Study of chemical reactivity and molecular interactions of the hydrochlorothiazide-4-aminobenzoic acid cocrystal using spectroscopic and quantum chemical approaches.

In this study, the molecular, electronic, and chemical properties of the drug hydrochlorothiazide (HCTZ) are determined after cocrystallization with 4-aminobenzoic acid (4-ABA). Analysis has been performed to understand how those variations lead to alteration of physical properties and chemical reactivity in the cocrystal HCTZ-4ABA. IR and Raman characterizations were performed along with quantum chemical calculations. A theoretical investigation of hydrogen bonding interactions in HCTZ-4ABA has been conducted using two functionals: B3LYP and wB97X-D. The results obtained by B3LYP and wB97X-D are compared which leads to the conclusion that B3LYP is the best applied function (density functional theory) to obtain suitable results for spectroscopy. The chemical reactivity descriptors are used to understand various aspects of pharmaceutical properties. Natural bond orbital (NBO) analysis and quantum theory of atoms (QTAIM) are used to analyze nature and strength of hydrogen bonding in HCTZ-4ABA. QTAIM analyzed moderate role of hydrogen bonding interactions in HCTZ-4ABA. The calculated HOMO-LUMO energy gap shows that HCTZ-4ABA is chemically more active than HCTZ drug. These chemical parameters suggest that HCTZ-4ABA is chemically more reactive and softer than HCTZ. The results of this study suggest that cocrystals can be a good alternative for enhancing physicochemical properties of a drug without altering its therapeutic properties.

Density Functional Theory Study of Cu6 Nanoclusters as a Phenylalanine Detector.

Research on amino acids is an attractive area because of their application in metabolism, cancer treatment, growth, and repair of body tissue, and RNA and DNA syntheses. Twenty amino acids are primarily responsible for protein synthesis. In our study, we used a Cu6 nanocluster as an amino acid detector. For the investigation, we adsorbed amino acids on the Cu6 nanocluster and studied their UV-visible spectra. It is observed that all of the Cu6-amino acid complexes have peaks at near 380 nm wavelength except the Cu-phenylalanine complex, where two UV-visible peaks are found at wavelengths 351 nm (excitation energy 3.49 eV) and 403 nm (excitation energy 3.02 eV), respectively, which originated from the HOMO - 2 to LUMO (28%) and HOMO - 1 to LUMO (38%) transitions. Due to this unique transition, the Cu6 nanocluster can be used for the detection of the phenylalanine amino acid out of the 20 amino acids.

Elucidation of novel SNPs affecting immune response to classical swine fever vaccination in pigs using immunogenomics approach.

The host genetic makeup plays a significant role in causing the within-breed variation among individuals after vaccination. The present study was undertaken to elucidate the genetic basis of differential immune response between high and low responder Landlly (Landrace X Ghurrah) piglets vis-à-vis CSF vaccination. For the purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measure of humoral immune response. Double-digestion restriction associated DNA (ddRAD) sequencing was undertaken on 96 randomly chosen Landlly piglets using Illumina HiSeq platform. SNP markers were called using standard methodology. Genome-wide association study (GWAS) was undertaken in PLINK program to identify the informative SNP markers significantly associated with differential immune response. The results revealed significant SNPs associated with E2 antibody response against CSF vaccination. The genome-wide informative SNPs for the humoral immune response against CSF vaccination were located on SSC10, SSC17, SSC9, SSC2, SSC3 and SSC6. The overlapping and flanking genes (500Kb upstream and downstream) of significant SNPs were CYB5R1, PCMTD2, WT1, IL9R, CD101, TMEM64, TLR6, PIGG, ADIPOR1, PRSS37, EIF3M, and DNAJC24. Functional enrichment and annotation analysis were undertaken for these genes in order to gain maximum insights into the association of these genes with immune system functionality in pigs. The genetic makeup was associated with differential immune response against CSF vaccination in Landlly piglets while the identified informative SNPs may be used as suitable markers for determining variation in host immune response against CSF vaccination in pigs.

Monitoring structural fluctuations of discotic liquid crystal during phase transitions.

The discotic liquid crystal 4-((2, 3, 4-tris (octyloxy) phenyl) diazenyl) benzoic acid, hereafter referred as DLC A8, exhibited in dimeric form has been studied using a combination of quantum chemical approaches and vibrational spectroscopy. This study investigates the structural alteration of DLC A8 associated with phase transition. The phase transitions of DLC A8 are Iso â†’ Discotic nematic â†’ Columnar â†’ Crystalline, which have been investigated using differential scanning calorimetry (DSC) accompanied with polarized optical microscopy (POM). Monotropic columnar mesophase was observed during the cooling cycle while discotic nematic mesophase was observed in both the heating and cooling cycles. Density functional theory (DFT) along with IR and Raman spectroscopic techniques were utilized to study the dynamics of molecules during phase transition. To predict the most stable conformation of the molecule, one-dimensional PES scans have been performed along 31 flexible bonds using DFT/B3LYP/6-311G++(d,p) method. Vibrational normal modes were analyzed in detail, taking potential energy contribution into account. The spectral analysis of FT-IR and FT-Raman was done by deconvoluting the structural sensitive bands. The agreement between the calculated IR and Raman spectra and the observed FT-IR and Raman spectra at room temperature confirms our theoretically predicted molecular model of investigated discotic liquid crystal. Moreover, our studies have unraveled the existence of intact intermolecular H-bonding of dimers throughout the phase transitions.

Allele mining in gene encoding fc fragment of IgG receptor, transporter, alpha (FCGRT) and association of nucleotide variants with passive transfer of immunity in neonatal buffalo calves.

BACKGROUND: Neonatal Fc receptors (FcRn) mediate the transcytosis of IgG present in colostrum across absorptive gut epithelium of newborn calves. FcRn receptor is a heterodimer composed of two polypeptides encoded by FCGRT (Fc fragment of IgG Receptor Transporter neonatal) and B2M (Beta 2 microglobulin) genes. Polymorphism in FCGRT gene may have a bearing on absorption of colostral immunoglobulins by neonatal buffalo calves, thereby affecting their immune status and susceptibility to diseases. The primary aim of our study was to mine alleles and single nucleotide polymorphs in the FCGRT gene and determine their association with the levels of IgG in serum of neonatal buffalo calves. METHODS AND RESULTS: On the basis of serum IgG levels estimated by indirect ELISA in 80 newborn calves, 20 calves each with highest and lowest IgG concentration were selected to study polymorphism in the FCGRT gene. The exonic regions of this gene were amplified in nine fragments which were subjected to PCR-SSCP to detect variations followed by the sequencing of variants to locate the SNPs. A total of nine SNPs (7 in introns and 2 in exons) were detected in four polymorphic fragments. Association study based on Odds ratios (ORs) with 95% Confidence Interval (CIs) established that the SNP G40T in fragment 3 has a significant (P < 0.05) bearing on IgG level in serum of neonatal buffalo calves. CONCLUSION: Genetic variation in FCGRT gene in buffalo calves was found to be associated with their serum IgG levels in neonatal stage which may have implications in calf survival and growth vis-à-vis inadequate transfer of passive immunity.

Spectroscopic and quantum chemical investigations to explore the effect of intermolecular interactions in a diuretic drug: Hydrochlorothiazide.

Hydrochlorothiazide (HCTZ) being a diuretic drug widely used in anti-hypertensive therapy as it lowers the blood pressure by reducing the reabsorption of electrolytes in kidney resulting an increment of urine output and lowering the blood pressure. The purpose of the present work is to study the structural, vibrational and chemical properties of HCTZ based on its monomeric, dimeric and trimeric models by utilizing computational methods and experimental techniques. Density functional theory (DFT) with functional B3LYP and 6-311++G (d, p) basis set was used for a detailed computational study. Monomeric, dimeric and trimeric models of HCTZ have been studied for a better understanding of inter- and intramolecular hydrogen bonding. FT-IR (400-3800 cm-1) and FT-Raman (100-3600 cm-1) spectroscopy have been utilized for the characterization of HCTZ. The shifting in wavenumber of NH2 and OSO group were observed in dimer and trimer due to the formation of intermolecular hydrogen bonding. Quantum theory of atoms in molecules (QTAIM) along with natural bond orbital (NBO) analysis were performed to examine the nature and strength of hydrogen bonding which showed that all the interactions were medium and partially covalent in nature; transition from LP(3)O15 â†’ σ*(H46 â†’ N32) and LP(3)O39 â†’ σ*(H74 â†’ N51) were responsible for the formation of O15•••H46 and O39•••H74 H-bonds, respectively. HOMO-LUMO energies predicted the chemical reactivity and stability of the molecule and the energy gap for dimer (4.6240 eV) and trimer (4.0493 eV) was found to be lesser than the monomer (5.0888 eV) which showed that the dimer and trimer have predicted more chemical reactivity in comparison to monomer. The most electronegative electrostatic potential was observed around the OSO group and the most electropositive potential around the amide group from MEPS analysis. Global as well as local reactivity descriptors have predicted the reactivity and hence, stability of the title molecule.

Detection of nucleotide variants in FCGRT (Fc fragment of IgG, receptor, transporter, alpha) gene and their influence on colostral IgG concentration in Indian water buffalo (Bubalus bubalis).

BACKGROUND: The neonatal Fc receptors (FcRn) mediate the transfer of immunoglobulin G (IgG) molecules from a dam's circulation to the colostrum produced by it immediately after parturition. In ruminants, the calves born are agammaglobulinemic therefore, ingestion of colostrum with high concentration of IgG imparts passive immunity to the newborn. The FcRn molecule is a heterodimer, coded by FCGRT (Fc fragment of IgG Receptor Transporter neonatal) and B2M (Beta 2 microglobulin) genes. Present study attempted to identify single nucleotide polymorphisms (SNPs) in the FCGRT gene in 40 buffaloes of Murrah breed and evaluated the association of these nucleotide variations and haplotypes with IgG concentration in their colostrum. METHODS AND RESULTS: Animals producing colostrum with high IgG and low IgG levels were identified by indirect ELISA and selected. SNPs were detected in the FCGRT gene sequence of selected animals by amplifying it in nine fragments covering all exons (with flanking introns) followed by PCR-single strand conformational polymorphism (PCR-SSCP). A total of nine SNPs were observed of which seven were present in flanking introns and two in exon 4 of the gene. The SNP A75G was non-synonymous and produced an amino acid change from isoleucine to valine. The exonic SNPs and corresponding haplotypes were found to be significantly (P < 0.01 and 0.05 respectively) associated with colostral IgG concentration based on Odds ratios at 95% confidence interval. CONCLUSION: Polymorphism in FCGRT gene is found to be associated with IgG concentration in colostrum and identification of females with desirable variations may prevent failure of passive transfer in neonatal ruminants.

High production of carotenoids by the green microalga Asterarcys quadricellulare PUMCC 5.1.1 under optimized culture conditions.

Since carotenoids are important as natural colorants, antioxidants, neutraceutics and pharmaceutics, the aim of the present study was to find a new good source of these pigments. We hereby report a green microalga Asterarcys quadricellulare PUMCC 5.1.1 as a new and good producer of carotenoids. The organism produced 35±1.75 µg carotenoids mg-1 dry biomass during stationary phase in control cultures. The growth and carotenoids production by the test microalga were optimized by varying nutrient growth media, pH, nitrogen and phosphate source, salinity, light quality, intensity and duration. The optimized conditions for carotenoid production were: Bold basal (BB) medium with pH 8.5, containing with10 mM nitrate, 3.5 mM phosphate and 0.17 mM salinity and illuminated with blue light with 60 µmol m-2 s-1 photon flux light intensity. Cultivation of cultures in the above mentioned optimized conditions resulted in nearly 3.0 fold increase in carotenoid production compared to the control cultures grown in unmodified BB medium. Using HPTLC, four carotenoids have been identified as ß-carotene, lutein, astaxanthin and canthaxanthin. Further, carotenoids were also separated and purified by flash chromatography and the amounts of purified carotenoids were determined by HPLC. The organism produced 47.0, 28.7, 15.5 and 14.0 µg ß-carotene, lutein, astaxanthin and canthaxanthin mg-1 dry biomass, respectively, under optimized conditions. The amount of total carotenoids (118 µg mg-1 dry biomass) produced by Asterarcys quadricellulare PUMCC 5.1.1 under optimized culture conditions was significantly higher than control cultures. Thus, this microalgal strain is a promising candidate for carotenoid production at commercial level.

Genome-wide integrated analysis of miRNA and mRNA expression profiles to identify differentially expressed miR-22-5p and miR-27b-5p in response to classical swine fever vaccine virus.

The present study was conducted to identify the differentially expressed miRNAs (DE miRNAs) in the peripheral blood mononuclear cells of crossbred pigs in response to CSF vaccination on 7 and 21 days of post vaccination as compared to unvaccinated control (0 dpv). Simultaneously, set of miRNA was predicted using mRNA seq data at same time point. The proportion of CD4-CD8+ and CD4+CD8+ increased after vaccination, and the mean percentage inhibition was 86.89% at 21 dpv. It was observed that 22 miRNAs were commonly expressed on both the time points. Out of predicted DE miRNAs, it was found that 40 and 35 DE miRNAs were common, obtained from miRNA seq analysis and predicted using mRNA seq data on 7 dpv versus 0 dpv and 21 dpv versus 0 dpv respectively. Two DE miRNAs, ssc-miR-22-5p and ssc-miR-27b-5p, were selected based on their log2 fold change and functions of their target genes in immune process/pathway of viral infections. The validations of DE miRNAs using qRT-PCR were in concordance with miRNA seq analysis. Two set of target genes, CD40 and SWAP70 (target gene of ssc-miR-22-5p) and TLR4 and Lyn (target gene of ssc-miR-27b-5p), were validated and were in concordance with results of RNA seq analysis at a particular time point (except TLR4). The first report of genome-wide identification of differentially expressed miRNA in response to live attenuated vaccine virus of classical swine fever revealed miR-22-5p and miR-27b-5p were differentially expressed at 7 dpv and 21 dpv.

Identification of sperm motility markers in bovine transition protein genes.

Transition proteins (TNPs) are essential in chromatin condensation during spermiogenesis, and hence, they are the candidate genes for identifying sperm motility markers. Coding and in silico predicted promoter regions of these genes were investigated in crossbred and purebred cattle, and also, their mRNA quantification was done to explore its use as a diagnostic tool of infertility. PCR-SSCP analysis revealed two band patterns in fragment III of TNP1 and fragment II of TNP2 gene. Sequence analysis revealed a deletion of "G" nucleotide in 3'UTR region of TNP1 and C>T SNP in intronic region of TNP2 gene. Least square analysis of variance did not reveal any significant influence of nucleotide deletion on any sperm motility parameters in both crossbred and purebred cattle. However, C>T SNP had a significant effect on initial progressive motility (p < 0.05) in purebred cattle and post-thaw motility in overall cattle population. RT-qPCR analysis did not reveal any significant variation in TNP1 and TNP2 gene expression among poorly motile and good quality spermatozoa of Vrindavani bulls.

Nucleotide variability of protamine genes influencing bull sperm motility variables.

Protamines (PRMs), important proteins of chromatin condensation in spermiogenesis, are promising candidate genes to explore markers of sperm motility. The coding and in-silico predicted promoter regions of these genes were investigated in 102 crossbred and 32 purebred cattle. Also, mRNA quantification was done to explore its possibility as diagnostic tool of infertility. The PCR-SSCP analysis indicated there were two band patterns only in fragment I of the PRM1 and fragment II of the PRM2 gene. The sequence analysis revealed A152G and G179A transitions in the PRM1 gene. Similarly, G35A, A49G and A64G transitions were identified in the PRM2 gene which resulted in altered amino acid sequences from arginine (R) to glutamine (Q), from arginine (R) to glycine (G) and from arginine (R) to glycine (G), respectively. This caused the reduction in molecular weight of PRM2 from 2157.66 to 1931.33 Da due to reduction in the number of basic amino acids. These altered properties of the PRM2 protein led to the reduction in Mass Motility (MM: P < 0.01), Initial Progressive Motility (IPM; P < 0.05) and Post Thaw Motility (PTM; P < 0.05) in crossbred bulls. The least squares analysis of variance indicated there was an effect of PRM2 haplotypes on MM (P = 0.0069), IPM (P = 0.0306) and PTM (P = 0.0500) in crossbred cattle and on PTM (P = 0.0408) in the overall cattle population. Based on the RT-qPCR analysis, however, there was not any significant variation of PRM1 and PRM2 gene expression among sperm of Vrindavani bulls with relatively lesser and greater sperm motility.

Single Nucleotide Polymorphisms in 5' Upstream Region of Bovine TLR4 Gene Affecting Expression Profile and Transcription Factor Binding Sites.

The present study in the 5' upstream region of TLR4 gene revealed four Single Nucleotide Polymorphisms (SNPs) in Vrindavani and Tharparkar cattle. The polymorphic information content (PIC), heterozygosity and allelic diversity values were low to moderate for these SNPs. In Vrindavani cattle, one SNP was found to be in Hardy-Weinberg Equilibrium (HWE) and the remaining three were found to be in linkage disequilibrium (LD) as indicated statistically (P > 0.05). In Tharparkar cattle, two SNPs were found to be in HWE and were not in LD as indicated statistically (P > 0.05). These SNPs were used for construction of haplotypes. In-silico analysis of these SNPs predicted abolition of eight transcription factor binding sites and creation of eight new sites. The quantitative real time PCR analysis did not show any significant variation of gene expression among haplotypes. However, gene expression between breed was found to be significant (P < 0.05) which suggested that upstream region of bovine TLR4 gene has a crucial role in its expression. These findings in TLR4 gene offer essential evidence that can be useful in future research exploring its role in immunity. TLR4 can be used as a marker for selection for disease resistance in bovines.

Expression Profiling and Identification of Novel SNPs in CatSper2 Gene and Their Influence on Sperm Motility Parameters in Bovines.

122 randomly selected Vrindavani cattle were studied to detect polymorphism in four fragments of the CatSper2 gene that were comprised of exon 2, 4, 5, and 6 with flanking regions. Using PCR-SSCP and sequencing analysis, three SNPs (T157C, C273A, and A274C) in the first fragment, one SNP (C30G) in the second fragment, and two SNPs (T86G and T292C) in the fourth fragment were identified. The third fragment did not reveal any polymorphism. The SNPs were used for construction of haplotypes and three haplotypes were found. The least square analysis of variance revealed a significant (P < 0.01) effect of haplotype on all three motility parameters. The haplotype II and III were nonsignificantly different from each other while being significantly (P < 0.01) different from haplotype I. The nonsignificant difference of haplotype II with III can lead to a hypothesis that T>G or C>T SNPs may not play a role in sperm motility. However, when the comparison was made between haplotype I and II, it can be inferred that C>T SNP may have a role in sperm motility, as haplotype II has better motility parameters. Expression profiling of Catper2 gene revealed nonsignificant down regulation of CatSper2 gene in poor motility sperm compared to good motility sperm.

Sequence Based Structural Characterization and Genetic Diversity Analysis of Full Length TLR4 CDS in Crossbred and Indigenous Cattle.

The exploration of candidate genes for immune response in cattle may be vital for improving our understanding regarding the species specific response to pathogens. Toll-like receptor 4 (TLR4) is mostly involved in protection against the deleterious effects of Gram negative pathogens. Approximately 2.6 kb long cDNA sequence of TLR4 gene covering the entire coding region was characterized in two Indian milk cattle (Vrindavani and Tharparkar). The phylogenetic analysis confirmed that the bovine TLR4 was apparently evolved from an ancestral form that predated the appearance of vertebrates, and it is grouped with buffalo, yak, and mithun TLR4s. Sequence analysis revealed a 2526-nucleotide long open reading frame (ORF) encoding 841 amino acids, similar to other cattle breeds. The calculated molecular weight of the translated ORF was 96144 and 96040.9 Da; the isoelectric point was 6.35 and 6.42 in Vrindavani and Tharparkar cattle, respectively. The Simple Modular Architecture Research Tool (SMART) analysis identified 14 leucine rich repeats (LRR) motifs in bovine TLR4 protein. The deduced TLR4 amino acid sequence of Tharparkar had 4 different substitutions as compared to Bos taurus, Sahiwal, and Vrindavani. The signal peptide cleavage site predicted to lie between 16th and 17th amino acid of mature peptide. The transmebrane helix was identified between 635-657 amino acids in the mature peptide.

Profiling of sperm gene transcripts in crossbred (Bos taurus x Bos indicus) bulls.

Crossbred cattle in some sectors of the world have a significant role in enhancing milk production thereby enhancing the per capita milk availability as a human food source. However, there are certain constraints associated with crossbred animals, such as disease susceptibility, increased reproductive problems, repeat breeding and poor seminal quality. The semen of crossbred bulls has a poor freezing capacity, increased cryo-damage, poor mass cell motility, greater percentages of dead/abnormal sperm and poor initial and post-freeze cell motility. The rejection rate of crossbred bulls for cryostorage of semen has been reported to be as great as 50% as a result of unacceptable semen quality. The identification of superior bulls using molecular technologies is needed which necessitates identification of the genes having a role in sperm function. The present study was, therefore, conducted to gain information on identification and expression of genes having a role in sperm motility in crossbred bulls. The gene transcripts in bulls with sperm of superior and inferior quality were profiled in Vrindavani crossbred cattle by microarray analyses and the results were verified by real time-quantitative PCR. Microarray analyses revealed 19,454 genes which were differentially expressed. At a two-fold cut off, 305 genes were differentially (P<0.01) expressed with 160 genes upregulated and 145 genes down regulated. Some of the upregulated candidate genes were further validated by RT-qPCR. These genes had a four to 16 fold upregulation in sperm with inferior motility as compared to sperm of crossbred bulls with superior motility.