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 In Silico Analysis of the Antigenic Properties of Iron-Regulated Proteins against Neisseria meningitidis

2020 ◽  
Vol 10 (17) ◽  
pp. 6113
Author(s):  
Md. Shahedur Rahman ◽  
Chayon Biswas ◽  
Polash Kumar Biswas ◽  
Md. Ashraful Kader ◽  
S. M. Nur Alam ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Outer Membrane Proteins ◽  
Treatment Strategies ◽  
In Silico Analysis ◽  
Analysis Data ◽  
Bioinformatic Tools ◽  
Antigenic Properties ◽  
Potential Vaccine

Neisseria meningitidis is a commensal pathogen that causes infectious cerebrospinal disease in people of all ages. The multivariate role of six disease-causing polysaccharide serotypes is found to play a crucial role in developing vaccines (or general treatment strategies) to treat this emerging pathogen. Iron is a crucial transition metal for N. meningitidis. Proteomic analysis data could be valuable for vaccine design. Here, we conduct a comparative study using computational bioinformatic tools to identify the most effective iron-regulated outer membrane proteins (OMPs) as immunogenic targets for a potential vaccine against N. meningitidis. The basic properties of N. meningitidis OMPs are explored for flexibility, solubility, hydrophilicity, beta-turns, and overall antigenic probability. Results of our study suggest that iron-regulated OMPs are flexible and soluble in water with high densities of conformational B-cell epitopes. As such, they can be recommended as a novel candidate for a vaccine against N. meningitidis both in vitro and in vivo.

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 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 Phages from Genus Bruynoghevirus and Phage Therapy: Pseudomonas Phage Delta Case

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1965
Author(s):  
Petar Knezevic ◽  
Aleksandra Petrovic Fabijan ◽  
Damir Gavric ◽  
Jovana Pejic ◽  
Zsolt Doffkay ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Phage Therapy ◽  
In Silico Analysis ◽  
Bacterial Toxin ◽  
Broad Host Range ◽  
Multiplicity Of Infection ◽  
Promising Candidate ◽  
A Genome ◽  
Silico Analysis

The applicability and safety of bacteriophage Delta as a potential anti-Pseudomonas aeruginosa agent belonging to genus Bruynoghevirus (family Podoviridae) was characterised. Phage Delta belongs to the species Pseudomonas virus PaP3, which has been described as a temperate, with cos sites at the end of the genome. The phage Delta possesses a genome of 45,970 bp that encodes tRNA for proline (Pro), aspartic acid (Asp) and asparagine (Asn) and does not encode any known protein involved in lysogeny formation or persistence. Analysis showed that phage Delta has 182 bp direct terminal repeats at the end of genome and lysogeny was confirmed, neither upon infection at low nor at high multiplicity of infection (MOI). The turbid plaques that appear on certain host lawns can result from bacteriophage insensitive mutants that occur with higher frequency (10−4). In silico analysis showed that the genome of Delta phage does not encode any known bacterial toxin or virulence factor, determinants of antibiotic resistance and known human allergens. Based on the broad host range and high lytic activity against planktonic and biofilm cells, phage Delta represents a promising candidate for phage therapy.

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 Genetics A Comprehensive In Silico Analysis of Deleterious SNPs of Paraplegin Protein Associated with Hereditary Spastic Paraplegia through Mitochondrial Dysfunction

2020 ◽  
Vol 2 (2) ◽  
pp. 1-14
Author(s):  
Ammara Akhtar ◽  
Sobia Nazir Choudhry ◽  
Rana Muhammad Mateen ◽  
Mureed Hussain
Keyword(s):  
Hereditary Spastic Paraplegia ◽  
In Silico ◽  
Mitochondrial Protein ◽  
In Silico Analysis ◽  
Missense Mutations ◽  
Spastic Paraplegia ◽  
Bioinformatic Tools ◽  
Pathogenic Variants ◽  
Structural And Functional Properties ◽  
Silico Analysis

Hereditary spastic paraplegia (HSP) is a heterogenous neurological disorder primarily associated with progressive spasticity. Paraplegin is a mitochondrial protein and mutations in this protein can lead to HSP. In this study, in silico analysis was carried out to identify the pathogenic variants of SPG7 (paraplegin protein). To find novel pathogenic mutations, missense and splicing variants were collected from gnomAD database and passed through a detailed and stringent analysis with the help of a variety of bioinformatic tools. The list of mutations was examined and compared in ClinVar. Altogether, 14 missense mutations and 18 splicing mutations were obtained and these mutations were predicted to have the potential of disrupting the normal structural and functional properties of paraplegin protein.

scholarly journals A comprehensive examination of ACE-2 receptor and prediction of spike glycoprotein and ACE-2 interaction based on in silico analysis of ACE-2 receptor

2021 ◽  
Author(s):  
Nehir Ozdemir Ozgenturk ◽  
Emre Aktaş
Keyword(s):  
Physical Properties ◽  
Critical Role ◽  
Transmembrane Helix ◽  
In Silico Analysis ◽  
Active Role ◽  
Vital Role ◽  
Surface Glycoprotein ◽  
Bioinformatic Tools ◽  
Essential Resource ◽  
Silico Analysis

ACE-2 receptor plays a vital role not only in the SARS-CoV-induced epidemic but also in some diseases. Studies have been carried out on the interactions of ACE-2- SARS-CoV proteins. However, comprehensive research has not been conducted on ACE2 protein by using bioinformatic tools. The present study especially two places, G104 and L108 points, which are effective in protecting the structure of the ACE-2 protein, play a critical role in the biological functioning of this protein, and play an essential role in determining the chemical-physical properties of this protein, and play a crucial role for ACE-2 protein-SARS CoV surface glycoprotein, were determined. It was also found that the G104 and L108 regions were more prone to possible mutations or deletions than the other ACE-2 protein regions. Moreover, it was determined that all possible mutations or deletions in these regions affect the chemical-physical properties, biological functions, and structure of the ACE-2 protein. Having a negative GRAVY value, one transmembrane helix, a significant molecular weight, a long-estimated half-life as well as most having unstable are results of G104 and L108 points mutations or deletions. Finally, it was determined that LQQNGSSVLS, which belong to the ACE-2 protein, may play an active role in binding the spike protein of SARS-CoV. All possible docking score results were estimated. It is thought that this study will bring a different perspective to ACE-2 _SARS-CoV interaction and other diseases in which ACE-2 plays an important role and will also be an essential resource for studies on ACE-2 protein.

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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