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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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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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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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Etiologic Determinants and Characteristics of Diabetes in Haitian Youth (EDDHY Study)

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Pediatric Diabetes 2025年第1期2025卷

作者： Eddy Jean-Baptiste Philippe Larco Julia E. Von Oettingen Janelle A. Noble Steven J. Mack Ningyi Song Harper R. N. Martin Erik Rozemuller Mark A. Atkinson Denira Govender Nancy Charles Larco Graham D. Ogle Fondation Haïtienne de Diabète et de Maladies Cardiovasculaires (FHADIMAC) Port-au-Prince Haiti Research Institute of the McGill University Health Centre Montreal Canada mcgill.ca Department of Endocrinology and Metabolism Montreal Children’s Hospital Montreal Canada *** Children’s Hospital Oakland Research Institute Oakland California USA *** Department of Pediatrics University of California San Francisco Oakland California USA berkeley.edu Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China *** GenDx Genome Diagnostics B.V. Utrecht Netherlands Department of Pathology Immunology and Laboratory Medicine College of Medicine Diabetes Institute University of Florida Gainesville Florida USA ufl.edu Department of Pediatrics College of Medicine Diabetes Institute University of Florida Gainesville Florida USA ufl.edu Life for a Child Program Diabetes Australia Glebe New South Wales Australia Sydney Medical School University of Sydney Sydney New South Wales Australia sydney.edu.au

Aims: Published information on youth-onset diabetes in Haiti is scarce, with limited data available on diabetes autoimmunity and genetic susceptibility to the disease. We determined the anthropometric, metabolic, and immunological characteristics and human leukocyte antigen (HLA)-associated risks in patients with youth-onset diabetes. Methods: One hundred and ten subjects with type 1 diabetes (T1D) aged <22 years and diagnosed for < 2 years were evaluated. Demographic and clinical information, as well as biochemical parameters, including blood glucose, hemoglobin A1c, fasting C-peptide (FCP), and T1D-associated autoantibodies, were assessed. DNA from 54 subjects and 66 controls was genotyped for classical HLA loci. Results: Of the 110 patients, 54% were male. Onset age was 13.5 ± 4.2 years (range 2–21), and disease duration was 11.7 ± 8.1 months (range 0–24). Idiopathic T1D was found in 62 (56.4%) patients and was diagnosed at an older age than immune-mediated T1D (14.4 ± 3.5 years vs., 12.3 ± 4.8 years, p = 0.01), with a higher BMI z-score in patients aged <14 years than in those aged ≥14 years (−0.29 ± 1.52 vs., −1.15 ± 1.18, p = 0.01). No correlation was found between immune-mediated T1D and BMI z-score. Diabetic ketoacidosis was present at diagnosis in 18 (16.4%) patients. Zinc transporter 8 autoantibodies (ZnT8A) were marginally more common in younger patients. Low FCP levels were found in 71 (64.5%) patients. Thyroid peroxidase antibodies (TPO-Ab) and thyroglobulin antibodies (TG-Ab) were positive in 1.1% and 2.2% of the patients, respectively. The alleles DRB1 ∗ 03:01 , DRB1 ∗ 09:01 , DQB1 ∗ 02:01 , and DQB1 ∗ 02:02 showed a significant T1D risk, whereas DRB1 ∗ 08:04 , DRB1 ∗ 15:03 , and DQB1 ∗ 06:02 were protective. Three DRB1~DQB1 haplotypes were strongly associated with T1D: DRB1 ∗ 03:01:01~DQB1 ∗ 02:01:01 , DRB1 ∗ 09:01:02~DQB1 ∗ 02:02:01 , both predisposing, and DRB1 ∗ 15:03:01~DQB1 ∗ 06:02:01 , protective . Conclusions: Idiopathic T1D is common among yo

关键词： autoimmunity genetics idiopathic type 1 diabetes youth-onset diabetes

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Whole-genome sequencing analyses suggest novel genetic factors associated with Alzheimer's disease and a cumulative effects model for risk liability

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Nature communications 2025年第1期16卷 4870页

作者： Jun Pyo Kim Minyoung Cho Chanhee Kim Hyunwoo Lee Beomjin Jang Sang-Hyuk Jung Yujin Kim In Gyeong Koh Seoyeon Kim Daeun Shin Eun Hye Lee Jong-Young Lee YoungChan Park Hyemin Jang Bo-Hyun Kim Hongki Ham Beomsu Kim A-Hyun Cho Towfique Raj Hee Jin Kim Duk L Na Sang Won Seo Joon-Yong An Hong-Hee Won Alzheimer's Disease Convergence Research Center Samsung Medical Center Seoul Republic of Korea. Department of Neurology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Republic of Korea. Neuroscience Center Samsung Medical Center Seoul Republic of Korea. Department of Digital Health Samsung Advanced Institute for Health Sciences & Technology (SAIHST) Sungkyunkwan University Seoul Republic of Korea. Department of Integrated Biomedical and Life Science Korea University Seoul Republic of Korea. L-HOPE Program for Community-Based Total Learning Health Systems Korea University Seoul Republic of Korea. Department of Health Sciences and Technology Samsung Advanced Institute for Health Sciences & Technology (SAIHST) Sungkyunkwan University Seoul Republic of Korea. Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York NY USA. Nash Family Department of Neuroscience & Friedman Brain Institute Icahn School of Medicine at Mount Sinai New York NY USA. Ronald M. Loeb Center for Alzheimer's Disease Icahn School of Medicine at Mount Sinai New York NY USA. Department of Medical Informatics Kangwon National University College of Medicine Chuncheon Republic of Korea. Department of Radiology and Imaging Sciences Indiana University School of Medicine Indianapolis IN USA. Indiana Alzheimer Disease Research Center Indiana University School of Medicine Indianapolis IN USA. Oneomics Co. Ltd Gyeonggi-do Republic of Korea. Division of Bio Bigdata Department of Precision Medicine Korea National Institution of Health Cheongju Republic of Korea. Department of Neurology Seoul National University Hospital Seoul National University School of Medicine Seoul Republic of Korea. Icahn Institute for Data Science and Genomic Technology Icahn School of Medicine at Mount Sinai New York NY USA. Estelle and Daniel Maggin Department of Neurology Icahn School of Medicine at Mount Sinai New York NY USA. Alzheimer's Disease Convergen

genome-wide association studies (GWAS) on Alzheimer's disease (AD) have predominantly focused on identifying common variants in Europeans. Here, we performed whole-genome sequencing (WGS) of 1,559 individuals from a Korean AD cohort to identify various genetic variants and biomarkers associated with AD. Our GWAS analysis identified a previously unreported locus for common variants (APCDD1) associated with AD. Our WGS analysis was extended to explore the less-characterized genetic factors contributing to AD risk. We identified rare noncoding variants located in cis-regulatory elements specific to excitatory neurons associated with cognitive impairment. Moreover, structural variation analysis showed that short tandem repeat expansion was associated with an increased risk of AD, and copy number variant at the HPSE2 locus showed borderline statistical significance. APOE ε4 carriers with high polygenic burden or structural variants exhibited severe cognitive impairment and increased amyloid beta levels, suggesting a cumulative effects model of AD risk.

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Advancing precision medicine through the integration of clinical cardiovascular genetics - An Asian perspective

Genetics in Medicine Open

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Genetics in Medicine Open 2024年 2卷 101877-101877页

作者： Balakrishnan, Iswaree D. Bylstra, Yasmin Fong, Nikki Chai, Nellie B.S. Kam, Sylvia Khoo, Chun Yuan Chan, Laura L.H. Koh, Angela S. Tang, Hak Chiaw Lim, Eric Tan, Ju Le Lim, Weng Khong Pua, Chee Jian Sim, David Cook, Stuart A. Tan, Ee Shien Yeo, Khung Keong Jamuar, Saumya S. Department of Cardiology National Heart Centre Singapore Singapore SingHealth Duke-NUS Genomic Medicine Centre Singapore SingHealth Duke-NUS Institute of Precision Medicine Singapore Genetics Service Department of Paediatrics KK Women's and Children's Hospital Singapore Cardiovascular and Metabolic Disorders Program Duke-NUS Medical School Singapore Singapore Cancer & Stem Cell Biology Program Duke-NUS Medical School Singapore Laboratory of Genome Variation Analytics Genome Institute of Singapore Agency for Science Technology and Research Singapore National Heart Research Institute Singapore National Heart Centre Singapore Singapore

Purpose: The integration of cardiovascular genetic (CVG) testing into clinical practice is gaining recognition, but its implementation in the Asian setting has not been widely reported. We present our experience developing a clinical CVG service and analyze its impact on patient care at our center. Methods: In 2020, the National Heart Centre Singapore collaborated with SingHealth Duke-NUS Genomic Medicine Centre, to establish a comprehensive clinical CVG service. We retrospectively gathered details regarding referral indication and the clinical utility of genetic counseling and testing. Results: Over a period of 2.5 years, 113 patients aged 17 to 94 years, were seen by the CVG team. The cohort included 79 males and 34 females: 82 of Chinese ancestry, 11 Indian, 7 Malay, and 13 from other ancestries. The most common reason for referral was for cardiomyopathy, followed by aortopathy. After clinical evaluation, 98 patients were offered genetic testing, of which 63 (64%) patients proceeded with genetic testing (diagnostic testing n = 51, predictive testing n = 10, familial segregation analysis n = 2). Eleven patients were referred for continuation of care. Overall, CVG testing added value to the care of 44 patients by clarifying clinical diagnosis, ruling out inherited cardiac disorders, aiding variant of uncertain significance resolution, and/or facilitating cascade testing. Conclusion: Our pilot initiative has provided insights into the practical value, obstacles, and opportunities for developing a clinical CVG service. The establishment of our clinical CVG service not only enhanced patient care but also demonstrated its scalability through collaborative partnerships with domain experts. © 2024 The Authors

关键词： Asian population Cardiovascular genetics Genetic counselling Precision medicine

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Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

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Plant Communications 2022年第1期3卷 53-70页

作者： Dmitry A.Semchonok Jyotirmoy Mondal Connor J.Cooper Katrina Schlum Meng Li Muhamed Amin Carlos O.S.Sorzano Erney Ramirez-Aportela Panagiotis L.Kastritis Egbert J.Boekema Albert Guskov Barry D.Bruce Groningen Biomolecular Sciences&Biotechnology Institute University of GroningenGroningenthe Netherlands Biochemistry&Cellular and Molecular Biology Department University of TennesseeKnoxvilleTNUSA Program in Genome Science and Technology University of TennesseeKnoxvilleTNUSA Bredesen Center for Interdisciplinary Research&Education University of TennesseeKnoxvilleTNUSA Department of Sciences University College GroningenGroningenthe Netherlands Biocomputing Unit National Center for Biotechnology(CSIC)Darwin 3Campus Universidad Auto´noma de MadridCantoblanco28049 MadridSpain Universidad CEU San Pablo Campus Urb.Monteprı´ncipeBoadilla del Monte28668 MadridSpain Institute of Biochemistry and Biotechnology Martin Luther University Halle-WittenbergHalle/SaaleGermany Microbiology Department University of TennesseeKnoxvilleTNUSA Present address:Institute of Biochemistry and Biotechnology Martin Luther University Halle-WittenbergHalle/SaaleGermany School of Oceanography University of WashingtonSeattleWAUSA

Photosystem I(PSI)is one of two photosystems involved in oxygenic *** of cyanobacteria exists in monomeric,trimeric,and tetrameric forms,in contrast to the strictly monomeric form of PSI in plants and *** tetrameric organization raises questions about its structural,physiological,and evolutionary *** we report the3.72 A˚resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic,unicellular cyanobacterium Chroococcidiopsis *** structure resolves 44 subunits and 448 cofactor *** conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers *** localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent *** analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric *** PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.

关键词： cryo-EM photosystem I non-heterocyst-forming cyanobacteria Chroococcidiopsis evolution of chloroplast high light adaptation

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Whole genome Gene Discovery in the Pathogenic Oomycete Pythium insidiosum by 454 Sequencing technology

Whole Genome Gene Discovery in the Pathogenic Oomycete Pythi...

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The Annual Oomycete Molecular Genetics Network Meeting(国际卵菌分子遗传学年会)

作者： Theerapong Krajaejun Shoba Ranganathan Rommanee Khositnithikul Tassanee Lerksuthirat Tassanee Lowhnoo Thidarat Rujirawat Wanta Yingyong Prapat Suriyaphol Sittichoke Tangphatsornruang Gagan Garg Department of Pathology Mahidol University Bangkok Department of Chemistry and Biomolecular Sciences Macquarie University Australia Molecular Medicine Program Multidisciplinary Unit Faculty of Science Mahidol University Bangkok Research Center Faculty of Medicine Ramathibodi HospitalMahidol University Bangkok Bioinformatics and Data Management for Research Office for Research and Development Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Genome Sequencing Laboratory National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency PathumthaniThailand

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