Current Research in Bioinformatics最新文献

The Development of New Molecules Having Antiemetic Activity Using Molecular Modeling 利用分子模拟技术开发具有止吐活性的新分子

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.21.28

K. E. Kanouni, Yacine Benguerba

引用次数: 0

In silico Assessment of the Arg85Trp Glucokinase Mutation Effects Arg85Trp葡萄糖激酶突变效应的计算机评价

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.38.41

F. Bouldjennet, S. Bouaziz-Terrachet, M. Azzouz, R. Raache

{"title":"In silico Assessment of the Arg85Trp Glucokinase Mutation Effects","authors":"F. Bouldjennet, S. Bouaziz-Terrachet, M. Azzouz, R. Raache","doi":"10.3844/ajbsp.2019.38.41","DOIUrl":"https://doi.org/10.3844/ajbsp.2019.38.41","url":null,"abstract":"Maturity Onset Diabetes of the Young (MODY) is a heterogeneous group of autosomal dominantly inherited, young-onset β-cell disorders that account for approximately 2% of non-insulin-dependent diabetics in Europe. MODY2 or GCK-MODY is caused by inactivating heterozygous mutations in the glucokinase. Linkage of MODY to the Arg85Trp GCK mutation, among Algerian diabetic patients has been established in our previous research. The main objective of this study is to strengthen the evidence for the pathogenicity of this mutation using bioinformatics tools. For this purpose, prediction of Arg85Trp mutation effect on glucokinase (PDB ID: 1V4T) stability was performed using I-Mutant 3.0, PoPMuSiC 3.1, DUET and mCSM web servers. Otherwise, structural analysis was performed after optimization of the native and the mutated structures (PDB ID: 1V4T). For that the steepest descent geometries optimization were applied using Nano Molecular Dynamics software (NAMD 2.12). Subsequently, interactions established between the native Arg85 or the mutated Trp85 and the surrounding residues were studied using Accelrys Discovery Studio Visualizer software. In silico analysis conducted through I-Mutant 3.0, PoPMuSiC 3.1, DUET and mCSM softwares, predicts the Arg85Trp as a destabilizing mutation. Structural modeling gives further evidence in favor of the pathogenicity of this mutation. Overall, our results corroborate with the previous metabolic and in silico studies which associate Arg85Trp mutation to MODY phenotype.","PeriodicalId":11025,"journal":{"name":"Current Research in Bioinformatics","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84472112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phylogeny and Molecular Study of Some Entomopathogenic Rhizobacteria Isolated from Two Regions in Algeria 阿尔及利亚两个地区分离的一些昆虫病原根细菌的系统发育和分子研究

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.55.61

Oulebsir-Mohandkaci Hakima, Benzina Farida, Khemili-Talbi Souad, M. Arezki, H. Fatma, Hadjouti Ryma

{"title":"Phylogeny and Molecular Study of Some Entomopathogenic Rhizobacteria Isolated from Two Regions in Algeria","authors":"Oulebsir-Mohandkaci Hakima, Benzina Farida, Khemili-Talbi Souad, M. Arezki, H. Fatma, Hadjouti Ryma","doi":"10.3844/ajbsp.2019.55.61","DOIUrl":"https://doi.org/10.3844/ajbsp.2019.55.61","url":null,"abstract":"The use of bacteria in the control of insect pests is a form of biological control whose practice is still not widespread. It is in this context that the present work falls. It concerns the isolation, characterization and identification of local bacterial strains for the purpose of their use in the control of certain pests. Indeed, 20 bacteria were isolated from soil cultivated in the region of Boumerdes (center of Algeria) with a total of 21 bacterial strains isolated from Adrar region (Desert Algerian). After carrying out the efficacy tests against 2 insect pests; Migratory locust (Locusta migratoria) and wax moth (Galleria mellonella), 8 potentially interesting strains were identified based on their genetic traits. Molecular characterization of these strains was performed by isolation of DNA, PCR and sequencing of the 16S rRNA gene, followed by phylogenetic analysis. The rDNA16S sequences of the 8 strains named B1, B2, B3, B4, B5, B6, H1 and H2 were recorded in the EMBL/EBI database and their phylogenetic analysis revealed that they belong to the genera Bacillus, Pseudomonas, Enterobacter and Delftia with a very high percentage of similarity with Bacillus thuringiensis strains (NR_043403) (99%) for isolate B1, Bacillus weihenstephanensis (NR_024697) (99%) for isolate B2, Pseudomonas fragi (JCM5420) (99%) for isolates B3 and B4, Bacillus thuringiensis (CMBLBT-5) (99%) for isolate B4, Enterobacter ludwigii (EN-119) for B5, Bacillus thuringiensis (4916) (99%) for isolate H1 and Delftia lacustris (R-54734) (100%) for isolate H2.","PeriodicalId":11025,"journal":{"name":"Current Research in Bioinformatics","volume":"95 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77088250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparison of IncL/M Plasmids Using the Neighbor-Joining Method on Basis repA and excA Genes 基于repA和excA基因的IncL/M质粒邻接法比较

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.14.17

Touati Abdelaziz, Mairi Assia

引用次数: 0

QSAR Modeling of Thirty Active Compounds for the Inhibition of the Acetylcholinesterase Enzyme 30种活性化合物抑制乙酰胆碱酯酶的QSAR模型

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.62.65

N. Hammoudi, Yacine Benguerba, W. Sobhi

引用次数: 4

In Silico Cholinesterase and Monoamine Oxidase Inhibitory Activities of Perillaldehyde and D-Limonene, Main Compounds of Essential Oil of Algerian Ammodaucus leucotrichus 阿尔及利亚白毛杉精油主要成分紫苏醛和d -柠檬烯对硅胆碱酯酶和单胺氧化酶抑制活性的研究

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.42.45

Nesrine Sadaoui-Smadhi, S. Khemili-Talbi, Wadood Abdul, S. Toubal, W. Mokhtari, N. Benhabyles, K. Arab, Khettal Bachra, R. Fazal

{"title":"In Silico Cholinesterase and Monoamine Oxidase Inhibitory Activities of Perillaldehyde and D-Limonene, Main Compounds of Essential Oil of Algerian Ammodaucus leucotrichus","authors":"Nesrine Sadaoui-Smadhi, S. Khemili-Talbi, Wadood Abdul, S. Toubal, W. Mokhtari, N. Benhabyles, K. Arab, Khettal Bachra, R. Fazal","doi":"10.3844/ajbsp.2019.42.45","DOIUrl":"https://doi.org/10.3844/ajbsp.2019.42.45","url":null,"abstract":"In a continuation of our previous work for the exploration of novel enzyme inhibitors, molecular modeling was used to inspect the binding mode of perillaldehyde and D-limonene, the major compounds of essential oil of Algerian Ammodaucus leucotrichus into the active site pocket of cholinesterase (AChE and BuChE) and Monoamine Oxidase (MAO). The molecular docking was carried out using Molecular Operating Environment (MOE) software package. Docking analysis showed that this compounds (perilladehyde and D-limonene) can interact with both the Catalytic Active Site (CAS) of AChE, BuChE and MAO. For D-limonene, molecular docking showed favorable H-phi interaction with catalytic residue of AchE and BuChE. The perillaldehyde showed best interaction profile with BuChE as compared with compound D-Limonene. The best interaction between perilladehyde and monoamine oxidase was also revealed. This paper shows best correlation between the in vitro study and the in silico molecular docking study of anti-cholinesterase and anti-monoamine oxidase activities.","PeriodicalId":11025,"journal":{"name":"Current Research in Bioinformatics","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88793589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Relevance of Bioinformatic Tools in the Study of Polymorphisms of the B4GALNT2 Gene and its Association with Cancer 生物信息学工具在研究B4GALNT2基因多态性及其与癌症的相关性

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.29.33

Eddaikra Atika, Haddouche Hayet, Touil-Boukoffa Chafia

{"title":"The Relevance of Bioinformatic Tools in the Study of Polymorphisms of the B4GALNT2 Gene and its Association with Cancer","authors":"Eddaikra Atika, Haddouche Hayet, Touil-Boukoffa Chafia","doi":"10.3844/ajbsp.2019.29.33","DOIUrl":"https://doi.org/10.3844/ajbsp.2019.29.33","url":null,"abstract":"The human gene B4GALNT2 encodes an enzyme (β1,4-N-acetylgalactosaminyltransferase II) that controls the expression of the blood group Sda carbohydrate’s antigen. This gene is located in position 17q21,32 and consists of 11 exons. The characterization and understanding of genetic variation is a real challenge in human genetics, both for healthy individuals and diseased ones. The in silico study of the B4GALNT2 gene’s polymorphism using a bioinformatic methodology by means of analyzing various databases and open source web browsers has shown that this gene is characterized by a polymorphic profile that has a very large number of Cosmic SNPs associated with different types of cancer. The prediction of the 3D structure in silico is an important step to better understand the overall architecture of the B4GALNT2 protein. The chosen model this study is one of chondroitin synthase with a recovery percentage of 20.10% relative to the target sequence. Our findings suggest that these cosmic polymorphisms are at the origin of a cellular disorder responsible for the initiation, birth and proliferation of tumors. Bioinformatics has become an indispensable tool in identifying and predicting the function of the B4GALNT2 gene and its relation to cancer.","PeriodicalId":11025,"journal":{"name":"Current Research in Bioinformatics","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74923203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Diversity of Culturable Halophilic Archaea and Bacteria from Chott Tinsilt and El Malah Salt-Lake in Algeria 阿尔及利亚Chott tin淤泥和El Malah盐湖可培养嗜盐古菌和细菌的多样性

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.46.54

Akmoussi-Toumi Siham, Khemili-Talbi Souad, Kebbouche-Gana Salima, Lenchi Nesrine, Khelfaoui Mohamed Amine, Sayah Amna, Bouarab Ghania, Ferrioune Imen, M. Wafa, Najjari Afef

{"title":"Diversity of Culturable Halophilic Archaea and Bacteria from Chott Tinsilt and El Malah Salt-Lake in Algeria","authors":"Akmoussi-Toumi Siham, Khemili-Talbi Souad, Kebbouche-Gana Salima, Lenchi Nesrine, Khelfaoui Mohamed Amine, Sayah Amna, Bouarab Ghania, Ferrioune Imen, M. Wafa, Najjari Afef","doi":"10.3844/ajbsp.2019.46.54","DOIUrl":"https://doi.org/10.3844/ajbsp.2019.46.54","url":null,"abstract":"At the limits of life, hyper-saline aquatic ecosystems; Chott and Sebkha are a model of choice of extreme environments, housing a halophilic microflora that had to adapt to these conditions. In Algeria, these ecosystems are poorly studied. However, our study was carried out on the waters of Chott Tinsilt and Sebkha El Malah. The study of this microflora revealed the presence of a significant morphological, physiological and metabolic diversity. The molecular study allowed us to access to a phylogenetic affiliation including an Archean Species (ATS1) and 7 bacterial species (A1, A2, A3, A4, B1, B4, B5). The results showed that these isolates were related to the genera Haloferax (for the strain ATS1) and Halomonas (strains A1, A2 and A4), Staphylococcus (strain A3), Salinivibrio (strain B1), Planococcus (strain B4) and Halobacillus (strain B5). Most isolates produced hydrolases at high salt concentrations. The Production yields obtained are very promising for applications in the biotechnology and industrial microbiology.","PeriodicalId":11025,"journal":{"name":"Current Research in Bioinformatics","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76244311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Molecular Docking of New Active Compounds Towards the Acetylcholinesterase Enzyme 新活性化合物与乙酰胆碱酯酶的分子对接

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.18.20

Lemaoui Tarek, Hammoudi Nour El Houda, Benguerba Yacine, Attoui Ayoub

引用次数: 6

Highlight of New Phosphodiesterase 10A Inhibitors Using Molecular Docking 新型磷酸二酯酶10A分子对接抑制剂研究进展

Current Research in Bioinformatics Pub Date : 2019-01-01 DOI: 10.3844/ajbsp.2019.34.37

Halla Belhoula, E. H. Mokrani, Abderrahmane Bensegueni, Djihane Bioud

引用次数: 1