CoViD-19 Susceptibility.
Abstract There have been over five million cases of infection with the second Corona virus to induce SARS (SARS-CoV2) and close to half a million deaths worldwide since the first report of Corona Virus Disease in late December 2019 (CoViD-19). Over two million CoViD-19 patients have recovered. The factors and variables that lead certain CoViD-19 patients to survive this otherwise aggressive and lethal viral infection are intensely researched, as is the development of productive anti-virals and of safe and effective vaccines. Several hypotheses invoke putative mutations of the ss-positive RNA SARS-CoV2 virus to sta...
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Chiappelli F Tags: Bioinformation Source Type: research

A short note on HBV infection.
Abstract HBV-related liver sickness or hepatocellular carcinoma is common worldwide. Therefore, it is of interest to document the current trends in hepatitis prevention, diagnosis, treatment and care. PMID: 32994674 [PubMed] (Source: Bioinformation)
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Muraleedharan A, Bupesh G Tags: Bioinformation Source Type: research

Critical comments on COViD-19 outbreak: succinct advice for dentists and oral healthcare professionals by Cirillo (2020).
This article informs dental professionals of timely and critical recommendations to keep the practice of dentistry safe for the patients, the staff, the hygienists and the dentists. Teaching of these recommendations are being integrated in the clinical curriculum of pre-DDS and pre-DMD professionals, as well as in dental hygiene and dental assisting schools. The paper provides an essential and clearly-written overview of new mandatory procedures and protocols for the practice of dentistry, which will spread world-wide in the near future. PMID: 32994675 [PubMed] (Source: Bioinformation)
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Kasar VR, Cajulis OS, Chiappelli F Tags: Bioinformation Source Type: research

Controlled drug release for inflammatory bowel disease (IBD).
Abstract Controlled drug release in formulation is an important area of research. Formulations using crospovidone as super-disintegrants to achieve immediate release once it reaches the ileo- cecal region is relevant. The Eudragit L30D pH dependent polymer that allows drug release after a lag time of 4-5 hrs to achieve desired drug release from the drug delivery system is critical. Hence, pre-formulation to study drug-polymer interaction is essential. The linear correlation between the predicted and actual values for all the batches of optimization is shown with high correlation coefficient (r-value). Therefore, t...
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Asha D, Jeganath S, Bupesh G, Sahoo UK, Bhaskar M, Pandian K Tags: Bioinformation Source Type: research

Inhibitory studies of HepG2 and human immune cells using Solanum nigrum.
Abstract It is of interest to document the inhibitory studies of HepG2 and human immune cells using Solanum nigrum. We have assessed the effect of ethanolic extract from Solanum nigrum for antiproliferative on HepG2 and on human PBMC. Treatment with Solanum nigrum separates the cells that are estimated by 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide measure. Results indicated improved cytotoxicity with expanding concentrations of extract. PMID: 32994677 [PubMed] (Source: Bioinformation)
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Kumar AG, Bupesh G, Sankarganesh P, Vasanth S, Nandagopal S, Joseph B Tags: Bioinformation Source Type: research

Comparative molecular docking analysis of the SARS CoV-2 Spike glycoprotein with the human ACE-2 receptors and thrombin.
Abstract Comparative molecular docking and vixualization analysis of the human thrombin with the SARS CoV-2 Spike glycoprotein and the human ACE-2 receptors is of interest. The data shows that residues spanning positions 30-41 in the ACE-2 have interaction with the spike glycoprotein (UniProt ID: Q9BYF1). Results also shows that thrombin binds with SER494 in the spike protein, and GLU37 in the ACE2 receptor. SER494 in the viral receptor-binding domain provides support for hotspot-353 reported elsewhere. These preliminary data provide insights for further probe. PMID: 32994678 [PubMed] (Source: Bioinformation)
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Bhanu P, Kumar NH, Kumar SH, Relekar M, Anand DA, Kumar J Tags: Bioinformation Source Type: research

An ANN model for the differential diagnosis of tuberculosis and sarcoidosis.
Abstract Sarcoidosis is often misdiagnosed as tuberculosis and consequently mistreated owing to inherent limitations in histopathological and radiological presentations. It is known that the differential diagnosis of Tuberculosis and Sarcoidosis is often non-trivial and requires expertise and experience from clinicians. Therefore, it is of interest to describe a multilayer neural network model to differentiate pulmonary tuberculosis from Sarcoidosis using signal intensity data from blood transcriptional microarray. Genes that are significantly upregulated in Pulmonary Tuberculosis and Sarcoidosis in comparison wit...
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Vijayaraj M, Abhinand PA, Venkatesan P, Ragunath PK Tags: Bioinformation Source Type: research

Comparative thermo-stability of two Rift Valley fever virus vaccine candidate CL13T with a recombinant arMP-12 ΔNSm21/384.
Comparative thermo-stability of two Rift Valley fever virus vaccine candidate CL13T with a recombinant arMP-12ΔNSm21/384. Bioinformation. 2020;16(7):547-554 Authors: Daouam S, Boumart Z, Elarkam A, Hamdi J, Tadlaoui KO, Ennaji MM, Harraka M Abstract Rift Valley fever (RVF) is a zoonotic, viral disease, transmitted by mosquitoes, characterized by high mortality rates in young animals. RVF is an endemic and enzootic disease in the Arabian Peninsula and Africa, causing public health and economic instability. Therefore, it is important to develop vaccines to minimize outbreaks and combat the disease...
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Daouam S, Boumart Z, Elarkam A, Hamdi J, Tadlaoui KO, Ennaji MM, Harraka M Tags: Bioinformation Source Type: research

Molecular docking analysis of capsaicin with apoptotic proteins.
We report the molecular binding features of capsaicin with apoptotic proteins such as Bcl-xl, Bcl-2 and Mcl-1 for further consideration. PMID: 32994681 [PubMed] (Source: Bioinformation)
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Roy A, Rasheed A, Sleeba AV, Rajagopal P Tags: Bioinformation Source Type: research

Molecular docking analysis of amyloid precursor protein with compounds from the Australian cowplant.
We report five compounds (Gymnemasaponin 5, Gymnemasin D, Gymnemoside A, Gymnemoside E, Gymnemoside F) derived from the Australian cowplant as the poteinal inhibitors of Amyloid precursor protein with optimal binding features for further consideration. PMID: 32994682 [PubMed] (Source: Bioinformation)
Source: Bioinformation - October 2, 2020 Category: Bioinformatics Authors: Selvaraj J, Sardar H, Vishnupriya V, Balakrishna JP, Mohan SK, Nivedha RP, Vijayalakshmi P, Ponnulakshmi R Tags: Bioinformation Source Type: research

Molecular docking analysis of docetaxel analogues as duel lipocalin 2 inhibitors.
Abstract Lipocalin 2 (Lcn2, also called as neutrophil gelatinase-associated lipocalin) is a member of the lipocalin family and a known target for breast cancer. Therefore, it is of interest to use Docetaxel as a scaffold to design molecules with improved efficiency from naturally derived phytochemicals. We document 10 analogues (4Deacetyltaxol, 7Acetyltaxol, Cabazitaxel, Cephalomannine, Docetaxal, Deacetyltaxol, Docetaxeltrihydrate, Ortataxel, Paclitaxel, Taxoline) having optimal binding with Lipocalin 2 in comparison with Docetaxel. This data is highly useful for consideration in the design and development of dru...
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Ponnulakshmi R, Rekha UV, Padmini R, Perumal S, Saravanan R, Vishnupriya V, Vijayalakshmi P, Selvaraj J Tags: Bioinformation Source Type: research

From sequence analysis of DPP-4 to molecular docking based searching of its inhibitors.
Abstract Literature data suggests that Dipeptidyl peptidase-4 (DPP-4) is a potential target for type 2 Diabetes Mellitus. Therefore, it is of interest to identify new DPP-4 inhibitors using molecular docking analysis. We document compounds such as STOCK1N-98884, STOCK1N-98881, and STOCK1N-98866 with optimal binding features with DPP-4 from the ligand database at https://www.ibscreen.com/ for further consideration. PMID: 32884207 [PubMed] (Source: Bioinformation)
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Alsamghan AS, Alwabli AS, Abadi M, Alsaleem SA, Anbari DM, Alomari AS, Alzahrani O, Alam Q, Tarique M Tags: Bioinformation Source Type: research

Comparative analyses of PAP smear data in pre and postmenopause Indian women.
Abstract PAP smear is one of the best screening tools available for early detection of cervical cancer. Hence, we conducted a retrospective study at the Department of Pathology, Sree Balaji Medical College and Hospital over a period of one year by collecting PAP smear data. A total of 978 smears were collected out of which 59% were premenopausal and 41% were post menopausal women. Data shows that the prevalence of pre malignant and malignant lesions were more among the women of post menopausal age group than the pre menopausal age group. PMID: 32884208 [PubMed] (Source: Bioinformation)
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Kannan A, Kiyam W, Bupesh G, Bhaskar M, Prasaad PR, Rao B Tags: Bioinformation Source Type: research

Molecular docking data of piperine with Bax, Caspase 3, Cox 2 and Caspase 9.
Abstract Several apoptotic signalling proteins such as Bax, Caspase 3, Cox 2 and Caspase 9 are known to be associated with colorectal cancer (CRC). It is of interest to study the interaction of these proteins with piperine a known drug candidate. We document the binding energy, hydrogen bond interaction and hydrophobic interaction between the piperine and apoptotic proteins for further consideration. PMID: 32884209 [PubMed] (Source: Bioinformation)
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Kirubhanand C, Selvaraj J, Rekha UV, Vishnupriya V, Nalini D, Mohan SK, Vijayalakshmi P, Rajalakshmi M, Ponnulakshmi R Tags: Bioinformation Source Type: research

Molecular docking of C-Jun-N-Terminal Kinase (Jnk) with amino-pyrimidine derivatives.
We report the optimal binding features (binding energy, interacting residues, inter atomic hydrogen bonding patterns) of 11 amino-pyrimidine derivatives with Jnk for further consideration. PMID: 32884210 [PubMed] (Source: Bioinformation)
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Meenakumari K, Bupesh G Tags: Bioinformation Source Type: research

Molecular docking analysis of Bcl-2 with phyto-compounds.
We report the optimal binding features of these compounds with Bcl-2 for further consideration towards in vitro and in vivo validation. PMID: 32884211 [PubMed] (Source: Bioinformation)
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Kirubhanand C, Selvaraj J, Rekha UV, Vishnupriya V, Sivabalan V, Manikannan M, Nalini D, Vijayalakshmi P, Rajalakshmi M, Ponnulakshmi R Tags: Bioinformation Source Type: research

Comments on "An insertion unique to SARS-CoV-2 exhibits super antigenic character strengthened by recent mutations" by Cheng MH et al.2020.
Comments on "An insertion unique to SARS-CoV-2 exhibits super antigenic character strengthened by recent mutations" by Cheng MH et al.2020. Bioinformation. 2020;16(6):474-476 Authors: Chiappelli F PMID: 32884212 [PubMed] (Source: Bioinformation)
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Chiappelli F Tags: Bioinformation Source Type: research

Predicted peptide patterns from the SARS-CoV-2 proteome for MS-MS based diagnosis.
Abstract COVID-19 caused by 2019 novel coronavirus (2019-nCoV2) also known as SARS-CoV-2 has manifested globally since January 2020. COVID-19 was declared as a pandemic by the WHO and has become a serious global health concern. Real-time PCR based and antibody-based assays are being used for the clinical detection of the virus in body fluids and nasopharyngeal swabs. Antibody variability linked to viral mutations is a big concern. Hence, it is of interest to use data patterns from mass spectrometry-based platforms for the identification of SARS-CoV-2. This dataset can be used to perform targeted mass-spectrometric...
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Kapoor S, Subba P Tags: Bioinformation Source Type: research

Molecular docking analysis of doronine derivatives with human COX-2.
We report the molecular docking, pharmacophore, ADMET and molecular properties analysis data of doronine and its similar compounds. Docking and ADMET Data shows that COX-2 binds with doronine with optimal features for further consideration. PMID: 32884214 [PubMed] (Source: Bioinformation)
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Hussain S, Guruvayoorappan C, Komal KP, Ennaganti S Tags: Bioinformation Source Type: research

Obesity, gestational weight gain, and polyunsaturated fatty acids profile in pregnant Saudi women.
Abstract Obesity and excessive gestational weight gain (GWG) are associated with a deficiency of essential fatty acids, affecting maternal health during and after pregnancy. Therefore, it is of interest to identify the associations of pre-pregnancy body mass index (BMI) and GWG with lipid profiles in Saudi women after giving birth. Hence, a cross-sectional study of 238 pregnant women aged 20-40 years was conducted at the King Abdul Aziz Hospital, in Al-Ahsa Governorate-Saudi Arabia. Thus, socio-demographic and anthropometric data were collected using a structured questionnaire. Poly-unsaturated fatty acids (PUFAs)...
Source: Bioinformation - September 6, 2020 Category: Bioinformatics Authors: Al-Otaibi H, Hussein N, Mustafa H, Al-Mudaires N Tags: Bioinformation Source Type: research

Molecular docking analysis of piperine with CDK2,CDK4,Cyclin D and Cyclin T proteins.
Abstract Piperine is a component of Piper nigrum (Black pepper). It is well known in ayurvedic formulations. Piperine is a bioenhancer as it reduces the activity of drug-metabolizing enzymes in rodents and thereby enhancing the plasma concentrations of several drugs, including the Pglycoprotein substrates. Therefore, it is of interest to understand the molecular docking interactions of piperine with several cell cycle proteins such as Cyclin dependent kinase 2 (CDK2), Cyclin-dependent kinase 4 (CDK4), Cyclin D and Cyclin T for further consideration in drug discovery related to oral cancer. PMID: 32831516 [Pub...
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Rekha UV, Anita M, Jayamathi G, Sadhana K, Deepa S, Hussain S, Bhuvaneswari J, Ramya V, Selvaraj J, Naveenraj NS Tags: Bioinformation Source Type: research

Male Sterility is linked to the Flavonoid Biosynthesis Pathways in Prunus mira.
We report 566 metabolites in six flower samples and 140 differentially accumulated metabolites (DAMs) between both flower types. Most of the DAMs belong to the phenyl propanoid biosynthesis pathway, particularly flavonoid, flavone and flavonol biosynthesis pathways, implying that alterations in these key pathways link to male sterility in P. mira. The known link between low levels of flavonoid metabolites, weak expression levels of several structural genes from the phenyl propanoid biosynthesis pathway and hyper accumulation of reactive oxygen species were highlighted for understanding the underlying mechanism leading to t...
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Zhang S, Pingcuo G, Ying H, Zhao F, Cui Y, Zeng X Tags: Bioinformation Source Type: research

Towards the design of epitope candidates for Coronavirus 2.
Abstract The severe acute respiratory syndrome coronavirus-2, formerly known as 2019 novel coronavirus, is a pandemic public health threat. This beta coronavirus potentially infects the alveolar cells of the lung leading to pneumonia. The disease may progress into acute respiratory distress syndrome especially in elderly patients with comorbidities. Therefore, it is of interest to design and develop candidates for treatment, therapy and prevention. The spike glycoprotein of the virus known to potentially interact with angiotensin converting enzyme 2 as a cell entry receptor is a suitable candidate for further cons...
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Odhar HA, Ahjel SW, Humadi SS Tags: Bioinformation Source Type: research

Molecular Docking analysis of the TNIK Receptor protein with a potential Inhibitor from the NPACT databas.
Abstract It is of interest to design and develop efficient inhibitors to the TNIK protein target in Wnt signaling pathways in the context of colorectal cancer (CRC) using molecular docking models. We show data to support that a compound named aglafoline (methyl (1R,2R,3S,3aR,8bS)-1,8b-dihydroxy-6,8-dimethoxy-3a-(4-methoxyphenyl)-3-phenyl-2,3-dihydro-1H cyclopenta [b] [1] from the NPACT (Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database) database have optimal binding features with the TNIK receptor for further consideration in this context. PMID: 32831519 [PubMed - as supplied by pu...
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Rosita AS, Begum TN Tags: Bioinformation Source Type: research

Views on GWAS statistical analysis.
Abstract Genome-wide association study (GWAS) is a popular approach to investigate relationships between genetic information and diseases. A number of associations are tested in a study and the results are often corrected using multiple adjustment methods. It is observed that GWAS studies suffer adequate statistical power for reliability. Hence, we document known models for reliability assessment using improved statistical power in GWAS analysis. PMID: 32831520 [PubMed - as supplied by publisher] (Source: Bioinformation)
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Cao X, Xing L, He H, Zhang X Tags: Bioinformation Source Type: research

Putative Natural History of CoViD-19.
Abstract The Severe Acute Respiratory Syndrome Corona Virus2 (SARS-CoV2) is responsible for Corona Virus Disease 2019 (CoViD-19), the pandemic that has afflicted close to two million people worldwide, and has taken the lives of over 120,000 patients since its first report in late December 2019. Per million people globally, the infection rate is close to 250 with a death rate of close to 14 (death rate average global death rate: 6.06%; for comparison, revised estimate of the 1918 influenza pandemic had an average global death rate of 5.4% [1]). About 400,000 SARS-CoV2-positive patients have been declared 'recovered...
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Chiappell F Tags: Bioinformation Source Type: research

Molecular docking analysis of N-substituted Oseltamivir derivatives with the SARS-CoV-2 main protease.
We describe the optimal binding features of Oseltamivir derivatives with the SARS-Cov-2 main protease (Code PDB: 6LU7) for further consideration. PMID: 32831522 [PubMed - as supplied by publisher] (Source: Bioinformation)
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Belhassan A, Chtita S, Zaki H, Lakhlifi T, Bouachrine M Tags: Bioinformation Source Type: research

Molecular docking analysis of Withaferin A from Withania somnifera with the Glucose regulated protein 78 (GRP78) receptor and the SARS-CoV-2 main protease.
Abstract Design and development of an effective compound to combat COVID-19 is clearly critical in the current circumstances. Therefore, it is of interest to document the molecular docking analysis data of the cellular receptor Glucose regulated protein 78 (GRP78) with Withaferin A from Withania somnifera in the context of COVID-19 pandemic for further consideration. Here, we report the optimal interaction features of withaferin A, artemisinin, curcumin and andrographolide with the GRP78 receptor having low binding energies (-8.7, -7.89, -6.21 and -6.17 kcal/mol respectively) in this report. In order to gain addit...
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Sudeep HV, Gouthamchandra K, Shyamprasad K Tags: Bioinformation Source Type: research

The COVID-19 Puzzle.
Abstract Viral diseases have affected humans since the dawn of humanity. Smallpox-now eradicated by vaccinations-serves as a particularly poignant example. More recently, the Spanish flu outbreak claimed a heavy toll in the early 20th century. The ongoing coronavirus pandemic appears no less threatening. The possible reason of highly variable course of disease is discussed. PMID: 32831524 [PubMed - as supplied by publisher] (Source: Bioinformation)
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Konieczny L, Roterman I Tags: Bioinformation Source Type: research

A report on DNA sequence determinants in gene expression.
Abstract The biased usage of nucleotides in coding sequence and its correlation with gene expression has been observed in several studies. A complex set of interactions between genes and other components of the expression system determine the amount of proteins produced from coding sequences. It is known that the elongation rate of polypeptide chain is affected by both codon usage bias and specific amino acid compositional constraints. Therefore, it is of interest to review local DNA-sequence elements and other positional as well as combinatorial constraints that play significant role in gene expression. PMID...
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Singh R, Sophiarani Y Tags: Bioinformation Source Type: research

Comments on Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease by Dai et al.(2020).
PMID: 32831526 [PubMed - as supplied by publisher] (Source: Bioinformation)
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Chiappelli F Tags: Bioinformation Source Type: research

Views on Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease by Dai et al. (2020).
PMID: 32831527 [PubMed - as supplied by publisher] (Source: Bioinformation)
Source: Bioinformation - August 25, 2020 Category: Bioinformatics Authors: Odhar HA Tags: Bioinformation Source Type: research

Towards Neuro-CoViD-19.
Abstract CoViD-19 is the current pandemic caused by the Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2). Infection by SARS-CoV-2 occurs via the binding of its S protein to the angiotensin-converting enzyme-2 receptor (ACE2-R). S binding to ACE2-R leads to a drop in ACE2, a homolog of angiotensin converting enzyme (ACE). In the central nervous system (CNS), ACE mediates neuroinflammation, neurodegeneration and neurotoxicity responsible for several CNS disorders. ACE2 counteracts the damaging effects of ACE on CNS neurons. SARS-CoV-2 can directly access the CNS via the circulation or via cranial nerve ...
Source: Bioinformation - August 13, 2020 Category: Bioinformatics Authors: Chiappelli F Tags: Bioinformation Source Type: research

COVID-19: Reduced Lung Function and Increased Psycho-emotional Stress.
Abstract The COVID-19 outbreak causing reduced lung function and increased psycho-emotional stress in the community worldwide. Therefore, it is of interest to document such viral outbreak related emotional stress data in the community with known molecular and patho-physiological parameters of the affected individuals. We provide a concise, coherent, critical, precise, specific and direct narration of such events from a community research viewpoint using known molecular data in this editorial. PMID: 32773987 [PubMed] (Source: Bioinformation)
Source: Bioinformation - August 13, 2020 Category: Bioinformatics Authors: Wu D, Ellis D, Datta S Tags: Bioinformation Source Type: research

Current Status on Population Genome Catalogues in different Countries.
Abstract Genomics has become indispensable for research in the last two decades. Completed and ongoing genome projects such as the UK Biobank, ICGC, TCGA and GenomeAsia100K have helped to understand several life-threatening diseases like cancer. Such initiatives from different countries have offered genomics-based diagnostics along with glues for therapies towards personalized healthcare. The Indian Agencies has started initiatives to catalogue the genome sequences of 20,000 individuals. The Department of Biotechnology (DBT) along with other scientific agencies has plans to sequence 10,000 healthy individuals and ...
Source: Bioinformation - August 13, 2020 Category: Bioinformatics Authors: Kumar R, Dhanda SK Tags: Bioinformation Source Type: research

Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis.
We report 10 candidates with optimal binding features to the active site of the protease for further consideration as potential drugs to treat patients infected with the emerging COVID-19 disease. PMID: 32773989 [PubMed] (Source: Bioinformation)
Source: Bioinformation - August 13, 2020 Category: Bioinformatics Authors: Hakmi M, Bouricha EM, Kandoussi I, Harti JE, Ibrahimi A Tags: Bioinformation Source Type: research

Design of non-viral vector with improved regulatory features towards therapeutic application.
We describe the design of a non-viral mammalian expression vector in which the primary transgene (a truncated dystrophin gene linked with Duchenne muscular dystrophy (DMD)) named microdystrophin delR4-R23/delCT (MD1) is under the transcriptional control of elements of desmin locus control region (DES-LCR). The designed vector, named as DES-LCR/MD1-EGFP, was constructed by cloning two fragments into the pBluescript backbone. Fragment 1 contains DES-LCR enhancer and DES-LCR promoter region while fragment 2 contains MD1 transgene and reporter EGFP (enhanced green fluorescent protein) gene separated by linker P2A (2A peptide)....
Source: Bioinformation - August 13, 2020 Category: Bioinformatics Authors: Sharma BS, Prabhakaran V, Verma RJ Tags: Bioinformation Source Type: research

Content analysis of vitamins, dietary fibers and amino acids in a wide collection of barley (Hordeum vulgare L.) from Tibet, China.
This study reveals a large nutritional diversity in barley cultivars from Tibet and represents an important reference for the exploitation of these germplasm in crop improvement and breeding programmes. PMID: 32773991 [PubMed] (Source: Bioinformation)
Source: Bioinformation - August 13, 2020 Category: Bioinformatics Authors: Huang H, Gao X, Li Y, Tian P, Nima Y, Laba Z, Ci Z, Wei X, Qu J, Guan W, Liao W Tags: Bioinformation Source Type: research

Modelling, docking and simulation analysis of Bisphenol A interaction with laccase from Trichoderma.
Abstract Fungal laccases are widely known for the degradation of recalcitrant xenobiotic compounds. Hence, it is of interest to study the interaction between laccase from Trichoderma laccase and Endocrine-Disrupting Chemical (EDC) named Bisphenol A. The molecular docking analysis of laccase from Trichoderma laccase with 23 xenobiotics and bisphenol A was completed. We show Bisphenol having optimal binding features (Glide score of -5.44 and the Glide energy -37.65 kcal/mol) with laccase from Trichoderma laccase. PMID: 32773992 [PubMed] (Source: Bioinformation)
Source: Bioinformation - August 13, 2020 Category: Bioinformatics Authors: Ramakrishnan SG, Sivaramakrishnan M, Chenthamara D, Kothandan R, Krishnaswami S, Subramaniam S Tags: Bioinformation Source Type: research

The impact of anthropogenic organic and inorganic pollutants on the Hasdeo River Water Quality in Korba Region, Chhattisgarh, India.
In this study, we assess the impact of organic and inorganic contaminations on Hasdeo River at Korba region, which is fifth critically polluted city in India. Hear, a new approach for water quality indexing like Water quality index (WQI), Heavy metal pollution index (HPI) and metal index (MI) has been proposed to represent pollution due to heavy metals in river system. The sample's pollution parameters and heavy metals contamination is exceed from BIS or WHO standards of drinking water (all p
Source: Bioinformation - August 13, 2020 Category: Bioinformatics Authors: Bhaskar M, Dixit AK, Ojha KK, Dubey S, Singh A, Abhishek A Tags: Bioinformation Source Type: research

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