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science (New York, N.Y.) 2025年第6753期388卷 1283-1284页

作者： Nasa Sinnott-Armstrong Desiree Forsythe Jane M Benoit Callie R Chappell Lisa S Y Coe Bruno Francesco Rodrigues de Oliveira Natalya Evans Anna C Fagre Jonathan M Gilligan Maria Hamilton Colin Moran Henneberry Suzanne L Ishaq Juliet Johnston Erin Krichilsky Jamie Alcira Lopez Kay McMonigal Melanie Ortiz Alvarez de la Campa Rahmeen Rahman Nicole E Schwartz Lauren Talluto Eric J Taylor José M Vargas-Muñiz J L Weissman Herbold Computational Biology Program Public Health Sciences Division Fred Hutchinson Cancer Center Seattle WA USA. Department of Genome Sciences University of Washington Seattle WA USA. Department of Biology Santa Clara University Santa Clara CA USA. Department of Biological Science Florida State University Tallahassee FL USA. Department of Biology Stanford University Stanford CA USA. Department of Biology and Genetics Institute University of Florida Gainesville FL USA. School of Teaching and Learning College of Education University of Florida Gainesville FL USA. Department of Microbiology and Parasitology Biomedical Institute Fluminense Federal University Niterói RJ Brazil. Marine Science Institute University of California Santa Barbara Santa Barbara CA USA. Department of Microbiology Immunology and Pathology Colorado State University Fort Collins CO USA. Department of Earth and Environmental Sciences Vanderbilt University Nashville TN USA. Department Civil and Environmental Engineering Vanderbilt University Nashville TN USA. Department of Marine Sciences University of Georgia Athens GA USA. Department of Ecology and Evolution Stony Brook University Stony Brook NY USA. Department of Animal and Veterinary Sciences University of Maine Orono ME USA. Microbes and Social Equity working group Orono ME USA. School of Science and Math Hampshire College Amherst MA USA. American Museum of Natural History Richard Gilder Graduate School New York NY USA. Department of Ecology Evolution and Environmental Biology Columbia University New York NY USA. Department of Bioengineering Stanford University Stanford CA USA. Department of Applied Physics Stanford University Stanford CA USA. College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks AK USA. Department of Molecular Microbiology and Immunology Brown University Providence RI USA.. Department of Infectious Disease Imperial College London London UK. Depar

Transgender and gender nonconforming (TGnC) people are a primary target of the Trump administration. Multiple executive orders seek to erase TGnC protections; mandate denial of gender identity; and ban diversity, equity, and inclusion (DEI) (1). Changes to federal funding policies related to TGnC individuals and DEI threaten to curtail academic diversity and freedom (2). Institutions have been hesitant to resist, but for many TGnC scientists—especially TGnC individuals of color, immigrants, and those with disabilities—invisibility is not an option. Anticipatory obedience (3, 4), and even passive allyship, is insufficient; institutions must abandon neutrality and defend targeted communities to minimize further harm (5, 6). As queer and TGnC scientists, we call on researchers at all levels—from undergraduates to university presidents—to take direct, consistent, and rapid action.

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Airr Community Curation and Standardised Representation for Immunoglobulin and T Cell Receptor Germline Sets

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SSRN 2022年

作者： Lees, William D. Christley, Scott Peres, Ayelet Kos, Justin T. Corrie, Brian Ralph, Duncan Breden, Felix Cowell, Lindsay G. Yaari, Gur Corcoran, Martin Karlsson Hedestam, Gunilla B. Ohlin, Mats Collins, Andrew M. Watson, Corey T. Busse, Christian E. Institute of Structural and Molecular Biology Birkbeck College London United Kingdom Human-Centered Computing and Information Science Institute for Systems and Computer Engineering Technology and Science Porto Portugal Peter O’Donnell Jr School of Public Health Department of Immunology UT Southwestern Medical Center Texas United States Bioengineering Program Faculty of Engineering Bar-Ilan University Ramat Gan Israel Department of Biochemistry and Molecular Genetics School of Medicine University of Louisville Kentucky United States Department of Biological Sciences Simon Fraser University BurnabyBC Canada Fred Hutchinson Cancer Research Center SeattleWA United States Department of Microbiology Tumor and Cell Biology Karolinska Institute Stockholm Sweden Department of Immunotechnology Lund University Lund Sweden School of Biotechnology and Biomolecular Sciences University of New South Wales SydneyNSW Australia Division of B Cell Immunology German Cancer Research Center Heidelberg Germany

Analysis of an individual’s immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes and provides transparency based on principles of findability, accessibility, interoperability, and reusability. We describe results obtained by applying the data model and associated principles within the AIRR Community, including supporting software and databases. © 2022, The Authors. All rights reserved.

关键词： Genes

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Engineering Osteogenic Spheroids: The Impact of Endothelial Cell Localization on Vascularization and Differentiation

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Advanced healthcare materials 2025年 e2501390页

作者： Yoonjoo Kang Tae Hoon Kang Hee Sang Ro Nathaniel S Hwang Hwan D Kim Department of IT Convergence (Brain Korea Plus 21) Korea National University of Transportation Chungju 27469 Republic of Korea. Interdisciplinary Program in Bioengineering Seoul National University Seoul 08826 Republic of Korea. School of Chemical and Biological Engineering The Institute of Chemical Processes Seoul National University Seoul 08826 Republic of Korea. Institute of Engineering Research BioMax/N-Bio Institute Institute of Bio Engineering Seoul National University Seoul 08826 Republic of Korea. Department of Polymer Science and Engineering Department of Biomedical Engineering Korea National University of Transportation Chungju 27469 Republic of Korea.

Bone tissue is highly vascularized, and robust blood flow is critical for successful bone regeneration. However, the intricate architecture of bone vascular networks and the mechanisms governing their development remain poorly understood, necessitating the development of in vitro models that replicate the native bone microenvironment. In this study, we investigated the influence of endothelial cell positioning within co-cultured spheroids on vascularization and osteogenic differentiation. Human umbilical vein endothelial cells (HUVECs) and human bone marrow-derived mesenchymal stem cells (hBMSCs) are employed to generate spheroids using two distinct co-culture strategies: core-shell and mixed configurations. Core-shell spheroids are fabricated in two arrangements: hBMSCs-core/HUVECs-outer layer (M2H) and HUVECs-core/hBMSCs-outer layer (H2M). Mixed spheroids are created by co-aggregation of HUVECs and hBMSCs. In vitro analyses revealed that endothelial cell localization significantly impacted spheroid morphology and function. Notably, M2H spheroids exhibited the highest VE-cadherin levels, suggesting enhanced endothelial cell-cell interactions. In Matrigel assays, M2H spheroids demonstrated superior angiogenic potential, evidenced by vascular network formation. Furthermore, we evaluated osteoblast differentiation within the spheroids to elucidate the interplay between endothelial cell positioning, vascularization, and bone development. This study provides valuable insights into the processes governing bone vascularization and offers a foundation for developing advanced tissue engineering strategies for regeneration.

关键词： cell differentiation co‐culture osteogenic spheroid vascularization

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Erratum to: Determining the Binding Constant of LANA Protein Fragment with Nucleosome

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Moscow University biological sciences Bulletin 2021年第1期76卷 39-39页

作者： Novikov, R. V. Bondarenko, E. A. Malyuchenko, N. V. Feofanov, A. V. Studitsky, V. M. Shaytan, A. K. Bioengineering Department Biological Faculty Moscow State University Moscow Russia Sirius Science and Technology University Sochi Russia Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Moscow Russia Cancer Epigenetics Program Fox Chase Cancer Center Philadelphia United States

An Erratum to this paper has been published: https://***/10.3103/S0096392521110018

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Plant, Cell & Environment 2021年第1期45卷

作者： Geun Cheol Song Je-Seung Jeon Hye Kyung Choi Hee-Jung Sim Sang-Gyu Kim Choong-Min Ryu Molecular Phytobacteriology Laboratory Infectious Disease Research Center KRIBB Daejeon South Korea Environmental Chemistry Research Group Korea Institute of Toxicology (KIT) Jinju South Korea Department of Biological Sciences Korea Advanced Institute of Science and Technology Daejeon South Korea Biosystems and Bioengineering Program University of Science and Technology (UST) Daejeon South Korea

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Author Correction: ML-enhanced peroxisome capacity enables compartmentalization of multienzyme pathway

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Nature chemical biology 2024年 2024 Nov 8页

作者： Jordan J Baker Jie Shi Shangying Wang Elena M Mujica Simone Bianco Sara Capponi John E Dueber Department of Bioengineering University of California Berkeley CA USA. UC Berkeley and UCSF Joint Graduate Program in Bioengineering University of California Berkeley CA USA. NSF Center for Cellular Construction University of California San Francisco CA USA. Department of Functional Genomics and Cellular Engineering IBM Almaden Research Center San Jose CA USA. Bay Area Institute of Science Altos Labs Redwood City CA USA. NSF Center for Cellular Construction University of California San Francisco CA USA. sara.capponi@***. Department of Functional Genomics and Cellular Engineering IBM Almaden Research Center San Jose CA USA. sara.capponi@***. Department of Bioengineering University of California Berkeley CA USA. jdueber@berkeley.edu. NSF Center for Cellular Construction University of California San Francisco CA USA. jdueber@berkeley.edu. Biological Systems and Engineering Division Lawrence Berkeley National Laboratory Berkeley CA USA. jdueber@berkeley.edu.

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Engineering Native biological Complexity from the Inside-out and Outside-in

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Nature chemical engineering 2024年第1期1卷 2-5页

作者： Cole A DeForest Bruce E Kirkpatrick Kristi S Anseth Department of Chemical Engineering University of Washington Seattle WA 98195 USA. Department of Bioengineering University of Washington Seattle WA 98195 USA. Department of Chemistry University of Washington Seattle WA 98195 USA. Institute of Stem Cell & Regenerative Medicine University of Washington Seattle WA 98109 USA. Molecular Engineering & Sciences Institute University of Washington Seattle WA 98195 USA. Institute for Protein Design University of Washington Seattle WA 98195 USA. Department of Chemical and Biological Engineering University of Colorado Boulder CO 80303 USA. The BioFrontiers Institute University of Colorado Boulder CO 80303 USA. Medical Scientist Training Program School of Medicine University of Colorado Aurora CO 80045 USA. Materials Science and Engineering Program University of Colorado Boulder CO 80303 USA.

Focusing on engineering control over cell function and fate, this article examines the critical balance of 'outside-in' and 'inside-ouť signaling in tissue development and regeneration. It highlights emerging strategies to manipulate these interactions, including biomaterial design and synthetic biology to influence this delicate equilibrium and fine tune cellular responses.

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De Novo Design of Integrin α5β1 Modulating Proteins to Enhance Biomaterial Properties

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Advanced materials (Deerfield Beach, Fla.) 2025年 e2500872页

作者： Xinru Wang Jordi Guillem-Marti Saurav Kumar David S Lee Daniel Cabrerizo-Aguado Rachel Werther Kevin Alexander Estrada Alamo Yan Ting Zhao Adam Nguyen Irina Kopyeva Buwei Huang Jing Li Yuxin Hao Xinting Li Aritza Brizuela-Velasco Analisa Murray Stacey Gerben Anindya Roy Cole A DeForest Timothy Springer Hannele Ruohola-Baker Jonathan A Cooper Melody G Campbell Jose Maria Manero Maria-Pau Ginebra David Baker Department of Biochemistry University of Washington Seattle WA USA. Institute for Protein Design University of Washington Seattle WA USA. Biomaterials Biomechanics and Tissue Engineering Group Department of Materials Science and Engineering Universitat Politècnica de Catalunya - BarcelonaTech (UPC) Barcelona Spain. Networking Research Centre of Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) Institute of Health Carlos III Madrid Spain. Division of Basic Sciences Fred Hutchinson Cancer Center Seattle WA USA. LILA Biologics Seattle WA USA. Department of Genome Sciences University of Washington Seattle WA USA. Oral Health Sciences School of Dentistry University of Washington Seattle WA USA. Institute for Stem Cell and Regenerative Medicine University of Washington Seattle WA USA. Graduate Program in Biological Physics Structure and Design University of Washington Seattle WA USA. Department of Bioengineering University of Washington Seattle WA USA. Program in Cellular and Molecular Medicine Boston Children's Hospital Boston MA 02115 USA. Department of Pediatrics Harvard Medical School Boston MA 02115 USA. Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA. DENS-ia Research Group Faculty of Health Sciences Miguel de Cervantes European University Valladolid Spain. Department of Chemical Engineering University of Washington Seattle WA USA. Department of Chemistry University of Washington Seattle WA USA. Molecular Engineering & Sciences Institute University of Washington Seattle WA USA. Institute for Bioengineering of Catalonia Barcelona Institute of Science and Technology Barcelona Spain. Howard Hughes Medical Institute University of Washington Seattle WA USA.

Integrin α5β1 is crucial for cell attachment and migration in development and tissue regeneration, and α5β1 binding proteins can have considerable utility in regenerative medicine and next-generation therapeutics. We use computational protein design to create de novo α5β1-specific modulating miniprotein binders, called NeoNectins, that bind to and stabilize the open state of α5β1. When immobilized onto titanium surfaces and throughout 3D hydrogels, the NeoNectins outperform native fibronectin (FN) and RGD peptides in enhancing cell attachment and spreading, and NeoNectin-grafted titanium implants outperformed FN- and RGD-grafted implants in animal models in promoting tissue integration and bone growth. NeoNectins should be broadly applicable for tissue engineering and biomedicine.

关键词： RGD biomaterial de novo protein design hydrogel integrin α5β1 regenerative medicine titanium

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The mechanism of action of T-705 as a unique delayed chain terminator on influenza viral polymerase transcription

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Biophysical Chemistry 2021年 277卷 106652页

作者： Wang, Yuqing Yuan, Congmin Xu, Xinzhou Chong, Tin Hang Zhang, Lu Cheung, Peter Pak-Hang Huang, Xuhui The Hong Kong University of Science and Technology-Shenzhen Research Institute Hi-Tech Park Nanshan Shenzhen 518057 China Bioengineering Graduate Program Department of Biological and Chemical Engineering The Hong Kong University of Science and Technology Clear Water Bay Hong Kong Department of Chemistry State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology Kowloon Hong Kong State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou 350002 Fujian China University of Chinese Academy of Sciences Beijing 100049 China Department of Chemical Pathology The Chinese University of Hong Kong Prince of Wales Hospital Shatin New Territories Hong Kong Li Ka Shing Institute of Health Sciences Li Ka Shing Medical Sciences Building The Chinese University of Hong Kong Shatin New Territories Hong Kong

Favipiravir (T-705) has been developed as a potent anti-influenza drug and exhibited a strong inhibition effect against a broad spectrum of RNA viruses. Its active form, ribofuranosyl-triphosphate (T-705-RTP), functions as a competitive substrate for the RNA-dependent RNA polymerase (RdRp) of the influenza A virus (IAV). However, the exact inhibitory mechanisms of T-705 remain elusive and subject to a long-standing debate. Although T-705 has been proposed to inhibit transcription by acting as a chain terminator, it is also paradoxically suggested to be a mutagen towards IAV RdRp by inducing mutations due to its ambiguous base pairing of C and U. Here, we combined biochemical assay with molecular dynamics (MD) simulations to elucidate the molecular mechanism underlying the inhibitory functions exerted by T-705 in IAV RdRp. Our in vitro transcription assay illustrated that IAV RdRp could recognize T-705 as a purine analogue and incorporate it into the nascent RNA strand. Incorporating a single T-705 is incapable of inhibiting transcription as extra natural nucleotides can be progressively added. However, when two consecutive T-705 are incorporated, viral transcription is completely terminated. MD simulations reveal that the sequential appearance of two T-705 in the nascent strand destabilizes the active site and disrupts the base stacking of the nascent RNA. Altogether, our results provide a plausible explanation for the inhibitory roles of T-705 targeting IAV RdRp by integrating the computational and experimental methods. Our study also offers a comprehensive platform to investigate the inhibition effect of antivirals and a novel explanation for the designing of anti-flu drugs. © 2021

关键词： Chain terminator Influenza Mutagen RNA polymerase T-705

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A flexible liposomal polymer complex as a platform of specific and regulable immune regulation for individual cancer immunotherapy

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Journal of Experimental and Clinical Cancer Research 2023年第1期42卷 29-29页

作者： Chen, Chia-Hung Weng, Tzu-Han Huang, Hsiao-Hsuan Huang, Ling-Ya Huang, Kai-Yao Chen, Pin-Rong Yeh, Kuang-Yu Huang, Chi-Ting Chien, Yu-Tzu Chuang, Po-Ya Lin, Yu-Ling Tsai, Nu-Man Liu, Shih-Jen Su, Yu-Cheng Weng, Shun-Long Liao, Kuang-Wen Department of Medical Research Hsinchu MacKay Memorial Hospital Hsinchu City 30071 Taiwan Department of Dermatology MacKay Memorial Hospital Taipei City 10449 Taiwan Industrial Development Graduate Program of College of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan Department of Medicine MacKay Medical College New Taipei City 25245 Taiwan Institute of Molecular Medicine and Bioengineering National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan Agricultural Biotechnology Research Center Academia Sinica Taipei 11529 Taiwan Department of Medical Laboratory and Biotechnology Chung Shan Medical University Taichung City 40201 Taiwan Department of Pathology and Clinical Laboratory Chung Shan Medical University Hospital Taichung City 40201 Taiwan National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Miaoli 350401 Taiwan Department of Obstetrics and Gynecology Hsinchu MacKay Memorial Hospital Hsinchu City 30071 Taiwan MacKay Junior College of Medicine Nursing and Management Taipei City 11260 Taiwan Graduate Institute of Medicine College of Medicine Kaohsiung Medical University Kaohsiung City 80708 Taiwan College of Dental Medicine Kaohsiung Medical University School of Dentistry Kaohsiung City 80708 Taiwan Department of Biotechnology and Bioindustry Sciences National Cheng Kung University Tainan City 70101 Taiwan Center for Intelligent Drug Systems and Smart Bio-Devices National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan

Background: The applicability and therapeutic efficacy of specific personalized immunotherapy for cancer patients is limited by the genetic diversity of the host or the tumor. Side-effects such as immune-related adverse events (IRAEs) derived from the administration of immunotherapy have also been observed. Therefore, regulatory immunotherapy is required for cancer patients and should be developed. Methods: The cationic lipo-PEG-PEI complex (LPPC) can stably and irreplaceably adsorb various proteins on its surface without covalent linkage, and the bound proteins maintain their original functions. In this study, LPPC was developed as an immunoregulatory platform for personalized immunotherapy for tumors to address the barriers related to the heterogenetic characteristics of MHC molecules or tumor associated antigens (TAAs) in the patient population. Here, the immune-suppressive and highly metastatic melanoma, B16F10 cells were used to examine the effects of this platform. Adsorption of anti-CD3 antibodies, HLA-A2/peptide, or dendritic cells’ membrane proteins (MP) could flexibly provide pan-T-cell responses, specific Th1 responses, or specific Th1 and Th2 responses, depending on the host needs. Furthermore, with regulatory antibodies, the immuno-LPPC complex properly mediated immune responses by adsorbing positive or negative antibodies, such as anti-CD28 or anti-CTLA4 antibodies. Results: The results clearly showed that treatment with LPPC/MP/CD28 complexes activated specific Th1 and Th2 responses, including cytokine release, CTL and prevented T-cell apoptosis. Moreover, LPPC/MP/CD28 complexes could eliminate metastatic B16F10 melanoma cells in the lung more efficiently than LPPC/MP. Interestingly, the melanoma resistance of mice treated with LPPC/MP/CD28 complexes would be reversed to susceptible after administration with LPPC/MP/CTLA4 complexes. NGS data revealed that LPPC/MP/CD28 complexes could enhance the gene expression of cytokine and chemokine pathways to st

关键词： Costimulatory molecules Immunotherapy LPPC personalized cancer therapy Tumor heterogenicity

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