scholarly journals In silico Analysis of Phylogeny and Virulence Genes in STEC Strains Associated with Outbreaks

2021 ◽  
Author(s):  
Mehmet Demirci ◽  
Akın Yiğin ◽  
Fadile Yıldız Zeyrek
Keyword(s):  
Foodborne Pathogens ◽  
In Silico ◽  
Virulence Genes ◽  
Genomic Analysis ◽  
In Silico Analysis ◽  
Comparative Genomic ◽  
Phylogeny Analysis ◽  
In Silico Study ◽  
The World ◽  
Different Parts

Objective: Shiga toxin-producing E. coli (STEC) strains are important foodborne pathogens. Significant outbreaks with STEC strains can be encountered, even if the geography, time or resources were different. The aim of our in silico study was to compare the virulance factors and phylogeny of STEC strains such as EDL933 and Sakai, which have been identified as an agent in important outbreaks in different parts of the world and whole genomic data were in open databases. Method: Genomic NCBI data of eight strains were included in our study, including seven different STEC strains associated with significant epidemics in different parts of the world, and one supershedder strain obtained from cattle feces. Results: According to phylogeny analysis, the most similar strain to EDL933 strain was TW14588, with 96.4% similarity. The most distant similarity was Sakai strains with 79.2%. According to the virulence genes analysis; the presence of 333 genes that constitute virulence factors under nine headings were detected. In the first STEC origin, EDL933, 45% of all virulence genes were found to be active. Adherence genes such as Ecp, Elf, Hcp and toxin genes such as clyA were active in all strains except stx genes. Conclusion: In our in silico study of comparative genomic analysis of STEC strains which are associated with outbreaks, it was determined that STEC strains used different virulence genes besides the stx gene. Indeed, they used certain virulence genes, even their sources, time and locations were different, in the pathogenesis

scholarly journals COMPARATIVE GENOME OF TWO STRAIN MORAXELLA CATARRHALIS USING IN SILICO ANALYSIS

2017 ◽  
Vol 2 (2) ◽  
pp. 1
Author(s):  
Oktira Roka Aji
Keyword(s):  
In Silico ◽  
Moraxella Catarrhalis ◽  
Computational Analysis ◽  
Genomic Analysis ◽  
In Silico Analysis ◽  
Comparative Genomic ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Comparative Genome ◽  
Silico Analysis

<p>Moraxella catarrhalis can cause otitis media and exacerbations of chronic obstructive pulmonary disease in human. Here we describe the comparison between two publicly available genomes of two strain of M.catarrhalis using computational analysis to obtain genomic features between them. Comparative genomic analysis were carried out using available tools in public domain websites. The aim of this study was to investigate the differences and similarities between two strains by comparing their genomic sequences. The results indicated that may be used to offer better understanding M.catarrhalis lifestyle.</p><p> </p><p><strong>Keywords:</strong> <em>Moraxella catarrhalis; In Silico; Comparative genome analysis</em></p>

In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

scholarly journals DETECTION OF VIRULENCE GENES phoP AND phoQ IN Salmonella spp. USING IN SILICO POLYMERASE CHAIN REACTION

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Stalis Norma Ethica ◽  
Hayatun Fuad ◽  
Nur Hidayah ◽  
Sri Sinto Dewi ◽  
Aditya Rahman Ernanto ◽  
...  
Keyword(s):  
In Silico ◽  
Salmonella Enterica ◽  
Virulence Genes ◽  
Gene Detection ◽  
Chain Reaction ◽  
Salmonella Spp ◽  
Detection Tool ◽  
In Silico Study ◽  
Polymerase Chain ◽  
In Silico Pcr

Detection of Salmonella bacteria based on their virulence genes is among essential steps in the eradication of clinical infection by bacteria. In this study, two pair of primers, PhoPF-PhoPR: 5’- CCGCGCAGGAAAAACTCAAA-3’ and 5’-ATCTGTTCCAGCATCACCGG -3’ as well as PhoQF-PhoQR: 5’-AGAGATGATGCGCGTACTGG-3’ and 5’- CAGACGCCCCATGAGAACAT-3’, had been successfully designed using Primer3Plus to detect the presence of phoP and phoQ genes in Salmonella spp. Using genomic DNA of 44 genomic data of Salmonella spp. as templates, PhoPF-PhoPR could produce 520-bp amplicon, while PhoQF-PhoQR could result in 598-bp amplicon. Results of in silico PCR showed that both pairs of primers PhoPF-PhoPR and PhoQF-PhoQR could detect only Salmonella enterica species, and no Salmonella bongori species could be detected based on phoP and phoQ sequences. Both pairs of PhoPF-PhoPR and PhoQF-PhoQR primers were also able to detect the virulence genes in most of the studied subspecies of Salmonella enterica available in silico database unless Arizona subspecies. As conclusion, based on this in silico study, phoP and phoQ genes appeared to be biomarkers for Salmonella enterica species. Both pairs of primers designed in this study has potential to be used as detection tool to differentiate species Salmonella enterica from Salmonella bongori, and also to distinguish S.enterica subsp. enterica from subsp. Arizonae.Keywords: Gene detection, bacterial virulence, phoP, phoQ, Salmonella spp.

scholarly journals IN SILICO STUDY OF THE ANTIMICROBIAL PROFILE OF β-CITRONELLOL: POTENTIAL AS AN ANTIFUNGAL

2019 ◽  
Vol 16 (32) ◽  
pp. 894-898
Author(s):  
D. F. SILVA ◽  
H. D. NETO ◽  
M. D. L. FERREIRA ◽  
A. A. O. FILHO ◽  
E. O. LIMA
Keyword(s):  
In Silico ◽  
Fungal Infections ◽  
In Silico Analysis ◽  
Fungal Species ◽  
In Silico Study ◽  
Pass Online ◽  
Therapeutic Alternatives ◽  
Bioactivity Profile ◽  
Silico Analysis

β-citronellol (3,7-dimethyl-6-octen-1-ol) has been exhibiting a number of pharmacological effects that creates interest about its antimicrobial potential, since several substances of the monoterpene class have already demonstrated to possess activity in this profile. In addition, the emergence of fungal species resistant to current pharmacotherapy poses a serious challenge to health systems, making it necessary to search for new effective therapeutic alternatives to deal with this problem. In this study, the antimicrobial profile of β-citronellol was analyzed. The Prediction of Activity Spectra for Substances (PASS) online software was used to study the antimicrobial activity of the β-citronellol molecule by the use of in silico analysis. In contrast, an in vitro antifungal study of this monoterpene was carried out. For this purpose, the Minimum Inhibitory Concentration (MIC) was determined by the microdilution technique in 96-well plates in Saboraud Dextrose Broth/RPMI against sensitive strains of Candida albicans, and this assay was performed in duplicate. In the in silico analysis of the antimicrobial profile, it was revealed that the monoterpene β-citronellol had a diverse antimicrobial bioactivity profile. For the antifungal activity, it presented a percentage value with Pa: 58.4% (predominant) and its MIC of 128 μg/mL, which was equivalent for all strains tested. The in silico study of the β-citronellol molecule allowed us to consider that the monoterpenoid is very likely to be bioactive against agents that cause fungal infections.

scholarly journals Influence of cantilever position and implant connection in a zirconia custom implant-supported fixed partial prosthesis: in silico analysis

2018 ◽  
Vol 47 (4) ◽  
pp. 223-229
Author(s):  
Juliana Maria Coutinho BASTOS ◽  
Dimorvan BORDIN ◽  
Andréa Araújo de VASCONCELLOS ◽  
Milton Edson MIRANDA
Keyword(s):  
In Silico ◽  
Maximum Stress ◽  
In Silico Analysis ◽  
Compression Stress ◽  
Vertical Load ◽  
Occlusal Force ◽  
Tension Distribution ◽  
Custom Implant ◽  
In Silico Study ◽  
Silico Analysis

Abstract Introduction A better tension distribution on implants and abutments in implant-supported fixed partial prosthesis is essential in the rehabilitation of posterior mandible area. Objective: To evaluate the influence of cantilever position and implant connection in a zircônia custom implant-supported fixed partial prosthesis using the 3-D finite element method. Material and method: Four models were made based on tomographic slices of the posterior mandible with a zirconia custom three-fixed screw-retained partial prosthesis. The investigated factors of the in silico study were: cantilever position (mesial or distal) and implant connection (external hexagon or morse taper). 100 N vertical load to premolar and 300 N to molar were used to simulate the occlusal force in each model to evaluate the distribution of stresses in implants, abutments, screws and cortical and cancellous bone. Result: The external hexagon (EH) connection showed higher cortical compression stress when compared to the morse taper (MT). For both connections, the molar cantilever position had the highest cortical compression. The maximum stress peak concentration was located at the cervical bone in contact with the threads of the first implant. The prosthetic and abutment screws associated with the molar cantilevers showed the highest stress concentration, especially with the EH connection. Conclusion: Morse taper implant connetions associated with a mesial cantilever showed a more favorable treatment option for posterior mandible rehabilitation.

Phytochemicals as Therapeutics Against COVID-19: An In-Silico Study

2020 ◽  
Author(s):  
Debraj Koiri ◽  
Ditam Chakraborty ◽  
Pranotosh Das ◽  
Rajkumar Rana ◽  
Soumyanil Chatterjee ◽  
...  
Keyword(s):  
In Silico ◽  
Therapeutic Agents ◽  
Binding Energies ◽  
Daily Lives ◽  
Lab Experiments ◽  
In Silico Studies ◽  
In Silico Study ◽  
The World ◽  
Wet Lab ◽  
Low Costs

Since December 2019, the worldwide spread of COVID-19 has brought the majority of the world to a standstill, affecting daily lives as well as economy. Under these conditions, it is imperative to develop a cure as soon as possible. On account of some of the adverse side effects of the existing conventional drugs, researchers all around the world are screening natural antiviral phytochemicals as potential therapeutic agents against COVID-19. This paper aims to review interactions of some specific phytochemicals with the receptor binding domain (RBD) of the Spike glycoprotein of SARS-CoV-2 and suggest their possible therapeutic applications. Literature search was done based on the wide array of in-silico studies conducted using broad spectrum phytochemicals against SARS-CoV-2 and other viruses. We shortlisted 26 such phytochemicals specifically targeting the S protein and its interactions with host receptors. To validate the previously published results, we also conducted molecular docking using the AutoDockVina application and identified 6 high potential phytochemicals for therapeutic use based on their binding energies. Besides this, availability of these compounds, their mode of action, toxicity data and cost-effectiveness were also taken into consideration. Our review specifically identifies 6 phytochemicals that can be used as potential treatments for COVID-19 based on their availability, toxicology results and low costs of production. However, all these compounds need to be further validated by wet lab experiments and should be approved for clinical use only after appropriate trials.

scholarly journals In silico Study of the Interactions between Schiff Base Polyphenols and HPV 16 E6/E6AP/p53 complex

2021 ◽  
pp. 3973-3980
Author(s):  
Jeremiah I. Ogah ◽  
Olatunji M. Kolawole ◽  
Steven O. Oguntoye ◽  
Muhammed Mustapha Suleiman
Keyword(s):  
Molecular Docking ◽  
Anticancer Agents ◽  
In Silico ◽  
In Silico Analysis ◽  
Docking Study ◽  
Hydrogen Atoms ◽  
Molecular Docking Study ◽  
Hpv 16 ◽  
In Silico Study

The rise in the incidence of cervical cancer globally has accentuate attention to the potential role of polyphenols as anticancer agents. Different studies have demonstrated the role of some polyphenols in altering Human Papillomavirus (HPV) carcinogenesis. Thus, this study was aimed at establishing the potentials of Schiff-based polyphenols from imesatin and satin as anticancer agents through in silico analysis. The polyphenols were synthesized and characterized using elemental analyses, spectroscopic analyses, UV-visible, Infrared, and Nuclear Magnetic Resonance (1H NMR and 13C, NMR). Molecular docking study of the polyphenols was carried out using Auto Dock Vina. The oncogenic E6 protein structure of HPV 16 was obtained from the protein bank (ID: 4XR8). The E6 proteins were prepared using AutoDock tools. Water molecules were removed from the protein molecules while hydrogen atoms were added. Also, the structures of Curcumin and Isomericitrin were obtained from PubChem. Results showed that three different Schiff based polyphenols were obtained from the synthesis; 3-(2’,4’-dimethoxy benzylidene hydrazono) indoline-2-one (DMBH), 3-(2’-hydroxy-4’-methoxy benzylidene hydrazono) indoline-2-one (HMBD), and 3-((4-4’-((2’’, 4’’-dimethoxy benzylidene amino) benzyl)phenyl)imino) indoline-2-one (DMBP). Higher ability of the docked polyphenols to bind to the E6/E6AP/p53 complex when compared to Curcumin was revealed. Also, results showed that the binding energy of Curcumin and Isomericitrin were -7.1kcal/mol and -8.4kcal/mol respectively while that of the polyphenols ranged from -7.4kcal/mol to -7.9kcal/mol. The molecular docking results of the polyphenols used in this study further confirm their potentials as strong anti-cancer agents.

scholarly journals Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19

2020 ◽  
Author(s):  
Romulo O. Barros ◽  
Fabio L. C. C. Junior ◽  
Wildrimak S. Pereira ◽  
Neiva M. N. Oliveira ◽  
Ricardo Ramos
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Social Health ◽  
Research Institutions ◽  
Health Measures ◽  
In Silico Study ◽  
The World ◽  
Anti Hiv ◽  
Society Research

The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for the COVID-19. In this work, molecular docking was used to study (in silico) the interaction of twenty-four ligands, divided into four groups, with four important SARS-CoV-2 receptors. The results showed that Metaquine (group 01), antimalarial substance and the anti-HIV antiretroviral Saquinavir (group 03), presented interaction with all the studied receptors, indicating that they are potentials candidates for muti-target drugs for COVID-19.

scholarly journals Inhibitory Effect of Phytochemicals from Azadirachta indica A Juss. and Tinospora cordifolia (Thunb.) Miers against SARS-CoV-2 M pro and Spike Protease- An In Silico Analysis

2020 ◽  
Author(s):  
RAMÀKRISHNAMACHARYA CH ◽  
VANITHA MURALIKUMAR ◽  
CHANDRASEKAR SESHACHALAM
Keyword(s):  
Medicinal Plants ◽  
Azadirachta Indica ◽  
In Silico ◽  
Viral Infections ◽  
In Silico Analysis ◽  
Inhibitory Effect ◽  
Tinospora Cordifolia ◽  
Reference Drug ◽  
In Silico Study ◽  
Silico Analysis

COVID 19 caused by SARS-CoV-2 is spreading worldwide and affected 10 million people with a mortality rate between 0.5 % to 5%. Medicinal plants from China, Morocco, Algeria, Africa and India were tested for antiviral efficacy in SARS-CoV-2. Ayurveda Medicine described many medicinal plants. The Nimba ( Azadirachta indica A. Juss) is used in fever, bacterial and viral infections, and Amrita ( Tinospora cordifolia (Thunb.) Miers) is used as antiviral, antipyretic, and anti-inflammatory purposes. The combination of both these plants is called Nimbamritam, and it is widely used in pyrexia, dermatitis, viral infections, etc. Spike protease (PDB ID 6VXX) and M pro (PDB ID 6LU) were retrieved from RCSB and 16 ligands from A. indica and 6 ligands from T. cordifolia were obtained from IMPPAT and PubChem. AutoDock Vina embedded PyRx was used for docking. Remdesivir was taken as a reference drug. In silico study of Cordifolide A of T cordifolia showed the highest scores with -8.2 Kcal/mol and -10.3Kcal/mol with M pro protease and Spike protease respectively. Cordifolide A had 4 H bonds and Kaempferol had 7 non-conventional bonds, including van der Waal with M pro (6LU7) protease. The interactions with 6VXX had 5 H bonds in each ligand Cordifolide A and Azadirachtin B. The prevention of virus entry by targeting spike protease host receptor ACE2 and restricting replication of the viral genome by targeting M pro residues were identified in our study. A. indica and T. cordifolia are promising therapeutic agents in COVID 19.

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