Genome-wide copy number variation regions in indigenous (Bos indicus) cattle breeds of Tamil Nadu, India.

Objective: Identification of large scale structural polymorphisms (Copy number variations) of more than 50 bp between the individuals of a species would help in knowing genetic diversity, phenotypic variability, adaptability to tropical environment and disease resistance.

Methods: Read depth-based method implemented in CNVnator was used for calling copy number variant regions on sequenced data obtained from WGS from 15 pooled samples belonging to five draught cattle breeds of Tamil Nadu.

Results: A total of 11,605 CNV regions (CNVRs) were observed covering a genome size of 18.

A cross sectional study on molecular prevalence of Orientia tsutsugamushi in household rat population of South India.

This study aimed to assess the molecular prevalence of mite-borne zoonotic pathogen O. tsutsugamushi in household rats of South India through nested polymerase chain reaction amplification of O. tsutsugamushi 47-kDa htrA gene and to determine the most suitable sample type for screening of O.

Genetic evaluation of semen production potential in Indigenous bulls using random regression models in a Bayesian framework.

Genetic potential of indigenous bulls with respect to semen production traits over the age of the bulls at semen collection was analyzed using random regression models (RRMs). Data pertaining to 59,641 ejaculates from 189 bulls of 18 indigenous breeds collected from BAIF (Bharatiya Agro Industries Foundation) was utilized for this study. Six semen production traits, viz.

Generation of single stranded DNA with selective affinity to bovine spermatozoa.

Objective: This study was conducted to generate single stranded DNA oligonucleotides with selective affinity to bovine spermatozoa, assess its binding potential and explore its potential utility in trapping spermatozoa from suspensions.

Methods: A combinatorial library of 94 mer long oligonucleotide was used for systematic evolution of ligands by exponential enrichment (SELEX) with bovine spermatozoa. The amplicons from sixth and seventh rounds of SELEX were sequenced, and the reads were clustered employing cluster database at high identity with tolerance (CD-HIT) and FASTAptamer.

RNAseq Reveals the Contribution of Interferon Stimulated Genes to the Increased Host Defense and Decreased PPR Viral Replication in Cattle.

(PPRV) is known to replicate in a wide variety of ruminants causing very species-specific clinical symptoms. Small ruminants (goats and sheep) are susceptible to disease while domesticated cattle and buffalo are dead-end hosts and do not display clinical symptoms. Understanding the host factors that influence differential pathogenesis and disease susceptibility could help the development of better diagnostics and control measures.

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing.

Background: The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence.

Methods: Here, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing.

Evaluating the efficacy of LaSota vaccination induced protection in chickens upon challenge with a genotype IV strain of Newcastle disease virus.

Newcastle disease (ND) is a major risk to the poultry industry which results in severe economic loss throughout the world even with vaccination. The vaccine viruses that are used in many countries include the LaSota and other live viruses that were isolated in the early and late 1950s. Reports from several laboratories including ours indicate a greater variance of the circulating strains and recent classification indicates the existence of XVIII different genotypes of NDV strains.

Co-culture: A quick approach for isolation of street rabies virus in murine neuroblastoma cells.

Background: Laboratory detection of rabies in most cases is based on detection of the antigen by fluorescent antibody test, however, in weak positive cases confirmative laboratory diagnosis depends on widely accepted mouse inoculation test. Cell lines like neuroblastoma have been used to isolate the virus with greater success not only to target for diagnosis, but also for molecular studies that determine the epidemiology of the circulating street rabies strains and in studies that look at the efficiency of the developed monoclonal antibodies to neutralize the different rabies strains. Due to the recent issues in obtaining ethical permission for mouse experimentation, and also the passages required in the cell lines to isolate the virus, we report herewith a co-culture protocol using the murine neuroblastoma (MNA) cells, which enable quicker isolation of street rabies virus with minimum passages.

Toll-like receptor responses to Peste des petits ruminants virus in goats and water buffalo.

Ovine rinderpest or goat plague is an economically important and contagious viral disease of sheep and goats, caused by the Peste des petits ruminants virus (PPRV). Differences in susceptibility to goat plague among different breeds and water buffalo exist. The host innate immune system discriminates between pathogen associated molecular patterns and self antigens through surveillance receptors known as Toll like receptors (TLR).

Complete Genome Sequence of a Newcastle Disease Virus from a Coturnix coturnix japonica (Japanese Quail) Covey in India.

The genome of a Newcastle disease virus isolated from a Japanese quail in 2003 is reported here. The genome is 15,192 nucleotides (nt) long, as found in the recent genotypes, and grouped as genotype VIIb, with a 6-nt insertion. This is the first report on the sequence of a genotype VII Newcastle disease virus (NDV) from India.

Comparative analysis of innate immune response following in vitro stimulation of sheep and goat peripheral blood mononuclear cells with bluetongue virus - serotype 23.

Bluetongue is an infectious disease caused by bluetongue virus (BTV), which affects sheep, goat, cattle and certain wild ruminants. However severe clinical signs are usually seen with significant mortality in sheep than cattle and goat. To date, comparative studies on innate immune responses of sheep and goat infected with BTV is lacking.

Homology modeling and structural comparison of leucine rich repeats of Toll like receptors 1-10 of ruminants.

Toll-like receptors (TLRs) are transmembrane receptors composed of extra cellular leucine rich repeats (LRRs) that identify specific pathogen associated molecular patterns triggering a innate immune cascade. The LRR regions of TLR 1-10 proteins of goat (Capra hircus), sheep (Ovis aries), buffalo (Bubalus bubalis) and bovine (Bos taurus) were modeled using MODELLER 9v7 tool and validated. The similarities and variations of these 10 TLRs extracellular regions of each species were compared using online servers like FATCAT, SSM and SSAP.

Comparative in vitro toll-like receptor ligand induced cytokine profiles of Toda and Murrah buffaloes-Identification of tumour necrosis factor alpha promoter polymorphism.

The objective of this study was to assess cytokine production upon activation of pattern recognition receptors responsible for sensing bacterial and viral pathogen associated molecular patterns in two genetically diverse buffalo breeds, Toda and Murrah. A very limited molecular-epidemiological analysis showed a higher prevalence of Anaplasma and Theileria in Murrah than Toda buffaloes. Toda buffalo peripheral blood mononuclear cells (PBMC) produced significantly higher levels of IFN γ and/or TNF α mRNAs in response to peptidoglycan, poly I:C, lipopolysaccharide, imiquimod and CpG.

Expression profile of toll-like receptor 2 mRNA in selected tissues of shark (Chiloscyllium sp.).

Sharks are a species of delight for immunologists from the evolutionary perspective since it is considered as the first species to have evolved the adaptive immune responses in addition to the innate immune system. One of the components of the highly conserved innate immune system is the toll-like receptors (TLR) which has a conserved overall protein structure throughout deuterostome evolution. There is no report that demonstrates the expression of these receptors in sharks.

Regulation of CD38 expression in human airway smooth muscle cells: role of class I phosphatidylinositol 3 kinases.

The ADP-ribosyl cyclase activity of CD38 generates cyclic ADP-ribose, a Ca(2+)-mobilizing agent. In human airway smooth muscle (HASM) cells, TNF-α mediates CD38 expression through mitogen-activated protein kinases and NF-κB and AP-1. The phosphatidylinositol-3 kinase/Akt (PI3K/Akt) pathway is involved in TNF-α signaling and contributes to airway hyperresponsiveness and airway remodeling.

Transcript profiling of pattern recognition receptors in a semi domesticated breed of buffalo, Toda, of India.

The primary objective of this study was to assess the expression profile and levels of toll-like receptor (TLR) mRNAs in the spleen, lung, mediastinal lymph node (MLN), jejunum, rectum, skin and peripheral blood mononuclear cells (PBMC) of Toda and Murrah buffalos. Spleen and PBMC had increased expression of TLR mRNAs 2, 4, 5, 6, 8, 9 and 10; lung had increased expression of TLR mRNAs 2, 4, 5, 6 and 8, MLN TLR mRNA 6, 9, 10 and decrease in TLR 3 and 7 mRNAs in skin. No significant differences were observed in the expression levels of any of the TLR mRNA in jejunum and rectum.

Genotypic and pathotypic characterization of Newcastle disease viruses from India.

Newcastle disease virus (NDV) is an avian paramyxovirus that causes significant economic losses to the poultry industry in most parts of the world. The susceptibility of a wide variety of avian species coupled with synanthropic bird reservoirs has contributed to the vast genomic diversity of this virus as well as diagnostic failures. Since the first panzootic in 1926, Newcastle disease (ND) became enzootic in India with recurrent outbreaks in multiple avian species.

Analysis of the Fusion Protein Cleavage Site of Newcastle disease virus Isolates from India Reveals Preliminary Evidence for the Existence of II, VI and VII Genotypes.

Newcastle disease virus (NDV) has been a threat to poultry industry in most of the developing countries with a wide variety of avian species being susceptible, coupled with the presence of mobile wild bird reservoirs contributing not only to the vast genomic diversity of this virus but also to the diagnostic failures. NDV of multiple genotypes (I-XI) is known to be prevalent and reported worldwide. However, there is a paucity of information on the circulating genotypes of NDV in India.

Sequence analysis of Toll-like receptor genes 1-10 of goat (Capra hircus).

This study involved cloning and sequencing of the coding regions of all 10 Toll-like receptor (TLR) genes of goat. Goat TLR 1-10 gene sequences revealed a high degree of nucleotide identity with sheep and cattle sequences (>90%) and 75-85% with pig, mouse and human sequences. At the amino acid level, 85-99% similarity was observed with sheep and cattle and 60-85% with pig, mouse and human.

Differential expression of toll-like receptor mRNA in corneal epithelium of ruminants.

Purpose: The present study was carried out to identify and assess the expression levels of toll-like receptors (TLRs) 1-10 mRNA in corneal epithelial cells of buffalo, goat, sheep and bull.

Materials And Methods: The globes from the respective species were collected and the corneal epithelium was denuded. The expression levels of the different TLR mRNAs were assessed by densitometry of the band intensities following reverse transcriptase polymerase chain reaction (RT-PCR).

Difference in the level of interferon gamma mRNA transcripts on stimulation of cattle and buffalo mononuclear cells with foot and mouth disease virus-antigen: a possible role of sequence variation in promoter region.

In an attempt to resolve the claim that buffaloes differ from cattle in disease progression, this study was undertaken to compare the mitogen (conA) or antigen (foot and mouth disease virus) induced expression levels of interferon gamma (IFN-γ mRNA in peripheral blood mononuclear cells (PBMCs) by real-time quantitative PCR. In general, the levels of IFN-γ mRNA were lower in buffaloes than in crossbred cattle. Significantly higher levels of IFN-γ mRNA were also observed in crossbred cattle when induced with FMD virus (1 μg).

Pathotyping of a Newcastle disease virus isolated from peacock (Pavo cristatus).

This report describes Newcastle disease in peacock and the isolation and characterization of the virus. The virus had an intracerbral pathogenicity index of 1.71 and mean death time of 47 h.

Differential expression of toll-like receptor mRNA in selected tissues of goat (Capra hircus).

Pattern recognition receptors (PRRs) expressed by various immune cells and tissues have been shown to play a pivotal role in the recognition of pathogens by the host. The present study was carried out to identify toll-like receptors (TLRs) 1-10 mRNA in goat peripheral blood mononuclear cells (PBMCs) and selected tissues including jejunum, lung, lymph node, skin, spleen and uterus using reverse transcriptase polymerase chain reaction (RT-PCR). Our results confirm earlier reports regarding the evolutionarily conserved nature of these receptors as successful amplification of the goat TLR mRNAs could be obtained with bovine TLR mRNA-specific primers.