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1.
PLoS Comput Biol ; 19(10): e1011527, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37851672

ABSTRACT

The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation of such results is essential for researchers to draw conclusions from obtained results. Although some tools are available, their functionality is limited. Here, we present AGouTI-a universal tool for flexible annotation of any genomic or transcriptomic coordinates using known genomic features deposited in different publicly available databases in the form of GTF or GFF files. In contrast to currently available tools, AGouTI is designed to provide a flexible selection of genomic features overlapping or adjacent to annotated intervals and can be used on custom column-based text files obtained from different data analysis pipelines. Although providing many unique options, AGouTI is straightforward in installation and usage, enabling effortless integration into existing data analysis workflows.


Subject(s)
Dasyproctidae , Animals , Transcriptome/genetics , Software , Genomics/methods , Genome/genetics , Molecular Sequence Annotation
2.
Antioxidants (Basel) ; 12(4)2023 Apr 01.
Article in English | MEDLINE | ID: mdl-37107222

ABSTRACT

BACKGROUND: Streptococcus agalactiae, referred to as Group B Streptococcus (GBS), is a prominent bacterium causing life-threatening neonatal infections. Although antibiotics are efficient against GBS, growing antibiotic resistance forces the search for alternative treatments and/or prevention approaches. Antimicrobial photodynamic inactivation (aPDI) appears to be a potent alternative non-antibiotic strategy against GBS. METHODS: The effect of rose bengal aPDI on various GBS serotypes, Lactobacillus species, human eukaryotic cell lines and microbial vaginal flora composition was evaluated. RESULTS: RB-mediated aPDI was evidenced to exert high bactericidal efficacy towards S. agalactiae in vitro (>4 log10 units of viability reduction for planktonic and >2 log10 units for multispecies biofilm culture) and in vivo (ca. 2 log10 units of viability reduction in mice vaginal GBS colonization model) in microbiological and metagenomic analyses. At the same time, RB-mediated aPDI was evidenced to be not mutagenic and safe for human vaginal cells, as well as capable of maintaining the balance and viability of vaginal microbial flora. CONCLUSIONS: aPDI can efficiently kill GBS and serve as an alternative approach against GBS vaginal colonization and/or infections.

3.
Database (Oxford) ; 20172017 01 01.
Article in English | MEDLINE | ID: mdl-29220443

ABSTRACT

Database URL: http://yeti.amu.edu.pl/retrogenedb. Secondary database URL: http://rhesus.amu.edu.pl/retrogenedb.


Subject(s)
Databases, Genetic , Eukaryota/genetics , Genome/genetics , Plants/genetics , RNA/genetics , Sequence Analysis, RNA , Animals , Expressed Sequence Tags , Phylogeny , User-Computer Interface
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