Publications

lengths of orthologous prokaryotic proteins are affected by evolutionary factors.	proteins of the same functional family (for example, kinases) may have significantly different lengths. it is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. the main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. we believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome ...	2015	26114113
the influence of smoking on the peri-implant microbiome.	smokers are at high risk for 2 bacterially driven oral diseases: peri-implant mucositis and peri-implantitis. therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the effect of smoking on the peri-implant microbiome in states of health and disease. peri-implant biofilm samples were collected from 80 partially edentulous subjects with peri-implant health, peri-implant mucositis, and peri-implantitis. bacterial dna was isolated and 16s ribsomal rna gene li ...	2015	26124222
oral campylobacter species: initiators of a subgroup of inflammatory bowel disease?	in recent years, a number of studies detected a significantly higher prevalence of campylobacter species such as campylobacter concisus (c. concisus) in intestinal biopsies and fecal samples collected from patients with inflammatory bowel disease (ibd) compared to controls. most of these campylobacter species are not of zoonotic origin but are human oral campylobacter species. bacterial species usually cause diseases in the location where they colonize. however, c. concisus and other oral campyl ...	2015	26309350
evolution of the selenoproteome in helicobacter pylori and epsilonproteobacteria.	by competing for the acquisition of essential nutrients, helicobacter pylori has the unique ability to persist in the human stomach, also causing nutritional insufficiencies in the host. although the h. pylori genome apparently encodes selenocysteine synthase (sela, hp1513), a key pyridoxal phosphate (plp)-dependent enzyme for the incorporation of selenium into bacterial proteins, nothing is known about the use of this essential element in protein synthesis by this pathogen. we analyzed the evol ...	2015	26342139
biochemical characterization and complete conversion of coenzyme specificity of isocitrate dehydrogenase from bifidobacterium longum.	bifidobacterium longum is a very important gram-positive non-pathogenic bacterium in the human gastrointestinal tract for keeping the digestive and immune system healthy. isocitrate dehydrogenase (idh) from b. longum (blidh), a novel member in type ii subfamily, was overexpressed, purified and biochemically characterized in detail. the active form of blidh was an 83-kda homodimer. kinetic analysis showed blidh was a nadp⁺-dependent idh (nadp-idh), with a 567- and 193-fold preference for nadp⁺ ov ...	2016	26927087
comparative genomic analysis of sulfurospirillum cavolei mes reconstructed from the metagenome of an electrosynthetic microbiome.	sulfurospirillum spp. play an important role in sulfur and nitrogen cycling, and contain metabolic versatility that enables reduction of a wide range of electron acceptors, including thiosulfate, tetrathionate, polysulfide, nitrate, and nitrite. here we describe the assembly of a sulfurospirillum genome obtained from the metagenome of an electrosynthetic microbiome. the ubiquity and persistence of this organism in microbial electrosynthesis systems suggest it plays an important role in reactor s ...	2016	26983005
novel immunomodulatory flagellin-like protein flac in campylobacter jejuni and other campylobacterales.	the human diarrheal pathogens campylobacter jejuni and campylobacter coli interfere with host innate immune signaling by different means, and their flagellins, flaa and flab, have a low intrinsic property to activate the innate immune receptor toll-like receptor 5 (tlr5). we have investigated here the hypothesis that the unusual secreted, flagellin-like molecule flac present in c. jejuni, c. coli, and other campylobacterales might activate cells via tlr5 and interact with tlr5. flac shows striki ...	2015	27303676
novel immunomodulatory flagellin-like protein flac in campylobacter jejuni and other campylobacterales.	the human diarrheal pathogens campylobacter jejuni and campylobacter coli interfere with host innate immune signaling by different means, and their flagellins, flaa and flab, have a low intrinsic property to activate the innate immune receptor toll-like receptor 5 (tlr5). we have investigated here the hypothesis that the unusual secreted, flagellin-like molecule flac present in c. jejuni, c. coli, and other campylobacterales might activate cells via tlr5 and interact with tlr5. flac shows striki ...	2015	27303676
unsupervised statistical discovery of spaced motifs in prokaryotic genomes.	dna sequences contain repetitive motifs which have various functions in the physiology of the organism. a number of methods have been developed for discovery of such sequence motifs with a primary focus on detection of regulatory motifs and particularly transcription factor binding sites. most motif-finding methods apply probabilistic models to detect motifs characterized by unusually high number of copies of the motif in the analyzed sequences.	2017	28056763
epsilonproteobacterial hydroxylamine oxidoreductase (εhao): characterization of a 'missing link' in the multihaem cytochrome c family.	members of the multihaem cytochrome c (mcc) family such as pentahaem cytochrome c nitrite reductase (nrfa) or octahaem hydroxylamine oxidoreductase (hao) are involved in various microbial respiratory electron transport chains. some members of the hao subfamily, here called εhao proteins, have been predicted from the genomes of nitrate/nitrite-ammonifying bacteria that usually lack nrfa. here, εhao proteins from the host-associated epsilonproteobacteria campylobacter fetus and campylobacter curvu ...	2017	28388834
empyema associated with campylobacter curvus infection.	we report the first case of thoracic empyema associated with campylobacter curvus infection. a 65-year-old woman with a history of bronchiectasis presented with acute cough and phlegm. the patient reported dyspnoea and left chest pain accompanied by left pleural effusion, despite treatment with sitafloxacin. curved gram-negative rods, eventually identified as c. curvus using 16s ribosomal rna- and atpa-specific polymerase chain reaction (pcr) and sequencing, were cultured in anaerobic condition ...	2017	28413685