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Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone

Scientific Data 2017年第1期4卷 170158页

作者： Hallam, Steven J. Torres-Beltrán, Mónica Hawley, Alyse K. Department of Microbiology and Immunology University of British Columbia Vancouver V6T 1Z3 BC Canada Peter Wall Institute for Advanced Studies University of British Columbia Vancouver V6T 1Z2 BC Canada Genome Science and Technology Program University of British Columbia Vancouver V6T 1Z4 BC Canada Graduate Program in Bioinformatics University of British Columbia Vancouver V6T 1Z4 BC Canada ECOSCOPE Training Program University of British Columbia Vancouver V6T 1Z4 BC Canada

Today in Scientific Data, two compendia of geochemical and multi-omic sequence information (DNA, RNA, protein) generated over almost a decade of time series monitoring in a seasonally anoxic coastal marine setting are presented to the scientific community. These data descriptors introduce a model ecosystem for the study of microbial responses to ocean deoxygenation, a phenotype that is currently expanding due to climate change. Public access to this time series information is intended to promote scientific collaborations and the generation of new hypotheses relevant to microbial ecology, biogeochemistry and global change issues. © The Author(s) 2017.

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Correction: Spatial organization of B lymphocytes and prognosis prediction in patients with gastric cancer

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Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association 2025年 2025 May 16页

作者： Ryan Yong Kiat Tay Manavi Sachdeva Haoran Ma Young-Woo Kim Myeong-Cherl Kook Hyunki Kim Jae-Ho Cheong Lindsay C Hewitt Katharina Nekolla Günter Schmidt Takaki Yoshikawa Takashi Oshima Tomio Arai Supriya Srivastava Ming Teh Xuewen Ong Su Ting Tay Taotao Sheng Joseph J Zhao Patrick Tan Heike I Grabsch Raghav Sundar Yong Loo Lin School of Medicine National University of Singapore 1E Kent Ridge Road Singapore 119228 Singapore. Department of Haematology-Oncology National University Cancer Institute National University Hospital Singapore Singapore. Cancer and Stem Cell Biology Program Duke-NUS Medical School Singapore Singapore. Department of Cancer Policy and Population Health National Cancer Center Graduate School of Cancer Science and Policy and Center for Gastric Cancer and Department of Surgery National Cancer Center Goyang Republic of Korea. Center for Gastric Cancer Department of Pathology National Cancer Center Goyang Republic of Korea. Department of Pathology Yonsei University College of Medicine Seoul Republic of Korea. Department of Surgery Yonsei University College of Medicine Seoul Republic of Korea. Department of Pathology GROW Research Institute for Oncology and Reproduction Maastricht University Medical Center+ Maastricht The Netherlands. Department of Precision Medicine GROW School for Oncology and Reproduction Maastricht University Center+ Maastricht The Netherlands. Computational Pathology Oncology R&D AstraZeneca Munich Germany. Department of Surgery Kanagawa Cancer Center Yokohama Japan. Department of Surgery Yokohama City University Yokohama Japan. Department of Surgery Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital Tokyo Japan. Department of Pathology Tokyo Metropolitan Institute for Geriatrics and Gerontology Tokyo Japan. Department of Medicine National University of Singapore Singapore Singapore. Department of Pathology National University Hospital Singapore Singapore. Genome Institute of Singapore Agency for Science Technology and Research Singapore Singapore. Cancer Science Institute of Singapore National University of Singapore Singapore Singapore. Cellular and Molecular Research National Cancer Centre Singapore Singapore. Singhealth/Duke-NUS Institute of Precision Medicine National Heart Centre Singapore

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Micropatterning of functional lipid bilayer assays for quantitative bioanalysis

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Biomicrofluidics 2023年第3期17卷 031302页

作者： Montalbo, Reynaldo Carlos K. Tu, Hsiung-Lin Institute of Chemistry Academia Sinica Taipei11529 Taiwan Nanoscience and Technology Taiwan International Graduate Program Academia Sinica Taipei11529 Taiwan Department of Engineering and System Science National Tsing-Hua University Hsinchu300044 Taiwan Genome and Systems Biology Degree Program Academia Sinica National Taiwan University Taipei10617 Taiwan

Interactions of the cell with its environment are mediated by the cell membrane and membrane-localized molecules. Supported lipid bilayers have enabled the recapitulation of the basic properties of cell membranes and have been broadly used to further our understanding of cellular behavior. Coupled with micropatterning techniques, lipid bilayer platforms have allowed for high throughput assays capable of performing quantitative analysis at a high spatiotemporal resolution. Here, an overview of the current methods of the lipid membrane patterning is presented. The fabrication and pattern characteristics are briefly described to present an idea of the quality and notable features of the methods, their utilizations for quantitative bioanalysis, as well as to highlight possible directions for the advanced micropatterning lipid membrane assays. © 2023 Author(s).

关键词： Lipid bilayers

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The Transcription Factor IRF8 is a Key Transcription Factor for Basophil Development

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BLOOD 2013年第21期122卷 1197-1197页

作者： Kurotaki, Daisuke Sasaki, Haruka Osato, Naoki Sasaki, Izumi Kaneda, Chika Sato, Hideaki Nishiyama, Akira Kaisho, Tsuneyasu Aburatani, Hiroyuki Morse, Herbert C., III Ozato, Keiko Tamura, Tomohiko Department of Immunology Yokohama City University Graduate School of Medicine Yokohama Japan Division of Genome Science Research Center for Advanced Science and Technology The University of Tokyo Tokyo Japan Laboratory for Immune Regulation Immunology Frontier Research Center Osaka University Osaka Japan Genome Science Division Research Center for Advanced Science and Technology The University of Tokyo Tokyo Japan Laboratory of Immunogenetics National Institute of Allergy and Infectious Disease NIH Rockville MD USA Program in Genomics of Differentiation National Institute of Child Health and Human Development NIH Bethesda MD USA

1197

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Building better interdisciplinary scientists: creating graduate level courses to address the communication gap in interdisciplinary research

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BMC Bioinformatics 2012年第12期13卷 1-2页

作者： Denise R Koessler Elizabeth G Johnson Jordan M Utley Harry A Richards Cynthia B Peterson Department of Electrical Engineering and Computer Science The University of Tennessee Knoxville TN 37996 USA Department of Microbiology The University of Tennessee Knoxville TN 37996 USA UT/ORNL Graduate School of Genome Science and Technology The University of Tennessee Knoxville TN 37996 USA SCALE-IT Program Administrator The University of Tennessee Knoxville TN 37996 USA Department of Biochemistry and Molecular Biology The University of Tennessee Knoxville TN 37996 USA

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Enhanced Heliothis virescens midgut regeneration and its role in resistance to Bacillus thuringiensis toxins

Enhanced Heliothis virescens midgut regeneration and its rol...

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第2届昆虫中肠生物学国际研讨会

作者： Ana(i)s S.Castagnola Omaththage P.Perera Cris Oppert Jerreme Jackson Fred Gould Juan Luis Jurat-Fuentes Department of Entomology and Plant Pathology University of TennesseeKnoxvilleTN 37996USA Southern Insect Management Research UnitUSDA-ARSStonevilleMS 38776USA Genome Science and Technology Graduate ProgramUniversity of TennesseeKnoxvilleTN 37996 Department of EntomologyNorth Carolina State UniversityRaleigh 27607USA

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Ultra-streamlined single cell proteomics by all-in-one chip and data-independent-acquisition mass spectrometry

Research Square

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Research Square 2021年

作者： Tu, Hsiung-Lin Gebreyesus, Sofani Tafesse Siyal, Asad Ali Kitata, Reta Birhanu Chen, Eric Sheng-Wen Enkhbayar, Bayarmaa Angata, Takashi Lin, Kuo-I Chen, Yu-Ju Institute of Chemistry Academia Sinica Taipei115 Taiwan Taiwan International Graduate program Nano Science and Technology program Academia Sinica Taipei115 Taiwan Department of Chemistry National Taiwan University Taipei106 Taiwan Taiwan International Graduate Program Chemical Biology and Molecular Biophysics Program Academia Sinica Taipei115 Taiwan Department of Chemistry National Tsing Hua University Hsinchu300 Taiwan Institute of Biological Chemistry Academia Sinica Taipei115 Taiwan Genomics Research Center Academia Sinica Taipei115 Taiwan Genome and Systems Biology Degree Program Academia Sinica and National Taiwan University Taiwan

Single cell proteomics provides the ultimate resolution to reveal cellular phenotypic heterogeneity and functional network underlying biological processes. Here, we present an ultra-streamlined workflow combining an integrated proteomic chip (iProChip) and data-independent-acquisition (DIA) mass spectrometry for sensitive microproteomics analysis down to single cell level. The iProChip offers multiplexed and automated all-in-one station from cell isolation/counting/imaging to complete proteomic processing within a single device. By mapping to project-specific spectra libraries, the iProChip-DIA enables profiling of 1160 protein groups from triplicate analysis of a single mammalian cell. Furthermore, the applicability of iProChip-DIA was demonstrated using both adherent and non-adherent malignant cells, which reveals 5 orders of proteome coverage, highly consistent ~100-fold protein quantification (1-100 cells) and high reproducibility with low missing values ( © , CC BY.

关键词： Mass spectrometry

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Α γ-tubulin complex-dependent pathway suppresses ciliogenesis by promoting cilia disassembly

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Cell Reports 2022年第7期41卷 000-000页

作者： Shankar, Sahana Hsu, Zi-Ting Ezquerra, Artur Li, Chien-Chien Huang, Tzu-Lun Coyaud, Etienne Viais, Ricardo Grauffel, Cédric Raught, Brian Lim, Carmay Lüders, Jens Tsai, Su-Yi Hsia, Kuo-Chiang Molecular and Cell Biology Taiwan International Graduate Program Academia Sinica and National Defense Medical Center Taipei 11490 Taiwan Institute of Molecular Biology Academia Sinica Taipei 11529 Taiwan Department of Life Science National Taiwan University Taipei 10617 Taiwan Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology Barcelona 08028 Spain Princess Margaret Cancer Centre University Health Network 101 College Street Toronto M5G 1L7 ON Canada Department of Medical Biophysics University of Toronto Toronto M5G 1L7 ON Canada Institute of Biomedical Sciences Academia Sinica Taipei Taiwan Research Center for Developmental Biology and Regenerative Medicine National Taiwan University Taipei 10617 Taiwan Genome and Systems Biology Degree Program National Taiwan University and Academia Sinica Taipei 10617 Taiwan Institute of Biochemistry and Molecular Biology College of Life Sciences National Yang-Ming University Taipei 11221 Taiwan

The primary cilium, a microtubule-based sensory organelle, undergoes cycles of assembly and disassembly that govern the cell cycle progression critical to cell proliferation and differentiation. Although cilia assembly has been studied extensively, the molecular mechanisms underlying cilia disassembly are less well understood. Here, we uncover a γ-tubulin ring complex (γ-TuRC)-dependent pathway that promotes cilia disassembly and thereby prevents cilia formation. We further demonstrate that Kif2A, a kinesin motor that bears microtubule-depolymerizing activity, is recruited to the cilium basal body in a γ-TuRC-dependent manner. Our mechanistic analyses show that γ-TuRC specifically recruits Kif2A via the GCP2 subunit and its binding partner Mzt2. Hence, despite the long-standing view that γ-TuRC acts mainly as a microtubule template, we illustrate that its functional heterogeneity at the basal body facilitates both microtubule nucleation and Kif2A recruitment-mediated regulation of ciliogenesis, ensuring cell cycle progression. © 2022 The Author(s)

关键词： cell cycle ciliogenesis CP: Molecular biology kinesin motor microtubule primary cilium γ-tubulin ring complex

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Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in hepatocellular carcinoma:the PLANET study

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National science Review 2022年第3期9卷 96-109页

作者： Weiwei Zhai Hannah Lai Neslihan Arife Kaya Jianbin Chen Hechuan Yang Bingxin Lu Jia Qi Lim Siming Ma Sin Chi Chew Khi Pin Chua Jacob Josiah Santiago Alvarez Pauline Jieqi Chen Mei Mei Chang Lingyan Wu Brian K.P.Goh Alexander Yaw-Fui Chung Chung Yip Chan Peng Chung Cheow Ser Yee Lee Juinn Huar Kam Alfred Wei-Chieh Kow Iyer Shridhar Ganpathi Rawisak Chanwat Jidapa Thammasiri Boon Koon Yoong Diana Bee-Lan Ong Vanessa H.de Villa Rouchelle D.Dela Cruz Tracy Jiezhen Loh Wei Keat Wan Zeng Zeng Anders Jacobsen Skanderup Yin Huei Pang Krishnakumar Madhavan Tony Kiat-Hon Lim Glenn Bonney Wei Qiang Leow Valerie Chew Yock Young Dan Wai Leong Tam Han Chong Toh Roger Sik-Yin Foo Pierce Kah-Hoe Chow Genome Institute of Singapore Agency for Science Technology and Research Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences School of Biological Sciences Nanyang Technological University Division of Biosciences Faculty of Life Sciences Division of Surgery and Surgical Oncology National Cancer Centre Department of Hepato-Pancreato-Biliary and Transplant Surgery Singapore General Hospital Division of Hepatobiliary and Pancreatic Surgery Department of Surgery University Surgical Cluster National University Health System Hepato-Pancreato-Biliary Surgery Unit Department of Surgery National Cancer Institute Division of Pathology National Cancer Institute Department of Surgery Faculty of Medicine University of Malaya Department of Surgery and Center for Liver Disease Management and Transplantation The Medical City Department of Laboratories The Medical City Department of Pathology Singapore General Hospital Institute for Infocomm Research ASTAR Department of Pathology National University Health System Translational Immunology Institute (TII) Sing Health Duke-NUS Academic Medical Centre Division of Gastroenterology and Hepatology University Medicine Cluster National University Hospital Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore Cancer Science Institute of Singapore National University of Singapore Division of Medical Oncology National Cancer Center Singapore Cardiovascular Research Institute National University of Singapore National University Healthcare System Singhealth-Duke-NUS Academic Surgery Program Duke-NUS Graduate Medical School Institute of Molecular and Cell Biology Agency for Science Technology and Research

Intra-tumor heterogeneity(ITH) is a key challenge in cancer treatment, but previous studies have focused mainly on the genomic alterations without exploring phenotypic(transcriptomic and immune)heterogeneity. Using one of the largest prospective surgical cohorts for hepatocellular carcinoma(HCC)with multi-region sampling, we sequenced whole genomes and paired transcriptomes from 67 HCC patients(331 samples). We found that while genomic ITH was rather constant across stages, phenotypic ITH had a very different trajectory and quickly diversified in stage Ⅱ patients. Most strikingly, 30% of patients were found to contain more than one transcriptomic subtype within a single tumor. Such phenotypic ITH was found to be much more informative in predicting patient survival than genomic ITH and explains the poor efficacy of single-target systemic therapies in HCC. Taken together, we not only revealed an unprecedentedly dynamic landscape of phenotypic heterogeneity in HCC, but also highlighted the importance of studying phenotypic evolution across cancer types.

关键词： hepatocellular carcinoma intra-tumor heterogeneity phenotypic evolution tumor evolution

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BSS1 as a negative regulator for brassinosteroid signaling that was identified by chemical biology using Brz

BSS1 as a negative regulator for brassinosteroid signaling t...

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The 2nd International Brassinosteroid Conference(第二届国际油菜素甾醇会议)

作者： Takeshi Nakano Setsuko Shimada Tomoyuki Komatsu Ayumi Yamagami Miki Nakazawa Minami Matsui Hiroshi Kawaide Masahiro Natsume Hiroyuki Osada Tadao Asami RIKEN Genome Science Center TsurumiYokohamaKanagawa 230-0045Japan Chemical Biology Group RIKEN Center for Sustainable Resource ScienceWakoSaitama 351-0198Japan Core Research for Evolutional Science and Technology(CREST) Japan Science and Technology Agency(JST)Japan Gene Discovery Research Group RIKEN Center for Sustainable Resource ScienceWakoSaitama 351-0198Japan United Graduate School of Agricultural Science Tokyo University of Agriculture and Technology(TUAT)Saiwai-ChoFuchuTokyo 183-8509Japan Synthetic Genomics Research Team Biomass Engineering Program Cooperation DivisionRIKEN Center for Sustainable Resource ScienceTsurumiYokohamaKanagawa 230-0045Japan Department of Applied Biological Chemistry The University of TokyoYayoiBunkyo-kuTokyo 113-8657Japan

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