Article
Immunology
Lei Zhang, Ting Chen, Ye Wang, Shengwei Zhang, Qingyu Lv, Decong Kong, Hua Jiang, Yuling Zheng, Yuhao Ren, Wenhua Huang, Peng Liu, Yongqiang Jiang
Summary: Metagenomic next-generation sequencing (mNGS) is a novel strategy increasingly used in clinic for pathogen detection. In this study, three DNA extraction methods were compared, and the enzymatic-based method was found to have excellent performance in long-read mNGS-based pathogen identification and potential diseases diagnosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Editorial Material
Microbiology
Ali Nabhani, Benjamin R. Morehouse
Summary: The study reveals that viral strategies to lyse host microbes can be as simple as a single gene, which produces a protein that inhibits host peptidoglycan synthesis and induces lysis.
CELL HOST & MICROBE
(2023)
Review
Biotechnology & Applied Microbiology
Pengyi Yang, Hao Huang, Chunlei Liu
Summary: Recent advances in single-cell biotechnologies have led to high-dimensional datasets with increased complexity, making feature selection an essential technique for single-cell data analysis. This review revisits and summarizes feature selection techniques, their applications, challenges, and future directions in the single-cell era. The scalability and general recommendations for each type of feature selection method are also considered for stimulating future research and applications in single-cell analysis.
Article
Multidisciplinary Sciences
James R. Rybarski, Kuang Hu, Alexis M. Hill, Claus O. Wilke, Ilya J. Finkelstein
Summary: A bioinformatic search has led to the discovery of new CRISPR-associated Tn7 transposons (CASTs), revealing different structures and evolution processes of the CAST systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Emily Crossette, Jordan Gumm, Kathryn Langenfeld, Lutgarde Raskin, Melissa Duhaime, Krista Wigginton
Summary: The study demonstrates an assembly-independent metagenomic quantification approach that can screen and quantify over 2,000 genes simultaneously, delivering absolute gene concentrations comparable to qPCR. By comparing with traditional qPCR methods, this approach avoids biases caused by primer specificity, and is capable of detecting orders of magnitude more genes than qPCR assays.
Editorial Material
Neurosciences
Ernest Arenas
Summary: This study reveals the existence of ten distinct dopamine-producing neuron subpopulations in the substantia nigra, but only one of them is associated with significant PD genetic risk and vulnerable to neurodegeneration in PD.
NATURE NEUROSCIENCE
(2022)
Review
Biotechnology & Applied Microbiology
Andy Tran, Pengyi Yang, Jean Y. H. Yang, John Ormerod
Summary: Recent advances in direct cell reprogramming offer a potential cell-based treatment for major diseases, but there are still obstacles to overcome, such as low efficiency and resource requirements. Computational algorithms, including transcription factor identification and perturbation methods, have been developed to guide experimental validation. We summarize the contributions and limitations of each method and discuss the innovation that single cell technologies bring to these approaches, as well as the future direction of the field.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2022)
Article
Chemistry, Multidisciplinary
Qi Zhang, Nuohan Xu, Chaotang Lei, Bingfeng Chen, Tingzhang Wang, Yunting Ma, Tao Lu, Josep Penuelas, Michael Gillings, Yong-Guan Zhu, Zhengwei Fu, Haifeng Qian
Summary: The global crisis in antimicrobial resistance continues to grow, with human feces found to be broadly representative of the global resistome and potentially a hub for accumulating and disseminating resistance genes across different habitats.
Article
Environmental Sciences
Manik Prabhu Narsing Rao, Zhen-Hao Luo, Zhou-Yan Dong, Qi Li, Bing-Bing Liu, Shu-Xian Guo, Guo-Xin Nie, Wen Jun Li
Summary: Chloroflexi members are widely distributed and extensively studied. In this study, the evolution and metabolic potentials of 17 newly obtained Chloroflexi MAGs were evaluated using genome and HGT analysis. The results suggest that the MAGs might be novel and clarify the evolution of anaerobic photosynthesis.
ENVIRONMENTAL RESEARCH
(2022)
Article
Biochemical Research Methods
Raissa Silva, Kleber Padovani, Fabiana Goes, Ronnie Alves
Summary: The study introduces a machine-learning based gene predictor, geneRFinder, which performs well in handling high-complexity metagenomic data. Compared to existing tools, geneRFinder shows significant differences in average prediction rates and higher specificity rates.
BMC BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Jun Lin, Wenqian Jiang, Lin Chen, Huilian Zhang, Yang Shi, Xin Liu, Weiwen Cai
Summary: Banknotes can serve as a valuable genetic resource for discovering novel microbial gene sequences, including potentially economically valuable enzymes. High-throughput genomic sequencing technology was used to characterize the microbial diversity on US dollars and Chinese Renminbis, leading to the discovery of a significant number of novel gene sequences, one of which was experimentally verified for its catalytic activity.
Review
Developmental Biology
Kuo-Chang Tseng, J. Gage Crump
Summary: The evolution of the craniofacial complex in vertebrates has enabled new adaptations in breathing, eating, communication, and environmental sensing. Recent advancements in genomics and single-cell technologies have provided a more comprehensive understanding of the genes and regulatory elements involved in craniofacial development, shedding light on human diseases and vertebrate evolution. These studies have the potential to uncover the causes of birth anomalies affecting the vertebrate head.
Article
Plant Sciences
Liam Le Lievre, Sreejith P. Chakkatu, Shiny Varghese, Robert C. Day, Sarah M. Pilkington, Lynette Brownfield
Summary: Pollen development is a complex process involving coordinated differentiation and functions of different cell types. However, studying gene expression during early stages of pollen development is challenging due to its inaccessibility. To overcome this, researchers have developed a protocol called SA RNA-Seq, which allows for the transcriptome analysis of isolated pollen from a single anther. This protocol has been successfully applied to Arabidopsis and kiwifruit, providing valuable insights into gene expression during pollen development.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Zhenwei Liu, Tao Zhang, Keke Wu, Zhongshan Li, Xiaomin Chen, Shan Jiang, Lifeng Du, Saisai Lu, Chongxiang Lin, Jinyu Wu, Xiaobing Wang
Summary: Periodontitis, an inflammatory disease characterized by progressive destruction of the periodontium and tooth loss, is associated with dysbiosis of the oral microflora. In this study, metagenomic sequencing was used to investigate the etiology, antibiotic resistance genes (ARGs), and virulence genes (VirGs) of periodontitis. The study revealed a shift in oral microbiota composition and identified functional pathways that were significantly more abundant in periodontitis patients. Furthermore, several positively selected ARGs and VirGs were identified, some of which were found in respiratory tract pathogens. These findings suggest a potential association between periodontitis and respiratory infection at the gene level.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Food Science & Technology
Lijun You, Chengcong Yang, Hao Jin, Lai-Yu Kwok, Zhihong Sun, Heping Zhang
Summary: This study utilized deep metagenomic sequencing to analyze the microbiomes of various fermented milk products, revealing microbial diversity and unique characteristics. New species belonging to Lactobacillus, Streptococcus, Acetobacter, and Rothia genera were identified, indicating potential influences on food flavor and quality. The common presence of bacteriocins and bacteriophage sequences in these products was also highlighted, showcasing their importance in controlling undesirable microorganisms and uncovering complex interactions within microbial communities.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Microbiology
Karthik R. Chamakura, Jennifer S. Tran, Ry Young
JOURNAL OF BACTERIOLOGY
(2017)
Article
Microbiology
Karthik R. Chamakura, Garrett B. Edwards, Ry Young
Article
Microbiology
Karthik R. Chamakura, Lok-To Sham, Rebecca M. Davis, Lorna Min, Hongbaek Cho, Natividad Ruiz, Thomas G. Bernhardt, Ry Young
NATURE MICROBIOLOGY
(2017)
Review
Biochemistry & Molecular Biology
Karthik Chamakura, Ry Young
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Multidisciplinary Sciences
Laith Harb, Karthik Chamakura, Pratick Khara, Peter J. Christie, Ry Young, Lanying Zeng
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Karthik R. Chamakura, Jennifer S. Tran, Chandler O'Leary, Hannah G. Lisciandro, Sophia F. Antillon, Kameron D. Garza, Elizabeth Tran, Lorna Min, Ry Young
NATURE COMMUNICATIONS
(2020)
Article
Engineering, Environmental
Harvey N. Summerlin, Cicero C. Pola, Karthikeyan R. Chamakura, Ry Young, Terry Gentry, Eric S. McLamore, Raghupathy Karthikeyan, Carmen L. Gomes
Summary: This study investigated the cultivation of romaine lettuce with inoculated wastewater effluent, tracking the prevalence of AP205 bacteriophage. Results showed a direct relationship between AP205 concentrations and contamination levels in foliage, leachate, and soil, with an increase in bacteriophage accumulation throughout cultivation.
JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART A-TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Benjamin A. Adler, Karthik Chamakura, Heloise Carion, Jonathan Krog, Adam M. Deutschbauer, Ry Young, Vivek K. Mutalik, Adam P. Arkin
Summary: This study used a high-throughput genetic screen to identify genome-wide host suppressors of diverse single-gene lysis factors (Sgls). In addition to validating known mechanisms, the researchers discovered that the Sgl of PP7, a Pseudomonas aeruginosa ssRNA phage, targets MurJ, the flippase responsible for lipid II export, which was previously shown to be the target of the Sgl of coliphage M. These unrelated Sgls, which are predicted to have opposite membrane topology, represent a case of convergent evolution. Furthermore, the genetic screens revealed a common set of multicopy suppressors for uncharacterized Sgls, suggesting a shared or similar mechanism of action.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Microbiology
James M. Grover, Adrian J. Luna, Thammajun L. Wood, Karthik R. Chamakura, Gabriel F. Kuty Everett
GENOME ANNOUNCEMENTS
(2015)
Article
Microbiology
Mariana S. Lopez, Mary K. Hodde, Karthik R. Chamakura, Gabriel F. Kuty Everett
GENOME ANNOUNCEMENTS
(2014)
Article
Microbiology
Adrian J. Luna, Thammajun L. Wood, Karthik R. Chamakura, Gabriel F. Kuty Everett
GENOME ANNOUNCEMENTS
(2013)
Article
Microbiology
Justin W. Maroun, Kelvin J. Whitcher, Karthik R. Chamakura, Gabriel F. Kuty Everett
GENOME ANNOUNCEMENTS
(2013)
Article
Microbiology
Rohit R. Kongari, Guichun W. Yao, Karthik R. Chamakura, Gabriel F. Kuty Everett
GENOME ANNOUNCEMENTS
(2013)
Article
Microbiology
Brontee E. Khatemi, Christopher C. Chung On, Karthik R. Chamakura, Gabriel F. Kuty Everett
GENOME ANNOUNCEMENTS
(2013)