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Although gene expansion plays an important role in evolution, its identification remains a challenge due to potential errors in genome assembly and annotation. Here, we describe a detailed step-by-step protocol for gene annotation, prediction of genomic gene expansion, and its computational and experimental validation. Finally, we also detail steps to discover functionality of each copy of replicated genes. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021).
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http://dx.doi.org/10.1016/j.xpro.2022.101692 | DOI Listing |
Plant Physiol Biochem
August 2025
School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China. Electronic address:
The PR10 (Pathogenesis-Related Protein 10) family plays a crucial role in plant defense and growth regulation, with unique hydrophobic cavities that bind various ligands, including phytohormones and alkaloids. Among them, Norcoclaurine Synthases (NCS) are key enzymes in benzylisoquinoline alkaloid (BIAs) biosynthesis, catalyzing the Pictet-Spengler reaction to form the precursor (S)-norcoclaurine. However, the evolutionary origins and functions of the PR10 family in BIA biosynthesis remain unclear.
View Article and Find Full Text PDFMicrob Genom
September 2025
National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan, ROC.
remains a leading respiratory pathogen for children and the elderly. In Taiwan, a national PCV13 catch-up vaccination programme for children began in March 2013. This study investigates the population structure and antimicrobial profiles of pneumococcal isolates in Taiwan from 2006 to 2022.
View Article and Find Full Text PDFJ Exp Med
November 2025
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
Host-pathogen interactions involve two critical strategies: resistance, whereby hosts clear invading microbes, and tolerance, whereby hosts carry high pathogen burden asymptomatically. Here, we investigate mechanisms by which Salmonella-superspreader (SSP) hosts maintain an asymptomatic state during chronic infection. We found that regulatory T cells (Tregs) are essential for this disease-tolerant state, limiting intestinal immunopathology and enabling SSP hosts to thrive, while facilitating Salmonella transmission.
View Article and Find Full Text PDFBiotechnol J
September 2025
Department of Biochemical Engineering, University College London, London, UK.
Chimeric antigen receptor T-cell (CAR-T) therapies have demonstrated clinical efficacy in treating haematological malignancies, resulting in multiple regulatory approvals. However, there is a need for robust manufacturing platforms and the use of GMP-aligned reagents to meet the clinical and commercial demands. This study investigates the impact of serum/xeno-free medium (SXFM) and cytokine supplementation on CAR-T cell production in static and agitated culture systems, using 24-well plate G-Rex vessels and 500 mL stirred tank bioreactors (STRs), respectively.
View Article and Find Full Text PDFAPMIS
September 2025
Laboratory of Parasitology, Department of Bacteria, Parasites and Fungi, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark.
Clinical microbiology involves the detection and differentiation of primarily bacteria, viruses, parasites and fungi in patients with infections. Billions of people may be colonised by one or more species of common luminal intestinal parasitic protists (CLIPPs) that are often detected in clinical microbiology laboratories; still, our knowledge on these organisms' impact on global health is very limited. The genera Blastocystis, Dientamoeba, Entamoeba, Endolimax and Iodamoeba comprise CLIPPs species, the life cycles of which, as opposed to single-celled pathogenic intestinal parasites (e.
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