Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats.

Thirty four distinct breeds and many non-descript populations represent the caprine diversity of India. Genetic characterization of breeds is an essential element in designing breeding strategies and preserving genetic diversity. Considering the popularity of mitochondrial DNA for phylogeographical studies, this study involved an extensive analysis of population structure and genetic diversity of 28 defined breeds and 5 lesser known populations representing all four major agro-climatic zones of India using mitochondrial DNA markers. Analysis of hypervariable region 1 of mtDNA control region in 443 goats together with 22 reference sequences, delineated 341 distinct haplotypes belonging to four maternal haplogroups; A, B, C and D, with haplogroup A representing 90% of the individuals. The haplotype and nucleotide diversity indices of Indian goats were 0.998 ± 0.001 and 0.028 ± 0.001, respectively indicating abundant genetic variability. Estimates of population demographic parameters from mismatch analysis suggested a relatively good fit to the model of either spatial or demographic expansion of Indian goats. AMOVA analysis and topology of MJ network suggested lack of phylogeographic structure in domestic goats, which can be attributed to unstructured animal breeding, dwindling pastures and nomadic pastoralism. Genetic differentiation between goats from different agro-ecological regions was in accordance with their geographical propinquity.

99mTc-MAG3 diuresis renography in differentiating renal obstruction: Using statistical parameters as new quantifiable indices.

OBJECTIVE: The aim of this study was to research, develop and assess the feasibility of using basic statistical parameters derived from renogram, "mean count value (MeanCV) and "median count value (MedianCV)", as novel indices in the diagnosis of renal obstruction through diuresis renography. SUBJECTS AND METHODS: First, we re-digitalized and normalized 132 renograms from 74 patients in order to derive the MeanCV and MedianCV. To improve the performance of the parameters, we extrapolated renograms by a two-compartmental modeling. After that, the cutoff points for diagnosis using each modified parameter were set and the sensitivity and specificity were calculated in order to determine the best variants of MeanCV and MedianCV that could differentiate renal obstruction status into 3 distinct classes - i) unobstructed, ii) slightly obstructed, and iii) heavily obstructed. RESULTS: The modified MeanCV and MedianCV derived from extended renograms predicted the severity of the renal obstruction. The most appropriate variants of MeanCV and MedianCV were found to be the MeanCV50 and the MedianCV60. The cutoff points of MeanCV50 in separating unobstructed and obstructed classes as well as slightly and heavily obstructed classes were 0.50 and 0.72, respectively. The cutoff points of MedianCV60 in separating unobstructed and obstructed classes as well as slightly and heavily obstructed classes were 0.35 and 0.69, respectively. Notably, MeanCV50 and MedianCV60 were not significantly influenced by either age or gender. CONCLUSIONS: The MeanCV50 and the MedianCV60 derived from a renogram could be incorporated with other quantifiable parameters to form a system that could provide a highly accurate diagnosis of renal obstructions.

Evidence of positive selection and concerted evolution in the rapidly evolving PRDM9 zinc finger domain in goats and sheep.

Meiotic recombination contributes to augmentation of genetic diversity, exclusion of deleterious alleles and proper segregation of chromatids. PRDM9 has been identified as the gene responsible for specifying the location of recombination hotspots during meiosis and is also the only known vertebrate gene associated with reproductive isolation between species. PRDM9 encodes a protein with a highly variable zinc finger (ZF) domain that varies between as well as within species. In the present study, the ZF domain of PRDM9 on chromosome 1 was characterized for the first time in 15 goat breeds and 25 sheep breeds of India. A remarkable variation in the number and sequence of ZF domains was observed. The number of ZF repeats in the ZF array varied from eight to 12 yielding five homozygous and 10 heterozygous genotypes. The number of different ZF domains was 84 and 52 producing 36 and 26 unique alleles in goats and sheep respectively. The posterior mean of dN/dS or omega values were calculated using the codeml tool of pamlx to identify amino acids that are evolving positively in goats and sheep, as positions -1, +3 and +6 in the ZF domain have been reported to experience strong positive selection across different lineages. Our study identified sites -5, -1, +3, +4 and +6 to be experiencing positive selection. Small ruminant zinc fingers were also found to be evolving under concerted evolution. Our results demonstrate the existence of a vast diversity of PRDM9 in goats and sheep, which is in concert with reports in many metazoans.

Nucleotide polymorphisms in the bovine lymphotoxin A gene and their distribution among Bos indicus zebu cattle breeds.

The present study was undertaken to characterize the genetic variation present in lymphoxin A gene (LTA gene) encoding for the lymphotoxin A protein also known as tumor necrosis factor beta, a cytokine produced by lymphocytes, known to be cytotoxic for a wide range of tumor cells both in vitro and in vivo, and, which is essential for normal immunological development; in 40 animals of 5 diverse Bos indicus Indian zebu cattle breeds. These breeds survive under the harsh and tough tropical climatic conditions of various parts of the Indian subcontinent. The LTA gene in the present study was observed to contain 33 SNPs and 3 small insertion/deletion polymorphisms. Four SNPs occurred in the coding regions of the gene viz. g.1327A>G and g.1400C>T in exon 2 and g.1840C>T and g.1942C>T in exon 3, of which the SNP g.1327A>G in exon 2 resulted in a non-synonymous amino acid change G38D. This amino acid change was however predicted not be affecting the protein function in any manner. The gene contained putative transcription factor binding sites for the c-Re1 and for Pax-4 transcription factors. A putative promoter region was also predicted on the reverse DNA strand from position 894 to 644. Several repeat elements and microsatellite repeats were detected to be occurring across the 3.2kb LTA gene sequence. The study showed the occurrence of 40 genotypes and 48 most probable haplotypes. The genotypes at the observed SNP positions in the LTA gene were in near Hardy-Weinberg equilibrium. A negative Tajima's D value that was not significant statistically at P>0.10 indicated that the neutral mutation hypothesis could not be excluded. The genetic variations observed in the LTA gene in the present study have not been reported earlier and these could possibly be used as molecular markers for further studies involving association of the gene variability with disease resistance/tolerance traits.

Locus minimization in breed prediction using artificial neural network approach.

Molecular markers, viz. microsatellites and single nucleotide polymorphisms, have revolutionized breed identification through the use of small samples of biological tissue or germplasm, such as blood, carcass samples, embryos, ova and semen, that show no evident phenotype. Classical tools of molecular data analysis for breed identification have limitations, such as the unavailability of referral breed data, causing increased cost of collection each time, compromised computational accuracy and complexity of the methodology used. We report here the successful use of an artificial neural network (ANN) in background to decrease the cost of genotyping by locus minimization. The webserver is freely accessible (http://nabg.iasri.res.in/bisgoat) to the research community. We demonstrate that the machine learning (ANN) approach for breed identification is capable of multifold advantages such as locus minimization, leading to a drastic reduction in cost, and web availability of reference breed data, alleviating the need for repeated genotyping each time one investigates the identity of an unknown breed. To develop this model web implementation based on ANN, we used 51,850 samples of allelic data of microsatellite-marker-based DNA fingerprinting on 25 loci covering 22 registered goat breeds of India for training. Minimizing loci to up to nine loci through the use of a multilayer perceptron model, we achieved 96.63% training accuracy. This server can be an indispensable tool for identification of existing breeds and new synthetic commercial breeds, leading to protection of intellectual property in case of sovereignty and bio-piracy disputes. This server can be widely used as a model for cost reduction by locus minimization for various other flora and fauna in terms of variety, breed and/or line identification, especially in conservation and improvement programs.

Genetic polymorphisms in the bovine toll-like receptor 4 (TLR4) and monocyte chemo attractant protein-1(CCL2) genes: SNPs distribution analysis in Bos indicus Sahiwal cattle breed.

Toll-like receptor 4 gene (TLR4) that recognizes the Gram negative bacterial ligand LPS was sequenced in the Bos indicus Sahiwal cattle breed. Ninety four single nucleotide polymorphisms (SNPs) were detected within 10.8 kb gene region. Seventeen of the SNPs were in the coding regions and the one at position 9589(A > G) in exon3 resulted in an amino acid change from Valine to Isoleucine. These SNPs led to generation of 27 TLR4 gene haplotypes. All the Sahiwal animals studied presently showed the occurrence of the genotype CC at gene position 9662, which codes for the amino acid threonine at position 674 of the TLR4 protein, and which had been reported to be associated with lower somatic cell score and, therefore, a lower susceptibility to mastitis, in Taurus cattle. This nucleotide configuration of the Toll-like receptor 4 gene of the Bos indicus Sahiwal cattle breed could possibly indicate toward a lower susceptibility to mastitis in the Sahiwal animals. Monocyte chemo-attractant protein-1 (CCL2) gene encoding for small inducible cytokine A2 that belongs to the CC chemokine family was also sequence characterized in these Sahiwal animals. The CCL2 gene was observed to have 12 polymorphic sites in 3.3 kb region of which one SNP at position 2500 (A > G) in exon 3 resulted in amino acid change from Valine to Isoleucine at position 46 of the mature CCL2 peptide. Seventeen haplotypes of the CCL2 gene were predicted corresponding to 12 genotypes detected.

Ankrd2 is a modulator of NF-κB-mediated inflammatory responses during muscle differentiation.

Adaptive responses of skeletal muscle regulate the nuclear shuttling of the sarcomeric protein Ankrd2 that can transduce different stimuli into specific adaptations by interacting with both structural and regulatory proteins. In a genome-wide expression study on Ankrd2-knockout or -overexpressing primary proliferating or differentiating myoblasts, we found an inverse correlation between Ankrd2 levels and the expression of proinflammatory genes and identified Ankrd2 as a potent repressor of inflammatory responses through direct interaction with the NF-κB repressor subunit p50. In particular, we identified Gsk3ß as a novel direct target of the p50/Ankrd2 repressosome dimer and found that the recruitment of p50 by Ankrd2 is dependent on Akt2-mediated phosphorylation of Ankrd2 upon oxidative stress during myogenic differentiation. Surprisingly, the absence of Ankrd2 in slow muscle negatively affected the expression of cytokines and key calcineurin-dependent genes associated with the slow-twitch muscle program. Thus, our findings support a model in which alterations in Ankrd2 protein and phosphorylation levels modulate the balance between physiological and pathological inflammatory responses in muscle.

Genetic structuring of nine Indian domestic goat breeds based on SNPs identified in IGF-1 gene.

The caprine Insulin like Growth Factor1 (IGF1) gene was analyzed for identification of single nucleotide polymorphisms (SNPs) and genetic structuring of Indian goat breeds. A panel of 80 samples belonging to nine Indian goat breeds (Capra hircus) including three large sized breeds (Jamunapari, Beetal and Jakhrana); three medium sized breeds (Sirohi, Barbari, and Osmanabadi) and three small sized breeds (Black Bengal, Changthangi, and Gaddi) were screened for SNP identification and diversity analysis. The comparative gene sequence analysis of all the nine goat breeds studied revealed a total of 18 SNPs in IGF1 gene. All the nucleotide changes were found to be synonymous. The mean observed heterozygosity was found to be maximum (0.074) in Sirohi, Beetal, Osmanabadi, and Gaddi breeds of goat, whereas it is found to be minimum (0.019) in Black Bengal breed of goat. The rest of the breeds were intermediate in terms of heterozygosity. The same has been confirmed by allele frequency distribution across the studied loci. Barbari and Gaddi were found to be more differentiated (0.0123), Changthangi and Jamunapari were least differentiated (0.00110) based on Nei's genetic distance.

The major histocompatibility complex in bovines: a review.

Productivity in dairy cattle and buffaloes depends on the genetic factors governing the production of milk and milk constituents as well as genetic factors controlling disease resistance or susceptibility. The immune system is the adaptive defense system that has evolved in vertebrates to protect them from invading pathogens and also carcinomas. It is remarkable in the sense that it is able to generate an enormous variety of cells and biomolecules which interact with each other in numerous ways to form a complex network that helps to recognize, counteract, and eliminate the apparently limitless number of foreign invading pathogens/molecules. The major histocompatibility complex which is found to occur in all mammalian species plays a central role in the development of the immune system. It is an important candidate gene involved in susceptibility/resistance to various diseases. It is associated with intercellular recognition and with self/nonself discrimination. It plays major role in determining whether transplanted tissue will be accepted as self or rejected as foreign.

Identification of newly recognized serotype 1c as the most prevalent Shigella flexneri serotype in northern rural Vietnam.

We investigated the identity of 37 Shigella flexneri strains that had previously been isolated from northern rural Vietnam (Son Tay Province) and described as untypable. Twenty-four isolates reacted with MASF 1c, a monoclonal antibody specific for S. flexneri serotype 1c. A further ten untypable isolates were found to be rough mutants (no longer expressing O-antigen) that were derived from serotype 1c strains. Pulsed-field gel electrophoresis demonstrated that these strains consisted of many different clones, indicating serotype 1c was well established in this region in the late 1990s. Serotype 1c was the most prevalent S. flexneri serotype isolated in the Son Tay Province, accounting for about 40% of S. flexneri isolates. Subsequent isolation of S. flexneri serotype 1c in this region and elsewhere in Vietnam confirmed that serotype 1c is of genuine importance in Vietnam.

Characterization of genetic polymorphism of the bovine lymphocyte antigen DRB3.2 locus in Kankrej cattle (Bos indicus).

Bovine lymphocyte antigen DRB 3.2 (BoLA-DRB3.2) gene encodes for the beta chain of the major histocompatibility complex (MHC) class II molecule in cattle, which is a glycoprotein present on the surface of antigen-presenting cells. This locus shows extensive polymorphism in it. The objective of the present study was to genotype the BoLA-DRB3.2 locus in Kankrej cattle (n = 50) by PCR-RFLP. Bovine DNA was isolated from aliquots of whole blood. Primers specific for exon 2 of the bovine lymphocyte antigen (BoLA)-DRB3 gene were used to amplify the region. The 304-bp amplified product of the DRB3 gene was separately digested with restriction endonucleases RsaI, BstYI, and Hae III. Twenty-four BoLA-DRB 3.2 alleles were identified with frequencies ranging from 1 to 22.0%. Twenty-one alleles of the total 24 alleles were similar to those reported earlier; 3 alleles were new and had not been reported previously. The allele BoLA-DRB3.2*34 occurred at the highest frequency of 22% (approx.) in the Kankrej animals studied. Six alleles (BoLA-DRB3.2 *34, *15, *06, *20, *37, and *20) accounted for almost 71% of the total alleles observed to be present in the Kankrej animals. All the new alleles observed were present at frequencies of 1%. The results obtained in the present study demonstrated that the BoLA DRB3.2 locus is highly polymorphic in the Kankrej cattle.

The anti-leishmanial drug miltefosine causes insulin resistance in skeletal muscle cells in vitro.

AIMS/HYPOTHESIS: Miltefosine, the first oral anti-leishmanial drug, is reported to inhibit phosphatidylinositol 3-kinase (PI3K)/Akt activity in carcinoma cell lines. Inhibition of the PI3K/Akt pathway is known to result in insulin resistance. Therefore, we investigated whether miltefosine has any deleterious effect(s) on insulin sensitivity in L6E9 skeletal muscle cells. MATERIALS AND METHODS: L6E9 myotubes were treated with miltefosine and its effect was observed on insulin-signalling proteins such as Akt, PI3K, insulin receptor-beta, IRS-1, c-Jun N-terminal kinase, p38 and glycogen synthase kinase beta, as well as on glucose uptake. RESULTS: Miltefosine caused skeletal muscle insulin resistance in vitro by interfering with the insulin-signalling pathway and inhibiting insulin-stimulated glucose uptake. CONCLUSIONS/INTERPRETATION: Miltefosine may contribute to the risk of type 2 diabetes and needs further clinical exploration.

Phytomitogen induced changes in levels of inositol phosphates in the bovine lymphocytes.

The changes in levels of inositol phosphates and phosphoinositides were studied in the bovine lymphocytes, in response to phytomitogens (lectins)-concanavalin A (con A) and phytohaemagglutinin (PHA). Addition of con A and PHA resulted in a rapid increase in the cpm of total inositol phosphates (from 8599 +/- 100 cpm/2 x 10(6) cells to 11228 +/- 126 cpm/2 x 10(6) and 9758 +/- 100 cpm/2 x10(6) cells, respectively) at 1 min after mitogen stimulation. There was a concomitant decrease in the phosphatidylinositol levels at 1 min, which continued up to 5 min. At 1 min of stimulation, inositol diphosphate fraction exhibited maximum increase, as compared to inositol mono- and triphosphates, suggesting that it contributed the most towards the overall increase in the total inositol phosphates levels. Results suggest that bovine lymphocytes respond to phytomitogens with a rapid turnover of phosphoinositides.

RNA-mediated gene silencing: mechanisms and its therapeutic applications.

RNA interference, part of a complicated network of interconnected pathways for cellular defence, RNA surveillance and development, has become a powerful tool for the experimental manipulation of gene expression. It is the process by which double-stranded (dsRNA) silences specific gene expression through homology-dependent degradation of cognate mRNA. The dsRNA is converted into 21nt small interfering RNAs (siRNAs), which directs a complex ribonuclease system to substrate mRNA targets. The degradation of the target mRNA is initiated with the cleavage at a position corresponding to the centre of the siRNA. Dissecting individual cellular pathways to reveal the function of numerous proteins is an approach to drug discovery. Interfering RNA (RNAi) serves as a rapid and convenient tool, which works in various organisms. RNAi technology has the potential to facilitate our understanding of biological processes and potentially lead to exciting new drugs. Here we review various experimental approaches adopted with RNAi and possible therapeutic applications.

Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri.

O-antigen modification (serotype conversion) in Shigella flexneri, which is an important virulence determinant, is conferred by temperate bacteriophages. Several serotype-converting phages have been isolated and preliminary characterization has identified the genes involved in O-antigen modification, and has also provided insight into the molecular biology of these phages.

A study of drug utilisation and cost of treatment in patients hospitalised with unstable angina.

OBJECTIVE: The current study was designed to investigate drug utilisation in the management of unstable angina in India and to calculate the costs incurred by patients in the treatment of a single episode of unstable angina. METHODS: We conducted a prescription survey to examine the use of antianginal drugs in patients with unstable angina in a tertiary care Indian hospital. The use of concurrent medications such as antidiabetic, antihypertensive and lipid-lowering agents was also examined. Data on the cost of treatment, investigations, income, and family size were collected from the case histories or direct interviews with the patients/relatives. RESULTS: A total of 336 consecutive prescriptions were evaluated. Aspirin was the most frequently prescribed drug (98%) followed by nitroglycerin infusion (90%) and enoxaparin (52%). One of the heparins was used by 89% of all patients and beta-blockers by up to 62% of the patients. Besides antianginals, antihypertensive (49%) and antidiabetic (16%) drugs were commonly coadministered. The mean (+/- SD) cost of treatment of a single episode of unstable angina in the hospital was US $494 (+/- 271) against an annual per capita income of US $245. The mean (+/- SD) cost incurred by the patients due to drugs alone during the hospital stay was US $70 (+/- 18) and enoxaparin accounted for 60% of the expenditure due to drugs. CONCLUSIONS: The results of our study show that low-molecular-weight heparin, enoxaparin, is replacing unfractionated heparin in the treatment of unstable angina. In view of the use of costly new drugs, there is an urgent need for carrying out pharmacoeconomic analysis in developing countries as the treatment of a single episode of unstable angina imparts a considerable economic burden on the patient.

Immune response to rotavirus VP4 expressed in an attenuated strain of Shigella flexneri.

An attenuated strain of Shigella flexneri was utilised to express viral protein (VP) 4 of rotavirus and the immunogenicity of the recombinant constructs was studied in BALB/c mice. VP4 was expressed as a fusion with maltose binding protein (MBP) in both the cytoplasm and periplasm, with a much higher level of expression occurring in the former. While all constructs induced a Shigella-specific response in mice, only the construct expressing MBP-VP4 in the cytoplasm of Shigella stimulated an immune response specific to rotavirus. This study demonstrates that Shigella can be used to deliver rotavirus antigens and induces an immune response directed towards both rotavirus and Shigella.

Serotype 1a O-antigen modification: molecular characterization of the genes involved and their novel organization in the Shigella flexneri chromosome.

The factors responsible for serotype 1a O-antigen modification in Shigella flexneri were localized to a 5.8-kb chromosomal HindIII fragment of serotype 1a strain Y53. The entire 5.8-kb fragment and regions up- and downstream of it (10.6-kb total) were sequenced. A putative three-gene operon, which showed homology with other serotype conversion genes, was identified and shown to confer serotype 1a O-antigen modification. The serotype conversion genes were flanked on either side by phage DNA. Multiple insertion sequence (IS) elements were located within and upstream of the phage DNA in a composite transposon-like structure. Host DNA homologous to the dsdC and the thrW proA genes was located upstream of the IS elements and downstream of the phage DNA, respectively. The sequence analysis indicates that the organization of the 10.6-kb region of the Y53 chromosome is unique and suggests that the serotype conversion genes were originally brought into the host by a bacteriophage. Several features of this region are also characteristic of pathogenicity islands.

Antigen-specific systemic and reproductive tract antibodies in foxes immunized with Salmonella typhimurium expressing bacterial and sperm proteins.

Attenuated Salmonella typhimurium strains are potential 'safe' delivery vectors of an oral immunocontraceptive vaccine for the European red fox (Vulpes vulpes). In the present study, model bacterial (Escherichia coli heat-labile enterotoxin B subunit, LTB) and fox sperm (fSP10) antigens were expressed in S. typhimurium SL3261 (delta aroA) under the control of the trc promoter. Adult female foxes were given three oral immunizations with SL3261 containing either LTB (SL3261/pLTB), fSP10 (SL3261/pFSP10) or a control plasmid (pKK233-2 or pTrc99A). All foxes raised serum (IgG) and vaginal (IgG and IgA) antibodies against S. typhimurium lipopolysaccharide (LPS). Each fox that received SL3261/pLTB raised high titre LTB-specific serum and vaginal IgG antibodies. However, only one of four foxes immunized with SL3261/pFSP10 raised an anti-fSP10 immune response, in the form of low titre serum and vaginal IgG antibodies. No vaginal IgA antibodies were raised against either LTB or fSP10 in these experiments. The immune responses against recombinant LTB and fSP10 resulted chiefly from the initial dose of antigen in the inocula and were minimally influenced by continued in vivo antigen expression. This study demonstrates for the first time in the female red fox that oral Salmonella can elicit specific systemic and reproductive tract antibodies against heterologous, recombinant proteins.

Serotype conversion of a Shigella flexneri candidate vaccine strain via a novel site-specific chromosome-integration system.

Shigella flexneri SFL124 (serotype Y) is a promising live oral vaccine candidate, which has been shown to be safe and immunogenic in human volunteers. To change the serotype of this vaccine strain, we inserted a serotype conversion gene cluster into the chromosome of SFL124 by using a bacteriophage-based site-specific integration system. By cloning an integrase gene (int), an attachment site (attP) and a glucosyl transfer gene cluster from bacteriophage SfX into a suicide vector, and subsequently introducing this construct into S. flexneri SFL124, we obtained a S. flexneri strain (designated SFL1213) expressing the serotype X somatic antigen specificity. The strain retained other characteristics of the parent strain, such as colony shape, growth rate, and Congo red binding property. Stability test showed that the serotype X O-antigen specificity in SFL1213 was 100% stable after being cultured approximately 72 successive hours under non-selective condition. In a mouse pulmonary model, the recombinant strain elicited a significant level of humoral antibodies which recognized the lipopolysaccharide (LPS) of a wild-type S. flexneri serotype X strain. The site-specific insertion system will be useful when stable expression of a cloned single copy gene is desired in the chromosome of S. flexneri vaccine candidate, SFL124.