SNPPicker: High quality tag SNP selection across multiple populations

<p>Abstract</p> <p>Background</p> <p>Linkage Disequilibrium (LD) bin-tagging algorithms identify a reduced set of tag SNPs that can capture the genetic variation in a population without genotyping every single SNP. However, existing tag SNP selection algorithms for designing custom genotyping panels do not take into account all platform dependent factors affecting the likelihood of a tag SNP to be successfully genotyped and many of the constraints that can be imposed by the user.</p> <p>Results</p> <p>SNPPicker optimizes the selection of tag SNPs from common bin-tagging programs to design custom genotyping panels. The application uses a multi-step search strategy in combination with a statistical model to maximize the genotyping success of the selected tag SNPs. User preference toward functional SNPs can also be taken into account as secondary criteria. SNPPicker can also optimize tag SNP selection for a panel tagging multiple populations. SNPPicker can optimize custom genotyping panels including all the assay-specific constraints of Illumina's GoldenGate and Infinium assays.</p> <p>Conclusions</p> <p>A new application has been developed to maximize the success of custom multi-population genotyping panels. SNPPicker also takes into account user constraints including options for controlling runtime. Perl Scripts, Java source code and executables are available under an open source license for download at <url>http://mayoresearch.mayo.edu/mayo/research/biostat/software.cfm</url></p

HLA homozygosity does not adversely affect measles vaccine-induced cytokine responses

AbstractThe association between HLA homozygosity and measles-specific Th1 (IFN-γ, IL-2 and IL-12p40) and Th2 (IL-4 and IL-10) cytokine responses were assessed in a group of 339 healthy schoolchildren 12–18 years of age previously immunized with two doses of live-attenuated measles virus vaccine. No associations were observed between class I HLA homozygosity and measles-specific cytokine levels. Children who were homozygous at the class II DRB1, DQA1, DPA1 and DPB1 loci had higher median IFN-γ secretion levels compared with children who were heterozygous for DRB1 (77.7 vs. 39.5 pg/ml, p=0.05), DQA1 (60.9 vs. 36.6 pg/ml, p=0.03), DPA1 (46.1 vs. 27.1 pg/ml, p=0.01) and DPB1 (61.5 vs. 36.0 pg/ml, p=0.01) loci, respectively. Homozygosity at increasing numbers of HLA loci ( >=4) was associated with increased IFN-γ secretion levels (test for trend p-value=0.01). Our results suggest that HLA homozygosity showed no disadvantage for measles-specific cytokine responses and instead was associated with increased IFN-γ levels

Mycobacterial proteins-Immune targets for antituberculous subunit vaccine

1157-1166Cellular and humoral immunity induced by Mycobacterium  tuberculosis has led to identification of newer vaccine candidates, but despite this, many questions concerning the protection against tuberculosis remain unanswered. Recent progress in this field has centered on T cell subset responses and cytokines that these cells secrete. There has been a steady progress in identification and characterization of several classes of major mycobacterial proteins which includes secretory/export proteins, cell wall associated proteins, heat shock proteins and cytoplasmic proteins. The protein antigens are now believed to represent the key protective immunity inducing antigens in the bacillus. In this review, various mycobacterial protein antigens of vaccination potential are compared for their efficacy in light of current immunological knowledge.</span

Hybrid caffeic acid derivatives as monoamine oxidases inhibitors: synthesis, radical scavenging activity, molecular docking studies and in silico ADMET analysis

Abstract Background Monoamine oxidase has been implicated in numerous neurological disorders. Although synthetic monoamine oxidase inhibitors (MAOI) have emerged with many side effects, the aspiration of natural based MAOI has greatly increased. As they exhibit fewer side effects and food interaction along with improved neuropharmacological profile. Results The in silico design of the caffeic acid derivatives led potent MAO inhibitors with remarkable antioxidant activity. The mechanistic insight of the compounds within the hMAO active site was achieved by molecular docking which led us to be more confident of the possible inhibition of MAO. Conclusions The synthesized eugenol based ester of caffeic acid compound 7 exhibited MAO-A inhibition with IC50 values of 07.03 ± 0.022 µM with good selectivity (SI = 0.291) towards MAO-A. Conversely, two anilides compounds 2 and 1, bearing chloro and nitro group at 2, 4 positions showed MAO-A inhibition with IC50 values of 08.51 ± 0.017 µM and 08.87 ± 0.005 µM, respectively. Only one compound 5 was found as a significant MAO-B inhibitor with the IC50 value of 10.80 ± 0.024 µM. Moreover, compounds 1, 2, 4 and 9 have profoundly appeared as potent antioxidants as evaluated in duel assay by scavenging DPPH and H2O2

In silico design and synthesis of hesperitin derivatives as new xanthine oxidase inhibitors

Abstract Background Hesperitin, a naturally occurring flavonoid was hybridized with phenolic acids to evaluate its potential to inhibit the activity of xanthine oxidase (XO), a key enzyme which catalyses xanthine to uric acid which is found to be associated with gout and many life style related disorders. Objective To develop new xanthine oxidase inhibitors from natural constituents along with antioxidant potential. Method In this report, we designed and synthesized hesperitin derivatives hybridized with natural phenolic acids to form ester linkage with the help of molecular docking. The synthesized compounds were evaluated for their antioxidant and xanthine oxidase inhibitory potential. Results The in vitro xanthine oxidase inhibitory activity and enzyme kinetics studies showed that hesperitin derivatives displayed a potential inhibition against XO in competitive manner with IC50 value ranging from 9.0 to 23.15 µM and HET4 was revealed as most active derivative. Molecular simulation revealed that new hesperitin derivatives interacted with the amino acid residues SER1080, PHE798, GLN1194, ARG912, THR1083, ALA1078 and MET1038 located within the active cavity of XO. Results of antioxidant activity revealed that all the derivatives showed very good antioxidant potential. Conclusion Taking advantage of molecular docking, this hybridization of two natural constituent could lead to desirable xanthine oxidase inhibitors with improved activity

Lead optimization for promising monoamine oxidase inhibitor from eugenol for the treatment of neurological disorder: synthesis and in silico based study

Abstract Natural based inhibitors of monoamine oxidase are promising drug candidates for the treatment of several neurodegenerative and neuropsychological disorders including depression, anxiety, Parkinson’s disease and Alzheimer’s disease. In the present study we designed and synthesized the eugenol based derivatives and investigated them for human MAO inhibitory potential as promising candidates for therapeutics of neurological disorders. Moreover, radical scavenging activity of designed derivatives was tested by and H2O2 and DPPH scavenging methods. Eugenol based derivatives were designed and synthesized for human MAO inhibitory action. The in silico and in vitro models were utilized for the evaluation of hMAO inhibition. The insight into molecular interactions among the compounds and both hMAO-A and hMAO-B active site was achieved by molecular docking studies. The two spectrophotometric titrations techniques were used to evaluate antioxidant potential. Compounds 5b and 16 were found as most active hMAO-A inhibitors with IC50 values of 5.989 ± 0.007 µM and 7.348 ± 0.027 µM respectively, through an appreciable selectivity index value of 0.19 and 0.14 respectively. In case of hMAO-B inhibition compounds 13a and 13b were found as most active hMAO-B inhibitors with IC50 values of 7.494 ± 0.014 µM and 9.183 ± 0.034 µM receptively and outstanding value of selectivity index of 5.14 and 5.72 respectively. Radical scavenging assay showed that compounds 5b, 5a, 9b, 9a were active antioxidants. The findings of present study indicated excellent correlation among dry lab and wet lab hMAO inhibitory experiments. Interestingly, the compounds exhibiting better MAO inhibition activity was also appeared as good antioxidant agents

A study of lambda hypernuclei within the Skyrme-Hartree-Fock model

Neelam Guleria, Shashi K. Dhiman, Radhey Shya

Poly (DL-lactide-co-glycolide) based delivery systems for vaccines and drugs

746-752Current vaccination and drug delivery strategies emphasize on the development of controlled release techniques for persistent and sustained effects. In the recent years, polymer based systems for the delivery of bioactive agents have gained considerable attention due to their marked adjuvanticity, established biodegradability and biocompatibility, excellent mechanical strength and controlled release profiles. This review deals with the potential applications of synthetic polymers mainly PLG polymers in delivery of vaccines and drugs

Quercetin and Related Chromenone Derivatives as Monoamine Oxidase Inhibitors: Targeting Neurological and Mental Disorders

Monoamine oxidase inhibitions are considered as important targets for the treatment of depression, anxiety, and neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases. This has encouraged many medicinal chemistry research groups for the development of most promising selective monoamine oxidase (MAO) inhibitors. A large number of plant isolates also reported for significant MAO inhibition potential in recent years. Differently substituted flavonoids have been prepared and investigated as MAO-A and MAO-B inhibitors. Flavonoid scaffold showed notable antidepressant and neuroprotective properties as revealed by various and established preclinical trials. The current review made an attempt to summarizing and critically evaluating the new findings on the quercetin and related flavonoid derivatives functions as potent MAO isoform inhibitors