scholarly journals In silico analysis of MGMT gene orthologous in the most ancient mammals Strepsirrhini

2020 ◽  
Vol 26 ◽  
pp. 305-310
Author(s):  
O. V. Pidpala ◽  
L. L. Lukash
Keyword(s):  
Gene Evolution ◽  
In Silico Analysis ◽  
Mobile Genetic Elements ◽  
Endogenous Retrovirus ◽  
Coding Region ◽  
Structural Units ◽  
Genetic Elements ◽  
Mgmt Gene ◽  
Evolutionary Changes ◽  
Silico Analysis

Aim. To analyze the evolution of the MGMT gene with using the example of primitive primates with an emphasis on the participation of mobile genetic elements (MGE) in this process. Methods. The homology between nucleotide sequences was determined by BLAST 2.6.1. The results of the search and identification of MGE were performed using the CENSOR program. Results. It was shown on the the example of variable exons, that non-coding sequences can play a coding role at various stages of gene evolution. In the case of the P.coquereli MGMT gene, it was found that exon sequences could be a source of an additional microintron. Based on a comparison of the sequences of Strepsirrhini primates and H.sapience, it can be assumed that fragmented sequences of the endogenous retrovirus HERV-Fc1 could participate in the formation of the coding region of human exon 5 and 3’UTR. Conclusions. The evolutionary changes in the MGMT gene occur at the level of various structural units (exons and introns), and the MGE can be not only components of introns, but also components of exons in the form of fragmented sequences which could not be identified as mobile genetic elements. Keywords: Strepsirrhini, MGMT gene, MGE, HERV-Fc1.

scholarly journals Species-specific mobile genetic elements in the gene of repair enzyme MGMT in new world monkeys

2021 ◽  
Vol 28 ◽  
pp. 128-134
Author(s):  
O. V. Pidpala ◽  
L. L. Lukash
Keyword(s):  
New World ◽  
Mobile Genetic Elements ◽  
Nucleotide Sequences ◽  
New World Monkeys ◽  
Repair Enzyme ◽  
Genetic Elements ◽  
Mgmt Gene ◽  
Evolutionary Changes ◽  
Species Specific ◽  
Human Specific

Aim.To analyze the distribution of species-specific mobile genetic elements (MGE) in orthologs of the MGMT gene in Platyrrhina. Methods. The homology between nucleotide sequences was determined by BLAST 2.6.1. The results of the search and identification of MGE were performed  using  the  CENSOR program. Results. On the example of orthologs of the MGMT gene in New World monkeys, it has been shown that different species-specific MGE identified in their intron sequences may have different evolutionary chronologies. In the case of the element Alu2_TS, which originated in the Tarsiiformes representative, it was found that in evolutionarily close primates it undergoes deletion degradation, while fragments of the human-specific L1Hs element are found in the genomes of evolutionarily distant primates long before the formation and emergence of this retroelement. Conclusions. The chronology of  evolutionary changes in the gene MGMT and its species-specific MGE can be of different nature and occur in parallele and independently. Keywords: Platyrrhina, MGMT gene, MGE, Alu2_TS, L1Hs.

scholarly journals Clostridioides difficile as a Dynamic Vehicle for the Dissemination of Antimicrobial-Resistance Determinants: Review and In Silico Analysis

2021 ◽  
Vol 9 (7) ◽  
pp. 1383
Author(s):  
Philip Kartalidis ◽  
Anargyros Skoulakis ◽  
Katerina Tsilipounidaki ◽  
Zoi Florou ◽  
Εfthymia Petinaki ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
In Silico ◽  
In Silico Analysis ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Clostridioides Difficile ◽  
Antimicrobial Resistance Genes ◽  
Silico Analysis

The present paper is divided into two parts. The first part focuses on the role of Clostridioides difficile in the accumulation of genes associated with antimicrobial resistance and then the transmission of them to other pathogenic bacteria occupying the same human intestinal niche. The second part describes an in silico analysis of the genomes of C. difficile available in GenBank, with regard to the presence of mobile genetic elements and antimicrobial resistance genes. The diversity of the C. difficile genome is discussed, and the current status of resistance of the organisms to various antimicrobial agents is reviewed. The role of transposons associated with antimicrobial resistance is appraised; the importance of plasmids associated with antimicrobial resistance is discussed, and the significance of bacteriophages as a potential shuttle for antimicrobial resistance genes is presented. In the in silico study, 1101 C. difficile genomes were found to harbor mobile genetic elements; Tn6009, Tn6105, CTn7 and Tn6192, Tn6194 and IS256 were the ones more frequently identified. The genes most commonly harbored therein were: ermB, blaCDD, vanT, vanR, vanG and vanS. Tn6194 was likely associated with resistance to erythromycin, Tn6192 and CTn7 with resistance to the β-lactams and vancomycin, IS256 with resistance to aminoglycoside and Tn6105 to vancomycin.

scholarly journals Novel mutation in the gonadotropin-releasing hormone receptor (GNRHR) gene in a patient with normosmic isolated hypogonadotropic hypogonadism

2012 ◽  
Vol 56 (8) ◽  
pp. 540-544 ◽  
Author(s):  
Daiane Beneduzzi ◽  
Ericka B. Trarbach ◽  
Ana Claudia Latronico ◽  
Berenice Bilharinho de Mendonca ◽  
Letícia F. G. Silveira
Keyword(s):  
In Silico ◽  
Novel Mutation ◽  
Hypogonadotropic Hypogonadism ◽  
In Silico Analysis ◽  
Control Group ◽  
Coding Region ◽  
Novel Variant ◽  
Gonadotropin Releasing Hormone Receptor ◽  
Inactivating Mutation ◽  
Silico Analysis

We report a novel GNRHR mutation in a male with normosmic isolated hypogonadotropic hypogonadism (nIHH). The coding region of the GNRHR gene was amplified and sequenced. Three variants p.[Asn10Lys;Gln11Lys]; [Tyr283His] were identified in the GNRHR coding region in a male with sporadic complete nIHH. The three variants were absent in the controls (130 normal adults). Familial segregation showed that the previously described p.Asn10Lys and p.Gln11Lys are in the same allele, in compound heterozygozity with the novel variant p.Tyr283His. The p.[Asn10Lys;Gln11Lys] are known inactivating mutations. The p.Tyr283His affects a well-conserved residue, and in silico analysis suggested it is a deleterious variant. We describe a novel GNRHR mutation in a male with nIHH. Absence of the mutation in the control group, conservation among species, in silico analysis, and familial segregation suggest that p.Tyr283His, which was identified in compound heterozygozity with the p.[Asn10Lys;Gln11Lys] variants, is an inactivating mutation. Arq Bras Endocrinol Metab. 2012;56(8):540-4

scholarly journals In Silico Analysis of B3GALTL Gene Reveling 13 Novel Mutations Associated with Peters’-plus syndrome

2020 ◽  
Author(s):  
Abdelrahman H. Abdelmoneim ◽  
Arwa A. Satti ◽  
Miysaa I. Abdelmageed ◽  
Naseem S. Murshed ◽  
Nafisa M. Elfadol ◽  
...  
Keyword(s):  
In Silico ◽  
Autosomal Recessive ◽  
In Silico Analysis ◽  
Autosomal Recessive Disorder ◽  
Coding Region ◽  
Novel Mutations ◽  
Physiochemical Properties ◽  
Peters Anomaly ◽  
Systemic Manifestations ◽  
Silico Analysis

AbstractBackgroundPeters’-plus syndrome is a rare autosomal recessive disorder, which is characterized by a specific malformation of the eye that includes corneal opaqueness and iridocorneal adhesions (Peters’ anomaly) along with other systemic manifestations. Furthermore, various researches report the association between B3GALTL gene and Peters’-plus syndrome. In the current work we aim to analyze the deleterious SNPs in B3GALTL gene that predispose to Peters’-plus syndrome.Methodthe associated SNPs of the coding region of the B3GALTL gene was acquired from National Center for Biotechnology Information and then analyzed by eight softwares (SIFT, Polyphen2, Proven, SNAP2, SNP@GO, PMut, Imutant and Mupro). The physiochemical properties of the resulted SNPs were then analyzed by Hope project website and visualized by chimera software.ResultThirteen novel mutations (Y172C, A222V, C260R, C260Y, D349G, I354K, R377C, G379C, G393R, G393E, G395E, G425E, R445W) are discovered in B3GALTL gene to cause deleterious effects leading to the development of Peters’-plus syndrome.ConclusionThirteen novel mutations in B3GALTL gene are predicted to cause Peters’-plus syndrome.

scholarly journals Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements

Microbiology ◽  
2009 ◽  
Vol 155 (9) ◽  
pp. 2962-2977 ◽  
Author(s):  
Timothy Sampson ◽  
Gregory W. Broussard ◽  
Laura J. Marinelli ◽  
Deborah Jacobs-Sera ◽  
Mondira Ray ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Analysis ◽  
Mycobacterium Smegmatis ◽  
Active Form ◽  
Mobile Genetic Elements ◽  
Mobile Elements ◽  
Comparative Genome Analysis ◽  
Coding Region ◽  
Comparative Genome ◽  
Genetic Elements

Mycobacteriophages BPs, Angel and Halo are closely related viruses isolated from Mycobacterium smegmatis, and possess the smallest known mycobacteriophage genomes, 41 901 bp, 42 289 bp and 41 441 bp, respectively. Comparative genome analysis reveals a novel class of ultra-small mobile genetic elements; BPs and Halo each contain an insertion of the proposed mobile elements MPME1 and MPME2, respectively, at different locations, while Angel contains neither. The close similarity of the genomes provides a comparison of the pre- and post-integration sequences, revealing an unusual 6 bp insertion at one end of the element and no target duplication. Nine additional copies of these mobile elements are identified in a variety of different contexts in other mycobacteriophage genomes. In addition, BPs, Angel and Halo have an unusual lysogeny module in which the repressor and integrase genes are closely linked. The attP site is located within the repressor-coding region, such that prophage formation results in expression of a C-terminally truncated, but active, form of the repressor.

scholarly journals Identification of SNPs in rice GPAT genes and in silico analysis of their functional impact on GPAT proteins

2021 ◽  
Vol 49 (3) ◽  
pp. 12346
Author(s):  
Imran SAFDER ◽  
Gaoneng SHAO ◽  
Zhonghua SHENG ◽  
Peisong HU ◽  
Shaoqing TANG
Keyword(s):  
In Silico ◽  
Association Studies ◽  
Rice Genome ◽  
In Silico Analysis ◽  
Gene Families ◽  
Coding Region ◽  
Rice Varieties ◽  
Functional Impact ◽  
Functional Snps ◽  
Silico Analysis

SNPs are the most common nucleotide variations in the genome. Functional SNPs in the coding region, known as nonsynonymous SNPs (nsSNPs), change amino acid residues and affect protein function. Identifying functional SNPs is an uphill task as it is difficult to correlate between variation and phenotypes in association studies. Computational in silico analysis provides an opportunity to understand the SNPs functional impact to proteins and facilitate experimental approaches in understanding the relationship between the phenotype and genotype. Advancement in sequencing technologies contributed to sequencing thousands of genomes. As a result, many public databases have been designed incorporating this sequenced data to explore nucleotide variations. In this study, we explored functional SNPs in the rice GPAT family (as a model plant gene family), using 3000 Rice Genome Sequencing Project data. We identified 1056 SNPs, among hundred rice varieties in 26 GPAT genes, and filtered 98 nsSNPs. We further investigated the structural and functional impact of these nsSNPs using various computational tools and shortlisted 13 SNPs having high damaging effects on protein structure. We found that rice GPAT genes can be influenced by nsSNPs and they might have a major effect on regulation and function of GPAT genes. This information will be useful to understand the possible relationships between genetic mutation and phenotypic variation, and their functional implication on rice GPAT proteins. The study will also provide a computational pathway to identify SNPs in other rice gene families.

scholarly journals Cloning, Sequencing and In Silico Analysis of Omp C of Salmonella Typhimurium

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Richa Jha ◽  
Anil Kumar ◽  
Anjani Saxena ◽  
Shantanu Tamuly ◽  
M. K. Saxena
Keyword(s):  
Dna Vaccine ◽  
Outer Membrane Proteins ◽  
In Silico Analysis ◽  
Broad Host Range ◽  
Coding Region ◽  
Bioinformatic Tools ◽  
Poultry Products ◽  
Histocompatibility Complex ◽  
Cell Mediated Immune Response ◽  
Silico Analysis

Salmonella Typhimurium is an important pathogen having a broad host range. In human population it causes mostly gastroenteritis but there are reports in which it was found to be responsible to cause several lethal diseases like endocarditis and meningitis. Poultry products are the major sources of this organism in India as these are consumed at various stages of cooking. The available vaccines have their own limitations such as short-term immunity. Outer membrane proteins have shown some promising potential, so in the present study Omp C of Salmonella Typhimurium was cloned and sequenced to explore the possibility of development of r-DNA vaccine against Salmonella Typhimurium for poultry. The sequence of Omp C was studied for antigenic indexing, epitope mapping, and MHC mapping using various bioinformatic tools. The ORF analysis revealed a complete coding region of approximately 1000 bp. Five major and 13 minor B-cell epitopes were identified having an antigenic index of 1.7. The sequences also showed major histocompatibility complex (MHC) class I and class II binding region indicating a potential of eliciting cell-mediated immune response. The findings indicate that Omp C may be proven as promising candidate for development of r-DNA vaccine against Salmonella Typhimurium.

scholarly journals Molecular characterization of OsCURT1A from upland rice in response to osmotic stress

2019 ◽  
pp. 1343-1352 ◽  
Author(s):  
Bernadette Toni ◽  
Nurulhikma Md Isa ◽  
Cheng Seng Tan ◽  
Ismanizan Ismail ◽  
Zamri Zainal
Keyword(s):  
Upland Rice ◽  
Crop Improvement ◽  
In Silico Analysis ◽  
Mutant Line ◽  
Potential Candidate ◽  
Rna Seq ◽  
Coding Region ◽  
Heterologous System ◽  
Silico Analysis

CURT1 proteins in Arabidopsis thaliana have been reported to be important for inducing grana curvature. Currently, we have identified transcript encoding CURT1A from Oryza sativa cv. indica through RNA-seq analysis and characterised using heterologous system in Arabidopsis. The OsCURT1A gene shares 80% of its amino acid sequence with Arabidopsis AtCURT1A. Phylogenetic analysis revealed that the OsCURT1A is also closely related to the CURT1 proteins in other choloroplast- conatining organisms. In silico analysis of OsCURT1A promoter shows that several cis-elements related to stress are present in the 5' upstream from the coding region. Under normal conditions, there were no notable changes in the phenotype and chlorophyll a;b ratio between three Arabidopsis genotypes, which were overexpressed (35S::OsCURT1A), T-DNA insertional mutant line (atcurt1a), and Wild type (Col-0). However, overexpression of OsCURT1A under salinity condition demonstrate high chlorophyll a:b compared to Col-0, whereas, the lack of atcurt1a gene in the mutant line showed reduced chlorophyll a:b ratio. These results indicate that the OsCURT1A might have a function as salt-stress related gene, which may indirectly regulate the chlorophyll a:b ratio. Therefore, OsCURT1A can be used as a potential candidate for salinity stress tolerance in crop improvement.

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