Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis

<p>Abstract</p> <p>Background</p> <p><it>Bordetella pertussis</it>, the causative agent of whooping cough, is a highly clonal pathogen of the respiratory tract. Its lack of genetic diversity, relative to many bacterial pathogens, could limit its ability to adapt to a hostile and changing host environment. This limitation might be overcome by phase variation, as observed for other mucosal pathogens. One of the most common mechanisms of phase variation is reversible expansion or contraction of homopolymeric tracts (HPTs).</p> <p>Results</p> <p>The genomes of <it>B. pertussis </it>and the two closely related species, <it>B. bronchiseptica </it>and <it>B. parapertussis</it>, were screened for homopolymeric tracts longer than expected on the basis of chance, given their nucleotide compositions. Sixty-nine such HPTs were found in total among the three genomes, 74% of which were polymorphic among the three species. Nine HPTs were genotyped in a collection of 90 geographically and temporally diverse <it>B. pertussis </it>strains using the polymerase chain reaction/ligase detection reaction (PCR/LDR) assay. Six HPTs were polymorphic in this collection of <it>B. pertussis </it>strains. Of note, one of these polymorphic HPTs was found in the <it>fimX </it>promoter, where a single base insertion variant was present in seven strains, all of which were isolated prior to introduction of the pertussis vaccine. Transcript abundance of <it>fimX </it>was found to be 3.8-fold lower in strains carrying the longer allele. HPTs in three other genes, <it>tcfA</it>, <it>bapC</it>, and BP3651, varied widely in composition across the strain collection and displayed allelic polymorphism within single cultures.</p> <p>Conclusion</p> <p>Allelic polymorphism at homopolymeric tracts is common within the <it>B. pertussis </it>genome. Phase variability may be an important mechanism in <it>B. pertussis </it>for evasion of the immune system and adaptation to different niches in the human host. High sensitivity and specificity make the PCR/LDR assay a powerful tool for investigating allelic variation at HPTs. Using this method, allelic diversity and phase variation were demonstrated at several <it>B. pertussis </it>loci.</p

Design of metallic nanoparticles gratings for filtering properties in the visible spectrum

Plasmonic resonances in metallic nanoparticles are exploited to create efficient optical filtering functions. A Finite Element Method is used to model metallic nanoparticles gratings. The accuracy of this method is shown by comparing numerical results with measurements on a two-dimensional grating of gold nanocylinders with elliptic cross section. Then a parametric analysis is performed in order to design efficient filters with polarization dependent properties together with high transparency over the visible range. The behavior of nanoparticle gratings is also modelled using the Maxwell-Garnett homogenization theory and analyzed by comparison with the diffraction by a single nanoparticle. The proposed structures are intended to be included in optical systems which could find innovative applications.Comment: submitted to Applied Optic

Retargeting transposon insertions by the adeno-associated virus Rep protein

The Sleeping Beauty (SB), piggyBac (PB) and Tol2 transposons are promising instruments for genome engineering. Integration site profiling of SB, PB and Tol2 in human cells showed that PB and Tol2 insertions were enriched in genes, whereas SB insertions were randomly distributed. We aimed to introduce a bias into the target site selection properties of the transposon systems by taking advantage of the locus-specific integration system of adeno-associated virus (AAV). The AAV Rep protein binds to Rep recognition sequences (RRSs) in the human genome, and mediates viral integration into nearby sites. A series of fusion constructs consisting of the N-terminal DNA-binding domain of Rep and the transposases or the N57 domain of SB were generated. A plasmid-based transposition assay showed that Rep/SB yielded a 15-fold enrichment of transposition at a particular site near a targeted RRS. Genome-wide insertion site analysis indicated that an approach based on interactions between the SB transposase and Rep/N57 enriched transgene insertions at RRSs. We also provide evidence of biased insertion of the PB and Tol2 transposons. This study provides a comparative insight into target site selection properties of transposons, as well as proof-of-principle for targeted chromosomal transposition by composite protein-protein and protein-DNA interactions

Somatoform disorders in the family doctor's practice.

Somatoform disorders – psycho­genic diseases are characterized by pathological physical symptoms that resemble somatic illness. Thus, any organic manifestations, which can be attributed to known diseases are not detected, but there are non-specific functional impairments. Somatoform disorders include somatization disorder, undifferentiated somatoform disorder, hypocho­n­driacal disorder, somatoform dysfunction of the autonomic nervous system and stable somatoform pain disorder. The first part of the article reviewes features of the clinical manifestations of somatization disorder and undifferentiated somatoform disorder. Role of non-benzodiazepine tranquilizers (ADAPTOL) and metabolic drugs (VASONAT) in the treatment of patients with somatoform disorders is discussed. In review article data of neurologists and cardiologists on the effectiveness of anxiolytic drug ADAPTOL and metabolic drug VASONAT in different clinical groups of patients (coronary artery disease, chronic ischemia of the brain), which can significantly improve quality of life, increase exercise tolerance, improve cognitive function and correct mental and emotional disorders are presented

Імунологічні показники зубоальвеолярного сегмента при зубовмісних кістах від тимчасових молярів

Проведено иммунологическое обследование 8 детей с зубосодержащими кистами от временных мо­ ляров нижней челюсти с определением основных популяций лимфоцитов в периферической крови зубо­ альвеолярного сегмента. Образование зубосодержащей кисты происходит на фоне уменьшения количе­ ства лимфоцитов с хелперно-индукторной функцией и увеличения количества лимфоцитов с иммуносу- прессивными свойствами. Вероятность образования кисты возрастает при снижении показателя имму- норегуляторного индекса до 1,3.Проведено імунологічне обстеження 8 дітей із зубовмісними кістами від тимчасових молярів нижньої щелепи з визначенням основних популяцій лімфоцитів у периферичній крові зубоальвеолярного сегмен­ Зубовмісна кіста утворюється на тлі зменшення кількості лімфоцитів із хелперно-індуктивною функці­ єю і збільшення кількості лімфоцитів з імуносупресивними властивостями. Імовірність утворення кісти зростає за зниження показника імунорегуляторного індексу до 1,3.The general populations of lymphocytes in peripheral blood of dentoalveolar segments have been deter­ mined during the examination of eight patients with dentigerous cyst from mandibular decidious molars. The dentigerous cyst formation is accompanied by decrease in the number of lymphocytes with helper-inductor function and increase in the number of lymphocytes with immunosuppressive properties. The chance of cyst formation increases with decrease in immunoregulatory index to 1.3

Amperometric flow-through biosensor for the determination of cholinesterase inhibitors

An amperometric flow-through biosensor based on epoxy-carbon electrode and butyrylcholinesterase immobilised on nylon, cellulose nitrate or white tracing paper has been developed and examined for the determination of reversible and irreversible inhibitors. The analytical characteristics of inhibitor determination depend on the hydrophobicity of the membrane material. Flow-through biosensor with various enzymatic membranes makes it possible to determine fluoride in the concentration range 1x10-4-25x10-4moll-1 and 3.5x10-5-1x10-2moll-1 when cholinesterase solution is used. The analytical characteristics of fluoride determination do not differ significantly from those obtained in batch conditions. For diazinon the immobilisation of cholinesterase results in the decrease of detection limits from 5x10-9moll-1 (native enzyme) to 4x10-9moll-1 (nylon membrane) and 1.5x10-9moll-1 (cellulose nitrate membrane). The influence of membrane material on analytical characteristics of FIA determination of inhibitors is due to the non-stationary distribution of reagents (fluoride) or sorptional preconcentration of the inhibitor (diazinon) in membrane. Copyright (C) 1999 Elsevier Science B.V

Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery

MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5' tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences

A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes

Helitron transposons capture and mobilize gene fragments in eukaryotes, but experimental evidence for their transposition is lacking in the absence of an isolated active element. Here we reconstruct Helraiser, an ancient element from the bat genome, and use this transposon as an experimental tool to unravel the mechanism of Helitron transposition. A hairpin close to the 3'-end of the transposon functions as a transposition terminator. However, the 3'-end can be bypassed by the transposase, resulting in transduction of flanking sequences to new genomic locations. Helraiser transposition generates covalently closed circular intermediates, suggestive of a replicative transposition mechanism, which provides a powerful means to disseminate captured transcriptional regulatory signals across the genome. Indeed, we document the generation of novel transcripts by Helitron promoter capture both experimentally and by transcriptome analysis in bats. Our results provide mechanistic insight into Helitron transposition, and its impact on diversification of gene function by genome shuffling