Article
Genetics & Heredity
Khaista Rahman, Muhammad Jamal, Xi Chen, Wei Zhou, Bin Yang, Yanyan Zou, Weize Xu, Yingying Lei, Chengchao Wu, Xiaojian Cao, Rohit Tyagi, Muhammad Ahsan Naeem, Da Lin, Zeshan Habib, Nan Peng, Zhen F. Fu, Gang Cao
Summary: In this study, the endogenous type III-A CRISPR/Cas10 system of M. tuberculosis was utilized for efficient gene editing and RNA interference. It was proven that this system can successfully and specifically knock in/out M. tuberculosis genes as confirmed by DNA high-throughput sequencing. Furthermore, genome-wide RNA interference screening was performed to identify M. tuberculosis genes regulating in vitro and intracellular growth. This system can be widely used for exploring the functional genomics of M. tuberculosis and facilitating the development of novel anti-TB drugs and vaccines.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Medicine, General & Internal
Sourya Shrestha, Emily A. Kendall, Rebekah Chang, Roy Joseph, Parastu Kasaie, Laura Gillini, Anthony Todd Fojo, Michael Campbell, Nimalan Arinaminpathy, David W. Dowdy
Summary: This study aimed to quantify the potential impact of a one-time, community-wide campaign on reducing the burden of tuberculosis. By successfully screening and treating 70% of the adult population, it was estimated that around 7800 cases and 1710 related deaths could be averted over a 10-year period. Preventive therapy and health system strengthening were identified as key components contributing to the avoided deaths.
Article
Microbiology
Denis Lagutkin, Anna Panova, Anatoly Vinokurov, Alexandra Gracheva, Anastasia Samoilova, Irina Vasilyeva
Summary: This study examined the variants associated with drug resistance in Mycobacterium tuberculosis (MTB) and the emergence of polymorphisms in MTB genomes after anti-tuberculosis treatment. The results revealed significant associations between specific genes and drug-resistant phenotypes, as well as different patterns of intra-host evolution and lineage-specific polymorphisms in post-treatment isolates. The authors propose that one specific insertion within a gene may play a role in cell wall biosynthesis and contribute to a compensatory mechanism in response to treatment.
Review
Microbiology
Hemant Joshi, Divya Kandari, Subhrangsu Sundar Maitra, Rakesh Bhatnagar
Summary: Tuberculosis (TB) infection is a major cause of death globally, and early detection of the pathogen is crucial for successful diagnosis. Recent advancements in TB biomarkers, specifically secretory proteins from Mycobacterium tuberculosis, have been explored for early diagnosis and treatment. This review discusses the latest developments in piezoelectric, magnetic, optical, and electrochemical biosensors, highlighting their strengths and limitations. Additionally, the review explores the construction of biosensors using integrated technologies, such as analytical chemistry, molecular biology, and nanotechnology.
CRITICAL REVIEWS IN MICROBIOLOGY
(2022)
Article
Microbiology
Francy J. Perez-Llanos, Viola Dreyer, Ivan Barilar, Christian Utpatel, Thomas A. Kohl, Martha Isabel Murcia, Susanne Homolka, Matthias Merker, Stefan Niemann
Summary: An outbreak of Mycobacterium tuberculosis complex (MTBC) bacteria was identified among the indigenous populations in the Colombian Amazon region. Whole genome sequencing (WGS) was used to analyze the transmission of MTBC strains and it was found that the use of an alternative reference genome and repetitive regions improved the phylogenetic resolution. The study also revealed the presence of multiple clones in some patients, indicating within-host MTBC diversity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Barbara De Kegel, Niall Quinn, Nicola A. Thompson, David J. Adams, Colm J. Ryan
Summary: Pairs of paralogs with shared protein-protein interactions and evolutionary conservation are likely to display synthetic lethal interactions. A machine-learning classifier has been developed to accurately predict which paralog pairs are most likely to be synthetic lethal based on these features.
Article
Infectious Diseases
Yiwang Chen, Qingyun Liu, Howard E. Takiff, Qian Gao
Summary: This study provides a global view of the correlation between common fitness-related genotypes and multidrug-resistant tuberculosis (MDR-TB) transmission. The results indicate that the factors commonly thought to increase bacterial fitness are not significantly associated with increased MDR-TB transmission.
JOURNAL OF INFECTION
(2022)
Article
Biotechnology & Applied Microbiology
Gabriel Morey-Leon, Derly Andrade-Molina, Juan Carlos Fernandez-Cadena, Luisa Berna
Summary: This study reveals for the first time the variability of circulating resistant strains between men and women in Ecuador. The use of whole genome sequencing allows for the identification of emerging resistance and an increase in fluoroquinolone resistance is detected. Further sampling efforts are needed to determine the overall variability and to generate better health policies.
Review
Immunology
Paolo Miotto, Rita Sorrentino, Stefano De Giorgi, Roberta Provvedi, Daniela Maria Cirillo, Riccardo Manganelli
Summary: Bacterial drug resistance poses a serious threat to human health, with tuberculosis being a high-risk infection due to limited drugs available against Mycobacterium tuberculosis. Drug resistance in bacteria is often caused by point mutations in drug targets, but changes in transcriptional regulation post-drug exposure also play a significant role and should be further explored for potential new drug targets and intervention strategies.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Caitlin Uren, Eileen G. Hoal, Marlo Moller
Summary: Research on the relationship between MTBC and human host is limited, with focus on genetic association studies that have shown inconsistent results. There is a need to reconsider research methods and understand the coupled evolution of the pathogen and host as a possible key to resolving the issue.
HUMAN MOLECULAR GENETICS
(2021)
Article
Multidisciplinary Sciences
Poonam Chitale, Alexander D. Lemenze, Emily C. Fogarty, Avi Shah, Courtney Grady, Aubrey R. Odom-Mabey, W. Evan Johnson, Jason H. Yang, A. Murat Eren, Roland Brosch, Pradeep Kumar, David Alland
Summary: This study presents a pipeline called Bact-Builder, which uses consensus building to generate accurate bacterial genome sequences. The pipeline was applied to the H37Rv strain and identified new regions and polymorphisms in the genome. The results suggest that Bact-Builder is an improved method for de novo assembly of bacterial genomes.
NATURE COMMUNICATIONS
(2022)
Article
Agricultural Engineering
Aatif Rashid, Manu Khajuria, Villayat Ali, Sheenam Faiz, Sumit Jamwal, Dhiraj Vyas
Summary: This study identified 48 WRKY transcription factors in Cannabis sativa through genome research, and classified them into different groups based on physiochemical and phylogeny analysis. The findings showed that CsWRKY genes remained conserved during evolution, and their upstream sequences contained stress-related elements. Functional analysis and protein-protein interaction revealed the regulatory network of CsWRKY. Additionally, several CsWRKY genes were found to play a potential role in inflorescence development and cannabinoid regulation.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Immunology
Tyler S. Brown, Linrui Tang, Shaheed Vally Omar, Lavania Joseph, Graeme Meintjes, Gary Maartens, Sean Wasserman, N. Sarita Shah, Maha R. Farhat, Neel R. Gandhi, Nazir Ismail, James C. M. Brust, Barun Mathema
Summary: Characterizing serial Mycobacterium tuberculosis (Mtb) isolates collected during bedaquiline (BDQ)-based treatment provides insights into the etiologies of BDQ resistance. The study found that BDQ-resistant TB can arise through multiple processes, including transmission of strains with pre-existing resistance. Capturing the within-host diversity of these infections could potentially improve clinical diagnosis, population-level surveillance, and molecular diagnostic test development.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Biochemistry & Molecular Biology
Yingjie Gao, Guanghui Jiang, Wenqian Yang, Weiwei Jin, Jing Gong, Xuewen Xu, Xiaohui Niu
Summary: In this study, we identified approximately 499 million high-quality SNPs from multiple animal species and developed the Animal-SNPAtlas database, which provides tools for functional annotation, genotype imputation, and more. This resource will be valuable for research in animal genomics, genetics, and breeding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Oscar Arrey-Salas, Jose Carlos Caris-Maldonado, Bairon Hernandez-Rojas, Enrique Gonzalez
Summary: A variety of C2H2 zinc-finger proteins are involved in pollen development in plants, including grapevine. The identification and characterization of 98 VviZFP genes in grapevine revealed significant changes and family expansion, with genes classified into three groups based on domain and phylogenetic analysis. Some VviZFP genes show differential expression patterns during flower development, providing insights into their role in grapevine reproductive development.
Article
Multidisciplinary Sciences
Roie Levy, Andrew T. Magis, John C. Earls, Ohad Manor, Tomasz Wilmanski, Jennifer Lovejoy, Sean M. Gibbons, Gilbert S. Omenn, Leroy Hood, Nathan D. Price
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Maxwell L. Neal, Ling Wei, Eliza Peterson, Mario L. Arrieta-Ortiz, Samuel A. Danziger, Nitin S. Baliga, Alexis Kaushansky, John D. Aitchison
Summary: Researchers developed a gene regulatory network model for Plasmodium falciparum using machine learning, which accurately predicted gene expression levels across diverse datasets. By investigating gene expression coherence, they found that artemisinin resistance in the parasite is associated with incoherent expression across multiple regulatory programs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Shuyi Ma, Robert Morrison, Samuel J. Hobbs, Vijay Soni, Jessica Farrow-Johnson, Andrew Frando, Neil Fleck, Christoph Grundner, Kyu Y. Rhee, Tige R. Rustad, David R. Sherman
Summary: The study utilizes a transcriptional regulator-induced phenotype screen coupled with network analysis to characterize adaptations of Mycobacterium tuberculosis to the first-line anti-tuberculosis drug isoniazid, identifying the transcriptional factor mce3R and the CtpD effector to have a role in Mycobacterium susceptibility to isoniazid.
NATURE MICROBIOLOGY
(2021)
Article
Environmental Sciences
Jacob J. Valenzuela, Justin Ashworth, Allison Cusick, Raffaela M. Abbriano, E. Virginia Armbrust, Mark Hildebrand, Monica Orellana, Nitin S. Baliga
Summary: This study identified a potential bioindicator for the resilience shift of diatoms under ocean acidification conditions, which is a putative Na+(K+)/H+ antiporter localized in plastid membrane that may play an important role in maintaining pH homeostasis. The differential in transcript levels of this antiporter between nighttime and daytime could serve as an indicator for the resilience shift of diatoms in response to high CO2 conditions in marine environments.
FRONTIERS IN MARINE SCIENCE
(2021)
Correction
Cell Biology
Eliza J. R. Peterson, Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga
Review
Oncology
James H. Park, Adrian Lopez Garcia de Lomana, Diego M. Marzese, Tiffany Juarez, Abdullah Feroze, Parvinder Hothi, Charles Cobbs, Anoop P. Patel, Santosh Kesari, Sui Huang, Nitin S. Baliga
Summary: Pronounced differences between individuals and cell-cell heterogeneity within tumors are major obstacles in effective brain tumor treatment, necessitating a personalized precision medicine approach. A systems biology approach is crucial for developing a multiscale understanding of disease mechanisms. Integrating patient tumor analysis with clinical medicine can optimize treatment strategies.
Article
Multidisciplinary Sciences
Charlotte Cooper, Eliza J. R. Peterson, Rebeca Bailo, Min Pan, Albel Singh, Patrick Moynihan, Makoto Nakaya, Nagatoshi Fujiwara, Nitin Baliga, Apoorva Bhatt
Summary: This study reveals that the mycolic acid desaturase regulator (MadR) controls mycolic acid desaturation and biosynthesis in response to cell envelope stress. This unique regulation mechanism is distinct to other regulators and MadR acts as a key regulatory checkpoint during infection to coordinate mycolic acid remodeling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Mathematical & Computational Biology
Selva Rupa Christinal Immanuel, Mario L. Arrieta-Ortiz, Rene A. Ruiz, Min Pan, Adrian Lopez Garcia de Lomana, Eliza J. R. Peterson, Nitin S. Baliga
Summary: The ability of Mycobacterium tuberculosis to adopt heterogeneous physiological states is crucial for its immune system evasion and antibiotic resistance. Developing new TB therapeutics requires a systems-level approach to understand the complexity of network-based adaptations of Mtb.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
Article
Microbiology
Mario L. Arrieta-Ortiz, Min Pan, Amardeep Kaur, Evan Pepper-Tunick, Vivek Srinivas, Ananya Dash, Selva Rupa Christinal Immanuel, Aaron N. Brooks, Tyson R. Shepherd, Nitin S. Baliga
Summary: There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Researchers found that tetracycline-resistant Escherichia coli undergo metabolic and transcriptional remodeling to support antibiotic resistance. They also discovered that sertraline, a drug, can resensitize tetracycline-resistant E. coli to the antibiotic.
Article
Microbiology
Alan P. R. Lorenzetti, Ulrike Kusebauch, Livia S. Zaramela, Wei-Ju Wu, Joao P. P. de Almeida, Serdar Turkarslan, Adrian L. G. de Lomana, Jose V. Gomes-Filho, Ricardo Z. N. Vencio, Robert L. Moritz, Tie Koide, Nitin S. Baliga
Summary: In this study, we investigated the scale of post-transcriptional regulation in the halophilic archaeon Halobacterium salinarum NRC-1. Our integrated analysis revealed that a large number of protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for post-transcriptional processing and regulation. Additionally, we found evidence for the conditional post-transcriptional regulation of a subset of genes involved in stressful environment acclimation. These findings provide valuable insights into the role of post-transcriptional regulation in environmental adaptation and are made available as an interactive atlas for further research.
Letter
Cardiac & Cardiovascular Systems
Janos Porszasz, Chu-Yi Wang, Carrie Ferguson, Shuyi Ma, Michele Girardi, William W. Stringer
RESPIRATORY MEDICINE
(2023)
Article
Multidisciplinary Sciences
Ulrike Kusebauch, Alan P. R. Lorenzetti, David S. Campbell, Min Pan, David Shteynberg, Charu Kapil, Mukul K. Midha, Adrian Lopez Garcia de Lomana, Nitin S. Baliga, Robert L. Moritz
Summary: Researchers have reported a comprehensive spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, which enables the measurement of a large fraction of its proteome. This library provides a valuable resource for confidently measuring and quantifying any protein of this archaeon.
Article
Biochemical Research Methods
Vivek Srinivas, Rene A. Ruiz, Min Pan, Selva Rupa Christinal Immanuel, Eliza J. R. Peterson, Nitin S. Baliga
Summary: The study presents a method named DRonA and MLSynergy, which uses transcriptome signature to detect drug responses of Mycobacterium tuberculosis and predict their cell killing effects, providing a new framework for rapid monitoring of drug effects and discovery of effective drug combinations.
CELL REPORTS METHODS
(2021)
Article
Oncology
Matthew A. Wall, Serdar Turkarslan, Wei-Ju Wu, Samuel A. Danziger, David J. Reiss, Mike J. Mason, Andrew P. Dervan, Matthew W. B. Trotter, Douglas Bassett, Robert M. Hershberg, Adrian Lopez Garcia de Lomana, Alexander V. Ratushny, Nitin S. Baliga
Summary: This study reports a transcriptional regulatory network inferred from multi-omics data that accurately predicts disease progression risk in multiple myeloma patients and provides insights into possible mechanisms and therapeutic vulnerabilities.
NPJ PRECISION ONCOLOGY
(2021)
Review
Gastroenterology & Hepatology
Tomasz Wilmanski, Noa Rappaport, Christian Diener, Sean M. Gibbons, Nathan D. Price
Summary: This review discusses current approaches for defining and monitoring gut microbiome health, emphasizes the importance of identifying gut microbial ecological features resonant with host molecular phenotypes, and highlights certain gut microbial metabolites as potential biomarkers of gut microbiome health. It further explores how omics measurements and gut microbiome profiles can be integrated into sophisticated host-microbiome mechanistic models for personalized interventions.