Article
Multidisciplinary Sciences
Bindu J. Subhadra, Dianjun Cao, Roderick Jensen, Clayton Caswell, Thomas Inzana
Summary: This study identified and partially characterized Hfq-associated sRNAs in Histophilus somni. Co-immunoprecipitation and sRNA sequencing identified 100 putative sRNAs, with 16 present in the pathogenic strain. Bioinformatics analysis suggested that certain sRNAs could bind to genes involved in virulence/biofilm formation. Further experiments confirmed sRNA-Hfq binding and determined the transcriptional start sites. This investigation provides insight into the regulatory roles of sRNAs in H. somni virulence and biofilm formation.
Article
Microbiology
Tamara Alhamami, Wai Yee Low, Yan Ren, Kara Taylor, Manouchehr Khazandi, Tania Veltman, Henrietta Venter, Mandi Carr, Conny Turni, Sam Abraham, Darren J. Trott
Summary: This study investigated the antimicrobial susceptibility and phylogenetic relationships of H. somni isolates from Australian feedlot cattle. The results showed that these isolates did not exhibit resistance to the tested antimicrobials and had limited genetic diversity.
VETERINARY MICROBIOLOGY
(2022)
Article
Microbiology
Qian Wang, Lei Zhang, Yiju Zhang, Huamin Chen, Jianghua Song, Mingjie Lyu, Rui Chen, Lixin Zhang
Summary: This study reveals the genome sequence of B. pumilus strain HM-7 and identifies its potential pathogenic mechanisms. The findings provide a foundation for developing effective prevention and control strategies against this pathogen in the future.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Environmental Sciences
Krittayapong Jantharadej, Akechai Kongprajug, Wuttichai Mhuantong, Tawan Limpiyakorn, Benjaporn Boonchayaanant Suwannasilp, Skorn Mongkolsuk, Kwanrawee Sirikanchana
Summary: This study used next-generation sequencing to investigate the microbial community structures, bacterial and viral pathogens, and antimicrobial resistance genes in water commuting in Thailand. The results showed different microbial clusters in different zones, with distinct separation between cultural and suburban sites. Various bacterial and viral pathogens were identified, as well as antimicrobial resistance genes. The abundance of resistance genes and certain pathogens in cultural sites differed significantly from other sites.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Mai Farghaly, Michael F. Hynes, Mohammad Nazari, Sylvia Checkley, Karen Liljebjelke
Summary: Integrative and conjugative elements (ICEs) are important in facilitating horizontal gene transfer and the dissemination of antimicrobial resistance between bacteria. A study identified an ICEHs02 in Histophilus somni that carries multiple antimicrobial resistance genes and can be transferred to other bacteria. The study found that tetracycline and ciprofloxacin induction significantly increased the transfer rates of ICEHs02, and the acquisition of ICEHs02 reduced the relative fitness of the host bacteria.
CANADIAN JOURNAL OF MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zhien He, Yongqiang Yang, Wei Li, Xiaoling Ma, Changfeng Zhang, Jingxiang Zhang, Baolin Sun, Tao Ding, Guo-Bao Tian
Summary: This study provides important information on Enterobacteriaceae bacteria carrying mcr-like genes and serves as a reference for the study of mcr-1 transmission in China and globally.
Article
Biochemistry & Molecular Biology
Peng Lu, Jiaqiao Zhou, Sibo Wei, Konosuke Takada, Hayato Masutani, Suguru Okuda, Ken Okamoto, Michio Suzuki, Tomoya Kitamura, Kentaro Masujin, Takehiro Kokuho, Hideaki Itoh, Koji Nagata
Summary: African swine fever (ASF) is a devastating disease caused by the African swine fever virus (ASFV) that threatens the pig industry and food security worldwide. This study identified potential vaccine targets for developing a broad-spectrum defense against ASFV by analyzing genomic and transcriptomic data of different ASFV strains. The results provide valuable candidate ORFs for ASF vaccine development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Agronomy
Jiaqi You, Min Lin, Zhenping Liu, Liuling Pei, Yuexuan Long, Lili Tu, Xianlong Zhang, Maojun Wang
Summary: This study characterizes the regulatory divergence of the transcriptional network in cotton after polyploidization. Conservation of promoter sites and transcription factor binding sites (TFBS) is associated with coordinated gene expression. Genomic variations in TFBS contribute to the formation of novel regulatory networks in tetraploid cotton. The turnover of TFBS is linked to expression pattern divergence of genes involved in fiber development.
Article
Biotechnology & Applied Microbiology
Fan Jiang, Yaoxin Jiang, Wenxuan Wang, Changyi Xiao, Ruiyi Lin, Tanghui Xie, Wing-Kin Sung, Shijun Li, Ivan Jakovlic, Jianhai Chen, Xiaoyong Du
Summary: This study conducted chromosome-level genome assembly of the Muscovy duck and comparative genomic analysis, revealing unique gene families in Muscovy duck compared to other bird species, with adaptive evolution signals in immune defence pathways. The results provide valuable resources for future molecular ecology studies and the evolutionary arms race between hosts and influenza viruses.
Article
Microbiology
Daoxin Dai, Huibin Lu, Peng Xing, Qinglong Wu
Summary: This study provides a comprehensive profile of the genomic features of the Nesterenkonia genus and reveals the possible mechanism for the survival of Nesterenkonia isolates in polar areas.
Article
Multidisciplinary Sciences
Steven Russum, Katie Jing Kay Lam, Nicholas Alan Wong, Vasu Iddamsetty, Kevin J. Hendargo, Jianing Wang, Aditi Dubey, Yichi Zhang, Arturo Medrano-Soto, Milton H. Saier
Summary: The Asgard superphylum of archaea, especially the Loki phylum, is closely related to eukaryotes and heavily relies on proton motive force for substrate transport, mainly organic molecules such as lipid precursors, amino acids, and sugars. The majority of identified transporters are more similar to prokaryotic transporters, supporting the mixotrophic and anaerobic nature of Asgard organisms while clarifying their metabolic potential and relation to eukaryotes.
Article
Microbiology
Hongchao Chen, Zhe Zhan, Xiaoyuan Jiang, Yang Qing, Zhe Yin, Lingling Mei, Dongsheng Zhou, Bin Ni, Yanjun Zhang
Summary: This study found that plasmids with single Inc(pA1763-KPC) replicons are less studied despite their emergence in some strains. Through genome sequencing and comparison, it was discovered that plasmids pA1763-KPC and p427113-2 from two clinical Klebsiella pneumoniae isolates showed different backbone structures compared to six previously sequenced representative Inc(pA1763-KPC) plasmids.
JOURNAL OF BASIC MICROBIOLOGY
(2021)
Article
Microbiology
Hongbo Jiang, Jie Bao, Yuenan Xing, Xiaodong Li, Qijun Chen
Summary: This study sequenced the whole genome of the pathogenic yeast M. bicuspidata LNES0119 and performed comparative genomic analysis, identifying several characteristics related to pathogenicity and virulence. The findings provide valuable insights into understanding the molecular basis of M. bicuspidata pathogenicity and potential therapeutic targets.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Yushan Lin, Jinge Han, Herman W. Barkema, Yue Wang, Jian Gao, John P. Kastelic, Bo Han, Shunyi Qin, Zhaoju Deng
Summary: This study provides important genomic insights into the bovine mastitis pathogen Lactococcus garvieae, revealing diverse genetic features and potential host adaptations.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Ling Xu, Mengting Cao, Qichao Wang, Jiahao Xu, Chenglin Liu, Najeeb Ullah, Juanjuan Li, Zhuoni Hou, Zongsuo Liang, Weijun Zhou, Ake Liu
Summary: This study investigates the periderm-like structure in the underground stem of Salvia castanea and explores the molecular evolutionary mechanisms of its adaptation to the Qinghai-Tibetan plateau (QTP). Through morphological observation and full-length transcriptome analysis, the study proposes a trunk-branches developmental model and identifies key transcription factors involved in the high accumulation of secondary metabolites in S. castanea tissues. Comparative genomic analyses reveal the phylogenetic position of S. castanea and the genetic changes associated with its morphogenesis and QTP adaptation.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Cardiac & Cardiovascular Systems
Matthew B. Carson, Denise M. Scholtens, Conor N. Frailey, Stephanie J. Gravenor, Emilie S. Powell, Amy Y. Wang, Gayle Shier Kricke, Faraz S. Ahmad, R. Kannan Mutharasan, Nicholas D. Soulakis
CIRCULATION-CARDIOVASCULAR QUALITY AND OUTCOMES
(2016)
Article
Cell Biology
Wenyi Qin, Guijun Zhao, Matthew Carson, Caiyan Jia, Hui Lu
IET SYSTEMS BIOLOGY
(2016)
Article
Computer Science, Information Systems
Gayle Shier Kricke, Matthew B. Carson, Young Ji Lee, Corrine Benacka, R. Kannan Mutharasan, Faraz S. Ahmad, Preeti Kansal, Clyde W. Yancy, Allen S. Anderson, Nicholas D. Soulakis
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2017)
Article
Medicine, Research & Experimental
Cliff Shunsheng Han
MEDICAL HYPOTHESES
(2016)
Article
Multidisciplinary Sciences
Caiyan Jia, Yafang Li, Matthew B. Carson, Xiaoyang Wang, Jian Yu
SCIENTIFIC REPORTS
(2017)
Article
Computer Science, Artificial Intelligence
Caiyan Jia, Matthew B. Carson, Xiaoyang Wang, Jian Yu
PATTERN RECOGNITION
(2018)
Article
Computer Science, Information Systems
Sara Gonzales, Matthew B. Carson, Guillaume Viger, Lisa O'Keefe, Norrina B. Allen, Joseph P. Ferrie, Kristi Holmes
Summary: Enabling and supporting discoverability of research outputs and datasets are crucial functions of university repositories, but adoption rates are hindered by usability issues. By incorporating agile development principles, user experience design, and observations of microinteractions, a multidisciplinary team at Galter Health Sciences Library & Learning Center has made their development effort more user-informed.
INFORMATION TECHNOLOGY AND LIBRARIES
(2021)
Article
Biochemical Research Methods
Sara Gonzales, Matthew B. Carson, Kristi Holmes
Summary: This article provides 10 key recommendations for creating a Data Management and Sharing Plan (DMSP) that is both maximally compliant and effective, in accordance with the National Institutes of Health's Policy for Data Management and Sharing.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Health Policy & Services
Matthew B. Carson, Sara Gonzales, Pamela Shaw, Daniel Schneider, Kristi Holmes
Summary: This article introduces a clinical research data management program launched by Northwestern University's Galter Health Sciences Library and the Northwestern Medicine Enterprise Data Warehouse. The program aims to enhance the capacity of clinical data workforce and improve the workflow of clinical research through training and collaboration.
LEARNING HEALTH SYSTEMS
(2023)
Article
Biochemical Research Methods
Robin Champieux, Anthony Solomonides, Marisa Conte, Svetlana Rojevsky, Jimmy Phuong, David A. A. Dorr, Elizabeth Zampino, Adam Wilcox, Matthew B. B. Carson, Kristi Holmes
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Matthew B. Carson, Cong Liu, Yao Lu, Caiyan Jia, Hui Lu
BMC MEDICAL GENOMICS
(2017)
Review
Public, Environmental & Occupational Health
Yuan Luo, William K. Thompson, Timothy M. Herr, Zexian Zeng, Mark A. Berendsen, Siddhartha R. Jonnalagadda, Matthew B. Carson, Justin Starren
Article
Microbiology
Hannah L. Woo, Kristen M. DeAngelis, Hazuki Teshima, Karen Davenport, Hajnalka Daligault, Tracy Erkkila, Lynne Goodwin, Wei Gu, Chien-Chi Lo, Christine Munk, Matthew Scholz, Yan Xu, Patrick Chain, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Blake A. Simmons, Terry C. Hazen
GENOME ANNOUNCEMENTS
(2017)
Article
Microbiology
Gary Xie, Ryan P. Chastain-Gross, Myriam Belanger, Dibyendu Kumar, Joan A. Whitlock, Li Liu, William G. Farmerie, Collin L. Zeng, Hajnalka E. Daligault, Cliff S. Han, Thomas S. Brettin, Ann Progulske-Fox
GENOME ANNOUNCEMENTS
(2017)
Article
Microbiology
Ryan P. Chastain-Gross, Gary Xie, Myriam Belanger, Dibyendu Kumar, Joan A. Whitlock, Li Liu, Sarah M. Raines, William G. Farmerie, Hajnalka E. Daligault, Cliff S. Han, Thomas S. Brettin, Ann Progulske-Fox
GENOME ANNOUNCEMENTS
(2017)