Structural Modeling and Validation of Rep protein of Begomovirus Strains (TLCBV and TYLCTHV)

Homology modeling involves taking a known sequence with an unknown structure and mapping it against a known structure of one or several similar (homologous) proteins. It would be expected that two proteins of similar origin and function would have reasonable structural similarity. Therefore it is possible to use the known structure as a template for modeling the structure of the unknown structure. Proteins that share the same function generally have similar structures. During alignment if two proteins show maximum sequence identity they also show a similar folding pattern. This principal has became the foundation of homology modeling. 
The Geminivirus taxonomic group of plant viruses is characterized by geminate particles and genomes consisting of single-stranded circular DNA molecules of about 2.5 to 2.8 kb in size. Agricultural plants are threatened by many diseases caused by whitefly-transmitted geminiviruses. Since these diseases are in a fast spreading phase, it is urgent to devise rapid diagnosis methods and to produce resistant plants. 
&#xa

In Silico Characterization of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A Proteins

We retrieved six protein sequences of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A [FJ345402] from GenBank-NCBI (ACJ03821, ACJ03822, ACJ03823, ACJ03824, ACJ03825 and ACJ03826) which were used for computational modeling structure prediction. Ramachandran plot of ACJ03826-AC4 had maximum 73.3% and ACJ03822-AV1 had 71% residues in core region therefore these models cannot be placed in a good quality category. ACJ03824-AC2 had only 18.6% residues in core and 13.6% residues in disallowed regions and therefore it was the least stable protein. Verify-3D graph profile scores for selected ToLCJV proteins were greater than zero. Therefore all the verify-3D graph corresponds to an acceptable environment for the model. Findings of the present study provide a base for docking and In-Silico anti-Begomoviral compound designing

Characterization of SARS-CoV-2 Isolate (MZ558159) Reported from India for in Silico Drug Designing

Background & Aims: There is inadequate information available about the genomics and proteomics characterization of SARS-CoV-2 isolates reported from India and other part of the globe. This characterization is important for the in-silico drug designing, as there are no approved medications available to treat SARS-CoV-2 infection. The present study based on the characterization of SARS-CoV-2 (MZ558159) isolate reported from India using homology modeling, validation, and in silico drug designing methods. Materials & Methods: Genome sequence of SARS-CoV-2 (MZ558159) was retrieved from NCBI, and four protein sequences e.g., QXN18496, QXN18498, QXN18504, and QXN18497 were selected for the homology modeling, validation, and in silico drug designing. SWISS-MODEL and UCLA-DOE server were used for homology modeling. Validation for structure model performed using PROCHECK and molecular docking using MCULE-1-Click server. Results: The surface glycoprotein (QXN18496) model corresponding to probability conformation with 93.6%, envelope protein (QXN18498) with 88.9%, nucleocapsid phosphoprotein (QXN18504) with 93.6%, and ORF3a protein (QXN18497) with 91.8% residues in core section of φ-ψ plot that specifies accuracy of prediction models. The corresponding ProSA Z-score score -12.67, -0.01, -4.4, and -2.87 indicates the good quality of the models. Molecular dynamic simulation and docking studies revealed that inhibitor binds effectively at the SARS-CoV-2 (MZ558159) proteins. Predicted inhibitor 2-acetamido-2-deoxy-beta-D-glucopyranose exhibited effective binding affinity against surface glycoprotein (QXN18496). Conclusion: The results of this study established inhibitor 2-Acetamido-2-deoxy-beta-D-glucopyranose as valuable lead molecule with great potential for surface glycoprotein (QXN18496)

Analysis the Effectiveness of Remdesivir, Galidesivir, Sofosbuvir, Tenofovir and Ribavirin as Potential Therapeutic Drug target against SARS-Cov-2 RNA-Dependent RNA Polymerase (RdRp): An in Silico Docking Study

Background & Aims:  The active site of RdRp-CoV is highly conserved, with two successive and surface-accessible aspartates in a beta-turn structure. Antiviral drugs Remdesivir, Galidesivir, Tenofovir, Sofosbuvir, and Ribavirin are known as inhibitors of RdRps, while lopinavir and rotinavir are known inhibitors of main protease (MPro) of coronavirus. The aim of the present study was to in silico test of the effectiveness of anti-polymerase drugs against SARS-CoV-2 RdRp, including 5 FDA-approved antiviral medications. Materials & Methods:  RdRp-CoV (nsp12) plays an important role in virus replication; therefore, it serves as a target to development of antiviral drugs. In this study, the RdRp is modeled, validated, and then targeted using different anti-polymerase drugs that approved for use against various viruses. Results:  The five approved drugs (Galidesivir, Remdesivir, Tenofovir, Sofosbuvir, and Ribavirin) were able to bind the SARS-CoV-2 RdRp with binding energies of 42.6, 1.7, 38.4, -1.4, and -3.9 kcal/mol, respectively. For the drug ribavirin, the only interactions established upon docking were the 11 H-bonds with F165, N459, R624, P677, N791, L460, N791, T462, N628, and T462 of the SARS-CoV-2 RdRp. Conclusion:  The results suggest the effectiveness of Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir as potent drugs against RdRp-CoV since they tightly bind to RdRp. The availability of FDA-approved anti-RdRp drugs can help treat the infection of new variant of SARS-CoV-2 strain specifically

Combined Effect of Vitamin C and E Dose on Type 2 Diabetes Patients

Abstract Diabetes is a metabolic disorder that causes vascular complications. As vitamin C and E is known for its beneficial effects on blood sugar, serum lipids and glycated haemoglobin (HbA1c). In the present study, we assess the combined effect of vitamin C and E on blood sugar (FBS), serum creatinine (SC), total cholesterol (TC), low and high density lipoprotein (LDL, HDL), and glycated haemoglobin (HbAIc) in type 2 diabetes mellitus patients. A total of 50 patients with type 2 diabetes referred to Rama Hospital (NCR), India, were included in the study. They received 500 mg daily twice of both vitamin C and E for 4 months. Fasting blood sugar (FBS), serum creatinine (SC), total cholesterol (TC), low and high density lipoprotein (LDL, HDL), and HbAIc were measured before and after vitamin C and E consumption and the results were analyzed. A significant decrease in FBS, TC level and non-significant decrease in SC, LDL, and HbA1c level was seen in the patients supplemented with 500 mg of both vitamin C and E twice in a day for 4 months. Results indicate that daily consumption of 500 mg of vitamin C and E for 4 months may be beneficial for decreasing the FBS, TC, SC, LDL, and HbA1c and slight raise in HDL and calcium level in patients with type II diabetes and thus reducing the risk of complications

EVALUATION OF SOME MINERALS AND VITAMINS IN CORD BLOOD FROM RURAL AND URBAN POPULATION OF UDAIPUR REGION

Objective: Vitamins and minerals collectively referred to as micronutrients have important influence on the health of pregnant women and the growing fetus. Pregnancy is related to increase demand of all nutrients and deficiency any of these can affect pregnancy, delivery, and outcome of pregnancy. Disorders in mineral element nutrition and metabolism can lead to wide variety of malformations. Data on mineral values in newborn are very less in contrast to adult. The present study was planned to analyze some of minerals in the umbilical cord blood of rural and urban population and compare them gender wise. Methods: Our study group consisted of 640 healthy term newborn. The cord blood was collected immediately after a normal delivery. The blood was tested to determine calcium (Ca), magnesium (Mg), Phosphorus (P), Iron (Fe), Vitamins D3, and Vitamin B12. Results: The results showed that the levels of Ca, Mg, P and Fe, Vitamin D3, and Vitamin B12 were higher in urban population than rural ones. All were statistically significant. The levels of Mg, P, Fe, and Vitamin B12 were lower in female urban neonates as compared to male urban neonates. All were significant when compared sex wise. The trend was same with increased levels of Mg, P, Fe, and Vitamin B12 in females of rural population than cord blood of male rural neonates. Conclusions: The result showed that rural and urban population also female and male neonates have genetic variation and difference in mineral metabolism

Preparation and Characterization of HgO and AgO Added La2CaBa2Cu5Oz Superconductors

We have prepared a series of La2CaBa2Cu5O (z) (La2125) compounds by the standard solid-state reaction method. The oxygen stoichiometry in this R-123 type compound has been homogenized by two different methods. The first method is heating the sample in flowing oxygen at 500 A degrees C for 6 hours and then slowly cooling to room temperature. The second method is to provide internal oxygen while sintering the sample by adding HgO or AgO. The addition of HgO or AgO in preparing oxide superconductors is advantageous when preparing them in bulk quantities, as HgO or AgO provide internal oxygen which is a much essential ingredient of the structure of oxide superconductors. Such a method of synthesis eliminates the need of additional oxygen annealing, thus enabling the synthesis in huge quantities at once. The composites referred to as La2125+xHgO and La2125+xAgO respectively, have been characterized by XRD, SEM, resistivity and magnetic measurements for their structural and superconducting properties. We compare the properties of oxygen-annealed and HgO/AgO added compounds and discuss the results in the light of applicability of such method in synthesizing bulk quantities of high-T (c) oxide superconductors