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Long non-coding RNA Databases in Cardiovascular Research

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Genomics, Proteomics & Bioinformatics 2016年第4期14卷 191-199页

作者： Frank Rühle Monika Stoll Institute of Human genetics Genetic EpidemiologyUniversity of Muenster48149 MuensterGermany Carmany Cardiovascular Research Institute Maastricht(CARIM) Genetic Epidemiology and Statistical GeneticsMaastricht Center for Systems Biology(MaCSBio)Maastricht University6211 LK MaastrichtThe Netherlands

With the rising interest in the regulatory functions of long non-coding RNAs （IncRNAs） in complex human diseases such as cardiovascular diseases, there is an increasing need in public databases offering comprehensive and integrative data for all aspects of these versatile molecules. Recently, a variety of public data repositories that specialized in lncRNAs have been developed, which make use of huge high-throughput data particularly from next-generation sequencing （NGS） approaches. Here, we provide an overview of current IncRNA databases covering basic and functional annotation, IncRNA expression and regulation, interactions with other biomolecules, and genomic variants influencing the structure and function of lncRNAs. The prominent IncRNA antisense noncoding RNA in the INK4 locus （ANRIL）, which has been unequivocally associated with coronary artery disease through genome-wide association studies （GWAS）, serves as an example to demonstrate the features of each individual database.

关键词： Database Non-coding IncRNA Gene regulation Cardiovascular disease ANRIL

In silico identification and characterization of common epitope-based peptide vaccine for Nipah and Hendra viruses

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Asian Pacific Journal of Tropical Medicine 2017年第6期10卷 601-608页

作者： Chayan Kumar Saha Mahbub Hasan Saddam Hossain Asraful Jahan Abul Kalam Azad department of genetic Engineering & Biotechnology Shahjalal University of Science and Technology department of genetic Engineering & Biotechnology University of Chittagong

Objective: To explore a common B-and T-cell epitope-based vaccine that can elicit an immune response against encephalitis causing genus Henipaviruses, Hendra virus(He V) and Nipah virus(Ni V). Methods: Membrane proteins F, G and M of He V and Ni V were retrieved from the protein database and subjected to different bioinformatics tools to predict antigenic B-cell epitopes. Best B-cell epitopes were then analyzed to predict their T-cell antigenic potentiality. Antigenic B-and T-cell epitopes that shared maximum identity with He V and Ni V were selected. Stability of the selected epitopes was predicted. Finally, the selected epitopes were subjected to molecular docking simulation with HLA-DR to confirm their antigenic potentiality in silico. Results: One epitope from G proteins, one from M proteins and none from F proteins were selected based on their antigenic potentiality. The epitope from the G proteins was stable whereas that from M was unstable. The M-epitope was made stable by adding flanking dipeptides. The 15-mer G-epitope(VDPLRVQWRNNSVIS) showed at least 66% identity with all Ni V and He V G protein sequences, while the 15-mer M-epitope(GKLEFRRNNAIAFKG) with the dipeptide flanking residues showed 73% identity with all Ni V and He V M protein sequences available in the database. Molecular docking simulation with most frequent MHC class-II(MHC II) and class-I(MHC I) molecules showed that these epitopes could bind within HLA binding grooves to elicit an immune response. Conclusions: Data in our present study revealed the notion that the epitopes from G and M proteins might be the target for peptide-based subunit vaccine design against He V and Ni V. However, the biochemical analysis is necessary to experimentally validate the interaction of epitopes individually with the MHC molecules through elucidation of immunity induction.

关键词： Hendra virus Nipah virus Epitope Encephalitis Docking Flanking dipeptides

Magnetic resonance spectroscopy to study hepatic metabolism in diffuse liver diseases, diabetes and cancer

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World Journal of Gastroenterology 2010年第13期16卷 1577-1586页

作者： Pieter C Dagnelie Susanne Leij-Halfwerk department of epidemiology Maastricht University

This review provides an overview of the current state of the art of magnetic resonance spectroscopy (MRS) in in vivo investigations of diffuse liver disease. So far, MRS of the human liver in vivo has mainly been used as a research tool rather than a clinical tool. The liver is particularly suitable for static and dynamic metabolic studies due to its high metabolic activity. Furthermore, its relatively superfi cial position allows excellent MRS localization, while its large volume allows detection of signals with relatively low intensity. This review describes the application of MRS to study the metabolic consequences of different conditions including diffuse and chronic liver diseases, congenital diseases, diabetes, and the presence of a distant malignancy on hepatic metabolism. In addition, future prospects of MRS are discussed. It is anticipated that future technical developments such as clinical MRS magnets with higher fi eld strength (3 T) and improved delineation of multicomponent signals such as phosphomonoester and phosphodiester using proton decoupling, especially if combined with price reductions for stable isotope tracers, will lead to intensifi ed research into metabolic syndrome, cardiovascular disease, hepato-biliary diseases, as well as non-metastatic liver metabolism in patients with a distant malignant tumor.

关键词： Cancer Cirrhosis Diabetes Diffuse liver disease Hepatitis Magnetic resonance spectroscopy

High affinity mouse-human chimeric Fab against Hepatitis B surface antigen

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World Journal of Gastroenterology 2005年第48期11卷 7569-7578页

作者： Biplab Bose Navin Khanna Subrat K Acharya Subrata Sinha department of Biochemistry International Center for genetic Engineering and Biotechnology department of Gastroenterology

AIM： Passive immunotherapy using antibody against hepatitis B surface antigen （HBsAg） has been advocated in certain cases of Hepatitis B infection. We had earlier reported on the cloning and expression of a high affinity scFv derived from a mouse monoclonal （5S） against HBsAg. However this mouse antibody cannot be used for therapeutic purposes as it may elicit anti-mouse immune responses. Chimerization by replacing mouse constant domains with human ones can reduce the immunogenicity of this antibody.METHODS： We cloned the VH and V, genes of this mouse antibody, and fused them with CH1 domain of human IgG1 and C, domain of human kappa chain respectively. These chimeric genes were cloned into a phagemid vector. After initial screening using the phage display system, the chimeric Fab was expressed in soluble form in E. coli.RESULTS： The chimeric Fab was purified from the bacterial periplasmic extract. We characterized the chimeric Fab using several in vitro techniques and it was observed that the chimeric molecule retained the high affinity and specificity of the original mouse monoclonal. This chimeric antibody fragment was further expressed in different strains of E. coli to increase the yield.CONCLUSION： We have generated a mouse-human chimeric Fab against HBsAg without any significant loss in binding and epitope specificity. This chimeric Fab fragment can be further modified to generate a fulllength chimeric antibody for therapeutic uses.

关键词： Chimeric Fab Hepatitis B surface antigen Phage display

Nonalcoholic fatty liver disease in developing countries

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World Journal of Gastroenterology 2005年第24期11卷 3808-3809页

作者： Hossein Bahrami department of epidemiology

TO THE EDITORNonalcoholic fatty liver disease (NAFLD) is an increasingly known medical entity with high prevalence, about 1 0 to 24 percent in general population and up to 74% in obese population[1]. The prevalence of the disease is expected to increase worldwide, as we are encountering the global obesity epidemic and the trend in developing countries toward the Western lifestyles. However, it looks that there are some differences between the demographic and epidemiologic features of NAFLD in developing and developed countries.

关键词： Nonalcoholic fatty liver Developing countries

Heterologous expression of Lolium perenne antifreeze protein confers chilling tolerance in tomato

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Journal of Integrative Agriculture 2018年第5期17卷 1128-1136页

作者： Srinivasan Balamurugan Jayan Susan Ann Inchakalody P Varghese Shanmugaraj Bala Murugan Mani ChANDra Harish Sarma Rajeev Kumar Ramalingam Sathishkumar Plant genetic Engineering Laboratory Department of BiotechnologyBharathiar University

Antifreeze proteins（AFP） are produced by certain plants, animals, fungi and bacteria that enable them to survive upon extremely low temperature. Perennial rye grass, Lolium perenne, was reported to possess AFP which protects them from cold environments. In the present investigation, we isolated AFP gene from L. perenne and expressed it in tomato plants to elucidate its role upon chilling stress. The T1 transgenic tomato lines were selected and subjected to molecular, biochemical and physiological analyses. Stable integration and transcription of Lp AFP in transgenic tomato plants was confirmed by Southern blot hybridization and RT-PCR, respectively. Physiological analyses under chilling conditions showed that the chilling stress induced physiological damage in wild type（WT） plants, while the transgenic plants remained healthy. Total sugar content increased gradually in both WT and transgenic plants throughout the chilling treatment. Interestingly, transgenic plants exhibited remarkable alterations in terms of relative water content（RWC） and electrolyte leakage index（ELI） than those of WT. RWC increased significantly by 3-fold and the electrolyte leakage was reduced by 2.6-fold in transgenic plants comparing with WT. Overall, this report proved that Lp AFP gene confers chilling tolerance in transgenic tomato plants and it could be a potential candidate to extrapolate the chilling tolerance on other chilling-sensitive food crops.

关键词： Lolium perenne antifreeze protein chilling tolerance genetic transformation transgenic tomato

Is prostate cancer a Lynch syndrome cancer？

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Asian Journal of Andrology 2013年第5期15卷 588-589页

作者： Aung Ko Win Centre for Molecular Environmental Genetic andAnalytic Epidemiology Melbourne School of Populationand G oba Heath Parkv e Vc. 3010 Austra a

The question of whether men with an inherited genetic condition called Lynch syndrome have an increased risk of developing prostate cancer has been controversial. It is important to answer this question, for understanding the role of DNA mismatch repair in carcinogenesis of prostate as well as for clinical implications for screening.

关键词： prostate cancer Lynch syndrome cancer

Relationship between ERCC2 Polymorphism and Risk of Lung Cancer in Chinese Nonsmoker

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Chinese Journal of Cancer Research 2007年第3期19卷 184-188页

作者：尹智华李鸣川崔泽实何钦成周宝森 department of epidemiology China Medical University

Objective： Excision repair cross-complimentary group 2 （ERCC2） is one of the important DNA repair genes. ERCC2 codon 751 polymorphism has been shown to modulate cancer risk. We therefore assessed the relationship between the ERCC2 polymorphism and the susceptibility to lung cancer in nonsmoking females via a hospital-based case-control study. Methods： There were 105 lung cancer cases and matched healthy controls in this study. Information concerning demographic and risk factors was obtained, each person donated 2 ml blood for biomarker testing. ERCC2 genotypes were determined by PCR-RFLP method. All of the statistical analyses were performed with SPSS （v 12.0）. Results： All of the subjects in this study were nonsmoking females in Shenyang. There was significant difference between the frequencies of ERCC2 polymorphism in cancer cases and controls （P〈0.05）. The frequencies of ERCC2 751 Gin allele were 6.2% in controls and 13.8% in cancer cases. The individuals with Lys/Gln＋Gln/Gln combined genotype were at an increased risk for lung cancer as compared with those carrying the Lys/Lys genotype （adjusted OR=2.80, 95%=CI 1.21-6.48）. We analyzed the environmental risk factors for lung cancer in nonsmoking females. The cancer patients showed a higher prevalence of exposure to cooking fumes compared with controls （OR=2.44, P〈0.05）. Furthermore, an interaction between exposure to cooking fumes and the variant ERCC2 751 Gin allele on the risk of lung cancer was observed. Individuals with both risk genotype and exposure to cooking fumes had a higher risk of cancer than those with only one of them. Conclusion： The above findings indicate that the genetic polymorphism in the ERCC2 codon 751 is associated with the risk of lung cancer in nonsmoking females.

关键词： ERCC2 gene Lung cancer Nonsmoker

Spatial and seasonal distribution of macroinvertebrates in high altitude reservoir (Beyler Reservoir, Turkey)

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Chinese Journal of Oceanology and Limnology 2013年第5期31卷 994-1001页

作者： zlem FINDIK Arts and Sciences Faculty Molecular Biology and Genetic DepartmentNevehir University

A highland reservoir in the West Black Sea region of Turkey which belongs to the Mediterranean climatic zone was *** littoral and profundal zones were sampled from October 2009 to September 2010,to determine taxonomic composition,biodiversity and abundance of benthic invertebrates as well as the seasonal variation of these measures.A total of 35 taxa were identified,of which 12 belong to Chironomidae and 10 to Oligochaeta *** highest diversity and abundance of benthic macroinvertebrates were found at the littoral *** showed significant positive correlations with water temperature and NO_2 and NO_3 concentrations,and negative correlation with dissolved oxygen.

关键词： macrofauna zoobenthos community structure littoral West Black Sea