Article
Biochemistry & Molecular Biology
Hao Chen, Jessica Wilson, Carson Ercanbrack, Hannah Smith, Qinglei Gan, Chenguang Fan
Summary: This study aimed to identify genes in E. coli cells that confer resistance to oxidizing agents through genome-wide screening. More than 100 genes associated with oxidative stress responses were discovered, which were previously unknown, potentially advancing basic studies on oxidative stress and the development of antibacterial agents.
Article
Microbiology
You Zhou, Dike Jiang, Xueping Yao, Yan Luo, Zexiao Yang, Meishen Ren, Ge Zhang, Yuanyuan Yu, Aiping Lu, Yin Wang
Summary: Glaesserella parasuis is a gram-negative bacterium that causes fibrotic polyserositis and arthritis in pigs, significantly impacting the pig industry. The pan-genome of G. parasuis is open and shows differences in the core and accessory genomes as the number of genes increases. The genes associated with virulence and biofilm formation in G. parasuis are still unclear due to its diversity. Therefore, a pan-genome-wide association study (Pan-GWAS) was conducted on 121 strains of G. parasuis. The study revealed the core genome consists of 1,133 genes associated with cytoskeleton, virulence, and basic biological processes. The accessory genome contributes to the genetic diversity of G. parasuis. Furthermore, the study identified 142 genes associated with strong virulence traits and their involvement in metabolic pathways, signal pathways, and virulence factors for bacterial survival and biofilm formation. This research provides a foundation for further investigation into virulence and biofilm formation and offers potential targets for drug and vaccine development against G. parasuis.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Entomology
Hao Sun, Jingya Chen, Ruolin Wang, Dan Liu, Na Zhang, Tong Zhang, Ling Jia, Sanyuan Ma, Qingyou Xia
Summary: This study used a genome-wide CRISPR/Cas9-based library and large-scale screening to analyze the key genes involved in the silkworm 20E signaling pathway and their mechanisms of action. Functional annotation revealed that 20E regulates key proteins in processes mainly occurring in the cytoplasm and nucleus. Pathway enrichment analysis showed that 20E can activate phosphorylation, may affect innate immunity, interfere with intracellular nutrition and energy metabolism, and ultimately lead to cell apoptosis. These findings provide a panoramic overview of the silkworm's response to 20E signaling, highlighting the utility of genome-wide CRISPR mutant libraries in deciphering hormone signaling pathways and metamorphosis regulation in insects.
Article
Multidisciplinary Sciences
Mangaljeet Singh, Kirandeep Kaur, Avinash Sharma, Rajvir Kaur, Dimple Joshi, Megha Chatterjee, Iman Dandapath, Amarjeet Kaur, Harpreet Singh, Prabhjeet Singh
Summary: Peptidyl-prolyl cis-trans isomerases (PPIases) are enzymes capable of cis-trans isomerization of the prolyl peptide bond, playing essential roles in various cellular processes. This study conducted a genome-wide analysis of PPIases in different Penicillium spp. and found variations in gene numbers and activities under salt stress. The halotolerant strain P. oxalicum showed significant enhancement in mycelial PPIase activity under salt stress, suggesting the importance of these enzymes in salt stress adaptation.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Pranas Grigaitis, Douwe A. J. Grundel, Eunice Van Pelt-KleinJan, Mirushe Isaku, Guixiang Xie, Sebastian Mendoza Farias, Bas Teusink, Johan H. Van Heerden
Summary: This study showcases the successful transfer of knowledge from Saccharomyces cerevisiae to Schizosaccharomyces pombe using computational models, exploring the metabolic behavior and resource allocation of the fission yeast.
Article
Biotechnology & Applied Microbiology
Fuchen Zhou, Shenghui Wang, Haojun Qin, Haiyu Zeng, Jian Ye, Jie Yang, Gengyuan Cai, Zhenfang Wu, Zebin Zhang
Summary: The Genome-Wide Association Study analysis on 216 Duroc pigs identified nine significant SNPs associated with Aplasia cutis congenita (ACC). The study also revealed the presence of two quantitative trait loci on SSC 5 and SSC13. Further annotation of candidate genes within a 1 Mb region surrounding the significant SNPs identified a total of 11 candidate genes on SSC5 and SSC13.
Article
Agriculture, Multidisciplinary
Baoqing Zhang, Yuxin Huang, Lijun Zhang, Zhongfeng Zhou, Shan Zhou, Weixing Duan, Cuifang Yang, Yijing Gao, Sicheng Li, Meiyan Chen, Yangrui Li, Xiping Yang, Gemin Zhang, Dongliang Huang
Summary: This study evaluated yield-related traits and identified markers and candidate genes for improving sugarcane yields using molecular techniques. The findings provide valuable information for marker-assisted breeding to increase sugarcane productivity.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Review
Biotechnology & Applied Microbiology
Luc Legon, Charalampos Rallis
Summary: Cellular models such as yeasts, which have simpler genomes, shorter lifespans and abundant genetic resources, play an important role in biogerontology research. Yeasts have contributed to the understanding of fundamental aspects of lifespan regulation, including nutrient response, protein translation, DNA damage, oxidative stress, mitochondrial function and autophagy. The use of automation and computational tools has allowed for the manipulation and analysis of genome-wide lifespan data, leading to a comprehensive view of cellular ageing.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2022)
Article
Endocrinology & Metabolism
Niina Sandholm, Joanne B. Cole, Viji Nair, Xin Sheng, Hongbo Liu, Emma Ahlqvist, Natalie van Zuydam, Emma H. Dahlstrom, Damian Fermin, Laura J. Smyth, Rany M. Salem, Carol Forsblom, Erkka Valo, Valma Harjutsalo, Eoin P. Brennan, Gareth J. McKay, Darrell Andrews, Ross Doyle, Helen C. Looker, Robert G. Nelson, Colin Palmer, Amy Jayne McKnight, Catherine Godson, Alexander P. Maxwell, Leif Groop, Mark I. McCarthy, Matthias Kretzler, Katalin Susztak, Joel N. Hirschhorn, Jose C. Florez, Per-Henrik Groop
Summary: By performing meta-analysis of previous genome-wide association studies (GWAS) on diabetic kidney disease (DKD) and integrating the results with renal transcriptomics datasets, novel genetic factors and genes contributing to DKD have been identified.
Article
Biology
Brandon R. Lowe, Rajesh K. Yadav, Ryan A. Henry, Patrick Schreiner, Atsushi Matsuda, Alfonso G. Fernandez, David Finkelstein, Margaret Campbell, Satish Kallappagoudar, Carolyn M. Jablonowski, Andrew J. Andrews, Yasushi Hiraoka, Janet F. Partridge
Summary: The study highlights the varied phenotypic effects and impact on DNA repair caused by mutations in different types of H3 histones, indicating the complexity associated with substitutions at a single residue in H3. Analysis using genetically tractable systems demonstrates the utility of such approaches in studying these mutations.
Article
Multidisciplinary Sciences
Alexandra Casey, Liam Dolan
Summary: By comparing protein sequences and generating phylogenetic trees, it was found that CYP and GST proteins existed in the common ancestor of Archaeplastida. Land plants have more genes encoding CYP and GST proteins compared to algae, primarily due to gene duplications in certain clans and classes. Variants in CYP71, CYP72, GST phi, and GST tau genes enable plants to develop herbicide resistance.
Article
Biochemistry & Molecular Biology
Mingzhe Sun, Maohong Cai, Qinzong Zeng, Yuliang Han, Siqi Zhang, Yingwei Wang, Qinyu Xie, Youheng Chen, Youling Zeng, Tao Chen
Summary: This study systematically classified the UBiA family and identified two abiotic stress candidate genes in sunflowers. It expands the understanding of the UBiA family and provides a theoretical basis for future abiotic stress studies in sunflowers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
M. Bohlouli, K. Halli, T. Yin, N. Gengler, S. Koenig
Summary: This study aimed to investigate the effects of climate on milk fatty acid composition, identify candidate genes associated with heat stress, and estimate breeding values and genetic parameters based on changes in the temperature-humidity index.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Lili Pan, Duncan Tormey, Nadine Bobon, Peter Baumann
Summary: The conserved Rap1 protein plays a critical role in chromosome end protection and telomere length regulation. Mutations in Rap1 can lead to genome instability, particularly in longer telomeres, which are protected by nuclear envelope attachment. This study provides insights into the mechanism of telomere length maintenance and explains the species-specific upper limits on telomere length.
Article
Biochemical Research Methods
Tanaz Abid, Amy B. Goodale, Zohra Kalani, Meghan Wyatt, Elizabeth M. Gonzalez, Kevin Ning Zhou, Kenin Qian, Dana Novikov, Alexandra-Larisa Condurat, Pratiti Bandopadhayay, Federica Piccioni, Nicole S. Persky, David E. Root
Summary: Spheroid culture systems have revolutionized cell propagation and modeling of tumor growth in vitro. Genome-wide CRISPR screening has proven valuable in understanding cancer cell lines, and similar screening methods for three-dimensional spheroid cultures will be crucial for future biological discovery.