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Rice transformation treatments leave specific epigenome changes beyond tissue culture

Plant physiology 2023年第2期193卷 1297-1312页

作者： Jo-Wei Allison Hsieh Pearl Chang Lin-Yun Kuang Yue-Ie C Hsing Pao-Yang Chen Institute of Plant and Microbial Biology Academia Sinica Taipei 115201 Taiwan. Genome and Systems Biology Degree Program Academia Sinica and National Taiwan University Taipei 10617 Taiwan. Department of Tropical Agriculture and International Cooperation/Department of Biological Science and Technology National Pingtung University of Science and Technology Pingtung 91201 Taiwan. The Transgenic Plant Core Facility Agricultural Biotechnology Research Center Academia Sinica Taipei 115201 Taiwan.

During transgenic plant production, tissue culture often carries epigenetic, and genetic changes that underlie somaclonal variations, leading to unpredictable phenotypes. Additionally, specific treatments for rice (Oryza sativa) transformation processes may individually or jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes toward transcriptional variations remain unknown. Here, the impact of individual transformation treatments on genome-wide DNA methylation and the transcriptome were examined. In addition to activating stress-responsive genes, individual transformation components targeted different gene expression modules that were enriched in specific functional categories. The transformation treatments strongly impacted DNA methylation and expression; 75% were independent of tissue culture. Furthermore, our genome-wide analysis showed that the transformation treatments consistently resulted in global hypo-CHH methylation enriched at promoters highly associated with downregulation, particularly when the promoters were colocalized with miniature inverted-repeat transposable elements. Our results clearly highlight the specificity of impacts triggered by individual transformation treatments during rice transformation with the potential association between DNA methylation and gene expression. These changes in gene expression and DNA methylation resulting from rice transformation treatments explain a significant portion of somaclonal variations, that is, way beyond the tissue culture effect.

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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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Porous FeAl alloys via powder sintering:Phase transformation,microstructure and aqueous corrosion behavior

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Journal of Materials science & technology 2021年第27期86卷 64-69页

作者： Gang Chen Klaus-Dieter Liss Chao Chen Yuehui He Xuanhui Qu Peng Cao Beijing Advanced Innovation Center for Materials Genome Engineering Institute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing100083PR China Materials and Engineering Science Program Guangdong Technion-Israel Institute of TechnologyShantouGuangdong515063PR China Technion-Israel Institute of Technology Haifa32000Israel School of Mechanical MaterialsMechatronic and Biomedical EngineeringFaculty of Engineering&Information SciencesUniversity of WollongongWollongongNSW2522Australia State Key Laboratory for Powder Metallurgy Central South UniversityChangsha410083PR China Department of Chemical and Materials Engineering The University of AucklandPrivate Bag 92019Auckland1142New Zealand MacDiarmid Institute of Advanced Materials and Nanotechnology Victoria University of WellingtonPO Box 600Wellington6140New Zealand

This study investigates the phase transformation and microstructure of porous Fe Al parts sintered from elemental powder mixtures using in-situ neutron diffraction and in-situ thermal dilatometry.A single B2 structured Fe Al phase was determined in the sintered Fe Al *** combined effects of the Kirkendall porosity,transient liquid phase,and phase transformations associated with powder sintering all contribute to the swelling phenomenon of the final sintered *** aqueous corrosion test indicates that the corrosion products include iron oxides in the porous Fe Al *** accumulation of corrosion products blocks the pore channel and decreases pore size and permeability over the soaking time.

关键词： Powder sintering Intermetallic Porous Corrosion Neutron diffraction

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BPS2025 - Elucidating the nanoscale clustering profiles of chimeric antigen receptors

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Biophysical Journal 2025年第3期124卷 105a-105a页

作者： Robert J. Pyron Sarah Binion Sarah A. Shelby Genome Science and Technology Program University of Tennessee Knoxville TN USA Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN USA

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High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry(Vaccinium darrowii)

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Horticulture Research 2021年第1期8卷 3321-3336页

作者： Jiali Yu Amanda M.Hulse-Kemp Ebrahiem Babiker Margaret Staton Genome Science and Technology Program University of TennesseeKnoxvilleTN 37996USA USDA-ARS Gen omics and Bioi nformatics Research Un it RaleighNCUSA Department of Crop and Soil Sciences North Carolina State UniversityRaleighNCUSA USDA-ARS Thad Cochran Southern Horticultural Laboratory PoplarvilleMSUSA Department of Entomology and Plant Pathology University of TennesseeKnoxvilleTN 37996USA

Vaccinium darrowii Camp(2 n=2×=24)is a native North American blueberry species and an important source oftraits such as low chill requirement in commercial southern highbush blueberry breeding(Vaccinium coymbosum,2n=4 ×=48).We present a chromosomal-scale genome of *** generated by the combination of PacBio sequencing and high throughput chromatin conformation capture(Hi-C)scaffolding technologies,yielding a total length of 1.06 Gigabases(Gb).Over 97.8%of the genome sequences are scaffolded into 24 chromosomes representing the two *** primary haplotype assembly of V,darrowii contains 34,809 protein-coding *** to a *** haplotype assembly reveals high collinearity between the two genomes with small intrachromosomal rearrangements in eight chromosome *** small RNA sequencing,the annotation was further expanded to include more than 200,000 small RNA loci and 638 microRNAs expressed in berry *** analysis across fruit development stages indicates that genes involved in photosynthesis are downregulated,while genes involved in flavonoid and anthocyanin biosynthesis are signi ficantly increased at the late stage of berry ripening.A high-quality reference genome and accompanying annotation of *** is a signi ficant new resource for assessing the evergreen blueberry contribution to the breeding of southern highbush blueberries.

关键词： breeding blue bases

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Artificial intelligence goes from predicting structure to predicting stability

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Magnetic Resonance Letters 2025年第1期5卷 75-76页

作者： Gary J.Pielak Conggang Li Maili Liu Department of Chemistry Department of Biochemistry&BiophysicsLineberger Cancer Centerand Integrative Program for Biological and Genome SciencesUniversity of North Carolina at Chapel HillChapel HillNC 27599United States Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular PhysicsNational Center for Magnetic Resonance in WuhanWuhan Institute of Physics and MathematicsInnovation Academy for Precision Measurement Science and TechnologyChinese Academy of SciencesWuhan430071China

AlphaFold[1]has turned everyone into a structural *** need for knowledge of Fourier transforms or spectral density,driven by artificial intelligence(AI),all one needs to do is enter the primary structure of a folded p... 详细信息

关键词： structure. structure predicting

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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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k-mer-based approaches to bridging pangenomics and population genetics

arXiv

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arXiv 2024年

作者： Roberts, Miles D. Davis, Olivia Josephs, Emily B. Williamson, Robert J. Genetics and Genome Sciences Program Michigan State University East LansingMI48824 United States Department of Computer Science and Software Engineering Rose-Hulman Institute of Technology Terre HauteIN47803 United States Department of Biology and Biomedical Engineering Rose-Hulman Institute of Technology Terre HauteIN47803 United States Department of Plant Biology Michigan State University East LansingMI48824 United States Ecology Evolution and Behavior Program Michigan State University East LansingMI48824 United States Plant Resilience Institute Michigan State University East LansingMI48824 United States

Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still lack multiple reference genomes and correctly aligning references to build pangenomes is challenging, limiting our ability to study this missing genomic variation in population genetics. Here, we argue that k-mers are a crucial stepping stone to bridging the reference-focused paradigms of population genetics with the reference-free paradigms of pangenomics. We review current literature on the uses of k-mers for performing three core components of most population genetics analyses: identifying, measuring, and explaining patterns of genetic variation. We also demonstrate how different k-mer-based measures of genetic variation behave in population genetic simulations according to the choice of k, depth of sequencing coverage, and degree of data compression. Overall, we find that k-mer-based measures of genetic diversity scale consistently with pairwise nucleotide diversity (π) up to values of about π = 0.025 (R2 = 0.97) for neutrally evolving populations. For populations with even more variation, using shorter k-mers will maintain the scalability up to at least π = 0.1. Furthermore, in our simulated populations, k-mer dissimilarity values can be reliably approximated from counting bloom filters, highlighting a potential avenue to decreasing the memory burden of k-mer based genomic dissimilarity analyses. For future studies, there is a great opportunity to further develop methods to identifying selected loci using k-mers. © 2024, CC BY.

关键词： genome

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Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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An integrated genetic-epigenetic analysis shed light on the mechanisms linking coronavirus disease 2019 (COVID-19) and cancer

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Cancer Communications 2021年第4期41卷 349-353页

作者： Zheng Dong Huiguang Yi Centre for Molecular Medicine and Therapeutics British Columbia Children’s Hospital Research InstituteUniversity of British ColumbiaVancouverBritish Columbia V5Z 4H4Canada Genome Science and Technology Graduate Program University of British ColumbiaVancouverBritish Columbia V5Z 4S6Canada Department of Epidemiology and Biostatistics University of GeorgiaAthensGeorgia 30602USA

Dear editor,The Coronavirus disease 2019(COVID-19)is an emerging disease caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection[1,2].It has spread rapidly across the world and caused a global health *** of 10 February 2021,COVID-19 has caused 2,333,446 deaths *** majority of COVID-19 deaths had comorbidities including cancer[1,2].

关键词： cancer acute respiratory

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