Dataset Information

Molecular identification of the occurrence of magnetotactic bacteria in fresh water sediments (Czech Republic).

ABSTRACT: Magnetotactic bacteria (MTB) are of considerable interest because of their importance in the manufacture of various bioinspired materials. In order to find out the status of magnetotactic bacteria at three different sediment in Czech Republic, samples collected from both standing and running freshwaters were subjected to molecular diversity analysis by using 16S rRNA gene approach. Total community DNA from sediment sample was isolated and used for PCR, cloning and sequence analysis. Of the 24 analyzed sequences, six clones are closely related to Magnetobacterium sp. affiliated with the Nitrospira phylum which showed the dominance of Magnetobacterium phylotypes in the sample. This study will provide useful insight about the community structure of MTB in this particular geographical region. However more detailed and specific studies are warranted in order to properly assess the community structure of MTB's in fresh water sediments.

SUBMITTER: Rulik M

PROVIDER: S-EPMC4323298 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Molecular identification of the occurrence of magnetotactic bacteria in fresh water sediments (Czech Republic).

Rulík Martin M Chaudhary Prem Prashant PP

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 20140101 4

Magnetotactic bacteria (MTB) are of considerable interest because of their importance in the manufacture of various bioinspired materials. In order to find out the status of magnetotactic bacteria at three different sediment in Czech Republic, samples collected from both standing and running freshwaters were subjected to molecular diversity analysis by using 16S rRNA gene approach. Total community DNA from sediment sample was isolated and used for PCR, cloning and sequence analysis. Of the 24 an ...[more]

PMID: 25763029

Similar Datasets

Project description:The aim of this study was to determine the occurrence of plasmid-mediated colistin resistance in domestic and imported meat and slaughter animals in the Czech Republic during 2020-2021 by using selective cultivation and direct PCR testing. A total of 111 colistin-resistant Escherichia coli isolates with mcr-1 gene were obtained from 65 (9.9%, n = 659) samples and subjected to whole-genome sequencing. Isolates with mcr were frequently found in fresh meat from domestic production (14.2%) as well as from import (28.8%). The mcr-1-positive E. coli isolates predominantly originated from meat samples (16.6%), mainly poultry (27.1%), and only minor part of the isolates came from the cecum (1.7%). In contrast to selective cultivation, 205 (31.1%) samples of whole-community DNA were positive for at least one mcr variant, and other genes besides mcr-1 were detected. Analysis of whole-genome data of sequenced E. coli isolates revealed diverse sequence types (STs) including pathogenic lineages and dominance of ST1011 (15.6%) and ST162 (12.8%). Most isolates showed multidrug-resistant profile, and 9% of isolates produced clinically important beta-lactamases. The mcr-1 gene was predominantly located on one of three conjugative plasmids of IncX4 (83.5%), IncI2 (7.3%), and IncHI2 (7.3%) groups. Seventy-two percent isolates of several STs carried ColV plasmids. The study revealed high prevalence of mcr genes in fresh meat of slaughter animals. Our results confirmed previous assumptions that the livestock, especially poultry production, is an important source of colistin-resistant E. coli with the potential of transfer to humans via the food chain. IMPORTANCE We present the first data on nation-wide surveillance of plasmid-mediated colistin resistance in the Czech Republic. High occurrence of plasmid-mediated colistin resistance was found in meat samples, especially in poultry from both domestic production and import, while the presence of mcr genes was lower in the gut of slaughter animals. In contrast to culture-based approach, testing of whole-community DNA showed higher prevalence of mcr and presence of various mcr variants. Our results support the importance of combining cultivation methods with direct culture-independent techniques and highlight the need for harmonized surveillance of plasmid-mediated colistin resistance. Our study confirmed the importance of livestock as a major reservoir of plasmid-mediated colistin resistance and pointed out the risks of poultry meat for the transmission of mcr genes toward humans. We identified several mcr-associated prevalent STs, especially ST1011, which should be monitored further as they represent zoonotic bacteria circulating between different environments.

Project description:BackgroundAlterations in the highly penetrant cancer susceptibility gene BRCA1 are responsible for the majority of hereditary breast and/or ovarian cancers. However, the number of detected germline mutations has been lower than expected based upon genetic linkage data. Undetected deleterious mutations in the BRCA1 gene in some high-risk families could be due to the presence of intragenic rearrangements as deletions, duplications or insertions spanning whole exons. Standard PCR-based screening methods are mainly focused on detecting point mutations and small insertions/deletions, but large rearrangements might escape detection.The purpose of this study was to determine the type and frequency of large genomic rearrangements in the BRCA1 gene in hereditary breast and ovarian cancer cases in the Czech Republic.MethodsMultiplex ligation-dependent probe amplification (MLPA) was used to examine BRCA1 rearrangements in 172 unrelated patients with hereditary breast and/or ovarian cancer syndrome without finding deleterious mutation after complete screening of whole coding regions of BRCA1/2 genes. Positive MLPA results were confirmed and located by long-range PCR. The breakpoints of detected rearrangements were characterized by sequencing.ResultsSix different large deletions in the BRCA1 gene were identified in 10 out of 172 unrelated high-risk patients: exons 1A/1B and 2 deletion; partial deletion of exon 11 and exon 12; exons 18 and 19 deletion; exon 20 deletion; exons 21 and 22 deletion; and deletion of exons 5 to 14. The breakpoint junctions were localized and further characterized. Destabilization and global unfolding of the mutated BRCT domains explain the molecular and genetic defects associated with the exon 20 in-frame deletion and the exon 21 and 22 in-frame deletion, respectively.ConclusionUsing MLPA, mutations were detected in 6% of high-risk patients previously designated as BRCA1/2 mutation-negative. The breakpoints of five out of six large deletions detected in Czech patients are novel. Screening for large genomic rearrangements in the BRCA1 gene in the Czech high-risk patients is highly supported by this study.

Dataset Information

Molecular identification of the occurrence of magnetotactic bacteria in fresh water sediments (Czech Republic).

Publications

Molecular identification of the occurrence of magnetotactic bacteria in fresh water sediments (Czech Republic).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets