Article
Biochemistry & Molecular Biology
Sergey Y. Morozov, Andrey G. Solovyev
Summary: This study discovered a novel putative-related movement gene module, called tetra-cistron movement block (TCMB), in the virus-like transcriptomes of moss and Antarctic flowering plant. These TCMBs are encoded by smaller RNA components of putative two-component viruses related to plant benyviruses. The involvement of replicative beny-like helicases in the evolution of the BMB and TCMB movement genetic modules was suggested based on phylogenetic analysis.
Article
Biochemistry & Molecular Biology
Yanjing Wang, Siyi Wang, Yuchen Niu, Buyong Ma, Jingjing Li
Summary: CXCL14 is a tumor suppressor gene in colorectal carcinoma that is initially activated and then silenced during tumor occurrence and deterioration. Its silencing is primarily caused by promoter hypermethylation. The methylation level of CXCL14 is associated with the anatomical site of tumor occurrence and is correlated with patient age and prognosis. Reversing the hypermethylation of CXCL14 may serve as an epigenetic therapy for colon cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Bing Wang, Mark Finazzo, Irina Artsimovitch
Summary: Plasmids mediate gene exchange between bacteria across different taxonomic groups through conjugation, shaping bacterial evolution. However, rapid plasmid-mediated spread of resistance genes has made most clinical antibiotics ineffective. To solve this problem, we used machine-learning models to identify important features for expanding the plasmid host range.
Article
Psychiatry
Yu Wang, Jinxue Wei, Ting Chen, Xiao Yang, Liansheng Zhao, Min Wang, Yikai Dou, Yue Du, Rongjun Ni, Tao Li, Xiaohong Ma
Summary: This study investigates the dysregulation of multiple RNA species in major depressive disorder (MDD) and explores the interaction between different types of RNA. The results suggest that energy metabolism and inflammation may play a role in the pathophysiology of MDD.
FRONTIERS IN PSYCHIATRY
(2022)
Article
Plant Sciences
Nils Poulicard, Israel Pagan, Pablo Gonzalez-Jara, Miguel angel Mora, Jean-Michel Hily, Aurora Fraile, Daniel Pinero, Fernando Garcia-Arenal
Summary: Specificity in plant-pathogen gene-for-gene interactions is determined by the recognition of pathogen proteins by the products of plant resistance genes. This study analyzes the evolution of the L resistance locus to tobamoviruses in wild pepper populations and finds that the frequency of resistance is lower in cultivated populations. The genetic diversity of the L locus shows a strong spatial structure, and different L alleles differ in specificity and expression of resistance.
Article
Cell Biology
Jeremy A. Schofield, Steven Hahn
Summary: Through studying upstream activating sequences (UASs), core promoters, and other gene features, it was found that most UASs can broadly activate different types of promoters, while a few have strong promoter specificity. However, matching UASs and promoters from the same gene class is generally important for optimal expression. Additionally, sensitivity to MED Tail and SAGA depletion depends on the identity of UAS and core promoter, while dependence on TFIID primarily localizes to the promoter.
Article
Microbiology
Diego Cortez, Gonzalo Neira, Carolina Gonzalez, Eva Vergara, David S. Holmes
Summary: The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. In this study, a comparative genomics investigation of acidophilic bacteria was performed to examine the correlation between genome size reduction and decreasing pH. The results indicate that genome streamlining in acidophilic bacteria is supported by gene loss and reduced gene sizes, independent of other genome size constraints.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Virology
Shaofu Qiu, Jinpeng Guo, Peihan Li, Peng Li, Xinying Du, Rongzhang Hao, Chaojie Yang, Qi Wang, Hongbo Liu, Haoran Zhang, Sai Tian, Hua Shi, Liang Wen, Daizhi An, Xiaocui Yang, Xiaoyuan An, Ligui Wang, Changjun Wang, Hongbin Song
Summary: Chikungunya fever, caused by CHIKV, has become a major global health concern with large outbreaks in various regions. The origin and spread of CHIKV in China remain poorly understood. The study identified Indian subcontinent and Southeast Asia as major hubs for recent global spread of CHIKV, leading to multiple outbreaks and epidemics.
Article
Oncology
Erik Knutsen, Saikat Das Sajib, Tonje Fiskaa, James Lorens, Thorarinn Gudjonsson, Gunhild M. Maelandsmo, Steinar Daae Johansen, Ole-Morten Seternes, Maria Perander
Summary: Epithelial-mesenchymal transition (EMT) is a cellular plasticity program critical for embryonic development and tissue regeneration. It is associated with breast cancer, which can be divided into distinct subgroups. Basal-like breast cancers exhibit partial-EMT and post-EMT gene expression patterns.
FRONTIERS IN ONCOLOGY
(2023)
Article
Plant Sciences
Nathan J. Scinto-Madonich, Shivranjani Baruah, Sameya Young, Katherine Vignona, Andrew C. Read, Sara C. D. Carpenter, Li Wang, Xinying Shi, Geoffrey Chang, Miguel A. Pineros, Adam J. Bogdanove
Summary: The type III secreted transcription activator-like effector Tal2g of the rice bacterial leaf streak (BLS) pathogen Xanthomonas oryzae pv. oryzicola promotes lesion development and bacterial exudation through stomata by upregulating a putative sulfate transporter gene in rice, OsSULTR3;6. The transport mechanics, subcellular localization, potential substrates, and phenotyping of OsSULTR3;6 knockout lines generated by genome editing are being characterized to understand its role in BLS disease development.
PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY
(2023)
Article
Genetics & Heredity
Maria Vlasenok, Sergey Margasyuk, Dmitri D. Pervouchine
Summary: Alternative splicing and alternative polyadenylation are crucial steps in the regulation of gene expression. Analysis of RNA-seq data reveals that intronic polyadenylation is more abundant than exonic polyadenylation. Some intronic polyadenylation events lack splicing support, suggesting they are products of spliced polyadenylated introns.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Md Khairul Islam, Md Rakibul Islam, Md Habibur Rahman, Md Zahidul Islam, Md Mehedi Hasan, Md Mainul Islam Mamun, Mohammad Ali Moni
Summary: Obesity is a chronic disease characterized by body fat accumulation and is associated with various metabolic-related disorders. Epidemiological data suggest a bidirectional relationship between obesity and neuro-psychiatric disorders such as schizophrenia and major depression. However, the biological interaction between obesity and these conditions is still unknown. In this study, a pipeline combining bioinformatics and statistical approaches was developed to identify differentially expressed genes and molecular mechanisms in patients with psychiatric disorders and obesity. The analysis revealed common genes, signaling pathways, and gene-disease associations between obesity and schizophrenia, as well as between obesity and major depressive disorder. These findings support the pathogenicity of psychiatric disorders and obesity and may contribute to the development of therapeutic approaches to improve the bidirectional relationship between the two. Validation using genome-wide association study and whole-genome sequence data further supported the involvement of significant genes in these conditions.
Article
Multidisciplinary Sciences
Md Khairul Islam, Md Rakibul Islam, Md Habibur Rahman, Md Zahidul Islam, Md Mehedi Hasan, Md Mainul Islam Mamun, Mohammad Ali Moni
Summary: Obesity and psychiatric disorders share common genes and pathways, which may contribute to the development and progression of the diseases. Integrating bioinformatics and statistical approaches can identify these key factors, providing insights into the relationship between obesity and neuro-psychiatric disorders, and guiding the development of treatment strategies.
Article
Dermatology
Julia Serrano-Lobo, Ana Gomez, Elena Reigadas, Patricia Munoz, Pilar Escribano, Jesus Guinea
Summary: This study evaluated the impact of not filtering conidial suspensions on the screening method for A. fumigatus isolates and found that unfiltered suspensions do not negatively affect the performance of the method.
Article
Mathematical & Computational Biology
Flemming Damgaard Nielsen, Jakob Moller-Jensen, Mikkel Girke Jorgensen
Summary: This study presents the complete pangenome of the important human pathogen Streptococcus pneumoniae, including both genes and intergenic regions (IGRs). It reveals a clear linkage between core genes and core IGRs, suggesting horizontal regulatory transfer between isolates involving core IGRs.
FRONTIERS IN BIOINFORMATICS
(2023)
Article
Virology
Eleni Kleanthous, Ingrida Olendraite, Nina I. Lukhovitskaya, Andrew E. Firth
ARCHIVES OF VIROLOGY
(2019)
Article
Virology
Jermilia Charles, Chandra S. Tangudu, Stefanie L. Hurt, Charlotte Tumescheit, Andrew E. Firth, Julian E. Garcia-Rejon, Carlos Machain-Williams, Bradley J. Blitvich
ARCHIVES OF VIROLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Hazel Stewart, Allan Olspert, Benjamin G. Butt, Andrew E. Firth
JOURNAL OF GENERAL VIROLOGY
(2019)
Article
Microbiology
Valeria Lulla, Adam M. Dinan, Myra Hosmillo, Yasmin Chaudhry, Lee Sherry, Nerea Irigoyen, Komal M. Nayak, Nicola J. Stonehouse, Matthias Zilbauer, Ian Goodfellow, Andrew E. Firth
NATURE MICROBIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Katherine Brown, Ingrida Olendraite, Steven M. Valles, Andrew E. Firth, Yanping Chen, Diego M. A. Guerin, Yoshifumi Hashimoto, Salvador Herrero, Joachim R. de Miranda, Eugene Ryabov, Elliot J. Lefkowitz, Andrew J. Davison, Stuart G. Siddell, Peter Simmonds, Sead Sabanadzovic, Donald B. Smith, Richard J. Orton, Nick J. Knowles
JOURNAL OF GENERAL VIROLOGY
(2019)
Article
Virology
Adam M. Dina, Sarah Keep, Erica Bickerton, Paul Britton, Andrew E. Firth, Ian Brierley
JOURNAL OF VIROLOGY
(2019)
Article
Virology
Yanhua Li, Andrew E. Firth, Ian Brierley, Yingyun Cai, Sawsan Napthine, Tao Wang, Xingyu Yan, Jens H. Kuhn, Ying Fang
JOURNAL OF VIROLOGY
(2019)
Article
Biochemistry & Molecular Biology
Sawsan Napthine, Susanne Bell, Chris H. Hill, Ian Brierley, Andrew E. Firth
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Shreekara Gopalakrishna, Sarah F. Pearce, Adam M. Dinan, Florian A. Schober, Miriam Cipullo, Henrik Spahr, Anas Khawaja, Camilla Maffezzini, Christoph Freyer, Anna Wredenberg, Ilian Atanassov, Andrew E. Firth, Joanna Rorbach
NUCLEIC ACIDS RESEARCH
(2019)
Article
Virology
Mattia Ficarelli, Irati Antzin-Anduetza, Rupert Hugh-White, Andrew E. Firth, Helin Sertkaya, Harry Wilson, Stuart J. D. Neil, Reiner Schulz, Chad M. Swanson
JOURNAL OF VIROLOGY
(2020)
Article
Multidisciplinary Sciences
Junhong Choi, Sinead O'Loughlin, John F. Atkins, Joseph D. Puglisi
Article
Multidisciplinary Sciences
Andrew M. Hudson, Gary Loughran, Nicholas L. Szabo, Norma M. Wills, John F. Atkins, Lynn Cooley
Summary: Translational stop codon readthrough allows for C-terminal extension of proteins encoded by certain genes. Efficiency of readthrough varies among different cell types, with the Drosophila CNS showing high levels of readthrough, particularly in neurons. Specific sequences downstream of the stop codon can stimulate readthrough efficiency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Letter
Multidisciplinary Sciences
Yousuf A. Khan, Gary Loughran, Anna-Lena Steckelberg, Katherine Brown, Stephen J. Kiniry, Hazel Stewart, Pavel Baranov, Jeffrey S. Kieft, Andrew E. Firth, John F. Atkins
Article
Multidisciplinary Sciences
Simon A. A. Fromm, Kate M. M. O'Connor, Michael Purdy, Pramod R. R. Bhatt, Gary Loughran, John F. F. Atkins, Ahmad Jomaa, Simone Mattei
Summary: The structure of the translating ribosome from Escherichia coli was determined at high resolution, allowing for identification of ribosome polymorphism sites and interpretation of ribosomal active and peripheral sites. This study improves our understanding of protein synthesis and enables more precise drug design to combat bacterial resistance.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Valeria Lulla, Andrew E. Firth