Article
Multidisciplinary Sciences
Alvaro Chiner-Oms, G. Mariana, Miguel Moreno-Molina, Victoria Furio, Inaki Comasa
Summary: This study used a dataset of MTBC strains to determine the impact of past and present selective forces on the variability of the pathogen population. It identified genome regions relevant for host-pathogen interaction and potential determinants of drug resistance in second-line tuberculosis treatments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Paula J. Gomez-Gonzalez, Susana Campino, Jody E. Phelan, Taane G. Clark
Summary: This study compared the genome sequencing of clinical isolates of Mycobacterium tuberculosis using Oxford Nanopore Technologies (ONT) sequencing and Illumina HiSeq sequencing. The analysis showed that ONT sequencing is robust for detecting single nucleotide polymorphisms and provides improved coverage in repetitive regions. It also demonstrated high concordance in variants associated with drug resistance. ONT sequencing is a promising tool for tuberculosis genomic investigations and can inform clinical and surveillance decision-making to reduce the disease burden.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Roger Vargas Jr, Michael J. Luna, Luca Freschi, Maximillian Marin, Ruby Froom, Kenan C. Murphy, Elizabeth A. Campbell, Thomas R. Ioerger, Christopher M. Sassetti, Maha Reda Farhat
Summary: This study investigates the role of insertions and deletions (INDELs) in genomic homopolymeric tracts (HT) in regulating gene expression in pathogenic bacteria, specifically within the Mycobacterium tuberculosis complex (MTBC). Through analysis of 31,428 clinical isolates, the researchers identified phase-variants of INDEL events that are under positive selection. Further experiments confirmed that a putatively adaptive phase-variant in the ESX-1 system alters the expression of the critical virulence mediator, espA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biotechnology & Applied Microbiology
Tiffany N. Batarseh, Abraham Morales-Cruz, Brian Ingel, M. Caroline Roper, Brandon S. Gaut
Summary: This study analyzed the genome sequences of Xylella fastidiosa and found evidence of specialization to specific plant hosts. It also identified genes that may play a role in the arms-race dynamics of the pathogen. These findings are significant for understanding the adaptability of Xylella fastidiosa to different host plants.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Philip M. Ashton, Jaeyoon Cha, Catherine Anscombe, Nguyen T. T. Thuong, Guy E. Thwaites, Timothy M. Walker
Summary: Molecular and genomic studies have shown that Mycobacterium tuberculosis Lineage 4 (L4) emerged in Europe and spread globally through trade routes, colonial migration, and historical connections. This study investigates the distribution of L4 in Southeast Asia and surrounding countries using public genomic data. The findings indicate that specific sub-lineages of L4 are predominantly found in East and Southeast Asia, suggesting a regional dispersal pattern. Further sampling and research are needed to determine the exact routes of dispersal.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Jessica Comin, Jesus Vinuelas, Carmen Lafoz, Alberto Cebollada, Daniel Ibarz, Maria-Jose Iglesias, Sofia Samper
Summary: In this study, the AmpliSeq method was used to directly identify lineage and drug resistance from clinical samples. The results showed that the lineage was identified in 100% of culture-derived samples, 95% of smear-positive samples, and 42.1% of smear-negative samples. The drug-resistance profile was accurately identified in most samples, with a few discrepancies.
Article
Microbiology
You-Ming Mei, Wen-Yue Zhang, Ji-Ya Sun, Hai-Qin Jiang, Ying Shi, Jing-Shu Xiong, Le Wang, Yan-Qing Chen, Si-Yu Long, Chun Pan, Tao Luo, Hong-Sheng Wang
Summary: This study investigated the pathogens associated with the occurrence and different types of cutaneous tuberculosis through the analysis of genomic characteristics of 58 Mycobacterium tuberculosis strains isolated over the last 20 years. The findings revealed that cutaneous tuberculosis and pulmonary tuberculosis shared similar genotypes and genomic composition. The drug-resistance rate was lower in cutaneous tuberculosis strains, and several SNPs in metabolism-related genes showed a strong correlation with different infection sites. Thus, while large genomic changes in M. tuberculosis isolates may not significantly affect the different infection sites of TB, the significant difference in SNPs of drug resistance genes and metabolism-related genes should be given more attention.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Matthew Silcocks, Xuling Chang, Nguyen Thuy Thuong Thuong, Youwen Qin, Dang Thi Minh Ha, Phan Vuong Khac Thai, Srinivasan Vijay, Do Dang Anh Thu, Vu Thi Ngoc Ha, Hoang Ngoc Nhung, Nguyen Huu Lan, Nguyen Thi Quynh Nhu, David Edwards, Artika Nath, Kym Pham, Nguyen Duc Bang, Tran Thi Hong Chau, Guy Thwaites, A. Dorothee Heemskerk, Chiea Chuen Khor, Yik Ying Teo, Michael Inouye, Rick Twee-Hee Ong, Maxine Caws, Kathryn E. Holt, Sarah J. Dunstan
Summary: In this study, the prevalence and evolutionary dynamics of drug resistance in Mycobacterium tuberculosis in Ho Chi Minh City, Vietnam were investigated. The accuracy of predicting drug resistance from sequencing data was assessed. The findings shed light on the transmission and evolution of drug resistance, as well as the need for rapid assays for drug resistance detection.
MICROBIOLOGY SPECTRUM
(2023)
Review
Microbiology
Ana Santos-Pereira, Carlos Magalhaes, Pedro M. M. Araujo, Nuno S. Osorio
Summary: The co-infection of Mycobacterium tuberculosis and HIV-1 can lead to a greater burden, despite differences in evolution rates genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 allow it to evade immune responses, generate drug-resistance and diversify the population-level reservoir of M group viral subtypes.
Review
Cell Biology
Rima Zein-Eddine, Guislaine Refregier, Jorge Cervantes, Noemi Kaoru Yokobori
Summary: CRISPR-Cas systems have become the most popular tool for genetic modifications, revolutionizing the study of microbial physiology. Recent research shows that M. tuberculosis has a partially functional CRISPR locus that provides a defense mechanism against foreign genetic elements. The advent of CRISPR-Cas based gene edition technologies has boosted our possibilities to explore the biology of M. tuberculosis and its interaction with the host immune system.
JOURNAL OF BIOMEDICAL SCIENCE
(2023)
Article
Microbiology
Allison F. Carey, Xin Wang, Nico Cicchetti, Caitlin N. Spaulding, Qingyun Liu, Forrest Hopkins, Jessica Brown, Jaimie Sixsmith, Rujapak Sutiwisesak, Samuel M. Behar, Thomas R. Ioerger, Sarah M. Fortune
Summary: There is evidence that genetic diversity in Mycobacterium tuberculosis affects infection outcomes and vaccination. Strains belonging to the mL2 sublineage of M. tuberculosis are associated with clinical features such as hypervirulence, treatment failure, and vaccine escape. These strains show distinct growth dynamics and vaccine resistance, which can be attributed to adaptive genetic changes in stress and host response pathways.
Article
Genetics & Heredity
Belen Saavedra Cervera, Mariana G. Lopez, Alvaro Chiner-Oms, Ana Maria Garcia, Irving Cancino-Munoz, Manuela Torres-Puente, Luis Villamayor, Carlos Madrazo-Moya, Edson Mambuque, Guillermo Victor Sequera, Durval Respeito, Silvia Blanco, Orvalho Augusto, Elisa Lopez-Varela, Alberto L. Garcia-Basteiro, Inaki Comas
Summary: In this study, a 1-year prospective surveillance-based study was conducted in Mozambique to investigate the population structure and transmission dynamics of Mycobacterium tuberculosis complex (MTBC). Whole-genome sequencing was applied to 295 positive cultures, and the MTBC isolates were fully characterized and analyzed for molecular epidemiology. The majority of the strains belonged to lineage 4, with a high proportion in genomic transmission clusters. Two "likely endemic" clades belonging to L1.2 were identified, dating back to the late 19th century and associated with recent spread among people living with HIV. The study reveals weaknesses in TB control activities and questions the role of HIV in TB transmission.
MICROBIAL GENOMICS
(2022)
Article
Biology
Ved Mehta, Basavraj Khanppnavar, Dina Schuster, Ilayda Kantarci, Irene Vercellino, Angela Kosturanova, Tarun Iype, Sasa Stefanic, Paola Picotti, Volodymyr M. Korkhov
Summary: Mycobacterium tuberculosis adenylyl cyclase Rv1625c/Cya, an ancestor of mammalian membrane ACs, serves as a model system for studying their structure and function. The transmembrane domain of the enzyme plays a crucial role in regulating the catalytic activity by guiding the assembly of the catalytic domain and responding to extracellular ligands.
Article
Biochemistry & Molecular Biology
Ali-Berenice Posada-Reyes, Yalbi I. Balderas-Martinez, Santiago avila-Rios, Pablo Vinuesa, Salvador Fonseca-Coronado
Summary: This study analyzed the polymorphic loci interactions in the genome of Mycobacterium tuberculosis, revealing key genes associated with pathogenicity and antibiotic resistance. The findings provide insights into the complex molecular interactions involved in the metabolism, virulence, and pathogenicity of M. tuberculosis, and can be applied to other bacterial populations.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Microbiology
Joshua M. Thiede, Nicholas A. Dillon, Michael D. Howe, Ranee Aflakpui, Samuel J. Modlin, Sven E. Hoffner, Faramarz Valafar, Yusuke Minato, Anthony D. Baughn
Summary: This study revealed the regulatory role of the cell envelope stress response in the action of PZA. Further research demonstrated that potentiation of PZA can be achieved by deleting the anti-Sigma factor gene rseA or exposing bacilli to drugs targeting the cell wall, independently of environmental pH. These findings necessitate a paradigm shift in the understanding of PZA action and offer new avenues for enhancing diagnostic and therapeutic tools for tuberculosis.
Article
Biology
Kunal Bhattacharya, Shikha Mahato, Satyendra Deka, Nongmaithem Randhoni Chanu, Amit Kumar Shrivastava, Pukar Khanal
Summary: Chemoresistance, a major challenge in cancer treatment, is associated with the cellular glutathione-related detoxification system. A study has identified GSTP1 enzyme as critical in the inactivation of anticancer drugs and suggests the need for GSTP1 inhibitors to combat chemoresistance. Through molecular docking and simulations, the study found that quercetin 7-O-beta-D-glucoside showed promise as a potential candidate for addressing chemoresistance in cancer patients.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Manwi Shankar, Majji Sai Sudha Rani, Priyanka Gopi, P. Arsha, Prateek Pandya
Summary: This study investigates the interaction between the food dye BBY and the serum protein BSA. The results show that BBY binds to a specific site on BSA through hydrophobic interactions, affecting the structural stability of the protein. These findings enhance our understanding of the molecular-level interactions between BBY and BSA.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Chi Zhang, Qian Gao, Ming Li, Tianfei Yu
Summary: In this study, we propose a graph neural network-based autoencoder model, AGraphSAGE, that effectively predicts protein-protein interactions across diverse biological species by integrating gene ontology.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Kangjie Wu, Liqian Xu, Xinxiang Li, Youhua Zhang, Zhenyu Yue, Yujia Gao, Yiqiong Chen
Summary: Named Entity Recognition (NER) is a crucial task in natural language processing (NLP) and big data analysis, with wide application range. This paper proposes an improved neural network method for NER of rice genes and phenotypes, which can learn semantic information in the context without feature engineering. Experimental results show that the proposed model outperforms other models.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Suman Hait, Sudip Kundu
Summary: Interactions between amino acids in proteins are crucial for stability and structural integrity. Thermophiles have more and more stable interactions to survive in extreme environments. Different types of interactions are enriched in different structural regions.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Kountay Dwivedi, Ankit Rajpal, Sheetal Rajpal, Virendra Kumar, Manoj Agarwal, Naveen Kumar
Summary: This study aims to identify biomarkers for non-small cell lung cancer (NSCLC) using copy number variation (CNV) data. A novel deep learning architecture, XL1R-Net, is proposed to improve the classification accuracy for NSCLC subtyping. Twenty NSCLC-relevant biomarkers are uncovered using explainable AI (XAI)-based feature identification. The results show that the identified biomarkers have high classification performance and clinical relevance. Additionally, twelve of the biomarkers are potentially druggable and eighteen of them have a high probability of predicting NSCLC patients' survival likelihood according to the Drug-Gene Interaction Database and the K-M Plotter tool, respectively. This research suggests that investigating these seven novel biomarkers can contribute to NSCLC therapy, and the integration of multiomics data and other sources will help better understand NSCLC heterogeneity.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Pengli Lu, Wenqi Zhang, Jinkai Wu
Summary: Researchers have developed a computational method, AMPCDA, to predict circRNA-disease associations using predefined metapaths, achieving high predictive accuracy. This method effectively combines node embeddings with higher-order neighborhood representations and provides valuable guidance for revealing new disease mechanisms in biological research.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)