Article
Biochemistry & Molecular Biology
Heladia Salgado, Socorro Gama-Castro, Paloma Lara, Citlalli Mejia-Almonte, Gabriel Alarcon-Carranza, Andres G. Lopez-Almazo, Felipe Betancourt-Figueroa, Pablo Pena-Loredo, Shirley Alquicira-Hernandez, Daniela Ledezma-Tejeida, Lizeth Arizmendi-Zagal, Francisco Mendez-Hernandez, Ana K. Diaz-Gomez, Elizabeth Ochoa-Praxedis, Luis J. Muniz-Rascado, Jair S. Garcia-Sotelo, Fanny A. Flores-Gallegos, Laura Gomez, Cesar Bonavides-Martinez, Victor M. del Moral-Chavez, Alfredo J. Hernandez-Alvarez, Alberto Santos-Zavaleta, Salvador Capella-Gutierrez, Josep Lluis Gelpi, Julio Collado-Vides
Summary: RegulonDB is a database that contains comprehensive knowledge on the regulation of transcription initiation of Escherichia coli K-12. The latest version, 12.0, offers improved data storage, retrieval, and accessibility, as well as intuitive graphical tools for data interpretation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Claudia Eberl, Anna S. Weiss, Lara M. Jochum, Abilash Chakravarthy Durai Raj, Diana Ring, Saib Hussain, Simone Herp, Chen Meng, Karin Kleigrewe, Michael Gigl, Marijana Basic, Barbel Stecher
Summary: The composition of the intrinsic microbial communities plays a crucial role in determining whether invading pathogens can establish colonization or be blocked by commensal bacteria. This study found that E. coli can provide colonization resistance against Salmonella Typhimurium by depleting specific carbon sources in a microbial context that supports the removal of simple sugars from the intestine. In certain cases, the presence of other bacterial groups is essential for the colonization resistance mediated by commensal E. coli.
CELL HOST & MICROBE
(2021)
Article
Biochemistry & Molecular Biology
Elizabeth Ramos-Morales, Efil Bayam, Jordi Del-Pozo-Rodriguez, Thalia Salinas-Giege, Martin Marek, Peggy Tilly, Philippe Wolff, Edouard Troesch, Eric Ennifar, Laurence Drouard, Juliette D. Godin, Christophe Romier
Summary: This study provides insights into the molecular mechanisms of tRNA deamination by ADAT2 and the importance of the ADAT3 N-terminal domain in tRNA binding and deamination. The rotation of the N-terminal domain with respect to the catalytic domain plays a crucial role in presenting and positioning the tRNA anticodon-stem-loop correctly in the ADAT2 active site. A founder mutation in the ADAT3 N-terminal domain, causing intellectual disability, is shown to hinder optimal presentation of the tRNA anticodon-stem-loop to ADAT2.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Immunology
Jianlin Zuo, Jinshuo Tang, Meng Lu, Zhongsheng Zhou, Yang Li, Hao Tian, Enbo Liu, Baoying Gao, Te Liu, Pu Shao
Summary: Rheumatoid arthritis is a classic autoimmune disease characterized by uncontrolled synovial proliferation, and the pathogenesis of which may involve glycolysis rate-limiting enzymes. By studying the expression characteristics of HK-II, PFK-1/PFKFB3, and PKM2, new insights may be gained for the treatment of RA.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Microbiology
Benjamin S. Beresford-Jones, Samuel C. Forster, Mark D. Stares, George Notley, Elisa Viciani, Hilary P. Browne, Daniel J. Boehmler, Amelia T. Soderholm, Nitin Kumar, Kevin Vervier, Justin R. Cross, Alexandre Almeida, Trevor D. Lawley, Virginia A. Pedicord
Summary: This study constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC) to identify functionally equivalent taxa between the gut microbiotas of humans and mice. It also provided a publicly deposited collection of bacterial isolates to facilitate experimental investigation of individual commensal bacteria functions.
CELL HOST & MICROBE
(2022)
Article
Cell Biology
Zhangding Wang, Yao Fu, Anliang Xia, Chen Chen, Jiamu Qu, Guifang Xu, Xiaoping Zou, Qiang Wang, Shouyu Wang
Summary: This study aimed to elucidate the comprehensive model of metabolic rate-limiting enzymes associated with the prognosis of hepatocellular carcinoma. A classifier based on three rate-limiting enzymes (RRM1, UCK2 and G6PD) was found to serve as an independent prognostic factor. Combining clinical risk score with signature risk score significantly improved the prediction accuracy of individual outcomes, highlighting the prognostic value of rate-limiting enzymes in guiding clinical management and treatment decisions for HCC.
CELL PROLIFERATION
(2021)
Article
Medicine, Research & Experimental
Chao Song, Yuexin Zhang, Hong Huang, Yuezhu Wang, Xilong Zhao, Guorui Zhang, Mingxue Yin, Chenchen Feng, Qiuyu Wang, Fengcui Qian, Desi Shang, Jian Zhang, Jiaqi Liu, Chunquan Li, Huifang Tang
Summary: Cis-Cardio is a valuable web server that collects and analyzes cardiovascular-related cis-regulatory data. It offers various tools and detailed annotations to study the regulatory cues of cardiovascular-specific cis-regulatory elements.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Multidisciplinary Sciences
Gaoyang Li, Li Liu, Wei Du, Huansheng Cao
Summary: The authors develop a method called Decrem, which integrates locally coupled reactions and global transcriptional regulation of metabolism, to reconstruct genome-scale metabolic networks. Decrem achieves accurate predictions of phenotypes and has broad applications in bioengineering, synthetic biology, and microbial pathology.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Mengyi Sun, Jianzhi Zhang
Summary: In this study, direct evidence for the translational accuracy hypothesis (TAH) of codon usage bias is presented through analyzing proteomic data from Escherichia coli. The experimentally measured codon-specific translational accuracies validate a sequence-based proxy and support the TAH across various taxa. The relative translational accuracies of synonymous codons vary among taxa and are strongly correlated with the amounts of cognate transfer RNAs (tRNAs) relative to those of near-cognate tRNAs, suggesting coevolution between codon usage bias and the tRNA pool.
Article
Biology
Angela R. Wild, Peter W. Hogg, Stephane Flibotte, Glory G. Nasseri, Rocio B. Hollman, Danya Abazari, Kurt Haas, Shernaz X. Bamji
Summary: Protein S-palmitoylation is a reversible post-translational lipid modification that plays a critical role in neuronal development and plasticity. This study analyzed the expression data of proteins involved in regulating S-palmitoylation in the mouse nervous system and developed a web-tool to visualize their expression patterns. The researchers found region and cell-type specific expression patterns that provide insights into the function of palmitoylating and de-palmitoylating enzymes in the brain and neurological disorders. ZDHHC expression patterns were also utilized to predict and validate palmitoylating enzyme-substrate interactions.
Article
Microbiology
Toshiyuki Ohtake, Naoki Kawase, Sammy Pontrelli, Katsuaki Nitta, Walter A. Lavina, Claire R. Shen, Sastia P. Putri, James C. Liao, Eiichiro Fukusaki
Summary: This study demonstrates the use of metabolomics as a powerful tool for systematically improving metabolic engineering microbial strains. By analyzing metabolic perturbations, targets for enhanced production of 1-propanol were identified. Strategies such as gene knockouts and overexpression were used to increase the concentration of intermediates, but also revealed negative effects such as toxicity and inadequate turnover rates. Finally, optimization of alcohol dehydrogenase activity resulted in further improvements in 1-propanol production and yield.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Medicine, Research & Experimental
Changpei Gan, Jing Wang, Yaogeng Wang, Alejandra Martinez-Chavez, Michel Hillebrand, Niels de Vries, Joke Beukers, Maria C. Lebre, Els Wagenaar, Hilde Rosing, Sjoerd Klarenbeek, Onno B. Bleijerveld, Ji-Ying Song, Maarten Altelaar, Jos H. Beijnen, Alfred H. Schinkel
Summary: Mammalian carboxylesterase 1 (Ces1) enzymes play a vital role in metabolism, hydrolyzing numerous xenobiotics and endogenous lipids. This study identified a mouse strain lacking three Ces1 genes (Ces1c, Ces1d, and Ces1e), and demonstrated that this deficiency impaired drug and lipid metabolism, leading to altered body weight, inflammation, and lipid accumulation in adipose tissue and liver. These findings emphasize the importance of Ces1 enzymes in maintaining metabolic homeostasis and suggest their potential role in obesity-related chronic inflammation and metabolic diseases.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Marcio L. Acencio, Miguel Vazquez, Konika Chawla, Astrid Laegreid, Martin Kuiper
Summary: Prior knowledge of transcription factors is crucial for understanding transcriptional regulation. TFCheckpoint 2.0 is an integrated resource that provides an easy and versatile cross-referencing system for viewing and downloading collections of transcription factors.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Martijn Wehrens, Laurens H. J. Krah, Benjamin D. Towbin, Rutger Hermsen, Sander J. Tans
Summary: This study reveals that catabolic enzyme expression in E. coli cells continuously responds to metabolic fluctuations, which is regulated by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) system. The study uses single-cell microscopy, genetic constructs, and mathematical modeling to show how fluctuations circulate through the metabolic and genetic network at sub-cell-cycle timescales. The findings suggest that the cAMP-CRP system may have evolved to control both internal metabolic fluctuations and external growth conditions.
Article
Biology
Rosemary Yu, Egor Vorontsov, Carina Sihlbom, Jens Nielsen
Summary: The study revealed that cell growth rate coordinately controls transcription and translation through RNA polymerase II and ribosome abundance, while nitrogen metabolism independently controls them through amino acid and nucleotide availabilities. Genes in central carbon metabolism are distinctly regulated compared to other genes in response to cell growth rate or nitrogen metabolism.
Article
Biology
Minglin Ou, Min Zhao, Chunhong Li, Donge Tang, Yong Xu, Weier Dai, Weiguo Sui, Yue Zhang, Zhen Xiang, Chune Mo, Hua Lin, Yong Dai
Summary: The study on human iPSC-derived cardiomyocytes revealed dynamic expression events related to oncogenes and tumor suppressor genes during cardiac differentiation, similar to patterns observed in oncogenesis. The oncogenic expression atlas obtained through single-cell sequencing is valuable for understanding the application of human iPSCs and potential carcinogenic risks associated with them.
Article
Multidisciplinary Sciences
YongKiat Wee, Yining Liu, Min Zhao
Summary: Acute lymphoblastic leukemia (ALL) in children is often caused by mutations in oncogenes and tumor suppressor genes, which play important roles in gene regulation at the post-translational level. Through integrative network analysis, it was found that oncogenes and tumor suppressor genes exhibit different functional regulatory patterns in childhood ALL progression.
Article
Biochemistry & Molecular Biology
Yining Liu, Min Zhao
Summary: By integrating single-cell transcriptome data from multiple cancer datasets, the similarities and variations of neuropeptide-mediated cell communication between different types of cancer were studied. Stable cell communication events showed common and distinct neuropeptide-receptor patterns, which are potentially associated with blood pressure regulation and patients' survival.
Article
Biotechnology & Applied Microbiology
Yalun Dong, Min Zhao, Renfu Shao
Summary: We analyzed the fragmentation of mitochondrial genomes in seal lice and gorilla louse, and found that minichromosome split contributes more than minichromosome merger in the evolution of fragmented mt genomes. We also observed multiple independent split events of ancestral mt minichromosomes in different lineages of sucking lice.
Article
Cell Biology
Lin Peng, Min Zhao, Tianqi Liu, Jiangbo Chen, Pin Gao, Lei Chen, Pu Xing, Zaozao Wang, Jiabo Di, Qiang Xu, Hong Qu, Beihai Jiang, Xiangqian Su
Summary: Genomic instability is crucial in the initiation and progression of CRC. Using whole-exome sequencing, two novel genes (GXYLT1 and GXYLT1(S212*)) associated with metastasis were identified, and their functional mechanisms were elucidated. GXYLT1 acts as a driver gene for metastasis, while GXYLT1(S212*) may serve as a potential indicator for therapies targeting the MAPK pathway in CRC.
CELL DEATH & DISEASE
(2022)
Article
Multidisciplinary Sciences
Phong Phan, Di Liang, Min Zhao, Russell C. Wyeth, Conor Fogarty, Mary G. Duke, Donald P. McManus, Tianfang Wang, Scott F. Cummins
Summary: The interactions between snails and parasites play a crucial role in blocking the development of schistosomes. Both snails and parasites have shared G protein-coupled receptors (GPCRs) that may aid in the parasite's ability to locate the snail hosts. These findings lay the foundation for potential development of novel interventions against schistosomiasis.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Salma Begum Bhyan, Scott Cummins, Mobashwer Alam, Min Zhao
Summary: In this study, the researchers collected 115 publicly available datasets for gene panel testing of breast cancer and identified 214 unique genes. They found eight highly penetrant and six moderately penetrant coding genes through large-scale cancer genomics data analysis. Additionally, they discovered two microRNAs that can be used as therapeutic tools for combating metastasis, chemo-resistance, and breast cancer recurrence.
Article
Biology
Yining Liu, Scott F. Cummins, Min Zhao
Summary: This study examined the genomes of edible seaweeds and discovered potential anticancer proteins and peptides. The findings contribute to our understanding of seaweed biology and have the potential to enhance the use of seaweed as a nutraceutical practice.
Article
Biology
Tianqi Liu, Yining Liu, Xiangqian Su, Lin Peng, Jiangbo Chen, Pu Xing, Xiaowen Qiao, Zaozao Wang, Jiabo Di, Min Zhao, Beihai Jiang, Hong Qu
Summary: Screening cancer genomes identified CNV-lncRNA-mRNA regulatory triplets associated with CNVs and aberrant expression of both mRNAs and lncRNAs. A patient-specific multi-dimensional integrative approach was implemented to uncover coherent signals from multiple independent platforms, which can identify reliable molecular signals for personalized medicine.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biology
Zubaida P. Patwary, Min Zhao, Tianfang Wang, Nicholas A. Paul, Scott F. Cummins
Summary: This study investigated the proteins in Asparagopsis taxiformis using different extraction methods and provided a comprehensive overview of expressed proteins in the seaweed. The findings offer insights into the potential functions of these proteins and lay a foundation for future targeted protein extraction and biodiscovery.
Article
Biology
Yining Liu, Min Zhao, Hong Qu
Summary: We developed a lung cancer-specific database that contains genetic and literature data from over 10,000 separate studies. The database includes meticulously curated and quality controlled cancer subtype information, allowing for novel exploration of subtype-specific genetics. Additionally, we created the Lung Cancer Gene (LCGene) database, an open-access web interface for researchers and clinicians to explore this data and conduct large-scale integrative analyses. On LCGene, users can perform gene list-based data integration to understand the shared and unique characteristics of different subtypes of lung cancer. The data from subtype-based survival analysis, comparative analysis, and CRISPR knockout provide valuable information for genome-wide gene/biomarker screening in lung cancer subtypes.
Article
Biology
Mingyu Luo, Yining Liu, Min Zhao
Summary: Blood-based detection of circulating cell-free DNA (cfDNA) is a non-invasive and easily accessible method for early cancer detection. However, there are challenges in developing clinical biomarkers, such as filtering out false-positive cfDNA mutations and detecting low-frequency genetic alterations.
Article
Biochemistry & Molecular Biology
Xianhui Ruan, Yue Huang, Lin Geng, Mengran Tian, Yu Liu, Mei Tao, Xiangqian Zheng, Peng Li, Min Zhao
Summary: Single-cell transcriptome sequencing provides higher resolution for cellular differences in papillary thyroid carcinoma. Through integrative analysis of two datasets, we identified 31 consistently differentially expressed genes across multiple cell types, which are related to adaptive immune response and autoimmune thyroid diseases. Experimental validation suggests that KRT7 may be a potential biomarker for PTC epithelial cells.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Mathematical & Computational Biology
Min Zhao, Yining Liu, Hong Qu
Summary: This study highlights the significance of circRNA as a stable and specific biomarker for cancer diagnosis and prognosis, showing differential expression in various cancer types. By curating data across multiple platforms, the authors identified numerous circRNAs with potential impact on patient survival, providing valuable insights for cancer research and personalized medicine.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Biotechnology & Applied Microbiology
Min Zhao, Hong Qu
