Periodontal pocket microbiocenosis and periodontal inflammatory diseases

Oral bacterial communities includes several microbiocenoses. Saliva, periodontal pocket and tunica mucosa of mouth is a habitat of a set of more that 700 different species of microorganisms. Some of them can cause periodontitis or gingivitis. Periodontitis is a common chronic inflammatory disease of tooth-supporting tissues caused by multibacterial infection. It has been shown that periodontitis patients carry higher number of disease-associated bacteria than healthy ones. The goal of the current review is to summarize knowledge about influence of periodontal pocket microbiocenosis composition on inflammatory diseases of tooth-supporting tissues.Полость рта представляет собой комплексную зкологическую систему. В таких биотопах как слюна, десневая жидкость, пародонтальный карман и биопленки обнаружено свыше 700 различных видов микроорганизмов. Нарушение соотношения нормальной и условно-патогенной флоры приводит к развитию дисбактериозов. Одним из проявлений такого дисбаланса является широко распространенное заболевание - пародонтит. В обзоре рассмотрены ключевые аспекты влияния состава микробного биоценоза пародонтального кармана на развитие воспалительных заболеваний пародонта

Association of collagen C0L1A1, C0L2A1 and C0L3A1 gene polymorphism with chronic periodontitis in Russians

Collagen is the main protein of connective tissue and may play a role in the development of periodontal disease. COL polymorphisms could alter transcription and function of these proteins. The aim of this study was to investigate C0L1A1. C0L2A1 and C0L3A1 gene polymorphisms (C0L1A1 -1997 G>T (rs1107946), C0L2A1 C>A (rs1635529) and C0L3A1 698 A>G (rs1800255)) in relation to susceptibility to severe chronic generalized periodontitis among the Russians. Our data suggest that COL2A1 С allele is associated with an increased risk for chronic generalized periodontitis in the Russian population.Коллаген составляет основу соединительной ткани, обеспечивает её прочность и эластичность и может играть роль в развитии заболеваний пародонта. Полиморфизм генов коллагенов влияет на уровень транскрипции и структуру кодируемого белка. В данной работе исследована взаимосвязь полиморфизмов C0L1A1 -1997 G>T (rs1107946), C0L2A1 С>А (rs1635529) и C0L3A1 698 A>G (rs1800255) с развитием хронического генерализованного пародонтита у жителей Москвы и Московской области. Установлена ассоциация варианта С полиморфизма C0L2A1 С>А (rs1635529) с развитием хронического генерализованного пародонтита

Complete genome sequence of a novel extrachromosomal virus-like element identified in planarian Girardia tigrina

BACKGROUND: Freshwater planarians are widely used as models for investigation of pattern formation and studies on genetic variation in populations. Despite extensive information on the biology and genetics of planaria, the occurrence and distribution of viruses in these animals remains an unexplored area of research. RESULTS: Using a combination of Suppression Subtractive Hybridization (SSH) and Mirror Orientation Selection (MOS), we compared the genomes of two strains of freshwater planarian, Girardia tigrina. The novel extrachromosomal DNA-containing virus-like element denoted PEVE (Planarian Extrachromosomal Virus-like Element) was identified in one planarian strain. The PEVE genome (about 7.5 kb) consists of two unique regions (Ul and Us) flanked by inverted repeats. Sequence analyses reveal that PEVE comprises two helicase-like sequences in the genome, of which the first is a homolog of a circoviral replication initiator protein (Rep), and the second is similar to the papillomavirus E1 helicase domain. PEVE genome exists in at least two variant forms with different arrangements of single-stranded and double-stranded DNA stretches that correspond to the Us and Ul regions. Using PCR analysis and whole-mount in situ hybridization, we characterized PEVE distribution and expression in the planarian body. CONCLUSIONS: PEVE is the first viral element identified in free-living flatworms. This element differs from all known viruses and viral elements, and comprises two potential helicases that are homologous to proteins from distant viral phyla. PEVE is unevenly distributed in the worm body, and is detected in specific parenchyma cells

Frequencies of eleven BRCA1 and BRCA2 mutations in random sample of russian breast cancer patients

In this study we were aiming to determine frequencies ot eleven known mutations in BRCA1 (185delAG, 4153delA, 5382insC, 3819delGTAAA, 3875delGTCT, Cys61 Gly, 2080delA, 2963del10) and BRCA2 (6174delT, 1528delAAAA, 9318delAAAA) in random sample of patients with breast cancer, Russian population (1091 cases). We found 64 mutation carriers (5,87%), primerily with 5382insC (BRCA1) mutation - 4,03% from the sample. We did not detect three mutations: 2963del10 (BRCA1), 1528delAAAA (BRCA2) and 9318delAAAA (BRCA2). We revealed 11 mutation carriers among patients without any anamnesis data supposing hereditary form of breast cancer. Taking into account the range of analyzed random sample and diagnostic panel and detection of listed below mutations in other Russian studies, we assume mutations in BRCA1 (185delAG, 4153delA, 5382insC, 3819delGTAAA, 3875delGTCT, 300T>G (Cys61Gly), 2080delA) and BRCA2 (6174delT) tests could be recommended for inclusion in screening programs for revelation of hereditary breast cancer cases.Целью работы было установление частот встречаемости одиннадцати ранее описанных мутаций в генах BRCA1 (185delAG, 4153delA, 5382insC, 3819delGTAAA, 3875delGTCT, Cys61Gly, 2080delA, 2963del10) и BRCA2 (6174delT, 1528delAAAA, 9318delAAAA) в неотобранной выборке больных раком молочной железы в Российской популяции (1091 человек). Мутации были найдены у 64 человек (5,87%), преобладала мутация 5382insC (BRCA1) -4,03% от выборки. Мутации 2963del10 (BRCA1), 1528delAAAA (BRCA2) и 9318delAAAA (BRCA2) не были обнаружены. В результате исследования выявлено 11 пациенток с мутацией в BRCA1 или BRCA2 без каких-либо данных в анамнезе, позволяющих предположить наследственную форму рака молочной железы. Учитывая размер тестированной неотобранной выборки, широту диагностической панели и нахождение зарегистрированных нами мутаций другими авторами, анализ на мутации в генах BRCA1 (185delAG, 4153delA, 5382insC, 3819delGTAAA, 3875delGTCT, 300T>G (Cys61Gly), 2080delA) и BRCA2 (6174delT) может быть рекомендован для включения в скрининговые программы по выявлению наследственных случаев рака молочной железы

Functional analysis and expression profiling of HcrVf1 and HcrVf2 for development of scab resistant cisgenic and intragenic apples

Apple scab resistance genes, HcrVf1 and HcrVf2, were isolated including their native promoter, coding and terminator sequences. Two fragment lengths (short and long) of the native gene promoters and the strong apple rubisco gene promoter (PMdRbc) were used for both HcrVf genes to test their effect on expression and phenotype. The scab susceptible cultivar ‘Gala’ was used for plant transformations and after selection of transformants, they were micrografted onto apple seedling rootstocks for scab disease tests. Apple transformants were also tested for HcrVf expression by quantitative RT-PCR (qRT-PCR). For HcrVf1 the long native promoter gave significantly higher expression that the short one; in case of HcrVf2 the difference between the two was not significant. The apple rubisco gene promoter proved to give the highest expression of both HcrVf1 and HcrVf2. The top four expanding leaves were used initially for inoculation with monoconidial isolate EU-B05 which belongs to race 1 of V. inaequalis. Later six other V. inaequalis isolates were used to study the resistance spectra of the individual HcrVf genes. The scab disease assays showed that HcrVf1 did not give resistance against any of the isolates tested regardless of the expression level. The HcrVf2 gene appeared to be the only functional gene for resistance against Vf avirulent isolates of V. inaequalis. HcrVf2 did not provide any resistance to Vf virulent strains, even not in case of overexpression. In conclusion, transformants carrying the apple-derived HcrVf2 gene in a cisgenic as well as in an intragenic configuration were able to reach scab resistance levels comparable to the Vf resistant control cultivar obtained by classical breeding, cv. ‘Santana’

Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)

Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value≤10-5) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies

Transcriptomic Analyses Reveal Novel Genes with Sexually Dimorphic Expression in the Zebrafish Gonad and Brain

Background Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs. Methodology/Principal Findings We have identified 116638 gonad-derived zebrafish expressed sequence tags (ESTs), 21% of which were isolated in our lab. Following in silico normalization, we constructed a gonad-derived microarray comprising 6370 unique, full-length cDNAs from differentiating and adult gonads. Labeled targets from adult gonad, brain, kidney and ‘rest-of-body’ from both sexes were hybridized onto the microarray. Our analyses revealed 1366, 881 and 656 differentially expressed transcripts (34.7% novel) that showed highest expression in ovary, testis and both gonads respectively. Hierarchical clustering showed correlation of the two gonadal transcriptomes and their similarities to those of the brains. In addition, we have identified 276 genes showing sexually dimorphic expression both between the brains and between the gonads. By in situ hybridization, we showed that the gonadal transcripts with the strongest array signal intensities were germline-expressed. We found that five members of the GTP-binding septin gene family, from which only one member (septin 4) has previously been implicated in reproduction in mice, were all strongly expressed in the gonads. Conclusions/Significance We have generated a gonad-derived zebrafish cDNA microarray and demonstrated its usefulness in identifying genes with sexually dimorphic co-expression in both the gonads and the brains. We have also provided the first evidence of large-scale differential gene expression between female and male brains of a teleost. Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations. Since several genes have been shown to play similar roles in gonadogenesis in zebrafish and other vertebrates, our array may even provide information on genetic disorders affecting gonadal phenotypes and fertility in mammals

Airborne Signals from a Wounded Leaf Facilitate Viral Spreading and Induce Antibacterial Resistance in Neighboring Plants

Many plants release airborne volatile compounds in response to wounding due to pathogenic assault. These compounds serve as plant defenses and are involved in plant signaling. Here, we study the effects of pectin methylesterase (PME)-generated methanol release from wounded plants (“emitters”) on the defensive reactions of neighboring “receiver” plants. Plant leaf wounding resulted in the synthesis of PME and a spike in methanol released into the air. Gaseous methanol or vapors from wounded PME-transgenic plants induced resistance to the bacterial pathogen Ralstonia solanacearum in the leaves of non-wounded neighboring “receiver” plants. In experiments with different volatile organic compounds, gaseous methanol was the only airborne factor that could induce antibacterial resistance in neighboring plants. In an effort to understand the mechanisms by which methanol stimulates the antibacterial resistance of “receiver” plants, we constructed forward and reverse suppression subtractive hybridization cDNA libraries from Nicotiana benthamiana plants exposed to methanol. We identified multiple methanol-inducible genes (MIGs), most of which are involved in defense or cell-to-cell trafficking. We then isolated the most affected genes for further analysis: β-1,3-glucanase (BG), a previously unidentified gene (MIG-21), and non-cell-autonomous pathway protein (NCAPP). Experiments with Tobacco mosaic virus (TMV) and a vector encoding two tandem copies of green fluorescent protein as a tracer of cell-to-cell movement showed the increased gating capacity of plasmodesmata in the presence of BG, MIG-21, and NCAPP. The increased gating capacity is accompanied by enhanced TMV reproduction in the “receivers”. Overall, our data indicate that methanol emitted by a wounded plant acts as a signal that enhances antibacterial resistance and facilitates viral spread in neighboring plants