scholarly journals Prediction of CTL epitope, in silico modeling and functional analysis of cytolethal distending toxin (CDT) protein of Campylobacter jejuni

2014 ◽  
Vol 7 (1) ◽  
Author(s):  
Arun G Ingale ◽  
Susumu Goto
Keyword(s):  
Functional Analysis ◽  
Campylobacter Jejuni ◽  
In Silico ◽  
Cytolethal Distending Toxin ◽  
Ctl Epitope ◽  
In Silico Modeling

scholarly journals IN SILICO OLIGONUCLEOTIDE PRIMER DESIGN FOR Campylobacter jejuni cytolethal distending toxin B GENE AMPLIFICATION

2021 ◽  
Vol 4 (1) ◽  
pp. 53
Author(s):  
Rian Ka Praja
Keyword(s):  
Campylobacter Jejuni ◽  
In Silico ◽  
Oligonucleotide Primer ◽  
Cytolethal Distending Toxin ◽  
Dna Double Strand Breaks ◽  
Toxin B ◽  
Strand Breaks ◽  
Cycle Arrest ◽  
M Phase ◽  
Reverse Primer

<p>Cytolethal distending toxin B (cdtB) is a genotoxinexpressed by <em>Campylobacter jejuni</em>. cdtB is a DNasethatinduces DNA double-strand breaks (DSB) in the nucleus causing cell cycle arrest at the G2/M phase and apoptosis. This study aimed to design and analyze in silico primer pairs to amplify cdtB gene of<em>C. jejuni</em>.The cdtB gene sequence with accession number AY445094.1was retrieved from GenBank NCBI and primer pairs were designed by using Primer-BLAST. Further analysis of primer quality such asself dimer, hairpin, repeats, and runwere done by NetPrimer. The results showed that forward primer pair 3 (5’-AGCAAGTGGAGTGTTAGCGT-3’) and reverse primer pair 3 (5’- TTGGAGTGGCTGTTCTTGGT-3’) met requirements as an ideal primer set to amplify cdtB gene in the term of primer length, Tm and GC% with a product length of 103 bp.In addition, based on NetPrimer analysis results, this primer pair had no self dimer, hairpin, repeats, and run. It can be concluded that a primer set to amplify cdtB gene of <em>C. jejuni</em>has been successfully designed<em>.</em>However, a wet experiment is needed to run this primer set in the laboratory setting.</p><p> </p><p>Keywords: <em>Campylobacter jejuni</em>, cdtB gene, in silico, primer.</p>

In Silico Modeling as a Tool to Predict and Characterize Plant Toxicity

2020 ◽  
pp. 367-378
Author(s):  
Charles Oluwaseun Adetunji ◽  
William Peter Mitembo ◽  
Chukwuebuka Egbuna ◽  
G.M. Narasimha Rao
Keyword(s):  
In Silico ◽  
Plant Toxicity ◽  
In Silico Modeling

scholarly journals In silico modeling gas molecules transfer through the biomembrane by kinks-solitons

2021 ◽  
Author(s):  
P. V. Mokrushnikov ◽  
E. V. Lezhnev ◽  
V. Ya. Rudyak
Keyword(s):  
In Silico ◽  
In Silico Modeling ◽  
Gas Molecules

scholarly journals Multidrug Antimicrobial Resistance and Molecular Detection of mcr-1 Gene in Salmonella Species Isolated from Chicken

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 206
Author(s):  
Md Bashir Uddin ◽  
S.M. Bayejed Hossain ◽  
Mahmudul Hasan ◽  
Mohammad Nurul Alam ◽  
Mita Debnath ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Antimicrobial Resistance ◽  
In Silico ◽  
Salmonella Enterica ◽  
Molecular Mechanisms ◽  
Antimicrobial Agents ◽  
Genetic Relationships ◽  
Evolutionary Relationship ◽  
Salmonella Spp ◽  
Gram Negative

Colistin (polymyxin E) is widely used in animal and human medicine and is increasingly used as one of the last-resort antibiotics against Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant Gram-negative bacteria, resistance to this antibiotic ought to be monitored. The study was undertaken to elucidate the molecular mechanisms, genetic relationships and phenotype correlations of colistin-resistant isolates. Here, we report the detection of the mcr-1 gene in chicken-associated Salmonella isolates in Bangladesh and its in-silico functional analysis. Out of 100 samples, 82 Salmonella spp. were isolated from chicken specimens (liver, intestine). Phenotypic disc diffusion and minimum inhibitory concentration (MIC) assay using different antimicrobial agents were performed. Salmonella isolates were characterized using PCR methods targeting genus-specific invA and mcr-1 genes with validation for the functional analysis. The majority of the tested Salmonella isolates were found resistant to colistin (92.68%), ciprofloxacin (73.17%), tigecycline (62.20%) and trimethoprim/sulfamethoxazole (60.98%). When screened using PCR, five out of ten Salmonella isolates were found to carry the mcr-1 gene. One isolate was confirmed for Salmonella enterica subsp. enterica serovar Enteritidis, and other four isolates were confirmed for Salmonella enterica subsp. enterica serovar Typhimurium. Sequencing and phylogenetic analysis revealed a divergent evolutionary relationship between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, rendering them resistant to colistin. Three-dimensional homology structural analysis of MCR-1 proteins and molecular docking interactions suggested that MCR-1 and LptA share a similar substrate binding cavity, which could be validated for the functional analysis. The comprehensive molecular and in-silico analyses of the colistin resistance mcr-1 gene of Salmonella spp. of chicken origin in the present study highlight the importance of continued monitoring and surveillance for antimicrobial resistance among pathogens in food chain animals.

scholarly journals A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Evangelina López de Maturana ◽  
◽  
Juan Antonio Rodríguez ◽  
Lola Alonso ◽  
Oscar Lao ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Functional Analysis ◽  
Genetic Susceptibility ◽  
In Silico ◽  
Complex Disease ◽  
Meta Analysis ◽  
Low Frequency ◽  
Acinar Cells ◽  
Pancreatic Acinar Cells ◽  
Phenotypic Variance

Abstract Background Pancreatic cancer (PC) is a complex disease in which both non-genetic and genetic factors interplay. To date, 40 GWAS hits have been associated with PC risk in individuals of European descent, explaining 4.1% of the phenotypic variance. Methods We complemented a new conventional PC GWAS (1D) with genome spatial autocorrelation analysis (2D) permitting to prioritize low frequency variants not detected by GWAS. These were further expanded via Hi-C map (3D) interactions to gain additional insight into the inherited basis of PC. In silico functional analysis of public genomic information allowed prioritization of potentially relevant candidate variants. Results We identified several new variants located in genes for which there is experimental evidence of their implication in the biology and function of pancreatic acinar cells. Among them is a novel independent variant in NR5A2 (rs3790840) with a meta-analysis p value = 5.91E−06 in 1D approach and a Local Moran’s Index (LMI) = 7.76 in 2D approach. We also identified a multi-hit region in CASC8—a lncRNA associated with pancreatic carcinogenesis—with a lowest p value = 6.91E−05. Importantly, two new PC loci were identified both by 2D and 3D approaches: SIAH3 (LMI = 18.24), CTRB2/BCAR1 (LMI = 6.03), in addition to a chromatin interacting region in XBP1—a major regulator of the ER stress and unfolded protein responses in acinar cells—identified by 3D; all of them with a strong in silico functional support. Conclusions This multi-step strategy, combined with an in-depth in silico functional analysis, offers a comprehensive approach to advance the study of PC genetic susceptibility and could be applied to other diseases.

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