Members of the Brachycladiidae are known to cause pathologies implicated in cetacean strandings and it is important to develop accurate diagnostic markers to differentiate these and other helminths found in cetaceans. Brachycladium goliath (van Beneden, 1858) is a large trematode found, as adults, usually in the hepatic (bile) and pancreatic ducts of various cetaceans. Complete sequences were determined for the entire mitochondrial genome, and phylogenetically informative nuclear genes contained within the ribosomal operon, from a small piece of an individual worm taken from a common minke whale Balaenoptera acutorostrata Lacépède, 1804. Genomic DNA was sequenced using an Illumina MiSeq platform. The mtDNA is 15,229 bp in length consisting of 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions of which the larger is comprised of 4 tandemly repeated units (260 bp each). The ribosomal RNA operon is 9297 bp long. These data provide a rich resource of molecular markers for diagnostics, phylogenetics and population genetics in order to better understand the role, and associated pathology of helminth infections in cetaceans.
- MeSH
- fylogeneze MeSH
- genom mitochondriální genetika MeSH
- mitochondriální DNA genetika MeSH
- nemoci ryb epidemiologie parazitologie MeSH
- operon genetika MeSH
- plejtvák malý parazitologie MeSH
- populační genetika MeSH
- sekvenční analýza DNA veterinární MeSH
- tandemové repetitivní sekvence genetika MeSH
- Trematoda genetika izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Set-level classification of gene expression data has received significant attention recently. In this setting, high-dimensional vectors of features corresponding to genes are converted into lower-dimensional vectors of features corresponding to biologically interpretable gene sets. The dimensionality reduction brings the promise of a decreased risk of overfitting, potentially resulting in improved accuracy of the learned classifiers. However, recent empirical research has not confirmed this expectation. Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. We hypothesize that such more correlated gene sets will enable to learn more accurate classifiers. METHODS: We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. From each of the two gene-set families, we first select the best-performing subtype. The two selected subtypes are then evaluated on independent (testing) data sets against state-of-the-art gene sets and against the conventional gene-level approach. RESULTS: The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. CONCLUSION: Novel gene sets defined on the basis of regulatory interactions improve set-level classification of gene expression data. The experimental scripts and other material needed to reproduce the experiments are available at http://ida.felk.cvut.cz/novelgenesets.tar.gz.
Treponema pallidum ssp. pallidum (TPA) causes over 10 million new cases of syphilis worldwide whereas T. pallidum ssp. pertenue (TPE), the causative agent of yaws, affects about 2.5 million people. Although penicillin remains the drug of choice in the treatment of syphilis, in penicillin-allergic patients, macrolides have been used in this indication since the 1950s. Failures of macrolides in syphilis treatment have been well documented in the literature and since 2000, there has been a dramatic increase in a number of clinical samples with macrolide-resistant TPA. Scarce data regarding the genetics of macrolide-resistant mutations in TPA suggest that although macrolide-resistance mutations have emerged independently several times, the increase in the proportion of TPA strains resistant to macrolides is mainly due to the spread of resistant strains, especially in developed countries. The emergence of macrolide resistance in TPA appears to require a two-step process including either A2058G or A2059G mutation in one copy of the 23S rRNA gene and a subsequent gene conversion unification of both rRNA genes. Given the enormous genetic similarity that was recently revealed between TPA and TPE strains, there is a low but reasonable risk of emergence and spread of macrolide-resistant yaws strains following azithromycin treatment.
- MeSH
- antibakteriální látky terapeutické užití MeSH
- azithromycin terapeutické užití MeSH
- bakteriální léková rezistence genetika MeSH
- frambézie farmakoterapie mikrobiologie MeSH
- lidé MeSH
- makrolidy terapeutické užití MeSH
- mutace genetika MeSH
- operon genetika MeSH
- RNA ribozomální 23S genetika MeSH
- syfilis farmakoterapie mikrobiologie MeSH
- terapie neúspěšná MeSH
- Treponema pallidum účinky léků genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Leptospira spp. are spirochete bacteria comprising both pathogenic and free-living species. The saprophyte L. biflexa is a model bacterium for studying leptospiral biology due to relative ease of culturing and genetic manipulation. In this study, we constructed a library of 4,996 random transposon mutants in L. biflexa. We screened the library for increased susceptibility to the DNA intercalating agent, ethidium bromide (EtBr), in order to identify genetic determinants that reduce L. biflexa susceptibility to antimicrobial agents. By phenotypic screening, using subinhibitory EtBr concentrations, we identified 29 genes that, when disrupted via transposon insertion, led to increased sensitivity of the bacteria to EtBr. At the functional level, these genes could be categorized by function as follows: regulation and signaling (n=11), transport (n=6), membrane structure (n=5), stress response (n=2), DNA damage repair (n=1), and other processes (n=3), while 1 gene had no predicted function. Genes involved in transport (including efflux pumps) and regulation (two-component systems, anti-sigma factor antagonists, etc.) were overrepresented, demonstrating that these genes are major contributors to EtBr tolerance. This finding suggests that transport genes which would prevent EtBr to enter the cell cytoplasm are critical for EtBr resistance. We identified genes required for the growth of L. biflexa in the presence of sublethal EtBr concentration and characterized their potential as antibiotic resistance determinants. This study will help to delineate mechanisms of adaptation to toxic compounds, as well as potential mechanisms of antibiotic resistance development in pathogenic L. interrogans.
- MeSH
- antiinfekční látky farmakologie MeSH
- bakteriální léková rezistence genetika MeSH
- bakteriální proteiny genetika MeSH
- biologický transport MeSH
- ethidium farmakologie MeSH
- fenotyp MeSH
- genová knihovna MeSH
- inzerční mutageneze MeSH
- Leptospira genetika fyziologie MeSH
- membránové transportní proteiny genetika MeSH
- mikrobiální testy citlivosti MeSH
- operon genetika MeSH
- tolerance léku genetika MeSH
- transpozibilní elementy DNA genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
An arsenic (ars) four-gene operon, containing genes encoding a putative membrane permease (ArsP), a transcriptional repressor (ArsR), an arsenate reductase (ArsC) and an arsenical-resistance membrane transporter (Acr3) was first identified in urease-positive thermophilic Campylobacter (UPTC) isolate, CF89-12. UPTC CF89-12 and some other Campylobacter lari isolates contained their ars four-genes, similarly, differing from that in the reference C. lari RM2100 strain. Two putative promoters and a putative terminator were identified for the operon in UPTC CF89-12. In vivo transcription of the operon was confirmed in the UPTC cells. PCR experiments using two primer pairs designed in silico to amplify two arsR and arsC-acr3 segments, respectively, generated two amplicons, approximately 200 and 350 base pairs, with all 31 of 31 and 19 of 31 C. lari isolates (n = 17 for UPTC; n = 14 for UN C. lari), respectively. An inverted repeat forming a dyad structure, a potential binding site for a transcriptional repressor, was identified in the promoter region. Within the deduced 61 amino acids sequence of the putative arsR open reading frame from the UPTC CF89-12, a metal binding box and a DNA-binding helix-turn-helix motif were identified. The UPTC CF89-12 and some other UPTC isolates isolated from natural environment were resistant to arsenate.
- MeSH
- arsen * MeSH
- arsenát reduktasy genetika MeSH
- bakteriální geny * MeSH
- bakteriální RNA genetika MeSH
- Campylobacter lari genetika izolace a purifikace MeSH
- DNA bakterií genetika MeSH
- DNA primery MeSH
- genetické lokusy MeSH
- konformace nukleové kyseliny MeSH
- molekulární sekvence - údaje MeSH
- motiv helix-turn-helix genetika MeSH
- operon genetika MeSH
- otevřené čtecí rámce MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- sekvence aminokyselin MeSH
- sekvenční analýza DNA MeSH
- sekvenční seřazení MeSH
- ureasa genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Anaplasma phagocytophilum is a tick-borne rickettsial pathogen that has measurable genetic heterogeneity across its geographical range and reservoir spectrum. In the present study, publicly available sequences of the genes that have prevailingly been used for typing A. phagocytophilum were analysed to identify the segments giving the highest resolution with respect to the predictability of host and geographical provenances of the strains. Selected partial sequences of 16S rRNA, groL, msp4 and ank genes were then employed in a tentative multilocus typing scheme used to characterize the strains causing equine granulocytic anaplasmosis (EGA). We were able to both identify alleles characteristic for equine strains of A. phagocytophilum and distinguish two unique genetic variants infecting horses in the Czech Republic. This resolution far exceeded the discriminatory potential of any of the four sequenced genes when used singly. The two novel A. phagocytophilum variants appeared to be phylogenetically closer to the strains reported as causing human disease in Slovenia than to strains thus far isolated from other European EGA cases. A decline in the quality of recently deposited A. phagocytophilum sequences was also demonstrated.
- MeSH
- Anaplasma phagocytophilum genetika klasifikace MeSH
- bakteriální geny MeSH
- bakteriální RNA genetika MeSH
- ehrlichióza epidemiologie mikrobiologie veterinární MeSH
- entropie MeSH
- financování organizované MeSH
- genotyp MeSH
- koně MeSH
- nemoci koní epidemiologie mikrobiologie MeSH
- operon genetika MeSH
- regulace genové exprese u bakterií MeSH
- RNA ribozomální 16S genetika MeSH
- techniky typizace bakterií MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Geografické názvy
- Česká republika MeSH
- MeSH
- biofilmy klasifikace MeSH
- hlen mikrobiologie MeSH
- operon genetika imunologie MeSH
- Staphylococcus epidermidis patogenita MeSH
- Publikační typ
- kongresy MeSH
