scholarly journals Metabolism of Daidzein and Genistein by Gut Bacteria of the Class Coriobacteriia

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2741
Author(s):  
Sebastian Tobias Soukup ◽  
Dominic Alexander Stoll ◽  
Nicolas Danylec ◽  
Alena Schoepf ◽  
Sabine Emma Kulling ◽  
...  
Keyword(s):  
Gene Cluster ◽  
In Silico ◽  
Pcr Amplification ◽  
Protein Sequences ◽  
In Silico Analysis ◽  
Gut Bacteria ◽  
Strictly Anaerobic ◽  
Bacterial Strains ◽  
Related Family ◽  
Pure Bacterial Cultures

The intake of isoflavones is presumed to be associated with health benefits in humans, but also potential adverse effects of isoflavones are controversially discussed. Isoflavones can be metabolized by gut bacteria leading to modulation of the bioactivity, such as estrogenic effects. Especially bacterial strains of the Eggerthellaceae, a well-known bacterial family of the human gut microbiota, are able to convert the isoflavone daidzein into equol. In addition, metabolization of genistein is also described for strains of the Eggerthellaceae. The aim of this study was to identify and investigate gut bacterial strains of the family Eggerthellaceae as well as the narrowly related family Coriobacteriaceae which are able to metabolize daidzein and genistein. This study provides a comprehensive, polyphasic approach comprising in silico analysis of the equol gene cluster, detection of genes associated with the daidzein, and genistein metabolism via PCR and fermentation of these isoflavones. The in silico search for protein sequences that are associated with daidzein metabolism identified sequences with high similarity values in already well-known equol-producing strains. Furthermore, protein sequences that are presumed to be associated with daidzein and genistein metabolism were detected in the two type strains ‘Hugonella massiliensis’ and Senegalimassilia faecalis which were not yet described to metabolize these isoflavones. An alignment of these protein sequences showed that the equol gene cluster is highly conserved. In addition, PCR amplification supported the presence of genes associated with daidzein and genistein metabolism. Furthermore, the metabolism of daidzein and genistein was investigated in fermentations of pure bacterial cultures under strictly anaerobic conditions and proofed the metabolism of daidzein and genistein by the strains ‘Hugonella massiliensis’ DSM 101782T and Senegalimassilia faecalis KGMB04484T.

scholarly journals In silico analysis of similar protein sequences between Sars-Cov-2 and BCG vaccine

2021 ◽  
Vol 132 ◽  
pp. S168-S169
Author(s):  
Busra Goksel Tulgar ◽  
Fahrettin Duymus ◽  
Deniz Esin ◽  
Fatma Betul Maden ◽  
Ebru Marzioglu Ozdemir ◽  
...  
Keyword(s):  
In Silico ◽  
Protein Sequences ◽  
In Silico Analysis ◽  
Bcg Vaccine ◽  
Similar Protein ◽  
Silico Analysis

scholarly journals Identification of a Novel Class of Membrane-Bound [NiFe]-Hydrogenases in Thermococcus onnurineus NA1 by In Silico Analysis

2010 ◽  
Vol 76 (18) ◽  
pp. 6286-6289 ◽  
Author(s):  
Jae Kyu Lim ◽  
Sung Gyun Kang ◽  
Alexander V. Lebedinsky ◽  
Jung-Hyun Lee ◽  
Hyun Sook Lee
Keyword(s):  
Gene Cluster ◽  
In Silico ◽  
In Silico Analysis ◽  
Sequence Motifs ◽  
Thermococcus Onnurineus Na1 ◽  
Hyperthermophilic Archaeon ◽  
Group 4 ◽  
Membrane Bound ◽  
Silico Analysis

ABSTRACT In silico analysis of group 4 [NiFe]-hydrogenases from a hyperthermophilic archaeon, Thermococcus onnurineus NA1, revealed a novel tripartite gene cluster consisting of dehydrogenase-hydrogenase-cation/proton antiporter subunits, which may be classified as the new subgroup 4b of [NiFe]-hydrogenases-based on sequence motifs.

scholarly journals The Genetic Perspective of Familial Glucocorticoid Deficiency: In Silico Analysis of Two Novel Variants

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Katayoun Heshmatzad ◽  
Nejat Mahdieh ◽  
Ali Rabbani ◽  
Abdolah Didban ◽  
Bahareh Rabbani
Keyword(s):  
In Silico ◽  
Clinical Symptoms ◽  
Genetic Disorder ◽  
Pcr Amplification ◽  
In Silico Analysis ◽  
Genetic Studies ◽  
Novel Variants ◽  
Comprehensive Search ◽  
Glucocorticoid Deficiency ◽  
Pathogenic Analysis

Familial glucocorticoid deficiency is a rare autosomal recessive genetic disorder which belongs to a group of primary adrenal insufficiency (PAI) and is mainly caused by mutations in the MC2R and MRAP genes. A comprehensive search was conducted to find the reported variants of MC2R and MRAP genes. In silico pathogenic analysis was performed for the reported variants. PCR amplification and sequencing were performed for three patients. Structural analysis, modeling, and interactome analysis were applied to characterize novel MC2R variants and their proteins. About 80% of MC2R-related cases showed the clinical symptoms which were diagnosed at <2 years old. 107 patients had MC2R mutations (85 homozygotes, 21 compound heterozygotes, and 1 simple heterozygote). 59 variants were found in the MC2R gene. Four mutations were responsible for half of patients. 39 homozygous patients had MRAP mutations; 14 variants were determined in the MRAP gene. Nine proteins were predicted by STRING to associate with the studied proteins. Two novel MC2R variants, c.128T > G (p.Leu43Arg) and c.251T > A (p.Ile84Asn), were found in two patients at the age of above and below 2 years, respectively. Mutations in MC2R and MRAP genes are the main cause of FGD. Genetic studies and in silico analysis will help to confirm the diagnosis.

scholarly journals Bioinformatics Resources for In Silico Proteome Analysis

2003 ◽  
Vol 2003 (4) ◽  
pp. 231-236 ◽  
Author(s):  
Manuela Pruess ◽  
Rolf Apweiler
Keyword(s):  
In Silico ◽  
Computational Analysis ◽  
Tertiary Structure ◽  
Protein Sequences ◽  
In Silico Analysis ◽  
Proteome Analysis ◽  
Protein Modelling ◽  
Similarity Searches ◽  
Silico Analysis

In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise this data for healthcare and drug development, first the characteristics of proteomes of entire species—mainly the human—have to be understood, before secondly differentiation between individuals can be surveyed. Specialised databases about nucleic acid sequences, protein sequences, protein tertiary structure, genome analysis, and proteome analysis represent useful resources for analysis, characterisation, and classification of protein sequences. Different from most proteomics tools focusing on similarity searches, structure analysis and prediction, detection of specific regions, alignments, data mining, 2D PAGE analysis, or protein modelling, respectively, comprehensive databases like the proteome analysis database benefit from the information stored in different databases and make use of different protein analysis tools to provide computational analysis of whole proteomes.

Geographical, Molecular, and Computational Analysis of Migraine-Causing Genes

2021 ◽  
Vol 20 (04) ◽  
pp. 391-403
Author(s):  
Muhammad Naveed ◽  
Bakhtawar Bukhari ◽  
Nadia Afzal ◽  
Haleema Sadia ◽  
Bisma Meer ◽  
...  
Keyword(s):  
In Silico ◽  
Computational Analysis ◽  
Pcr Amplification ◽  
In Silico Analysis ◽  
Bivariate Analysis ◽  
Headache Disorders ◽  
Gender And Age ◽  
Migraine Pathophysiology ◽  
Silico Analysis

Migraine is a re-occurring type of headache and causes moderate-to-severe pain that is troubling or pulsing. The pain occurs in half of the head, and common symptoms are photophobia, phonophobia, nausea, depression, anxiety, vomiting, etc. This study evaluates the prevalence of migraine and responsible genes through molecular modeling in the region of Bahawalpur, Pakistan. This research was aimed to determine the prevalence of migraine-causing genes in the population of Bahawalpur and also to do molecular and in-silico analysis of migraine-causing gene as no similar research was conducted before. The disease was characterized and diagnosed under the criteria of the Second Edition of the International Classification of Headache Disorders and molecular identification of migraine-causing genes, i.e. GRIA1, GRIA3, and ESR1, by PCR amplification. The total number of samples collected for migraine patients was 230, out of which 30 were positive for PCR amplification of the genes GRIA1, GRIA3, and ESR1. Therapeutic potentials of commercial drugs, namely Cyclobenzaprine, Divalproex, Ergotamine, and Sumatriptan, were analyzed in silico through molecular docking. Ergotamine demonstrated the highest binding affinity of [Formula: see text]8.4 kcal/mol for the target molecule and, hence, the highest potential. The bivariate analysis showed that the prevalence of migraine concerning gender and age was significantly correlated ([Formula: see text], [Formula: see text]). It was observed that almost 31.4% of women suffered from headaches daily, 70% weekly, 28.1% monthly, and 23.5% rarely. Comparatively, only 8.3% of males suffered from daily headaches, 34% weekly, 12.8% monthly, and 14.9% rarely. The study shows promising results and encourages future researchers to conduct such a comprehensive epidemiological study on an even larger population to justify a more precise association of risk factors involved in migraine pathophysiology.

scholarly journals In silico analysis to elect superior bacterial alkaline protease for detergent and leather industries

2015 ◽  
Vol 5 (3) ◽  
pp. 685-698 ◽  
Author(s):  
Kamonashis Das ◽  
Sourav Chakraborty ◽  
Mahmudul Hasan ◽  
Abdullah Maruf Rahman Shovo
Keyword(s):  
High Temperature ◽  
Bacillus Megaterium ◽  
In Silico ◽  
Alkaline Protease ◽  
Protein Sequences ◽  
In Silico Analysis ◽  
Alkaline Proteases ◽  
Leather Industry ◽  
Catalytic Function ◽  
Common Motif

Alkaline protease contributes 40% of the total worldwide enzyme sales. Alkaline protease that is stable at very high temperature and pH is massively desirable for detergent industry and leather industry specially in tanning process. So the present study aims to elect superior bacterial alkaline protease (high temperature and pH stable) as compared to the alkaline proteases of currently industrially used bacteria (Bacillus subtilis and Bacillus cereus). A total of 50 protein sequences of alkaline proteases of different bacteria were analyzed through in silico characterization. ProtParam result revealed that isoelectric point and aliphatic index of alkaline protease of Bacillus megaterium were 8.83 and 93.35 respectively. In case of alkaline protease of B. megaterium, these two properties were significant in comparison to alkaline proteases of industrially used bacteria and other considered bacteria. A common motif of 28 amino acid residues i.e., IQSTYPGEDYEYMSGTSMATPHVAGVAA was found using MEME software in 46 protein sequences. It can be concluded that alkaline protease of Bacillus megaterium may be superior to alkaline proteases of industrially used bacteria and other considered bacteria. In addition, obtained common motif indicates its probable role in catalytic function and structure of alkaline proteases. 

A systematic review with in silico analysis on transcriptomic profile of gallbladder carcinoma

2020 ◽  
Vol 47 (6) ◽  
pp. 398-408
Author(s):  
Sonam Tulsyan ◽  
Showket Hussain ◽  
Balraj Mittal ◽  
Sundeep Singh Saluja ◽  
Pranay Tanwar ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gallbladder Carcinoma ◽  
In Silico ◽  
In Silico Analysis ◽  
Transcriptomic Profile ◽  
Silico Analysis
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