2019-nCoV - Towards a 4th generation vaccine.
Abstract The first report of the unusual manifestation of pneumonia-like symptoms in Wuhan City, China was made on 31 December 2019. Within one week, the Chinese authorities reported that they had identified the causative agent as a new member of the Coronavirus family, the same family of that was responsible for MERS and SARS not so many years ago. The new virus was called Novel Coronavirus 2019 (2019-nCoV). Three weeks later, the World Health Organization declared that 2019-nCoV was capable of direct human-to-human transmission, the virus had spread across several countries in three continents, and had infected ...
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Chiappelli F Tags: Bioinformation Source Type: research

Classification of thyroid nodules using ultrasound images.
Abstract Medical imaging using image sensors play an essential role in effective diagnosis. Therefore, it is of interest to use medical imaging techniques for the diagnosis of thyroid-linked dysfunction. Ultrasound is the low-cost image processing technique to study internal organs and blood flow in blood vessels. Digital processed images help to distinguish between normal, benign and malignant tissue stages in organs.Hence, it is of importance to discuss the design and development of a computer-aided image-processing model for thyroid nodule identification, classification and diagnosis. PMID: 32405165 [PubMe...
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Manivannan T, Ayyappan N Tags: Bioinformation Source Type: research

GenPop-An Online Tool to Analyze Human Population Genetic Data.
Abstract GenPop is a web based online cross platform tool developed to help Geneticist and Epidemiologist to deal with association studies in analyzing human population genetic data. The tool features include descriptive analysis such as Hardy-Weinberg equilibrium test, chi-square p-value and analysis of single nucleotide polymorphisms (SNPs) with multiple inheritance models such as dominant, recessive, allelic, genotype, odd's ratio and relative risk at 95% confidence interval and analysis of multiple SNPs including haplotype frequencies and linkage disequilibrium for a pair of biallelic markers. This is a user-d...
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Mahesh BA, Kannan E, Davis GDJ, Venkatesan P, Ragunath PK Tags: Bioinformation Source Type: research

Docking analysis of importin-11 homology model with the phyto compounds towards colorectal cancer treatment.
Abstract Colorectal cancer (CRC) is the most familiar malignancy worldwide. Hence, searching for novel therapeutic options is of highest priority. Therefore, it is of interest to design inhibitors to the protein target importin-11, which transports β-catenin linked to colon cancer cells. However, the structure of importin-11 is not known. Hence, we use a homology model of importin-11 to dock potential interactions with five phyto compounds using molecular interaction features for further consideration. PMID: 32405167 [PubMed] (Source: Bioinformation)
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Selvaraj J, Ponnulakshmi R, Abilasha S, Nalini D, Vijayalakshmi P, Vishnupriya V, Mohan SK Tags: Bioinformation Source Type: research

Decoding the vital segments in human ATP-dependent RNA helicase.
We describe the enzyme protein model developed using modeller to identify active site residues. We used consurf to estimate the structural conservation and is evolutionary relationship is inferred using known close sequence homologs. The active site is predicted using castp and its topological flexibility is estimated through cabs-flex. The protein is annotated as a hydrolase using available data and ddx58 is found as its top-ranked interacting protein partner. We show that about 124 residues are found to be highly conserved among 259 homologs, clustered in 7 clades with the active-site showing low sequence conservation. I...
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Kamjula V, Kanneganti A, Metla R, Nidamanuri K, Idupulapati S, Runthala A Tags: Bioinformation Source Type: research

CpGDB : A Comprehensive Database of Chloroplast Genomes.
Abstract Chloroplast Genome Database (CpGDB) is user friendly, web-based, freely available and dynamic relational database which provides a platform for researchers to search and download complete chloroplast genome sequences, individual gene sequences and feature records of plant species belonging to same or different families of spermatophytes. Presently, the database consists of genome sequences, individual gene sequences and feature records of chloroplast genomes of 3823 plant species belonging to 1527 genera from 256 families, which will be updated regularly with the availability of new sequences at NCBI. Ext...
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Singh BP, Kumar A, Kaur H, Singh H, Nagpal AK Tags: Bioinformation Source Type: research

Increased Gonadotropins and prolactin are linked to infertility in males.
Abstract Infertility has become a significant issue among married couples worldwide. The association of variations in reproductive hormones with infertility is evaluated at a tertiary care hospital in North India. A total of 220 infertile males having infertility longer than one year (cases) and 220 age-matched fertile males with confirmed paternity in past two to three years (controls) were enrolled for the study. Serum levels of LH, FSH, testosterone and PRL were measured by Roche e411 autoanalyzer using electrochemiluminescense immunoassay technique. Significant higher levels of serum hormone (mean±SD) w...
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Gangwar PK, Sankhwar SN, Pant S, Krishna A, Singh BP, Mahdi AA, Singh R Tags: Bioinformation Source Type: research

Molecular modeling and docking analysis of aspirin with pde7b in the context of neuro-inflammation.
Abstract The PDE7B gene encodes 3'5'-cyclic nucleotide phosphodiesterase (PDE) and a known target in cognitive impairments. Therefore, it is of interest to design and development of potential inhibitors with PDE7B with improved binding features. We document that the amino acid residues such as H186, K190, and G113 of PDE7B protein showed crucial interactions with aspirin for further consideration in this context. PMID: 32405171 [PubMed] (Source: Bioinformation)
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Balasundaram A, David DC Tags: Bioinformation Source Type: research

Molecular docking analysis of phytochemicals from ethanolic extract of crescentia cujete with the auto inhibited parkin catalytic domain.
We report the docking features of the phytochemical named 1, 2-Ethanediamine, N-(2-aminoethyl) with the target protein for further consideration towards the design and development of anti-Parkinson agents. PMID: 32405172 [PubMed] (Source: Bioinformation)
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Anitha P, Kumar PK, Shanmughavel P, Nazeema TH, Lalitha G Tags: Bioinformation Source Type: research

Linking gut microbiota with the human diseases.
We report a review of known data for the correction of dysbiosis (imbalance in microbe population) towards improved human health. PMID: 32405173 [PubMed] (Source: Bioinformation)
Source: Bioinformation - May 16, 2020 Category: Bioinformatics Authors: Vandana UK, Barlaskar NH, Gulzar ABM, Laskar IH, Kumar D, Paul P, Pandey P, Mazumder PB Tags: Bioinformation Source Type: research

Molecular dynamics analysis of conserved water mediated inter-domain recognition of His667-Trp669 in human ceruloplasmin.
Abstract The human ceruloplasmin (hCP) is the copper containing ferroxidase enzyme with multifunctional activities (NO-oxidase, NO2-synthase,oxidation of neurotransmitters including antioxidants). Therefore, it is of interest to probe the multi-domain hCP using moleculardynamics simulation. Results explain the role played by several conserved water centers in the intra and inter-domain recognition throughH-bond interaction with the interacting residues. We observed seventeen conserved water centers in the inter-domain recognition. Weshow that five invariant water centers W13, W14, W18, W23 and W26 connect the Doma...
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Mukhopadhyay BP Tags: Bioinformation Source Type: research

CoViD-19 Immunopathology and Immunotherapy.
Abstract New evidence on the T-cell immuno-pathology in patient's with Corona Virus Disease 2019 (CoViD-19) was reported by Diao et al. in MedRxiv (doi: 10.1101/2020.02.18.20024364) [1]. It reports observations on 522 patients with confirmed CoViD-19 symptomatology, compared to 40 control subjects. In brief, notable T cytopoenia was recorded by flow cytometry in the CD4+ and the CD8+ populations, which were significantly yet inversely correlated with remarkably increased serum levels of the pro-inflammatory cytokines IL-6, IL-10 and TNF-a. Flow cytometry established a progressive increase in the expression of prog...
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Chiappelli F, Khakshooy A, Greenberg G Tags: Bioinformation Source Type: research

Analysis of predicted proteasomal cleavages in the methyltransferase domain from JEV.
Abstract The methyltransferase (MTase, a 265 amino acid residues long region at the N-terminal end of the viral nonfunctional supermolecule NS5 domain) is key for viral replication in Japanese Encephalitis Virus (JEV). Sequence to structure to functional information with adequate knowledge on MTase from JEV is currently limited. Therefore, it is of interest to document a report on the comprehensive analysis of predicted proteasomal cleavage data in the methyltransferase domain from JEV. This data is relevant in the design and development of vaccine and other therapeutic candidates for further consideration. P...
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Afaq S, Malik A, Akhtar MS, Alwabli AS, Alzahrani DA, Al-Solami HM, Alzahrani O, Alam Q, Kamal MA, Abulfaraj AA, Tarique M Tags: Bioinformation Source Type: research

Analysis of methyltransferase (MTase) domain from Zika virus (ZIKV).
Abstract A comprehensive analysis of methyltransferase (MTase) from Zika virus (ZIKV) is of interest in the development of drugs and biomarkers in the combat and care of ZIKA fever with impulsive joint pain and conjunctivitis. MTase sequence is homologous in several viral species. We analyzed the MTase domain from ZIKV using Bioinformatics tools such as SMART, PROSITE, PFAM, PANTHER, and InterProScan to glean insights on the sequence to structure to function data. We document inclusive information on MTase from ZIKV for application in the design of drugs and biomarkers to fight against the disease. PMID: 3230...
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Afaq S, Atiya A, Malik A, Alwabli AS, Alzahrani DA, Al-Solami HM, Alzahrani O, Alam Q, Kamal MA, Abulfaraj AA, Alhebshi AM, Tarique M Tags: Bioinformation Source Type: research

Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus.
Abstract Design and development of an effective drug to combat the 2019 novel coronavirus remains a challenge. Therefore, it is of interest to study the binding features of 1615 FDA approved drugs with the recently known 2019-nCoV main protease structure having high sequence homology with that from SARS-CoV. We document the binding features of top 10 drugs with the target protein. We further report that Conivaptan and Azelastine are mainly involved in hydrophobic interactions with active site residues. Both drugs can maintain close proximity to the binding pocket of main protease during simulation. However, these ...
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Odhar HA, Ahjel SW, Albeer AAMA, Hashim AF, Rayshan AM, Humadi SS Tags: Bioinformation Source Type: research

Mining of miRNAs from EST data in Dendrobium nobile.
We report 14 potential miRNAs from three ESTs of D. nobile. They belong to 3 miRNA families (miR390, miR528 and miR414) linking to transcription factor regulation, signal transduction, DNA and protein binding, and various cellular processes covering 34 different metabolic networks in KEGG. These results help in the understanding of miRNA-mRNAs functional networks in Dendrobium nobile. PMID: 32308267 [PubMed] (Source: Bioinformation)
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Krishnatreya DB, Baruah PM, Dowarah B, Bordoloi KS, Agarwal H, Agarwala N Tags: Bioinformation Source Type: research

Distinctive features gleaned from the comparative genomes analysis of clinical and non-clinical isolates of Klebsiella pneumoniae.
Abstract It is of interest to describe the distinctive features gleaned from the comparative genome analysis of clinical and non-clinical isolates of Klebsiella pneumoniae. The core genome of K. pneumoinae consisted of 3568 genes. Comparative genome analysis shows that mdtABCD, toxin-antitoxin systems are unique to clinical isolates and catB, benA, and transporter genes for citrate utilization are exclusive to non-clinical isolates. We further noted aromatic compound degrading genes in non-clinical isolates unlike in the later isolates. We grouped 88 core genes into 3 groups linked to infections, drug-resistance o...
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Rajkumari J, Chakraborty S, Pandey P Tags: Bioinformation Source Type: research

A comparative study of antibacterial and antifungal activities of extracts from four indigenous plants.
In this study, we assessed comparative antibacterial and antifungal effects of extracts from four Indigenous plants (Nerium sp; Mentha sp; Aloe vera and Eucalyptus sp). Total phenolic and flavonoid content were extracted by microwave-assisted extractor and used for phytochemical assay. Antimicrobial experiment was done by micro dilution technique. A post hoc analysis inbuilt with one-way ANOVA test was used for the compilation of antibiotic sensitivity data and percent inhibition. Total phenolic content was significantly high in Mentha sp. and low in Nerium sp. (All p
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Mehta R, Dhruv S, Kaushik V, Sen KK, Khan NS, Abhishek A, Dixit AK, Tripathi VN Tags: Bioinformation Source Type: research

Towards the revival of oscillation from complete cessation in stochastic systems for application in molecular biology.
Abstract Delay and noise are inevitable in complex systems that are common in biochemical networks. The system is often disturbed at various states irrespective of the size (small or large) of delay and noise. Therefore, it is of interest to describe the significance of delay and noise in stochastic Willamowski-Rossler chemical oscillator model using a delay stochastic (having random probability distribution) simulation algorithm. Oscillating dynamics moves to stable fixed point when delay at a fixed magnitude of noise drives the system from oscillating state to stochastic amplitude death state (complete cessation...
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Singh SN, Malik MZ, Singh RB Tags: Bioinformation Source Type: research

Molecular docking analysis of alkaloid compounds with beta-catenin towards the treatment of colon cancer.
In this study, we report the molecular docking analysis of alkaloid compounds (aristolochicacid, cryptopleurine, demecolcine, fagaronine and thalicarpine) with beta-catenin for further consideration towards the design and development of potential inhintors for the treatmnet of colon cancer. PMID: 32308271 [PubMed] (Source: Bioinformation)
Source: Bioinformation - April 22, 2020 Category: Bioinformatics Authors: Ponnulakshmi R, Vishnupriya V, Mohan SK, Abilasha S, Ramajayam G, Vijayalakshmi P, Rajalakshmi M, Selvaraj J Tags: Bioinformation Source Type: research

Drug Discovery: Today and Tomorrow.
Abstract Drug discovery continues to underperform relative to unmet medical need. Driven by profit not societal need, the search for new drugs is neither properly funded nor sufficiently systematic. Many innovative approaches are significantly underused yet extant methodology is replete with problems. In and of itself, technical innovation is unlikely to fulfill the potential of drug discovery if the supporting infrastructure remains unchanged. PMID: 32025152 [PubMed] (Source: Bioinformation)
Source: Bioinformation - February 8, 2020 Category: Bioinformatics Authors: Flower DR Tags: Bioinformation Source Type: research

Metascience in Bioinformation.
Abstract Metascience refers to the systematic process that uncovers, builds, evaluates, organizes and disseminates scientific advances. It is the principal tool at the disposal of the society to combat the debilitating effects of "false information" on health related data and its constituents. PMID: 32025153 [PubMed] (Source: Bioinformation)
Source: Bioinformation - February 8, 2020 Category: Bioinformatics Authors: Khakshooy A, Bach Q, Kasar V, Chiappelli F Tags: Bioinformation Source Type: research

Revisiting the Micropipetting Techniques in Biomedical Sciences: A Fundamental Prerequisite in Good Laboratory Practice.
Abstract The underlying technical and operational knowledge of micro-pipetting is essential for scientists, technicians, and students to achieve precise results from their experiments in Biomedical Sciences and other related disciplines. Since it is one of the crucial prerequisites for Good Laboratory Practices (GLPs), the key fundamentals of the micro-pipetting methods, such as forward and reverse pipetting and the importance of ergonomics and maintenance etc., are revisited in this Editorial report. PMID: 32025154 [PubMed] (Source: Bioinformation)
Source: Bioinformation - February 8, 2020 Category: Bioinformatics Authors: Pushparaj PN Tags: Bioinformation Source Type: research

Bioinformatics drives discovery in Biomedicine.
Abstract Bioinformatics has evolved from providing basic solutions, such as sequence alignment, structure predictions, and phylogenetic analysis to an independent data-driven field. The unprecedented growth of genomic technologies and the enormous data have opened an avenue for bioinformaticians (Bioinformatics professionals) never been seen before in the history of mankind. The novel opportunity also requires creative solutions that need skills to deal with noisy, unstructured information to offer valuable biological insights. Currently, we are seeing only the tip of an iceberg and the future will revolve around ...
Source: Bioinformation - February 8, 2020 Category: Bioinformatics Authors: Gujar R, Panwar B, Dhanda SK Tags: Bioinformation Source Type: research

Gaining new insights on the Hsp90 regulatory network.
Abstract The heat shock protein Hsp90 is a molecular chaperon that uses ATP and interacts with various co-chaperone proteins, acting as adapters, in order to carry out the maturation of its target proteins. In physiological conditions, the heat shock proteins (HSPs) favour post-translational modification, protein folding and sub-cellular transport of their "client" proteins. In stress conditions, many misfolded proteins accumulate exposing their hydrophobic residues and these are recognized by HSPs which prevent the aggregation and favour the correct folding. In case this is no longer possible, HSPs medi...
Source: Bioinformation - February 8, 2020 Category: Bioinformatics Authors: Piva F, Cecati M, Giulietti M Tags: Bioinformation Source Type: research

Identification of tunnels as in potato hydrolases.
Abstract Enzymes with an active center hidden in the middle of the molecule in a tunnel-like cavity constitute an interesting object of analysis due to the highly specialized environment for the course of the catalytic reaction. Identifying the tunnel is a challenge in itself. Moreover, the structural conditioning for the course of the reaction provides information on the diversity of the environment, which must necessarily meet the conditions of high specificity. The use of a fuzzy oil drop model to identify residues constituting the walls of the tunnel located in the center of the protein seems highly justified....
Source: Bioinformation - February 8, 2020 Category: Bioinformatics Authors: Banach M, Piotr F, Katarzyna S, Leszek K, Roterman I Tags: Bioinformation Source Type: research

Impact of airway dysfunction on dental health.
Abstract The airway encompasses the mouth, jaw, nasal passages, tongue, and throat. Dentists in collaboration with other health professionals can recognize the early signs of the disorder, perform proper assessment of facial and dental structures, and provide treatment to help prevent and manage the dysfunction. Therefore, it is of interest to discuss the impact of airway development and dysfunction on dental health. PMID: 32025158 [PubMed] (Source: Bioinformation)
Source: Bioinformation - February 8, 2020 Category: Bioinformatics Authors: Tamkin J Tags: Bioinformation Source Type: research

Importance of customized (task oriented) software tools for biomedical applications.
Abstract Biomedical scientists and clinicians often require customized and user-friendly software tools due to the unavailability of specific software, complexity of existing software or high cost of commercial software. This editorial provides a short update on recently published task-oriented biomedical software tools. The novelty and applications of some customized software tools including CALCFISHER, CALCNTCP, CALCDOSE, and SCEW are also summarized in this editorial. PMID: 32025159 [PubMed] (Source: Bioinformation)
Source: Bioinformation - February 8, 2020 Category: Bioinformatics Authors: Khan HA Tags: Bioinformation Source Type: research

Science for service in a society is the success story of scientists with serenity.
Abstract Available data on science is constantly gleaned for gathering valuable information to create concise yet precise knowledge on specific subjects (especially, the biology oriented agriculture and biomedicine) for service in the society. These sacrifices surmounts as success stories for scientists worldwide. Data in the form of known literature plays a radical role in serving the society with improved infrastructure and facilities making associated resources available, accessible and affordable. This is possible by making known literature available and accessible for application in a modern economy dominant ...
Source: Bioinformation - February 8, 2020 Category: Bioinformatics Authors: Kangueane P, Pavithra S Tags: Bioinformation Source Type: research

Data enabled prediction analysis assigns folate/biopterin transporter (BT1) family to 36 hypothetical membrane proteins in Leishmania donovani.
Abstract Leishmaniasis is a neglected tropical disease caused by the pathogenic protozoan Leishmania donovani and it is transmitted by an infected sand fly. Approximately 0.4 million cases of Visceral Leishmaniasis are reported across the globe every year, of which 67% is from the Indian subcontinent. The currently available drugs have not been effective owing to their high toxicity levels, inadequate specificity, drug resistance, extended treatment periods and/or prohibitive prices. For this reason, hypothetical proteins in this pathogen, which constitute about 67% of its proteome, must be distinctly characterize...
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Ravooru N, Paul OS, Nagendra HG, Sathyanarayanan N Tags: Bioinformation Source Type: research

Combined e-pharmacophore based screening and docking of PI3 kinase with potential inhibitors from a database of natural compounds.
Abstract Phospho inositide 3-kinase (PI3 K) is a promising target for the design of anticancer drugs and is of significant concern in developing selective isoforms as inhibitors for cancer treatments. The results obtained from the computational analysis were selected based on Glide score and drug binding interaction features. Molecular docking studies and prime MM-GBSA energy calculations showed STOCK1N-77648 with optimal binding features for further consideration. The hydrogen bonding patterns between the top three molecules STOCK1N-91335, STOCK1N-70036 and STOCK1N-77648 and the target protein based on G-scores i...
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Eda SR, Jinka R Tags: Bioinformation Source Type: research

The combined effect of Trigonella foenum seeds and Coriandrum sativum leaf extracts in alloxan-induced diabetes mellitus wistar albino rats.
Abstract Diabetes mellitus is a group of heterogeneous disorders commonly presenting with episodes of hyperglycemia and glucose intolerance, as a result of lack of insulin, ineffective insulin action, and/or both. It is our interest to study the effect of ethanolic extract of Trigonella foenum seeds (fenugreek) and Coriandrum sativum leaves (dhaniya) or its combination in alloxan induced diabetes mellitus wistar albino rats. Rats were randomly separated into six groups where group 1 animals received 2% acacia, group 2 animals received alloxan dose of 150 mg/kg, group 3 animals received glibenclamide dose of 0.5 mg...
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Yella SST, Kumar RN, Ayyanna C, Varghese AM, Amaravathi P, Vangoori Y Tags: Bioinformation Source Type: research

Effect of non-synonymous SNP on JAK1 protein structure and subsequent function.
We report 3 deleterious nsSNPs (F78L, Q644R and S646F) in the coding region of JAK1 with predicted structure and function linking to diseases. However, further studies are needed to validate this preliminary observation. PMID: 31831954 [PubMed] (Source: Bioinformation)
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Liza R, Tanima S, Tahsin N, Reaz MM Tags: Bioinformation Source Type: research

Molecular docking analysis of zanamavir with haem agglutinin neuraminidase of human para influenza virus type 3.
Abstract The human para influenza virus (HPIV) type 3 is an imperative respiratory virus which cause upper and lower respiratory infections. The receptor involved in the viral infection is haem agglutinin neuraminidase. It is of interest to study the interaction of haem agglutinin neuraminidase with zanamavir (4-GU-DANA), a known antiviral drug. We used the PDB structures with PDB IDs 1V2I, 1V3B, 1V3D and 1V3E for studying the interactions with zanamavir. The binding features of zanamavir with 1V2I (1.41kcal/mol) and 1V3E (11.81kcal/mol) having optimal interactions is reported for further consideration. PMID:...
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Indumathi CP, Bupesh G, Vasanth S, Senthilkumar V, Anandh AV, Pandian K Tags: Bioinformation Source Type: research

Linking Helicobacter pylori with gallbladder and biliary tract cancer in Moroccan population using clinical and pathological profiles.
Abstract It is of interest to assess the clinical and pathological aspects of Gallbladder and biliary tract carcinomas confirmed by histological data. It is also of further interest to evaluate the link between Helicobacter pylori and biliary tract cancers. Eighty-nine (89) cases (mean age 60±12 years) of Gallbladder and biliary tract cancer confirmed by histological data were enrolled for the study at the Department of Pathology in Mohammed VI University Hospital, in Morocco. The data such as age, sex, clinical and histo pathological features were collected. Bile duct specimens were investigated for H. pyl...
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Cherif S, Rais H, Hakmaoui A, Sellami S, Elantri S, Amine A Tags: Bioinformation Source Type: research

Molecular docking based virtual screening of carbonic anhydrase IX with coumarin (a cinnamon compound) derived ligands.
We report ligands #41, #42, #19 and #15 showed good docking score, glide energy and hydrogen bond interactions without vdW clash. We further show that N-(3,4,5-trimethoxy-phenylcarbamoylmethyl) designated as compound #41 have the highest binding energy (-61.58) with optimal interactions with the catalytic residues (THR 199, PRO 201, HIS 119, HIS 94) of CAIX. PMID: 31831957 [PubMed] (Source: Bioinformation)
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Meenakumari K, Bupesh G, Vasanth S, Vasu CA, Pandian K, Prabhu K, Prasath S Tags: Bioinformation Source Type: research

Insights from molecular dynamics simulation of human ceruloplasmin (ferroxidase enzyme) binding with biogenic monoamines.
Abstract Human ceruloplasmin (hCP) is a multi-copper oxidase with ferroxidase and amine oxidase activities. Molecular dynamics simulation (MDS) and docking analysis of biogenic monoamines with ceruloplasmin explain the role of Asp1025, Glu935, Glu272, Glu232 and Glu230 together with the binding site water molecules (referred as conserved water molecules) in the stabilization of neurotransmitter (Serotonin, Norepinephrine and Epinephrine) molecules within the binding cavity of hCP. Conserved water molecules are found at specific positions interacting with the protein structures that have sequence similarity. The et...
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Mukhopadhyay BP Tags: Bioinformation Source Type: research

From EST to structure models for functional inference of APP, BACE1, PSEN1, PSEN2 genes.
Abstract Successive oxidative stress and biochemical changes results in neuronal death and neuritic plaques growth in Alzheimer's disease (AD). Therefore, it is interest to analyze amyloid-βeta precursor protein (APP), beta-secretase 1 (BACE1), presenilin (PSEN1 and PSEN2) genes from brain tissues to gain insights. Development of potential inhibitors for these targets is of significance. EST sequences of 2898 (APP), 539 (BACE1), 786 (PSEN1) and 314 (PSEN2) genes were analyzed in this study. A contig sequences with APP (contigs 1-4), BACE1 (contigs 5-7), PSEN1 (contigs 8, 9, 10, 11), PSEN2 (contigs 13, 14) exc...
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Aathi M, Piramanayagam S Tags: Bioinformation Source Type: research

Detection and analysis of stable and flexible genes towards a genome signature framework in cancer.
Abstract Comparison and detection of stable cancer genes across cancer types is of interest. The gene expression data of 6 different cancer types (colon, breast, lung, ovarian, brain and renal) and a control group from The Cancer Genome Atlas (TCGA) database were used in this study. The comparison of gene expression data together with the calculation standard deviations of such data was completed using a statistical model for the detection of stable genes. Genes having similar expression (referred as flexible genes) pattern to the control group in four out of six cancer types are PATE, NEUROD4 and TRAFD1. Moreover...
Source: Bioinformation - December 14, 2019 Category: Bioinformatics Authors: Sehovic E, Hadrovic A, Dogan S Tags: Bioinformation Source Type: research

Virtual screening,docking and molecular dynamics simulation of selected phytochemical compounds bound to receptor tyrosine kinases:A correlative anti angiogenic study.
Abstract Screening of phytochemicals for their anti angiogenic potential has been a growing area of research in the current decade. The following study proposes virtual screening, drug likeliness and ADME filtering of specific phytochemical based compounds retrieved from "TIP - A Database of Taiwan Indigenous Plants". The study further subjects the filtered phytochemicals for their molecular docking analysis and molecular dynamics simulation studies against the prominent receptor tyrosine kinases EGFR, VEGFR-1 and VEGFR-2 involved in angiogenesis phenomenon. Among the various in silico analysis done and ...
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Saxena G, Akhtar S, Sharma N, Sharma M, Siddiqui MH, Khan MKA Tags: Bioinformation Source Type: research

Identification and analysis of pathogenic nsSNPs in human LSP1 gene.
Abstract LSP1 (Lymphocyte-specific protein 1) protein plays an important role in neutrophil motility, fibrinogen matrix proteins adhesion, and trans-endothelial migration. Variation in the LSP1 gene is associated with leukemia and lymphomas in tumor cells of Hodgkin's disease and breast cancer. Despite extensive study on the human LSP1, a comprehensive analysis on the Single Nucleotide Polymorphism (SNPs) of the gene is not available. Therefore, it is of interest to identify, collect, store and analyze the SNPs of the LSP1 gene in relation to several known diseases. Hence, the SNP data (398 rsids) from dbSNP datab...
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Ali HM Tags: Bioinformation Source Type: research

Molecular docking enabled updated screening of the matrix protein VP40 from Ebola virus with millions of compounds in the MCULE database for potential inhibitors.
We report a candidate lead (compound #5: ((10R)-10-(4-hydroxyphenyl)-11,12,14,16-tetraazatetracyclo[7.7.0.02,7.011,15] hexadeca-1(16), 2(7),3,5,8,12,14-heptaen-8-ol)) with high drug-likeness score, promising lead-likeness behaviour and high median lethal dose. The candidate lead compound #5 engages in hydrogen bonding and hydrophobic interactions with VP40 active site residues. Thus, the lead compound #5 is recommended for further in vitro and in vivo validations for further consideration. PMID: 31787811 [PubMed] (Source: Bioinformation)
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Odhar HA, Rayshan AM, Ahjel SW, Hashim AA, Albeer AAMA Tags: Bioinformation Source Type: research

Differential prolactin levels among male and female patients with thyroid related complains in the Hail regions of Saudi Arabia.
Abstract Thyroid diseases are caused by autoimmunity due to hormone imbalance both in male and female patients. Therefore, it is of acute importance to measure, analyze and compare thyroid hormone levels among populations with thyroid-related complications. Hence, we examined 202 male and female thyroid patients in the Hail regions of Saudi Arabia and estimated their hormone levels. Blood samples were collected from patients and processed for the hormonal profiling such as prolactin, luteinizing hormone (LH), FSH, free T3 (FT3), free T4 (FT4) and TSH3. Further, measurement of thyroid gland size in the Hail populat...
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Ahmed GME, Alcantara JC, Alharbi SA, Alshammari WM, Alshammari FD, Elnaem IS, Hassan AOA, Alrashedi KS, Tayyar AAA, Alreshidi TAK Tags: Bioinformation Source Type: research

Characterization of influenza A(H1N1)pdm09 isolates of Peru using HRM, a post PCR molecular biology method.
Abstract Influenza caused by A(H1N1)pdm09 is a public health issue with severe conditions in vulnerable populations leading to death. Therefore, it is of interest to characterize and monitor influenza A(H1N1)pdm09 genotypes using High Resolution Melting (HRM), a post PCR molecular biology method. We used HRM analysis (using RotorGene Q thermocycler) to characterize A(H1N1)pdm09 genotypes from several places of Peru. RNA was purified from nasal and pharyngeal swab samples referred to LRNVR-INS, synthesized cDNA, and then the hemagglutinin gene and matrix fragment were amplified. Thus, 287 samples positive for influ...
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Lope P, Maribel H, Egma M, Henri B, Carlos P Tags: Bioinformation Source Type: research

Molecular docking analysis of flavonoid compounds with HIV-1 Reverse transcriptase for the identification of potential effective inhibitors.
Abstract It is of interest to elucidate the binding mode analysis of 18 sulphonated flavones in the non nucleoside inhibitory binding pocket of the HIV-1 reverse transcriptase (PDB ID: 1RTD). We further compared them with the known Non Nucleosidic Reverse Transcriptase Inhibitors (NNRTI) drug molecules such as delaviridine, nevirapine and etravirine. Molecular docking studies of sulphonated flavones were performed in the binding pocket of reverse transcriptase using the PatchDock server. The flavones have different binding energies with RT and the atomic contact energy (ACE) value of sulfonated flavones range from...
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Alaoui MAE, Fartah SE, Alaoui N, Fahime EME, Habsaoui A Tags: Bioinformation Source Type: research

Effect of Myristica fragrans extract on total body composition in cafeteria diet induced obese rats.
Abstract It is of interest to evaluate the effect of Myristica fragrans on body composition of cafeteria diet induced obese rats. Thirty rats (150-160g) grouped into 5 and each group contains 6 rats. Group-1 was normal control and 2-5 groups were fed with cafeteria diet for 15 weeks to induce obesity. From 16th week to 25th week test drugs were given as mentioned in the experimental protocol. Body weight, BMI, changes in body composition was measured by TOBEC, adipose tissue weights, organ weights, abdominal circumference were measured according to standard methods. After 70days of treatment with MFE 200mg/kg, 400...
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Yakaiah V, Dakshinamoorthi A, Kavimani S Tags: Bioinformation Source Type: research

Insights into evolutionary interaction patterns of the 'Phosphorylation Activation Segment' in kinase.
Abstract We are interested in studying the phosphorylation of the kinase activation loop, distinguishing the passage from the unphosphorylated to the phosphorylated form without allostery. We performed an interaction study to trace the change of interactions between the activation segment and the kinase catalytic core, before and after phosphorylation. Results show that the structural changes are mainly due to the attraction between the phosphate group and guanidine groups of the arginine side chains of RD-pocket, which are constituted mainly of guanidine groups of the catalytic loop, the β9, and the αC...
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Ahiri A, Garmes H, Podlipnik C, Aboulmouhajir A Tags: Bioinformation Source Type: research

Analysis of glycoside hydrolases from oat (Avena sativa) seedling extract.
In this study, we characterized novel sequences of class I chitinases from seedlings extract of the common oat (Avena sativa L.) using proteomics and sequence-structure-function analysis. These enzymes, which belong to the GH19 family of protein, were extracted from oat and identified using SDS-PAGE, trypsin digestion, LC-MS-MS, and sequence-structure-function analysis. The amino acid sequences of the oat tryptic peptides were used to identify cDNAs from the Avena sativa databases of the expressed sequence tags (ESTs) and transcriptome shotgun assembly (TSA). Based upon the Avena sativa sequences of ESTs and TSA, at least ...
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Halima NB Tags: Bioinformation Source Type: research

Genome wide identification and functional assignments of C2H2 Zinc-finger family transcription factors in Dichanthelium oligosanthes.
Abstract Transcription factors (TFs) are biological regulators of gene function in response to various internal and external stimuli. C2H2 zinc finger proteins (C2H2-ZFPs) are a large family of TFs that play crucial roles in plant growth and development, hormone signalling and response to biotic and abiotic stresses. While C2H2-ZFPs have been well characterized in many model and crop plants, they are yet to be ascertained in the evolutionarily important C3 plant Dichanthelium oligosanthes (Heller's rosette grass). In the present study, we report 32 C2H2-ZF genes (DoZFs) belonging to three different classes-Q type,...
Source: Bioinformation - December 4, 2019 Category: Bioinformatics Authors: Mahapatra M, Mahanty B, Joshi RK Tags: Bioinformation Source Type: research

Phyllanthus amarus protects against spatial memory impairment induced by lipopolysaccharide in mice.
Abstract Phyllanthus amarus Schumach. and Thonn. is a wide spread medicinal herb with various traditional uses. It is well documented for its antioxidant, anti-inflammatory, and hepatoprotective activities. Therefore, it is of interest to evaluate the 80% ethanol extract of Phyllanthus amarus (PA) on spatial memory using the 8-radial arm maze (8-RAM) in mice after induction of neuro inflammation by lipopolysaccharide (LPS) in a 14- and 28-days treatment study. LC-MS/MS was performed to profile the chemical composition in PA extract. Mice were treated orally with 5% v/v tween 20, PA extract (100, 200 and 400 mg/kg)...
Source: Bioinformation - November 14, 2019 Category: Bioinformatics Authors: Alagan A, Jantan I, Kumolosasi E, Azmi N Tags: Bioinformation Source Type: research