We have screened the genome of Saccharomyces cerevisiae for fragments that confer a growth-retardation phenotype when overexpressed in a multicopy plasmid with a tetracycline-regulatable (Tet-off) promoter. We selected 714 such fragments with a mean size of 700 base-pairs out of around 84,000 clones tested. These include 493 in-frame open reading frame fragments corresponding to 454 distinct genes (of which 91 are of unknown function), and 162 out-of-frame, antisense and intergenic genomic fragments, representing the largest collection of toxic inserts published so far in yeast.
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http://dx.doi.org/10.1186/gb-2004-5-9-r72 | DOI Listing |
BMC Bioinformatics
January 2025
Department of Radiology, University of Minnesota, Minneapolis, MN, 55455, USA.
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic determinants of various diseases. Naturally, the accuracy of these tests should be verified and improved if possible.
View Article and Find Full Text PDFJ Int AIDS Soc
February 2025
AP-HP, Hôpital Bichat Claude Bernard, Service de Virologie, INSERM, IAME, Paris, France.
Introduction: Molecular surveillance is an important tool for detecting chains of transmission and controlling the HIV epidemic. This can also improve our knowledge of molecular and epidemiological factors for the optimization of prevention. Our objective was to illustrate this by studying the molecular and epidemiological evolution of the cluster including the new circulating recombinant form (CRF) 94_cpx of HIV-1, detected in 2017 and targeted by preventive actions in 2018.
View Article and Find Full Text PDFRev Argent Microbiol
January 2025
Instituto De Química Biológica de la Facultad de Ciencias Exactas y Naturales-CONICET, Buenos Aires, Argentina; Departamento de Química Biológica, FCEyN-UBA, Buenos Aires, Argentina. Electronic address:
DNA extraction is crucial for conducting procedures, such as whole-genome sequencing, which demand methods that are reproducible and cost-effective. Lysing Staphylococcus aureus cells is particularly challenging due to their peptidoglycan layer that is resistant to common treatments. Traditional methods involve costly enzymatic lysis using lysostaphin.
View Article and Find Full Text PDFBMC Biol
January 2025
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.
Background: Silver arowana (Osteoglossum bicirrhosum) is a basal fish species with sexual monomorphism, while its sex determination mechanism has been poorly understood, posing a significant challenge to its captive breeding efforts.
Results: We constructed two high-quality chromosome-level genome assemblies for both female and male silver arowana, with scaffold N50 values over 10 Mb. Combining re-sequencing data of 109 individuals, we identified a female-specific region, which was localized in a non-coding region, i.
AIDS Res Hum Retroviruses
January 2025
Clinical Laboratory, The People's Hospital of Baoding, Baoding, China.
Many new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) of human immunodeficiency virus type-1 (HIV-1) have been discovered in populations with multiple circulating HIV-1 genotypes. In this study, we report two novel URFs derived from two HIV-1-positive individuals in Hebei, China, who were infected through homosexual (BDD142) and heterosexual (BDD154) contact. Phylogenetic and recombinant analyses of the two NFLG revealed that they are second-generation recombinant strains originating from the CRF01_AE cluster 4/B and CRF01_AE cluster 5/B strains.
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