Editor's choice: Functional classification of 15 million SNPs detected from diverse chicken populations

Next-generation sequencing has prompted a surge of discovery of millions of genetic variants from vertebrate genomes. Besides applications in genetic association and linkage studies, a fraction of these variants will have functional consequences. This study describes detection and characterization of 15 million SNPs from chicken genome with the goal to predict variants with potential functional implications (pfVars) from both coding and non-coding regions. The study reports: 183K amino acid-altering SNPs of which 48% predicted as evolutionary intolerant, 13K splicing variants, 51K likely to alter RNA secondary structures, 500K within most conserved elements and 3K from non-coding RNAs. Regions of local fixation within commercial broiler and layer lines were investigated as potential selective sweeps using genome-wide SNP data. Relationships with phenotypes, if any, of the pfVars were explored by overlaying the sweep regions with known QTLs. Based on this, the candidate genes and/or causal mutations for a number of important traits are discussed. Although the fixed variants within sweep regions were enriched with non-coding SNPs, some non-synonymous-intolerant mutations reached fixation, suggesting their possible adaptive advantage. The results presented in this study are expected to have important implications for future genomic research to identify candidate causal mutations and in poultry breeding.     

Enzyme-catalysed production of n-butyl palmitate using ultrasound-assisted esterification of palmitic acid in a solvent-free system

Bioprocess and Biosystems Engineering - This work exhibits the implementation of ultrasound technology in solvent-free synthesis study of n-butyl palmitate using Fermase CALB™10000....     

Synthesis, biological evaluation, and molecular docking studies of benzyl, alkyl and glycosyl [2-(arylamino)-4,4-dimethyl-6-oxo-cyclohex-1-ene]carbodithioates, as potential immunomodulatory and immunosuppressive agents

The immunomodulating properties of functionalized [2-(arylamino)-4,4-dimethyl-6-oxo-cyclohex-1-ene] carbodithioates and 6,6-dimethyl-4-(2-(propan-2-ylidene)hydrazinyl)-6,7-dihydro-2H-indazole-3(5H)-thione compounds have been investigated. Four of them, 13, 18, 19 and 20 inhibited PBMC proliferation induced by phytohemagglutinin (PHA) in a dose dependent manner with an IC(50) of ≤ 20 μM. The Th-1 cytokine, interleukin-2 (IL-2) in PHA/PMA-stimulated peripheral blood mononuclear cells (PBMCs) is significantly inhibited by 13, 19 and 20 with an IC(50) of 8.4 ± 0.4, 5.34 ± 0.15 and 4.9 ± 0.7 μM, respectively. They also inhibited the PMA/lipopolysaccharide-induced proinflammatory cytokines, IL-1β and TNF-α production in human monocytic leukemia cells (THP-1), by 86%, 46% and 59.2% for IL-1β and by 83.8%, 48.2% and 58.7% for TNF-α, respectively. Only 20 showed significant suppressive activity against the phagocyte oxidative burst in a dose dependent manner, with an IC(50) of 23.8 μM. LPS-induced nitrites in mouse macrophages were found to be inhibited by compounds 6, 8, 13-15 and 19 with an IC(50), which range between 7.7 and 63 μM. The cytotoxicity for the active compounds was also studied on Rat Wistar Hepatocyte cell line, CC1 and the Mouse Fibroblast cell line 3T3 NIH in the presence of compounds using a standard MTT assay. Furthermore, structural-activity relationship using automated docking software revealed that active compounds 7, 13 and 19, adapted the same binding mode, however the most active compound 20 is found deeply inserted within the ligand binding site of IL-2, as multiple hydrophobic and hydrophilic key interactions stabilize the compound inside the binding site, thus contributing higher activity.     

Development of a sensitive high-performance thin-layer chromatography method for estimation of ranitidine in urine and its application for bioequivalence decision for ranitidine tablet formulations

A sensitive and simple HPTLC method was developed for estimation of ranitidine in human urine. The drug was extracted from urine after basification using dichloromethane. Dichloromethane extract was spotted on silica gel 60 F254 TLC plate and was developed in a mixture of ethyl acetate-methanol-ammonia (35:10:5 v/v) as the mobile phase and scanned at 320 nm. The RF value obtained for the drug was 0.67 +/- 0.03. The method was validated in terms of linearity (50-400 ng/spot), precision and accuracy. The average recovery of ranitidine from urine was 89.35%. The proposed method was applied to evaluate bioequivalence of two marketed ranitidine tablet formulations (150 mg, Formulation I and Formulation 2) using a crossover design by comparing urinary excretion data for unchanged ranitidine in six healthy volunteers. Various pharmacokinetic parameters like peak excretion rate [(dAU/dt)max], time for peak excretion rate (tmax), AUC0-24, AUC0-infinity, cumulative amount excreted were calculated for both formulations and subjected to statistical analysis. The relative bioavailability of Formulation 2 with respect to Formulation 1 was 93.76 and 95.31% on the basis of AUC0-24 and cumulative amount excreted, respectively. Statistical comparison of various pharmacokinetic parameters indicated that the two ranitidine tablet formulations are bioequivalent.     

Design, synthesis, and pharmacological evaluation of some 2-[4-morpholino]-3-aryl-5-substituted thiophenes as novel anti-inflammatory agents: generation of a novel anti-inflammatory pharmacophore

Compounds incorporating a thiophene moiety, a pi excess five membered heterocycle, have attracted a great deal of research interest owing to the therapeutic utility of the template as useful drug molecular scaffolding. Recently we reported the anti-inflammatory activity profile exhibited by two thiophene analogs, AP84 and AP82 in acute and chronic models of inflammation. The good activity profile exhibited by AP84, a 3-(substituted aryl)-2-(4-morpholino)-5-heteroaryl substituted analog of thiophene, in the formalin induced rat paw edema chronic model as compared to a weak activity in acute carrageenin induced rat paw edema, and the slightly better protection exhibited in the acute model by AP82 (27%), the 5-aroyl analog provided an impetus for a proper exploration of their structural types. In this paper we report the synthesis and pharmacological evaluation of some novel, 2-(4-morpholino)-3-(substituted aryl)-5-substituted thiophenes, as possible anti-inflammatory leads. The 3-(4-chlorophenyl)-2-(4-morpholino) thiophene analogs AP49, AP158, and AP88 provided a protection of 20%, 23%, and 20%, respectively, when screened for anti-inflammatory activity in carrageenin induced rat paw edema, an acute in vivo model, comparable to that of AP82, at a dose level of 100mg/kg body weight p.o. compared to ibuprofen as standard. The replacement of the 3-(4-chlorophenyl) moiety with the 3-phenyl moiety gave rise to AP50 (30%), AP159 (38%), AP27 (0%), and AP92 (38%), with three analogs being more active in the acute model. Alteration of the group para to the phenyl ring at third position, from chloro, to methyl mercapto gave rise to the 3-(4-methylmercapto-phenyl) analogs AP54 (20%), AP160 (0%), and AP73 (52%), with only one analog appearing to be better than AP82. These results indicate that 4-methane sulfonyl aroyl group at 5-position and other substituents of different quadrants of Craig plot on the phenyl moiety at the third position could lead to more potent candidates. However, alteration of aroyl to substituted pyridyl at 5-position with a phenyl group at the third position as in AP26 gave rise to much better protection (66%) again reinforcing the importance of the heteroaryl ring at the fifth position and implying its utility in the composition of a novel pharmacophore for designing better trisubstituted thiophenes as anti-inflammatory agents.     

The majority of currently circulating human immunodeficiency virus type 1 clade B viruses fail to prime cytotoxic T-lymphocyte responses against an otherwise immunodominant HLA-A2-restricted epitope: implications for vaccine design

Human immunodeficiency virus type 1 (HIV-1) mutates to escape immune selection pressure, but there is little evidence of selection mediated through HLA-A2, the dominant class I allele in persons infected with clade B virus. Moreover, HLA-A2-restricted responses are largely absent in the acute phase of infection as the viral load is being reduced, suggesting that circulating viruses may lack immunodominant epitopes targeted through HLA-A2. Here we demonstrate an A2-restricted epitope within Vpr (Vpr59-67) that is targeted by acute-phase HIV-1-specific CD8+ T cells, but only in a subset of persons expressing HLA-A2. Individuals in the acute stage of infection with viruses containing the most common current sequence within this epitope (consensus sequence) were unable to mount epitope-specific T-cell responses, whereas subjects infected with the less frequent I60L variant all developed these responses. The I60L variant epitope was a stronger binder to HLA-A2 and was recognized by epitope-specific T cells at lower peptide concentrations than the consensus sequence epitope. These data demonstrate that HLA-A2 is capable of contributing to the acute-phase cytotoxic T-lymphocyte response in infected subjects, but that most currently circulating viruses lack a dominant immunogenic epitope presented by this allele, and suggest that immunodominant epitopes restricted by common HLA alleles may be lost as the epidemic matures.     

Independent Origin and Global Distribution of Distinct Plasmodium vivax Duffy Binding Protein Gene Duplications

BackgroundPlasmodium vivax causes the majority of malaria episodes outside Africa, but remains a relatively understudied pathogen. The pathology of P. vivax infection depends critically on the parasite’s ability to recognize and invade human erythrocytes. This invasion process involves an interaction between P. vivax Duffy Binding Protein (PvDBP) in merozoites and the Duffy antigen receptor for chemokines (DARC) on the erythrocyte surface. Whole-genome sequencing of clinical isolates recently established that some P. vivax genomes contain two copies of the PvDBP gene. The frequency of this duplication is particularly high in Madagascar, where there is also evidence for P. vivax infection in DARC-negative individuals. The functional significance and global prevalence of this duplication, and whether there are other copy number variations at the PvDBP locus, is unknown.Conclusions/SignificancePvDBP duplications are much more widespread and complex than previously thought, and at least two distinct duplications are circulating globally. The same duplication boundaries were identified in parasites from three continents, and were found at high prevalence in human populations where DARC-negativity is essentially absent. It is therefore unlikely that PvDBP duplication is associated with infection of DARC-negative individuals, but functional tests will be required to confirm this hypothesis.