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arXiv 2017年

作者： Deforet, Maxime Carmona-Fontaine, Carlos Korolev, Kirill S. Xavier, Joao B. Sorbonne Université Centre National de la Recherche Rcientifique Laboratoire Jean Perrin LJP Paris75005 France Center for Genomics and Systems Biology Department of Biology New York University New York CityNY10003 United States Department of Physics Graduate Program in Bioinformatics Boston University BostonMA02215 Program in Computational Biology Memorial Sloan-Kettering Cancer Center New York CityNY10065 United States

Predicting evolution of expanding populations is critical to control biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of evolution where organisms pay a reproductive cost to disperse faster. When does selection favor this 'survival of the fastest?' We searched for a simple rule, motivated by evolution experiments where swarming bacteria evolved into an hyperswarmer mutant which disperses ∼ 100% faster but pays a growth cost of ∼ 10% to make many copies of its flagellum. We analyzed a two-species model based on the Fisher equation to explain this observation: the population expansion rate (v) results from an interplay of growth (r) and dispersal (D) and is independent of the carrying capacity: v = 2 √rD. A mutant can take over the edge only if its expansion rate (v2) exceeds the expansion rate of the established species' (v1);this simple condition (v2> v1) determines the maximum cost in slower growth that a faster mutant can pay and still be able to take over. Numerical simulations and time-course experiments where we tracked evolution by imaging bacteria suggest that our findings are general: less favorable conditions delay but do not entirely prevent the success of the fastest. Thus, the expansion rate defines a traveling wave fitness, which could be combined with trade-offs to predict evolution of expanding populations. Copyright © 2017, The Authors. All rights reserved.

关键词： Bacteria

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Graph Representation Learning in Biomedicine

arXiv

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arXiv 2021年

作者： Li, Michelle M. Huang, Kexin Zitnik, Marinka Bioinformatics and Integrative Genomics Program Harvard Medical School BostonMA02115 United States Health Data Science Program Harvard T.H. Chan School of Public Health BostonMA02115 United States Department of Biomedical Informatics Harvard Medical School BostonMA02115 United States Broad Institute of MIT and Harvard CambridgeMA02142 United States Harvard Data Science Initiative CambridgeMA02138 United States

Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence, specifically deep learning, have enabled us to model, analyze, and learn with such networked data. In this review, we put forward an observation that long-standing principles of systems biology and medicine-while often unspoken in machine learning research-provide the conceptual grounding for representation learning on graphs, explain its current successes and limitations, and even inform future advancements. We synthesize a spectrum of algorithmic approaches that, at their core, leverage graph topology to embed networks into compact vector spaces. We also capture the breadth of ways in which representation learning has dramatically improved the state-of-the-art in biomedical machine learning. Exemplary domains covered include identifying variants underlying complex traits, disentangling behaviors of single cells and their effects on health, assisting in diagnosis and treatment of patients, and developing safe and effective medicines. © 2021, CC BY.

关键词： Vector spaces

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Remarkable sequence signatures in archaeal genomes

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Archaea 2003年第3期1卷 185-190页

作者： Fadiel, Ahmed Lithwick, Stuart Ganji, Gopi Scherer, Stephen W. Center for Applied Genomics Hospital for Sick Children Toronto Ont. M5G 1Z8 Canada Bioinformatics Supercomputing Centre Genom. and Genetics Biology Program Hospital for Sick Children Toronto Ont. M5G 1Z8 Canada

Complete archaeal genomes were probed for the presence of long (≥ 25 bp) oligonucleotide repeats (words). We detected the presence of many words distributed in tandem with narrow ranges of periodicity (i.e., spacer length between repeats). Similar words were not identified in genomes of non-archaeal species, namely Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Mycoplasma genitalium and Mycoplasma pneumoniae. BLAST similarity searches against the GenBank nucleotide sequence database revealed that these words were archaeal species-specific, indicating that they are of a signature character. Sequence analysis and genome viewing tools showed these repeats to be restricted to non-coding regions. Thus, archaea appear to possess a non-coding genomic signature that is absent in bacterial species. The identification of a species-specific genomic signature would be of great value to archaeal genome mapping, evolutionary studies and analyses of genome complexity.

关键词： Archaea bioinformatics Comparative genomics Genome signature Oligonucleotide frequencies

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SYSTEMS BIOLOGY IN BARLEY POWDERY MILDEW INTERACTIONS

SYSTEMS BIOLOGY IN BARLEY POWDERY MILDEW INTERACTIONS

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The 13th International Cereal Rusts and Powdery Mildews Conference(第13届国际禾谷类锈病与白粉病大会)

作者： Roger WISE Priyanka SURANA Greg FUERST Ruo XU Dan NETTLETON Divya MISTRY Julie DICKERSON Lin WANG Tom BRUTNELL Department of Plant Pathology and Microbiology Center for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011USA Department of Statistics Iowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate Program Iowa State UniversityAmesIowa 50011USA Department of Plant Pathology and MicrobiologyCenter for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011USA Crop and Insect Genetics Genomicsand Informatics Research UnitU.S.Department of Agriculture-Agricultural Research ServiceIowa State UniversityAmesIowa 50011USA Department of Plant Pathology and Microbiology Center for Plant Responses to Environmental StressesIowa State UniversityAmesIowa 50011USA Department of StatisticsIowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesIowa 50011USA Bioinformatics and Computational Biology Graduate Program Iowa State UniversityAmesIowa 50011USA Crop and Insect GeneticsGenomicsand Informatics Research UnitU.S.Department of Agriculture-Agricultural Research ServiceIowa State UniversityAmesIowa 50011USA Department of Electrical and Computer Engineering Iowa State UniversityAmesIowa 50011USA Boyce Thompson Institute for Plant ResearchCornell UniversityIthacaNY

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Targeting protein-protein interaction interfaces with antiviral N protein inhibitor in SARS-CoV-2

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Biophysical Journal 2024年第4期123卷 478-488页

作者： Hong, Jhen-Yi Lin, Shih-Chao Kehn-Hall, Kylene Zhang, Kai-Min Luo, Shun-Yuan Wu, Hung-Yi Chang, Sui-Yuan Hou, Ming-Hon Institute of Genomics and Bioinformatics and Department of Life Sciences National Chung Hsing University Taichung Taiwan Bachelor Degree Program in Marine Biotechnology College of Life Sciences National Taiwan Ocean University Keelung Taiwan Department of Biomedical Sciences and Pathobiology Virginia-Maryland College of Veterinary Medicine Virginia Polytechnic Institute and State University Blacksburg VA United States Center for Emerging Zoonotic and Arthropod-borne Pathogens Virginia Polytechnic Institute and State University Blacksburg VA United States Department of Chemistry National Chung Hsing University Taichung Taiwan Graduate Institute of Veterinary Pathobiology College of Veterinary Medicine National Chung Hsing University. Taichung Taiwan Department of Clinical Laboratory Sciences and Medical Biotechnology College of Medicine National Taiwan University Taipei Taiwan PhD Program in Medical Biotechnology National Chung Hsing University Taichung Taiwan Biotechnology Center National Chung Hsing University Taichung Taiwan

Coronaviruses not only pose significant global public health threats but also cause extensive damage to livestock-based industries. Previous studies have shown that 5-benzyloxygramine (P3) targets the Middle East respiratory syndrome coronavirus (MERS-CoV) nucleocapsid (N) protein N-terminal domain (N-NTD), inducing non-native protein-protein interactions (PPIs) that impair N protein function. Moreover, P3 exhibits broad-spectrum antiviral activity against CoVs. The sequence similarity of N proteins is relatively low among CoVs, further exhibiting notable variations in the hydrophobic residue responsible for non-native PPIs in the N-NTD. Therefore, to ascertain the mechanism by which P3 demonstrates broad-spectrum anti-CoV activity, we determined the crystal structure of the SARS-CoV-2 N-NTD:P3 complex. We found that P3 was positioned in the dimeric N-NTD via hydrophobic contacts. Compared with the interfaces in MERS-CoV N-NTD, P3 had a reversed orientation in SARS-CoV-2 N-NTD. The Phe residue in the MERS-CoV N-NTD:P3 complex stabilized both P3 moieties. However, in the SARS-CoV-2 N-NTD:P3 complex, the Ile residue formed only one interaction with the P3 benzene ring. Moreover, the pocket in the SARS-CoV-2 N-NTD:P3 complex was more hydrophobic, favoring the insertion of the P3 benzene ring into the complex. Nevertheless, hydrophobic interactions remained the primary stabilizing force in both complexes. These findings suggested that despite the differences in the sequence, P3 can accommodate a hydrophobic pocket in N-NTD to mediate a non-native PPI, enabling its effectiveness against various CoVs. © 2024 Biophysical Society

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High Resolution Imaging of Virus in Liquid Droplets: The Application of Cryo-TEM Methodology to Improve Liquid-phase TEM Imaging of Biological Materials

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Microscopy and Microanalysis 2021年第S2期27卷 19-20页

作者： Madeline J. Dukes GM Jonaid William J. Dearnaley Michael A. Casasanta Deborah F. Kelly Protochips Inc.Morrisville NC USA. Bioinformatics and Genomics Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA USA. Department of Biomedical Engineering Pennsylvania State University University Park PA USA. Materials Research Institute Pennsylvania State University University Park PA USA. Center for Structural Oncology Pennsylvania State University University Park PA16802 USA.

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Evolution of olfactory receptor genes in East Asian loaches

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Zoological Studies 2009年第2期48卷 223-237页

作者： Wang, Daryi Wang, Tzi-Yuan Weng, Li-Chuan Emori, Yasufumi Tzeng, Chyng-Shyan Li, Wen-Hsiung Biodiversity Research Center Academia Sinica Taipei 115 Taiwan Genomics Research Center Academia Sinica Taipei 115 Taiwan Department of Biophysics and Biochemistry Graduate School of Science University of Tokyo Bunkyo Tokyo 113-0033 7-3-1 Hongo Japan Undergraduate Program for Bioinformatics and System Biology University of Tokyo Bunkyo Tokyo 113-0033 7-3-1 Hongo Japan Institute of Bioinformatics and Structural Biology Department of Life Sciences National Tsing Hua University Hsinchu 300 Taiwan

Daryi Wang, Tzi-Yuan Wang, Li-Chuan Weng, Yasufumi Emori, Chyng-Shyan Tzeng, and Wen-Hsiung Li (2009) Evolution of olfactory receptor genes in East Asian loaches. Zoological Studies 48(2): 223-237. It is well known that fish have fewer olfactory receptor (OR) genes than mammals do. In order to investigate the divergence of and evolutionary changes in OR genes in fish, 2 loach OR gene families (D1/3 and D32) from Taiwanese and Chinese populations of 2 species (Misgurnus anguillicaudatus and Paramisgurnus dabryanus) were analyzed. We found duplications in both D1/3 and D32 that had accumulated after the separation of the island of Taiwan from the Asian mainland ~5 million yrs ago. The accumulation of duplicate copies in a relatively short time suggests that gaining extra copies of OR genes may have been selectively advantageous for adapting to local environments. On the other hand, the loss of some OR genes in the 2 species in Taiwan may reflect loss of selective constraints on some OR genes. Moreover, unlike the situation in mammals in which pseudogenes are found in each family, pseudogenes are clustered in an expanding gene family in P. dabryanus in Taiwan. The presence of pseudogenes and the limited number of functional OR genes in fish suggest that fish do not need a large number of OR genes. Finally, the dynamic changes in OR gene number and the possible explanation for a lower OR gene number in fish are discussed. http://***/Journals/48.2/***.

关键词： Adaptation Misgurnus anguillicaudatus Multigene family Olfaction Paramisgurnus dabryanus

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Artificial intelligence in gastrointestinal radiology: A review with special focus on recent development of magnetic resonance and computed tomography

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Artificial Intelligence in Gastroenterology 2021年第2期2卷 27-41页

作者： Kai-Po Chang Shih-Huan Lin Yen-Wei Chu PhD Program in Medical Biotechnology National Chung Hsing UniversityTaichung 40227Taiwan Department of Pathology China Medical University HospitalTaichung 40447Taiwan Institute of Genomics and Bioinformatics National Chung Hsing UniversityTaichung 40227Taiwan Institute of Molecular Biology National Chung Hsing UniversityTaichung 40227Taiwan Agricultural Biotechnology Center National Chung Hsing UniversityTaichung 40227Taiwan Biotechnology Center National Chung Hsing UniversityTaichung 40227Taiwan PhD Program in Translational Medicine National Chung Hsing UniversityTaichung 40227Taiwan Rong Hsing Research Center for Translational Medicine Taichung 40227Taiwan

Artificial intelligence(AI),particularly the deep learning technology,have been proven influential to radiology in the recent *** ability in image classification,segmentation,detection and reconstruction tasks have substantially assisted diagnostic radiology,and has even been viewed as having the potential to perform better than radiologists in some *** radiology,an important subspecialty dealing with complex anatomy and various modalities including endoscopy,have especially attracted the attention of AI researchers and engineers ***,recently many tools have been developed for lesion detection and image construction in gastrointestinal radiology,particularly in the fields for which public databases are available,such as diagnostic abdominal magnetic resonance imaging(MRI)and computed tomography(CT).This review will provide a framework for understanding recent advancements of AI in gastrointestinal radiology,with a special focus on hepatic and pancreatobiliary diagnostic radiology with MRI and *** fields where AI is less developed,this review will also explain the difficulty in AI model training and possible strategies to overcome the technical *** authors’insights of possible future development will be addressed in the last section.

关键词： Artificial intelligence Deep learning Image diagnosis Radiology Magnetic resonance imaging Computed tomography

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Array-Based High-Throughput Screening UNIT 5C.3 in Mouse Embryonic Stem Cells with shRNAs

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Current Protocols in Stem Cell Biology 2013年第SUPPL.26期1卷 5C.3.1-5C.3.19页

作者： Wang, Chia-Hui Ma, Nianhan Lin, Yu-Tsen Wu, Cheng-Chung Wu, Hong-Jin Yu, Ching-Chia Hsiao, Michael Lu, Frank Leigh Schuyler, Scott C. Lu, Jean Genomics Research Center Academia Sinica Taipei Taiwan Institute of Systems Biology and Bioinformatics National Central University Taoyuan Taiwan Graduate Institute of Life Sciences National Defense Medical Center Taipei Taiwan Department of Pediatrics National Taiwan University Hospital and National Taiwan University Medical College Taipei Taiwan Department of Biomedical Sciences College of Medicine Chang Gung University Taoyuan County Taiwan Genomics and System Biology Program College of Life Science National Taiwan University Taipei Taiwan National Core Facility Program for Biotechnology National RNAi Platform Taipei Taiwan

High-throughput short-hairpin RNA (shRNA) lentivirus screening is a powerful tool for identifying multiple functional regulators in embryonic stem cells (ESCs). shRNA libraries can efficiently down-regulate target genes persistently with high efficiency. The concurrent measurement of relative cell number by alamarBlue (AB) assay and undifferentiated ESC markers via an alkaline phosphatase (ALP) activity assay in the same cell culture well provides an efficient and economical way to pinpoint factors crucial for ESC pluripotency and/or expansion. Most of the renewal pathways affect ALP activity. Thus, multiple positive and negative regulators can be identified by this method. In addition, morphological changes and/or the expression levels of specific pluripotency or differentiation markers examined by immunofluorescence can be used as secondary screens for target-gene selection. In summary, we describe an efficient way to identify multiple regulators of ESC renewal using shRNAs. © 2013 by John Wiley & Sons, Inc.

关键词： Embryonic stem cells High-throughput screening RNA interference Short-hairpin RNA

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Enhancement of cellulase activity from a new strain of bacillus subtilis by medium optimization and analysis with various cellulosic substrates

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Enzyme Research 2011年第1期2011卷 151656页

作者： Deka, Deepmoni Bhargavi, P. Sharma, Ashish Goyal, Dinesh Jawed, M. Goyal, Arun Centre for the Environment Indian Institute of Technology Guwahati Assam Guwahati 781039 India Department of Biotechnology Indian Institute of Technology Guwahati Assam Guwahati 781039 India Bioinformatics and Genomics Program Pennsylvania State University University Park PA 16802-5301 United States Department of Biotechnology and Environmental Sciences Thapar University Punjab Patiala 140007 Bhadson Road India

The cellulase activity of Bacillus subtilis AS3 was enhanced by optimizing the medium composition by statistical methods. The enzyme activity with unoptimised medium with carboxymethylcellulose (CMC) was 0.07 U/mL and that was significantly enhanced by CMC, peptone, and yeast extract using Placket-Burman design. The combined effects of these nutrients on cellulase activity were studied using 2² full factorial central composite design. The optimal levels of medium components determined were CMC (1.8%), peptone (0.8%), and yeast extract (0.479%). The maximum enzyme activity predicted by the model was 0.49 U/mL which was in good agreement with the experimental value 0.43 U/mL showing 6-fold increase as compared to unoptimised medium. The enzyme showed multisubstrate specificity, showing significantly higher activity with lichenan and -glucan and lower activity with laminarin, hydroxyethylcellulose, and steam exploded bagasse. The optimised medium with lichenan or -glucan showed 2.5- or 2.8-fold higher activity, respectively, at same concentration as of CMC. © 2011 Deepmoni Deka et al.

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