Transport", "author": [ { "family_name": "Hendel", "given_name": "Nathan L.", "clpid": "Hendel-N-L" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Marshall", "given_name": "Wallace F.", "clpid": "Marshall-W-F" } ], "abstract": "An important question in cell biology is how cells know how big to make their organelles. The eukaryotic flagellum is an ideal model for studying size control because its linear geometry makes it essentially one-dimensional, greatly simplifying mathematical modeling. The assembly of flagella is regulated by intraflagellar transport (IFT), in which trains of kinesin motors walk to the tip of the flagellum and deposit the cargo necessary for the flagellum to grow. The competing length control factor is a length-independent decay of the flagellum. In Chlamydomonas reinhardtii flagella, this process results in initial rapid growth followed by convergence to a steady-state length. Curiously, the rate at which motors are recruited to begin transport is indirectly proportional to the length, implying some kind of communication between the base and the tip. We propose a model in which motors unbind after cargo delivery and diffuse back to the base, and are reused in IFT. In this model, the diffusion time of the motors serves as a proxy for length measurement. To explore the viability of this diffusion-based length control, we computationally built this model in three different ways. First, we built an agent-based model in which we used object-oriented programming to explicitly model flagella and motors, including time dynamics. Second, we modeled the number density along the flagellum as a vector, and built a stochastic matrix to simulate time dynamics and determine a steady-state. Third, we used differential equations to directly solve for the steady-state length. In all three, we found that the diffusion model can achieve steady-state length and an inverse relationship between length and recruitment rate. This is remarkable because this is perhaps the simplest explanation of length control, giving it credence in light of evolution.", "doi": "10.1016/j.bpj.2017.11.1877", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2018-02-02", "series_number": "3", "volume": "114", "issue": "3", "pages": "335A-336A" }, { "id": "authors:7efyr-ajm67", "collection": "authors", "collection_id": "7efyr-ajm67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180202-090924087", "type": "article", "title": "Adult Neurogenesis Is Sustained by Symmetric Self-Renewal and Differentiation", "author": [ { "family_name": "Obernier", "given_name": "Kirsten", "clpid": "Obernier-Kirsten" }, { "family_name": "Cebrian-Silla", "given_name": "Arantxa", "clpid": "Cebrian-Silla-Arantxa" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Parraguez", "given_name": "Jos\u00e9 Ignacio", "clpid": "Parraguez-Jos\u00e9-Ignacio" }, { "family_name": "Anderson", "given_name": "Rio", "clpid": "Anderson-Rio" }, { "family_name": "Guinto", "given_name": "Cristina", "clpid": "Guinto-Cristina" }, { "family_name": "Rodriguez", "given_name": "Jos\u00e9 Rodas", "clpid": "Rodriguez-Jos\u00e9-Rodas" }, { "family_name": "Garcia-Verdugo", "given_name": "Jos\u00e9-Manuel", "orcid": "0000-0001-9872-6499", "clpid": "Garcia-Verdugo-J-M" }, { "family_name": "Alvarez-Buylla", "given_name": "Arturo", "orcid": "0000-0003-4426-8925", "clpid": "Alvarez-Buylla-A" } ], "abstract": "Somatic stem cells have been identified in multiple adult tissues. Whether self-renewal occurs symmetrically or asymmetrically is key to understanding long-term stem cell maintenance and generation of progeny for cell replacement. In the adult mouse brain, neural stem cells (NSCs) (B1 cells) are retained in the walls of the lateral ventricles (ventricular-subventricular zone [V-SVZ]). The mechanism of B1 cell retention into adulthood for lifelong neurogenesis is unknown. Using multiple clonal labeling techniques, we show that the vast majority of B1 cells divide symmetrically. Whereas 20%\u201330% symmetrically self-renew and can remain in the niche for several months before generating neurons, 70%\u201380% undergo consuming divisions generating progeny, resulting in the depletion of B1 cells over time. This cellular mechanism decouples self-renewal from the generation of progeny. Limited rounds of symmetric self-renewal and consuming symmetric differentiation divisions can explain the levels of neurogenesis observed throughout life.", "doi": "10.1016/j.stem.2018.01.003", "pmcid": "PMC5802882", "issn": "1934-5909", "publisher": "Cell Press", "publication": "Cell Stem Cell", "publication_date": "2018-02-01", "series_number": "2", "volume": "22", "issue": "2", "pages": "221-234" }, { "id": "authors:11k8x-brh50", "collection": "authors", "collection_id": "11k8x-brh50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180321-144810107", "type": "article", "title": "Diffusion as a ruler: Modeling kinesin diffusion as a length sensor for intraflagellar transport", "author": [ { "family_name": "Hendel", "given_name": "N. L.", "clpid": "Hendel-Nathan-L" }, { "family_name": "Thomson", "given_name": "M.", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Marshall", "given_name": "W. F.", "clpid": "Marshall-Wallace-F" } ], "abstract": "An important question in cell biology is whether cells are able to measure size, either whole cell size or organelle size. Perhaps cells have an internal chemical representation of size that can be used to precisely regulate growth, or perhaps size is just an accident that emerges due to constraint of nutrients. The eukaryotic flagellum is an ideal model for studying size sensing and control because its linear geometry makes it essentially one\u2010dimensional, greatly simplifying mathematical modeling. The\nassembly of flagella is regulated by intraflagellar transport (IFT), in which kinesin motors carry cargo\nadaptors for flagellar proteins along the flagellum and then deposit them at the tip, lengthening the flagellum. The rate at which IFT motors are recruited to begin transport into the flagellum is anticorrelated with the flagellar length, implying some kind of communication between the base and the tip and possibly indicating that cells contain some mechanism for measuring flagellar length. Although it is possible to imagine many complex scenarios in which additional signaling molecules sense length and carry feedback signals to the cell body to control IFT, might the already\u2010known components of the IFT\nsystem be sufficient to allow length dependence of IFT? Here, we investigate a model in which the anterograde kinesin motors unbind after cargo delivery, diffuse back to the base, and are subsequently reused to power entry of new IFT trains into the flagellum. By modeling such a system at three different levels of abstraction we are able to show that the diffusion time of the motors can in principle be\nsufficient to serve as a proxy for length measurement. In all three implementations, we found that the diffusion model can not only achieve a stable steady\u2010state length without the addition of any other signaling molecules or pathways, but also is able to produce the anticorrelation between length and IFT recruitment rate that has been observed in quantitative imaging studies.", "doi": "10.1091/mbc.E17-10-0618", "issn": "1059-1524", "publisher": "American Society for Cell Biology", "publication": "Molecular Biology of the Cell", "publication_date": "2017-12-15", "series_number": "26", "volume": "28", "issue": "26", "pages": "Art. No. M196" }, { "id": "authors:3p2m6-a5p97", "collection": "authors", "collection_id": "3p2m6-a5p97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170612-083933304", "type": "article", "title": "Transient Thresholding: A Mechanism Enabling Noncooperative Transcriptional Circuitry to Form a Switch", "author": [ { "family_name": "Aull", "given_name": "Katherine H.", "clpid": "Aull-K-H" }, { "family_name": "Tanner", "given_name": "Elizabeth J.", "clpid": "Tanner-E-J" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Weinberger", "given_name": "Leor S.", "clpid": "Weinberger-L-S" } ], "abstract": "Threshold generation in fate-selection circuits is often achieved through deterministic bistability, which requires cooperativity (i.e., nonlinear activation) and associated hysteresis. However, the Tat positive-feedback loop that controls HIV's fate decision between replication and proviral latency lacks self-cooperativity and deterministic bistability. Absent cooperativity, it is unclear how HIV can temporarily remain in an off-state long enough for the kinetically slower epigenetic silencing mechanisms to act\u2014expression fluctuations should rapidly trigger active positive feedback and replication, precluding establishment of latency. Here, using flow cytometry and single-cell imaging, we find that the Tat circuit exhibits a transient activation threshold. This threshold largely disappears after \u223c40 h\u2014accounting for the lack of deterministic bistability\u2014and promoter activation shortens the lifetime of this transient threshold. Continuous differential equation models do not recapitulate this phenomenon. However, chemical reaction (master equation) models where the transcriptional transactivator and promoter toggle between inactive and active states can recapitulate the phenomenon because they intrinsically create a single-molecule threshold transiently requiring excess molecules in the inactive state to achieve at least one molecule (rather than a continuous fractional value) in the active state. Given the widespread nature of promoter toggling and transcription factor modifications, transient thresholds may be a general feature of inducible promoters.", "doi": "10.1016/j.bpj.2017.05.002", "pmcid": "PMC5474885", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2017-06-06", "series_number": "11", "volume": "112", "issue": "11", "pages": "2428-2438" }, { "id": "authors:73et7-25x08", "collection": "authors", "collection_id": "73et7-25x08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161121-084221387", "type": "article", "title": "Signaling Boundary Conditions Drive Self-Organization of Human \"Gastruloids\"", "author": [ { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Morphogenesis requires tissues to sense and respond to their geometry. In this issue of Developmental Cell, Etoc et al. (2016) show that a confined colony of human embryonic stem cells can spontaneously sense its boundary, generating a self-organized TGF-\u03b2 signaling gradient that patterns it into a tissue resembling a gastrulating embryo.", "doi": "10.1016/j.devcel.2016.10.016", "issn": "1534-5807", "publisher": "Cell Press", "publication": "Developmental Cell", "publication_date": "2016-11-07", "series_number": "3", "volume": "39", "issue": "3", "pages": "279-280" }, { "id": "authors:kb19k-wzt94", "collection": "authors", "collection_id": "kb19k-wzt94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170203-145417665", "type": "article", "title": "Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing", "author": [ { "family_name": "Heimberg", "given_name": "Graham", "clpid": "Heimberg-G" }, { "family_name": "Bhatnagar", "given_name": "Rajat", "clpid": "Bhatnagar-R" }, { "family_name": "El-Samad", "given_name": "Hana", "orcid": "0000-0001-6239-9916", "clpid": "El-Samad-H" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "A tradeoff between precision and throughput constrains all biological measurements, including sequencing-based technologies. Here, we develop a mathematical framework that defines this tradeoff between mRNA-sequencing depth and error in the extraction of biological information. We find that transcriptional programs can be reproducibly identified at 1% of conventional read depths. We demonstrate that this resilience to noise of \"shallow\" sequencing derives from a natural property, low dimensionality, which is a fundamental feature of gene expression data. Accordingly, our conclusions hold for \u223c350 single-cell and bulk gene expression datasets across yeast, mouse, and human. In total, our approach provides quantitative guidelines for the choice of sequencing depth necessary to achieve a desired level of analytical resolution. We codify these guidelines in an open-source read depth calculator. This work demonstrates that the structure inherent in biological networks can be productively exploited to increase measurement throughput, an idea that is now common in many branches of science, such as image processing.", "doi": "10.1016/j.cels.2016.04.001", "pmcid": "PMC4856162", "issn": "2405-4712", "publisher": "Elsevier", "publication": "Cell Systems", "publication_date": "2016-04-27", "series_number": "4", "volume": "2", "issue": "4", "pages": "239-250" }, { "id": "authors:8n4r3-btc28", "collection": "authors", "collection_id": "8n4r3-btc28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170217-152208931", "type": "article", "title": "SOX2O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells", "author": [ { "family_name": "Myers", "given_name": "Samuel A.", "clpid": "Myers-S-A" }, { "family_name": "Peddada", "given_name": "Sailaja", "clpid": "Peddada-S" }, { "family_name": "Chatterjee", "given_name": "Nilanjana", "clpid": "Chatterjee-N" }, { "family_name": "Friedrich", "given_name": "Tara", "clpid": "Friedrich-T" }, { "family_name": "Tomoda", "given_name": "Kiichrio", "clpid": "Tomoda-Kiichrio" }, { "family_name": "Krings", "given_name": "Gregor", "clpid": "Krings-G" }, { "family_name": "Thomas", "given_name": "Sean", "clpid": "Thomas-S" }, { "family_name": "Maynard", "given_name": "Jason", "clpid": "Maynard-J" }, { "family_name": "Broeker", "given_name": "Michael", "clpid": "Broeker-M" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Pollard", "given_name": "Katherine", "clpid": "Pollard-K" }, { "family_name": "Yamanaka", "given_name": "Shinya", "clpid": "Yamanaka-Shinya" }, { "family_name": "Burlingame", "given_name": "Alma L.", "clpid": "Burlingame-A-L" }, { "family_name": "Panning", "given_name": "Barbara", "orcid": "0000-0002-8301-1172", "clpid": "Panning-B" } ], "abstract": "The transcription factor SOX2 is central in establishing and maintaining pluripotency. The processes that modulate SOX2 activity to promote pluripotency are not well understood. Here, we show SOX2 is O-GlcNAc modified in its transactivation domain during reprogramming and in mouse embryonic stem cells (mESCs). Upon induction of differentiation SOX2 O-GlcNAcylation at serine 248 is decreased. Replacing wild type with an O-GlcNAc-deficient SOX2 (S248A) increases reprogramming efficiency. ESCs with O-GlcNAc-deficient SOX2 exhibit alterations in gene expression. This change correlates with altered protein-protein interactions and genomic occupancy of the O-GlcNAc-deficient SOX2 compared to wild type. In addition, SOX2 O-GlcNAcylation impairs the SOX2-PARP1 interaction, which has been shown to regulate ESC self-renewal. These findings show that SOX2 activity is modulated by O-GlcNAc, and provide a novel regulatory mechanism for this crucial pluripotency transcription factor.", "doi": "10.7554/eLife.10647", "pmcid": "PMC4841768", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2016-03-07", "volume": "5", "pages": "Art. No. e10647" }, { "id": "authors:2z7q3-72409", "collection": "authors", "collection_id": "2z7q3-72409", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170217-155108197", "type": "article", "title": "Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors", "author": [ { "family_name": "Morsut", "given_name": "Leonardo", "clpid": "Morsut-L" }, { "family_name": "Roybal", "given_name": "Kole T.", "clpid": "Roybal-K-T" }, { "family_name": "Xiong", "given_name": "Xin", "clpid": "Xiong-Xin" }, { "family_name": "Gordley", "given_name": "Russell M.", "clpid": "Gordley-R-M" }, { "family_name": "Coyle", "given_name": "Scott M.", "clpid": "Coyle-S-M" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Lim", "given_name": "Wendell A.", "clpid": "Lim-W-A" } ], "abstract": "The Notch protein is one of the most mechanistically direct transmembrane receptors\u2014the intracellular domain contains a transcriptional regulator that is released from the membrane when engagement of the cognate extracellular ligand induces intramembrane proteolysis. We find that chimeric forms of Notch, in which both the extracellular sensor module and the intracellular transcriptional module are replaced with heterologous protein domains, can serve as a general platform for generating novel cell-cell contact signaling pathways. Synthetic Notch (synNotch) pathways can drive user-defined functional responses in diverse mammalian cell types. Because individual synNotch pathways do not share common signaling intermediates, the pathways are functionally orthogonal. Thus, multiple synNotch receptors can be used in the same cell to achieve combinatorial integration of environmental cues, including Boolean response programs, multi-cellular signaling cascades, and self-organized cellular patterns. SynNotch receptors provide extraordinary flexibility in engineering cells with customized sensing/response behaviors to user-specified extracellular cues.", "doi": "10.1016/j.cell.2016.01.012", "pmcid": "PMC4752866", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "2016-02-11", "series_number": "4", "volume": "164", "issue": "4", "pages": "780-791" }, { "id": "authors:j8q2p-50k32", "collection": "authors", "collection_id": "j8q2p-50k32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170206-125245319", "type": "article", "title": "Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise", "author": [ { "family_name": "Sokolik", "given_name": "Cameron", "clpid": "Sokolik-C" }, { "family_name": "Liu", "given_name": "Yanxia", "clpid": "Liu-Yanxia" }, { "family_name": "Bauer", "given_name": "David", "clpid": "Bauer-D" }, { "family_name": "McPherson", "given_name": "Jade", "clpid": "McPherson-J" }, { "family_name": "Broeker", "given_name": "Michael", "clpid": "Broeker-M" }, { "family_name": "Heimberg", "given_name": "Graham", "clpid": "Heimberg-G" }, { "family_name": "Qi", "given_name": "Lei S.", "clpid": "Qi-Lei-S" }, { "family_name": "Sivak", "given_name": "David A.", "clpid": "Sivak-D-A" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Stem cells occupy variable environments where they must distinguish stochastic fluctuations from developmental cues. Here, we use optogenetics to investigate how the pluripotency network in embryonic stem cells (ESCs) achieves a robust response to differentiation cues but not to gene expression fluctuations. We engineered mouse ESCs to allow quantitative control over the endogenous mechanism of neural differentiation through a light-inducible Brn2 transgene and monitored differentiation status through a genome-integrated Nanog-GFP reporter. By exposing cells to pulses of Brn2, we find that the pluripotency network rejects Brn2 inputs that are below specific magnitude or duration thresholds, but allows rapid differentiation when both thresholds are satisfied. The filtering properties of the network arise through its positive feedback architecture and the intrinsic half-life of Nanog, which determines the duration threshold in the network. Together our results suggest that the dynamic properties of positive feedback networks might determine how inputs are classified as signal or noise by stem cells.", "doi": "10.1016/j.cels.2015.08.001", "pmcid": "PMC4576702", "issn": "2405-4712", "publisher": "Elsevier", "publication": "Cell Systems", "publication_date": "2015-08-26", "series_number": "2", "volume": "1", "issue": "2", "pages": "117-129" }, { "id": "authors:tk9ge-wfm60", "collection": "authors", "collection_id": "tk9ge-wfm60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170217-155108581", "type": "article", "title": "Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo", "author": [ { "family_name": "Finkbeiner", "given_name": "Stacy R.", "clpid": "Finkbeiner-S-R" }, { "family_name": "Hill", "given_name": "David R.", "clpid": "Hill-D-R" }, { "family_name": "Altheim", "given_name": "Christopher H.", "clpid": "Altheim-C-H" }, { "family_name": "Dedhia", "given_name": "Priya H.", "clpid": "Dedhia-P-H" }, { "family_name": "Taylor", "given_name": "Matthew J.", "clpid": "Taylor-M-J" }, { "family_name": "Tsai", "given_name": "Yu-Hwai", "clpid": "Tsai-Yu-Hwai" }, { "family_name": "Chin", "given_name": "Alana M.", "clpid": "Chin-Alana-M" }, { "family_name": "Mahe", "given_name": "Maxime M.", "clpid": "Mahe-M-M" }, { "family_name": "Watson", "given_name": "Carey L.", "clpid": "Watson-C-L" }, { "family_name": "Freeman", "given_name": "Jennifer J.", "clpid": "Freeman-J-J" }, { "family_name": "Nattiv", "given_name": "Roy", "clpid": "Nattiv-R" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Klein", "given_name": "Ophir D.", "clpid": "Klein-O-D" }, { "family_name": "Shroyer", "given_name": "Noah F.", "clpid": "Shroyer-N-F" }, { "family_name": "Helmrath", "given_name": "Michael A.", "clpid": "Helmrath-M-A" }, { "family_name": "Teitelbaum", "given_name": "Daniel H.", "clpid": "Teitelbaum-D-H" }, { "family_name": "Dempsey", "given_name": "Peter J.", "clpid": "Dempsey-P-J" }, { "family_name": "Spence", "given_name": "Jason R.", "clpid": "Spence-J-R" } ], "abstract": "Human intestinal organoids (HIOs) are a tissue culture model in which small intestine-like tissue is generated from pluripotent stem cells. By carrying out unsupervised hierarchical clustering of RNA-sequencing data, we demonstrate that HIOs most closely resemble human fetal intestine.We observed that genes involved in digestive tract development are enriched in both fetal intestine and HIOs compared to adult tissue, whereas genes related to digestive function and Paneth cell host defense are expressed at higher levels in adult intestine. Our study also revealed that the intestinal stem cell marker OLFM4 is expressed at very low levels in fetal intestine and in HIOs, but is robust in adult crypts.We validated our findings using in vivo transplantation to show that HIOs become more adult-like after transplantation. Our study emphasizes important maturation events that occur in the intestine during human development and demonstrates that HIOs can be used to model fetal-to-adult maturation.", "doi": "10.1016/j.stemcr.2015.04.010", "pmcid": "PMC4471827", "issn": "2213-6711", "publisher": "Elsevier", "publication": "Stem Cell Reports", "publication_date": "2015-06-09", "series_number": "6", "volume": "4", "issue": "6", "pages": "1140-1155" }, { "id": "authors:tany3-s7t55", "collection": "authors", "collection_id": "tany3-s7t55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170206-125245656", "type": "article", "title": "A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity", "author": [ { "family_name": "Cerchiari", "given_name": "Alec E.", "clpid": "Cerchiari-A-E" }, { "family_name": "Garbe", "given_name": "James C.", "clpid": "Garbe-J-C" }, { "family_name": "Jee", "given_name": "Noel Y.", "clpid": "Jee-Noel-Y" }, { "family_name": "Todhunter", "given_name": "Michael E.", "clpid": "Todhunter-M-E" }, { "family_name": "Broaders", "given_name": "Kyle E.", "clpid": "Broaders-K-E" }, { "family_name": "Peehl", "given_name": "Donna M.", "clpid": "Peehl-D-M" }, { "family_name": "Desai", "given_name": "Tejal A.", "orcid": "0000-0003-3409-9208", "clpid": "Desai-T-A" }, { "family_name": "LaBarge", "given_name": "Mark A.", "clpid": "LaBarge-M-A" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Gartner", "given_name": "Zev J.", "clpid": "Gartner-Z-J" } ], "abstract": "Developing tissues contain motile populations of cells that can self-organize into spatially ordered tissues based on differences in their interfacial surface energies. However, it is unclear how self-organization by this mechanism remains robust when interfacial energies become heterogeneous in either time or space. The ducts and acini of the human mammary gland are prototypical heterogeneous and dynamic tissues comprising two concentrically arranged cell types. To investigate the consequences of cellular heterogeneity and plasticity on cell positioning in the mammary gland, we reconstituted its self-organization from aggregates of primary cells in vitro. We find that self-organization is dominated by the interfacial energy of the tissue\u2013ECM boundary, rather than by differential homo- and heterotypic energies of cell\u2013cell interaction. Surprisingly, interactions with the tissue\u2013ECM boundary are binary, in that only one cell type interacts appreciably with the boundary. Using mathematical modeling and cell-type-specific knockdown of key regulators of cell\u2013cell cohesion, we show that this strategy of self-organization is robust to severe perturbations affecting cell\u2013cell contact formation. We also find that this mechanism of self-organization is conserved in the human prostate. Therefore, a binary interfacial interaction with the tissue boundary provides a flexible and generalizable strategy for forming and maintaining the structure of two-component tissues that exhibit abundant heterogeneity and plasticity. Our model also predicts that mutations affecting binary cell\u2013ECM interactions are catastrophic and could contribute to loss of tissue architecture in diseases such as breast cancer.", "doi": "10.1073/pnas.1410776112", "pmcid": "PMC4343104", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2015-02-17", "series_number": "7", "volume": "112", "issue": "7", "pages": "2287-2292" }, { "id": "authors:h17dy-k1z79", "collection": "authors", "collection_id": "h17dy-k1z79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170217-150644261", "type": "article", "title": "Environmental Statistics and Optimal Regulation", "author": [ { "family_name": "Sivak", "given_name": "David A.", "clpid": "Sivak-D-A" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "[no abstract]", "doi": "10.1016/j.bpj.2014.11.1999", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2015-01-27", "series_number": "2, Supp. 1", "volume": "108", "issue": "2, Supp. 1", "pages": "364a-365a" }, { "id": "authors:eqsfg-syx61", "collection": "authors", "collection_id": "eqsfg-syx61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170206-153034371", "type": "article", "title": "Environmental Statistics and Optimal Regulation", "author": [ { "family_name": "Sivak", "given_name": "David A.", "clpid": "Sivak-D-A" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "abstract": "Any organism is embedded in an environment that changes over time. The timescale for and statistics of environmental change, the precision with which the organism can detect its environment, and the costs and benefits of particular protein expression levels all will affect the suitability of different strategies\u2013such as constitutive expression or graded response\u2013for regulating protein levels in response to environmental inputs. We propose a general framework\u2013here specifically applied to the enzymatic regulation of metabolism in response to changing concentrations of a basic nutrient\u2013to predict the optimal regulatory strategy given the statistics of fluctuations in the environment and measurement apparatus, respectively, and the costs associated with enzyme production. We use this framework to address three fundamental questions: (i) when a cell should prefer thresholding to a graded response; (ii) when there is a fitness advantage to implementing a Bayesian decision rule; and (iii) when retaining memory of the past provides a selective advantage. We specifically find that: (i) relative convexity of enzyme expression cost and benefit influences the fitness of thresholding or graded responses; (ii) intermediate levels of measurement uncertainty call for a sophisticated Bayesian decision rule; and (iii) in dynamic contexts, intermediate levels of uncertainty call for retaining memory of the past. Statistical properties of the environment, such as variability and correlation times, set optimal biochemical parameters, such as thresholds and decay rates in signaling pathways. Our framework provides a theoretical basis for interpreting molecular signal processing algorithms and a classification scheme that organizes known regulatory strategies and may help conceptualize heretofore unknown ones.", "doi": "10.1371/journal.pcbi.1003826", "pmcid": "PMC4177669", "issn": "1553-7358", "publisher": "Public Library of Science", "publication": "PLOS Computational Biology", "publication_date": "2014-09", "series_number": "9", "volume": "10", "issue": "9", "pages": "Art. No. e1003826" }, { "id": "authors:yedxt-2ne26", "collection": "authors", "collection_id": "yedxt-2ne26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170127-224411366", "type": "article", "title": "Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers", "author": [ { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Liu", "given_name": "Siyuan John", "clpid": "Liu-Siyuan-John" }, { "family_name": "Zou", "given_name": "Ling-Nan", "clpid": "Zou-Ling-Nan" }, { "family_name": "Smith", "given_name": "Zack", "clpid": "Smith-Zack" }, { "family_name": "Meissner", "given_name": "Alexander", "clpid": "Meissner-A" }, { "family_name": "Ramanathan", "given_name": "Sharad", "clpid": "Ramanathan-S" } ], "abstract": "Cell fate decisions are fundamental for development, but we do not know how transcriptional networks reorganize during the transition from a pluripotent to a differentiated cell state. Here, we asked how mouse embryonic stem cells (ESCs) leave the pluripotent state and choose between germ layer fates. By analyzing the dynamics of the transcriptional circuit that maintains pluripotency, we found that Oct4 and Sox2, proteins that maintain ESC identity, also orchestrate germ layer fate selection. Oct4 suppresses neural ectodermal differentiation and promotes mesendodermal differentiation; Sox2 inhibits mesendodermal differentiation and promotes neural ectodermal differentiation. Differentiation signals continuously and asymmetrically modulate Oct4 and Sox2 protein levels, altering their binding pattern in the genome, and leading to cell fate choice. The same factors that maintain pluripotency thus also integrate external signals and control lineage selection. Our study provides a framework for understanding how complex transcription factor networks control cell fate decisions in progenitor cells.", "doi": "10.1016/j.cell.2011.05.017", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "2011-06-10", "series_number": "6", "volume": "145", "issue": "6", "pages": "875-889" }, { "id": "authors:jt54h-2yp89", "collection": "authors", "collection_id": "jt54h-2yp89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170206-154848264", "type": "article", "title": "The rational parameterisation theorem for multisite post-translational modification systems", "author": [ { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Gunawardena", "given_name": "Jeremy", "clpid": "Gunawardena-J" } ], "abstract": "Post-translational modification of proteins plays a central role in cellular regulation but its study has been hampered by the exponential increase in substrate modification forms (\"modforms\") with increasing numbers of sites. We consider here biochemical networks arising from post-translational modification under mass-action kinetics, allowing for multiple substrates, having different types of modification (phosphorylation, methylation, acetylation, etc.) on multiple sites, acted upon by multiple forward and reverse enzymes (in total number L), using general enzymatic mechanisms. These assumptions are substantially more general than in previous studies. We show that the steady-state modform concentrations constitute an algebraic variety that can be parameterised by rational functions of the L free enzyme concentrations, with coefficients which are rational functions of the rate constants. The parameterisation allows steady states to be calculated by solving L algebraic equations, a dramatic reduction compared to simulating an exponentially large number of differential equations. This complexity collapse enables analysis in contexts that were previously intractable and leads to biological predictions that we review. Our results lay a foundation for the systems biology of post-translational modification and suggest deeper connections between biochemical networks and algebraic geometry.", "doi": "10.1016/j.jtbi.2009.09.003", "pmcid": "PMC2800989", "issn": "0022-5193", "publisher": "Elsevier", "publication": "Journal of Theoretical Biology", "publication_date": "2009-12-21", "series_number": "4", "volume": "261", "issue": "4", "pages": "626-636" }, { "id": "authors:q50de-jv517", "collection": "authors", "collection_id": "q50de-jv517", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170206-154848538", "type": "article", "title": "Unlimited multistability in multisite phosphorylation systems", "author": [ { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Gunawardena", "given_name": "Jeremy", "clpid": "Gunawardena-J" } ], "abstract": "Reversible phosphorylation on serine, threonine and tyrosine is the most widely studied posttranslational modification of proteins (1, 2). The number of phosphorylated sites on a protein (n) shows a significant increase from prokaryotes, with n less than or equal to 7 sites, to eukaryotes, with examples having n greater than or equal to 150 sites (3). Multisite phosphorylation has many roles (4, 5) and site conservation indicates that increasing numbers of sites cannot be due merely to promiscuous phosphorylation. A substrate with n sites has an exponential number (2^n) of phospho-forms and individual phospho-forms may have distinct biological effects (6, 7). The distribution of these phospho-forms and how this distribution is regulated have remained unknown. Here we show that, when kinase and phosphatase act in opposition on a multisite substrate, the system can exhibit distinct stable phospho-form distributions at steady state and that the maximum number of such distributions increases with n. Whereas some stable distributions are focused on a single phospho-form, others are more diffuse, giving the phospho-proteome the potential to behave as a fluid regulatory network able to encode information and flexibly respond to varying demands. Such plasticity may underlie complex information processing in eukaryotic cells (8) and suggests a functional advantage in having many sites. Our results follow from the unusual geometry of the steady-state phospho-form concentrations, which we show to constitute a rational algebraic curve, irrespective of n. We thereby reduce the complexity of calculating steady states from simulating 3 times 2^n differential equations to solving two algebraic equations, while treating parameters symbolically. We anticipate that these methods can be extended to systems with multiple substrates and multiple enzymes catalysing different modifications, as found in posttranslational modification 'codes' (9) such as the histone code (10, 11). Whereas simulations struggle with exponentially increasing molecular complexity, mathematical methods of the kind developed here can provide a new language in which to articulate the principles of cellular information processing (12).", "doi": "10.1038/nature08102", "pmcid": "PMC2859978", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2009-07-09", "series_number": "7252", "volume": "460", "issue": "7252", "pages": "274-277" }, { "id": "authors:222s0-j1978", "collection": "authors", "collection_id": "222s0-j1978", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170206-154848804", "type": "article", "title": "Programming with models: modularity and abstraction provide powerful capabilities for systems biology", "author": [ { "family_name": "Mallavarapu", "given_name": "Aneil", "clpid": "Mallavarapu-A" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Ullian", "given_name": "Benjamin", "clpid": "Ullian-B" }, { "family_name": "Gunawardena", "given_name": "Jeremy", "clpid": "Gunawardena-J" } ], "abstract": "Mathematical models are increasingly used to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations presents a fundamental barrier to progress. Overcoming this requires modularity, enabling sub-systems to be specified independently and combined incrementally, and abstraction, enabling generic properties of biological processes to be specified independently of specific instances. These, in turn, require models to be represented as programs rather than as datatypes. Programmable modularity and abstraction enables libraries of modules to be created, which can be instantiated and reused repeatedly in different contexts with different components. We have developed a computational infrastructure that accomplishes this. We show here why such capabilities are needed, what is required to implement them and what can be accomplished with them that could not be done previously.", "doi": "10.1098/rsif.2008.0205", "pmcid": "PMC2659579", "issn": "1742-5689", "publisher": "The Royal Society", "publication": "Journal of the Royal Society Interface", "publication_date": "2009-03-06", "series_number": "32", "volume": "6", "issue": "32", "pages": "257-270" }, { "id": "authors:0pa0n-jye66", "collection": "authors", "collection_id": "0pa0n-jye66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170217-132836548", "type": "article", "title": "An embryonic stem cell\u2013like gene expression signature in poorly differentiated aggressive human tumors", "author": [ { "family_name": "Ben-Porath", "given_name": "Ittai", "clpid": "Ben-Porath-I" }, { "family_name": "Thomson", "given_name": "Matthew W.", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Carey", "given_name": "Vincent J.", "clpid": "Carey-V-J" }, { "family_name": "Ge", "given_name": "Ruping", "clpid": "Ge-Ruping" }, { "family_name": "Bell", "given_name": "George W.", "clpid": "Bell-G-W" }, { "family_name": "Regev", "given_name": "Aviv", "orcid": "0000-0003-3293-3158", "clpid": "Regev-A" }, { "family_name": "Weinberg", "given_name": "Robert A.", "clpid": "Weinberg-R-A" } ], "abstract": "Cancer cells possess traits reminiscent of those ascribed to normal stem cells. It is unclear, however, whether these phenotypic similarities reflect the activity of common molecular pathways. Here, we analyze the enrichment patterns of gene sets associated with embryonic stem (ES) cell identity in the expression profiles of various human tumor types. We find that histologically poorly differentiated tumors show preferential overexpression of genes normally enriched in ES cells, combined with preferential repression of Polycomb-regulated genes. Moreover, activation targets of Nanog, Oct4, Sox2 and c-Myc are more frequently overexpressed in poorly differentiated tumors than in well-differentiated tumors. In breast cancers, this ES-like signature is associated with high-grade estrogen receptor (ER)-negative tumors, often of the basal-like subtype, and with poor clinical outcome. The ES signature is also present in poorly differentiated glioblastomas and bladder carcinomas. We identify a subset of ES cell-associated transcription regulators that are highly expressed in poorly differentiated tumors. Our results reveal a previously unknown link between genes associated with ES cell identity and the histopathological traits of tumors and support the possibility that these genes contribute to stem cell\u2013like phenotypes shown by many tumors.", "doi": "10.1038/ng.127", "pmcid": "PMC2912221", "issn": "1061-4036", "publisher": "Nature Publishing Group", "publication": "Nature Genetics", "publication_date": "2008-05", "series_number": "5", "volume": "40", "issue": "5", "pages": "499-507" } ]