Bioinformatics

Clustering is widely used in different field such as biology, psychology, and economics. The result of clustering varies as number of cluster parameter changes hence main challenge of cluster analysis is that the number of clusters or the number of model parameters is seldom known, and it must be determined before clustering. The several clustering algorithm has been proposed. Among them k-means method is a simple and fast clustering technique. We address the problem of cluster number selection by using a k-means approach We can ask end users to provide a number of clusters in advance, but it is not feasible end user requires domain knowledge of each data set. There are many methods available to estimate the number of clusters such as statistical indices, variance based method, Information Theoretic, goodness of fit method etc...The paper explores six different approaches to determine the right number of clusters in a dataset

A considerable section of males suffered from COVID-19, with many experiencing long-term repercussions. Recovered males have been documented to have compromised fertility, albeit the mechanisms remain unclear. We investigated the impact of COVID-19 on semen proteome following complete clinical recovery using mass spectrometry. A label-free quantitative proteomics study involved 10 healthy fertile subjects and 17 COVID-19-recovered men. With 1% false discovery rate and >1 unique peptide stringency, MaxQuant analysis found 1099 proteins and 8503 peptides. Of the 48 differentially expressed proteins between the healthy and COVID-19-recovered groups, 21 proteins were downregulated and 27 were upregulated in COVID-19-recovered males. The major pathways involved in reproductive functions, such as sperm-oocyte recognition, testosterone response, cell motility regulation, adhesion regulation, extracellular matrix adhesion, and endopeptidase activity, were downregulated in COVID-19-recovered patients according to bioinformatics analysis. Furthermore, the targeted approach revealed significant downregulation of semenogelin 1 and prosaposin, two proteins related to male fertility. Therefore, we demonstrate the alteration of semen proteome in response to COVID-19, thus disrupting the male reproductive function despite the patient's clinical remission. Hence, to understand fertility-related biological processes triggered by this infection, a protracted evaluation of the consequences of COVID-19 in recovered men is warranted.

Malaria caused by the parasite Plasmodium falciparum is a major public health concern. The parasite lacks a functional Tricarboxylic acid cycle (TCA), making glycolysis its sole energy source. One such enzyme is triose phosphate isomerase. This catalyzes the isomerization of D-Glyceraldehyde 3 phosphate to dihydroxy acetone phosphate. An attempt was made to identify the potential phyto inhibitors and inhibit the enzyme as well as to modify their side chain to impure the binding efficiently. Here, two datasets are made such as training set and testing set, in which first, is training set, contain 19 known inhibitors against Triosephosphate isomerase and second is testing set which contain 6 phyto-inhibitors to be tested. Autodock Vina, a docking tool, is used for molecular docking that utilizes information on conformational variability from ensembles of experimental receptor structure of Triosephosphate isomerase. We showed that experimentally determined binding orientations and comp...

The principal objective of the present research work was to determine the antibacterial potential of A. marmelos against four standard pathogenic bacterial strains. To evaluate antibacterial activity the agar-well diffusion assay was used. All the four extracts showed the highest and significant antibacterial activity against both Gram negative and Gram-positive bacteria. It is the strain Bacillus subtilis that is almost resistant to the four extracts of A. marmelos.

PBIT (Pipeline Builder for Identification of drug Targets) is an online webserver that has been developed for screening of microbial proteomes for critical features of human drug targets such as being non-homologous to human proteome as well as the human gut microbiota, essential for the pathogen's survival, participation in pathogen-specific pathways etc. The tool has been validated by analyzing 57 putative targets of Candida albicans documented in literature. PBIT integrates various in silico approaches known for drug target identification and will facilitate highthroughput prediction of drug targets for infectious diseases, including multi-pathogenic infections.

The rapid dissemination of antimicrobial resistance (AMR) has emerged as a serious health problem on an unprecedented global scale. AMR is predicted to kill more than 10 million people annually by 2050 leading to huge economic losses worldwide. Therefore, urgent action is required at the national as well as international levels to avert this looming crisis. Effective surveillance can play an important role in the containment of AMR spread by providing data to help determine AMR hotspots, predict an outbreak, maintain proper stewardship and propose immediate and future plans of action in this respect. Although many existing databases provide genetic and molecular information on AMR in microorganisms, there is no dedicated database of AMR from non-clinical samples. The FEAMR database is a one-of-its-kind database to provide manually collated and curated information on the prevalence of AMR in food and the environment. For designing the FEAMR webpage, Microsoft Visual Studio with HTML, CSS, ASP.NET, Bootstrap for the front-end and C# for the back-end were used. The FEAMR database is a free access resource ( https://feamrudbt-amrlab.mu.ac.in/ ), accepting verified food- and environment-related AMR submissions from across the globe. To the best of our knowledge, it is probably the first database providing AMR-related surveillance data from non-clinical samples. It is designed from the 'One Health Approach' perspective to help in the containment of global AMR spread. Flowsheet of steps for making FEAMR database 1. Research articles relating to Antimicrobial Resistance (AMR) were searched on the internet. 2. Data relating to AMR were retrieved from these articles and stored in an MS-Excel sheet. 3. The web pages of the FEAMR database (DB) were created using Microsoft Visual Studio (MVS) and its various tools. HTML, CSS, ASP.NET and Bootstrap were used for the front end and C# used for the back-end of the website. 4. The DB of FEAMR was created using MS SQL Server which was controlled by SQL Server Management Studio (SSMS). 5. The data from the MS-Excel sheet in step 2 was stored in the SQL server and displayed on the web page using GridView tool of MVS and C#. The database created was then uploaded on the University of Mumbai (UoM) website, where it can be accessed by all users having the link to the DB ( https://feamrudbt-amrlab.mu.ac.in/ ).

Carissa carandas is a useful food and medicinal plant of India, found to be widely distributed throughout subtropical and topical regions. The plant has been used as a traditional medicinal plant over thousands of years in the Ayurvedic, Unani, and Homoeopathic system of medicine. Traditionally, whole plant and its parts were used in the treatment of various ailments. The major bioactive constituents, which impart medicinal value to the herb, are alkaloids, flavonoids, saponins and large amounts of cardiac glycosides, triterpenoids, phenolic compounds and tannins. Roots were reported to contain volatile principles including 2-acetyl phenol, lignan, carinol, sesquiterpenes (carissone, carindone), lupeol, β-sitosterol, 16β-hydroxybetulinic acid, α-amyrin, β-sitosterol glycoside, and des-Nmethylnoracronycine, whereas leaves were reported to contain triterpenoid constitutes as well as tannins. While, fruits have been reported to contain carisol, epimer of α-amyrin, linalool, β-caryophyllene, carissone, carissic acid, carindone, ursolic acid, carinol, ascorbic acid, lupeol, and β-sitosterol. Ethnopharmacological significance of the plant has been ascribed due to anti-cancer, anti-convulsant, anti-oxidant, analgesic, anti-inflammatoryAQ1, anti-ulcer, anthelmintic activity, cardiovascular, anti-nociceptive, anti-diabetic, antipyretic, hepatoprotective, neuropharmacological, and diuretic activities, antimicrobial activities and cytotoxic potentials, in-vitro anti-oxidant, and DNA damage inhibition, and constipation and diarrheal activities. The review also dealt with describing micropropagation strategies for effective conservation of this important food and medicinal plant. The review has been written with the aim to provide a direction for further clinical research to promote safe and effective herbal treatments to cure a number of diseases.

Background: Candida auris is associated with invasive and severe candidemia, multi-drug resistance and high mortalities. Azoles and Flucytosine are commonly used antifungal drugs. Lanosterol alpha-demethylase (ERG11), Uracil phosphoribosyl transferase (FUR1) are two principal proteins involved in ergosterol biosynthesis and pyrimidine metabolism. However, crystal structures of these proteins from C. auris have not yet been established. We constructed structural model of ERG11 and FUR1 proteins for South-African Clade using homology modelling, molecular docking and molecular dynamics simulations. To investigate how point mutations affect drug interaction, we used the same methods on ERG11 mutants (Y132F, K143R) and FUR1 mutants (F211I). Methodology: Homology modelling was used to construct 3D structure of proteins. Reliability of models was analysed by using validation tools. The drug interaction in wild and mutant variants was studied using molecular docking, and binding energy was ...

COVID-19, a new strain of coronavirus (CoV), was identified in Wuhan, China, in 2019. No specific therapies are available, and investigations regarding COVID-19 treatment are lacking. Crystallised COVID-19 main protease (Mpro), which is a potential drug target. The present study aimed to assess drugs found in literature as potential COVID-19 Mpro inhibitors, using a molecular docking study. Molecular docking was performed using Autodock 4.2, with the Lamarckian Genetic Algorithm, to analyse the probability of docking. The docking was cross-validated using Swiss Dock. COVID-19 Mpro was docked with several compounds, and docking was analysed by Biovia Discovery Studio 2020. Quinine and hydroxychloroquine were used as standards for comparison. The binding energies obtained from the docking of 6LU7, 2GTB with screened drugs viz., Quinine, Artesunate, Clotrimazol, Artemether, Quercetin, Mefloquine, ciprofloxacin, clindamycin, cipargamin, SJ-733 were in between -7.0 to -9.6 kcal/mol. On c...

IntroductionThe concept of personalized medicine in cancer has emerged rapidly with the advancement of genome sequencing and the identification of clinically relevant variants that contribute to disease prognosis and facilitates targeted therapy options. In this study, we propose to validate a whole exome-based tumor molecular profiling for DNA and RNA from formalin-fixed paraffin-embedded (FFPE) tumor tissue.MethodsThe study included 166 patients across 17 different cancer types. The scope of this study includes the identification of single-nucleotide variants (SNVs), insertions/deletions (INDELS), copy number alterations (CNAs), gene fusions, tumor mutational burden (TMB), and microsatellite instability (MSI). The assay yielded a mean read depth of 200×, with >80% of on-target reads and a mean uniformity of >90%. Clinical maturation of whole exome sequencing (WES) (DNA and RNA)- based assay was achieved by analytical and clinical validations for all the types of genomic alte...

Corona is an avian and mammalian Ribovirus which generally evade host immune mechanism hampering respiratory tract of the host. Structurally it has an envelope of protein enclosing a single-stranded positively coiled RNA genome. Coronavirus uses around 4-5 different classes of protein for its replication in the host cell. Due to the high mutation rate of the viral genome development of a vaccine against corona has been a difficult task. In the current scenario, the world is facing a problem with CoViD-19 as the biggest pandemic. Several combinations of drugs like Hydroxychloroquine, Plaquine, Chloroquine, etc. targeting viral protein have been utilized for controlling viral infection. The possibility of insect brain proteins was checked against the selected non-structural proteins of CoViD-19 that take an active role in the replication of the virus in the host. Molecular docking methodology plays an important role in predicting interaction between the insect proteins with non-structural protein (nsp) of coronavirus. The results predict good bonding affinity with possible interaction as hydrogen bond and salt bridge between antibacterial protein and nsp of CoViD-19 indicating as afuture alternative medications.