Primary Analysis on mtDNA D-loop Hypervariable Region in Eutamias sibiricus

This study analyzed the mitochondrial DNA D-loop hypervariable region 601 bp sequence in 12 Eutamias sibiricus from Heilongjiang area. The result showed that the average contents of A, T, G and C were 33.2%, 30.5%, 11.8% and 24.5% respectively, the A＋T content （63.7%） was obviously higher than the G＋C content （36.3%）. Thirty-six, mutation （approximately 6.0%） sites were found and 9 haplotypes were defined. The mutations types, including transition, transversion and deletion were all found in the detected mtDNA D-loop regions, most of which was transition. The average nucleotide mutational ratio was 1.22%. The nucleotide mutation sites affected the restriction site appearance or disappearance of the restriction site. The research on mtDNA D-loop is focused on the domestic animals and there is no report on Eutamias sibiricus, This study analyzed the mitochondrial DNA D-loop hypervariable in Eutamias sibiricus so as to provide some useful informations for related research in the future.

Antibody-Like Phosphorylation Sites in Focus of Statistically Based Bilingual Approach

In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequently, we look here for the sequences 1) composing human and mouse proteins different from antigen receptors, 2) identical with or highly similar to nucleotide sequence representatives of conserved variable immunoglobulin segments and 3) identical with or closely related to phosphorylation sites. More precisely, we searched for the corresponding actual pairs of DNA and protein sequence segments using five-step bilingual approach employing among others a) different types of BLAST searches, b) two in-principle-different machine-learning methods predicting phosphorylated sites and c) two large databases recording existing phosphorylation sites. The approach identified seven existing phosphorylation sites and thirty-seven related human and mouse segments achieving limits for several predictions or phylogenic parameters. Mostly serines phosporylated with ataxia-telangiectasia-related kinase (involved in regulation of DNA-double-strand-break repair) were indicated or predicted in this study. Hypermutation motifs, located in effective positions of the selected sequence segments, occurred significantly less frequently in transcribed than non-transcribed DNA strands suggesting thus the incidence of mutation events. In addition, marked differences between the numbers and proportions of human and mouse cancer-related sequence items were found in different steps of selection process. The possible role of hypermutation changes within the selected segments and the observed structural relationships are discussed here with respect to DNA damage, carcinogenesis, cancer vaccination, ageing and evolution. Taken together, our data represent additional and sometimes perhaps complementary information to the existing databases of empirically proven phosphorylation sites or pathogenically important spots.

Comparison of 16S rRNA Gene Primers on Studying Microbial Community Composition in Bottom Water and Sediment of Artificial Reefs in Laoshan Bay, China

Marine microorganisms are indispensable regulators of nutrient cycling and energy flow,which are crucial for artificial reefs(ARs)ecosystems.However,little is known about the microbial communities in the bottom water and sediment of ARs.Studies of microbial diversities have greatly advanced due to the development of high-throughput sequencing technologies,whereas the results may vary significantly due to the primers’choice.This study investigated the influences of two 16S ribosomal RNA gene primer choices(V4 and V3-V4)on microbial community compositions and structures.The results showed that the taxonomic assignment de-tected by primer V3-V4 was higher compared with that obtained by primer V4,whereas microbial community compositions had strong correlations between the two primers.Microbial beta diversities of ARs can be uncovered by both primers,but the relation-ships between communities and environmental parameters were inconsistent.The performances of the two primers for water samples were highly consistent,but the inconformity was evident for sediment samples.Given the relatively lower taxonomic classification of primer V4 for sediment samples,primer V3-V4 was recommended for later studies.With the development and advancement of ARs in China,our findings provide a meaningful reference for ecologists focusing on the microbial diversities and ecological functions of these artificial habitats in the future.

Evaluation of cross-reactive antibody response to HVR1 in chronic hepatitis C

AIM:To evaluate the presence and cross-reactive anti-bodies against hypervariable region 1(HVR1) in hepatitis C virus(HCV) infected patients and its relationship with the progression of the disease.METHODS:Sixteen representative HVR1 proteins selected from a unique set of 1600 natural sequences were used to semiquantitate the cross-reactivity of HVR1 antibodies in the sera of HCV patients.Fifty-five chronic HCV patients including 23 with asymptomatic mild hepatitis,18 with chronic hepatitis and 16 with liver cirrhosis patients were studied.RESULTS:The degree of the cross-reactivity of anti-HVR1 antibodies in 23 patients with mild asymptomatic hepatitis was 3.09 ± 2.68,which was signif icantly lower than in those with chronic hepatitis(5.44 ± 3.93,P < 0.05) and liver cirrhosis(7.44 ± 3.90,P < 0.01).No correlation was observed between the broadness of the cross-reactivity anti-HVR1 antibodies and patient's age,infection time,serum alanine aminotransferase activity,or serum HCV-RNA concentration.It was the breath of cross-reactivity rather than the presence of anti-HVR1 antibody in HCV sera that was associated with the progression of liver disease.CONCLUSION:The broadly cross-reactive HVR1 antibodies generated in natural HCV patients can not neutralize the virus,which results in persistent infection in patients with chronic hepatitis.

Antibody-Like Phosphorylation Sites. Theme for Studies of Cancer, Aging and Evolution

Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indicated in the majority of the corresponding non-IgV nucleotide sequences. According to database confirmations or double prediction of phosphorylation sites, 80% of the selected human and mouse IgV-related phosphorylation sites or their highly probable candidates exhibited substrate relationship to ataxia-telangiectasia-mutated kinase known as ATM. In accordance with literature data, inactivation of ATM by mutations can participate in the mechanisms of carcinogenesis, neurodegeneration and possibly also in aging. In agreement with this relationship, some of the selected IgV-/ATM-related segments formed molecules specifically involved in carcinogenesis. The selected IgV-related sequence segments were also similar to certain segments of higher plants containing immunoglobulin-like repeats and related regions. Bioinformatic analysis of some selected plant sequences then indicated the presence of catalytic domains composing serine/threonine/tyrosine receptor/receptor-like kinases, which are considered important structures for evolution of very early and part of later Ig-domain-related immunity. The analyzed conserved domain similarities also suggested certain interesting structural and phylogenic relationships, which need to be further investigated. This review in fact briefly summarizes the findings on the subject from the last twenty years.

Sequence variations of the hypervariable region of hepatitis C virus and their clinical significance

To understand the clinical significance of sequence variations in the hypervariable region (HVR) of hepatitis C virus during infection Methods Eight patients with acute hepatitis C and 20 patients with chronic hepatitis C were followed up for two years Blood samples were taken at intervals of six months for analysis of HCV HVR sequences by reverse transcription polymerase chain reaction (RT PCR) and direct sequencing methods Results HCV HVR sequences of the 28 patients changed in various degrees 92% of these nucleotide substitutions led to changes of corresponding amino acid sequences Only 8% of changed nucleotide were synonymous substitutions Of 27 amino acids variation of amino acid ranged from 1 to 20 (mean 8, 30%) The most common nucleotide substitution (62%) occurred in the first position of codon, 31% in the second and the rest in the third HVR variation rate was 0 89×10 1 per genome site per year in acute hepatitis C, compared with 2 31×10 1 per genome site per year in chronic hepatitis C ( P <0 05), but had no relation to HCV subtype Variation of HVR in the flare up type (ALT>150?μ/L) was much more than that in the quiescent type (ALT<100?μ/L) Conclusion Our results suggested that sequence variation of HVR during HCV chronic infection seems to be an adaptive response to HCV to evade the host immune pressure and might play a major role in the establishment of persistent infection as well as in the flare up of hepatitis

Haplotype Diversity of Mitochondrial DNA in the Jat Population of Haryana

Background:The genetic representation of various population groups has been successfully attempted by studying hypervariable regions of human mitochondrial DNA(mtDNA)for forensic purposes.In this view of the fact,there are very few studies in the northern region of India focusing on mtDNA variations.The usage of mtDNA typing for forensic purposes has however been delayed in most states,especially Haryana,due to lack of mtDNA pool database for Haryana populations.Aims and Objectives:Since,there has been no elaborated mtDNA study on Jat population of Haryana,thus,the genetic variability of Jat population of Haryana was estimated by examining the hypervariable regions(HVI,HVII,and HVIII)of mtDNA.Materials and Methods:Blood samples of maternally unrelated individuals have been collected.Statistical Analysis Used:Different parameters and molecular diversity indices were computed.Results:The polymorphism has been observed with their corresponding haplogroups.The phylogenetic relationship was inferred between different haplogroups.Conclusion:A high level of variation and a low random match probability was observed in all the three hypervariable regions of mtDNA,indicating its utility for forensic purposes.

High-throughput sequencing identifies salivary microbiota in Chinese caries-free preschool children with primary dentition

Objectives:The study aimed at identifying salivary microbiota in caries-free Chinese preschool children using highthroughput sequencing.Methods:Saliva samples were obtained from 35 caries-free preschool children(18 boys and 17 girls)with primary dentition,and 16 S ribosomal DNA(r DNA)V3–V4 hypervariable regions of the microorganisms were analyzed using Illumina MiSeq.Results:At 97%similarity level,all of these reads were clustered into 334 operational taxonomic units(OTUs).Among these,five phyla(Firmicutes,Proteobacteria,Actinobacteria,Bacteroidetes,and Candidate division TM7)and13 genera(Streptococcus,Rothia,Granulicatella,Prevotella,Enterobacter,Veillonella,Neisseria,Staphylococcus,Janthinobacterium,Pseudomonas,Brevundimonas,Devosia,and Gemella)were the most dominant,constituting 99.4%and 89.9%of the salivary microbiota,respectively.The core salivary microbiome comprised nine genera(Actinomyces,Capnocytophaga,Gemella,Granulicatella,Lachnoanaerobaculum,Neisseria,Porphyromonas,Rothia,and Streptococcus).Analysis of microbial diversity and community structure revealed a similar pattern between male and female subjects.The difference in microbial community composition between them was mainly attributed to Neisseria(P=0.023).Furthermore,functional prediction revealed that the most abundant genes were related to amino acid transport and metabolism.Conclusions:Our results revealed the diversity and composition of salivary microbiota in caries-free preschool children,with little difference between male and female subjects.Identity of the core microbiome,coupled with prediction of gene function,deepens our understanding of oral microbiota in cariesfree populations and provides basic information for associating salivary microecology and oral health.