Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), represents a significant problem for the agriculture industry as well as posing a risk for human health. Current diagnostic tests ...for bTB target the cell-mediated immune (CMI) response to infection with M. bovis, primarily through screening of animals with the tuberculin skin test. Epigenetic modifications have been shown to alter the course of the immune response and differentially methylated regions (DMRs) might also influence the outcome of the skin test in cattle. Whole Genome Bisulphite Sequencing (WGBS) was used to profile DNA methylation levels from peripheral blood of a group of cattle identified as test positive for M. bovis (positive for the single intradermal comparative tuberculin test (SICTT) and/or the interferon-gamma release assay compared to a test negative control group n = 8/group, total of 16 WGBS libraries. Although global methylation profiles were similar for both groups across the genome, 223 DMRs and 159 Differentially Promoter Methylated Genes (DPMGs) were identified between groups with an excess of hypermethylated sites in SICTT positive cattle (threshold > 15% differential methylation). Genes located within these DMRs included the Interleukin 1 receptor (IL1R1) and MHC related genes (BOLA and BOLA-DQB). KEGG pathway analysis identified enrichment of genes involved in Calcium and MAPK signalling, as well as metabolism pathways. Analysis of DMRs in a subset of SICTT negative cattle that were IFN-gamma positive showed differential methylation of genes including Interleukin 10 Receptor, alpha (IL10RA), Interleukin 17 F (IL17F) and host defence peptides (DEFB and BDEF109). This study has identified a number of immune gene loci at which differential methylation is associated with SICTT test results and the degree of methylation could influence effective host immune responses.
We used an embryo lethality assay (ELA) to assess virulence for different isolates from cases of bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Lameness is among the most significant ...animal welfare issues in the poultry industry. Bacterial infections are a major cause of lameness and different bacterial species have been obtained from lame broilers. Reliable lab-based assays are required to assess relative virulence of bacteria obtained from lame broilers. ELA has been used to assess lethal dosage of Enterococcus faecalis and Enterococcus cecorum. We hypothesized that ELA could substitute for more laborious and costly assessments of BCO isolate pathogenicity using live birds. We evaluated 2 different levels of bacteria injected into eggs from layer and commercial broiler embryos. Significant findings include 1) Escherichia coli from neighboring farms operated by the same integrator had very different embryo lethality, 2) isolate Staphylococcus agnetis 908 had low virulence in ELA, even though this isolate can induce more than 50% BCO lameness, 3) Enterococcus cecorum 1415 also had low pathogenicity; even though it was recovered from severe bilateral tibial dyschondroplasia, 4) human and chicken BCO isolates of S. aureus had significant pathogenicity, 5) virulence for some isolates was highly variable possibly corresponding with quality of the embryos/fertile eggs used, and 6) ELA pathogenicity was much lower for our BCO isolates than previous reports which may reflect maternal environment. Overall, ELA virulence and BCO virulence are not always concordant indicating that ELA may not be an effective measure for assessing virulence with respect to BCO.
Ascites syndrome is the most severe manifestation of pulmonary hypertension in fast-growing broilers. The disease can be attributed to increased body weights of birds, where the higher metabolic load ...is not matched by sufficient oxygen supply to the cells and tissues. Although there are environmental components, the disease exhibits moderate to high heritability. The current study uses high throughput whole genome resequencing (WGR) to identify genes and chromosomal regions associated with ascites.
The WGR data identified the CPQ gene on chromosome 2. The association was confirmed by genotyping a large collection of DNAs from phenotyped birds from three distinct broiler lines using SNPs in intron 6 and exon 8 of the CPQ gene. By combining the genotype data for these two SNP loci, we identified three different alleles segregating in the three broiler lines. Particular genotypes could be associated with resistance to ascites. We further determined that particular genotypes most associated with resistance overexpress CPQ mRNA in three tissues which might explain the role of these alleles in contributing to resistance.
Our findings indicate CPQ is an important determinant of pulmonary hypertension syndrome leading to ascites in broilers. We identified particular SNPs that can be used for marker-assisted selection of broilers for resistance to the disease. Our findings validate WGR as a highly efficient approach to map determinants contributing to complex phenotypic or disease-related traits. The CPQ gene has been associated with pulmonary hypertension in genome-wide association studies in humans. Therefore, ascites investigations in broilers are likely to provide insights into some forms of hypertension in humans.
Tea is an economical and most widely used beverage across the globe owing to its unique fragrance and flavor. Plant microbe interaction has emerged as an important topic which got the attention of ...scientists to improve plant performance. Tea microbes remained a prominent research topic for scientists over the years as tea microbes helps in nutrient cycling and stress management which in turn improve the tea growth, yield and quality. The roots of tea plants are colonized by various microbes including arbuscular mycorrhizal fungi (AMF), bacterial communities, and endophytes increase root growth, development and nutrient uptake which in turn improve tea growth, yield and quality. These microbes also increase the concentration of nutrients, amino acids, soluble proteins, flavonoids, catechuic acid, glucose, fructose, sucrose contents caffeine, and polyphenols concentration in tea plants. Besides this, these microbes also protect the tea plants from harmful pest and diseases which in turn leads to an appreciable improvement in plant growth and development. The most important goal of any farming system is to establish a system with production of maximum food while minimizing impacts on the environment. The present review article highlights the role of various microbes in improving the growth, yield and quality of tea plants. In addition, we also discussed the research gaps to improve our understanding about the role of tea microbes in improving tea growth, yield, pest and diseases resistance. We believe that this review will provide a better insight into the existing knowledge of tea microbes in improving tea growth and yield.
Due to the availability of huge amount of molecular biology data, our main focus was to determine the protein structures, functions and their role in different molecular pathways. The 3-D structure ...prediction of protein is important in medicine and biotechnology. Molecular docking not only finds the interaction between proteins but also the accurate models of energy of these interacting proteins and helps in further designing of the better drug for that particular protein. The drug targeting is either to inhibit, restore or for the modification of the protein structure. CatSper protein family is calcium ion permeable channels, located in the plasma membrane of sperm tail. It contains a conserved domain of six trans-membrane helices in their protein sequence. These four CatSper proteins (1 to 4) assemble and form tetramer, calcium selective channel. It has been found that all members of CatSper protein family (1-4) have a role in hyperactivation in sperm and fertilization processes. As a result of deletion of certain regions (bps) containing these genes along with some other genes, male infertility occurs. We have predicted and analyzed the 3D structures of all members of CatSper protein family in this article. Docking of predicted 3D structures of CatSper protein family, with calcium ion was also performed to verify their interactions.
Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has ...been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations.
The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype.
The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.
We are using whole genome resequencing to identify chromosomal regions associated with resistance or susceptibility to ascites, a form of pulmonary hypertension syndrome, meat-type chickens. Previous ...Genome Wide Association Studies (GWAS) based on Single Nucleotide Polymorphisms (SNPs) have identified regions on chromosomes 2, 9 and Z. Despite several GWAS and further genotyping, there are no reliable or potential markers for ascites phenotype. We have completed screening of Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms in ascites resistant and susceptible birds from the relaxed, REL, line derived from a commercial elite broiler line. DNA samples from resistant and susceptible birds were purified, quantified and pooled in two pools of 10 DNAs from each phenotype for both genders. Eight pools (2 pools x 2 phenotypes x 2 genders) were generated. Each pool was submitted for bar-coded library generation, and 2x125 paired end reads on Illumina HiSeq 2500 and with 66X genome coverage. The sequence reads were mapped onto Galgal5 using Bowtie for initial CNV mapping cn.mops (R package). Further mapping to chromosomes were done using NGen and ArrayStar (DNAStar ver 13). So far, we have identified two potential regions for CNVs and 31 regions for SNPs with potential association with ascites phenotype. CPQ gene on chromosome 2 and LRRTM4 gene on chromosome 22 have been validated for containing ascites QTLs. However, their exact role in ascites is yet to be discovered. Further, we screened the regions from REL line in DNAs from an unrelated commercial broiler line using WGR.
Mung bean (Vigna radiata L.) grown under heavy metals such as cadmium stress shows poor growth patterns and yield attributes which can be extenuated by the application of calcium and organic manure ...to the contaminated soil. The present study was designed to decipher the calcium oxide nanoparticles and farmyard manure-induced Cd stress tolerance through improvement in physiological and biochemical attributes of mung bean plants. A pot experiment was conducted by defining appropriate positive and negative controls under differential soil treatments with farmyard manure (1% and 2%) and calcium oxide nanoparticles (0, 5, 10, and 20 mg/L). Root treatment of 20 mg/L calcium oxide nanoparticles (CaONPs) and 2% farmyard manure (FM) reduced the cadmium acquisition from the soil and improved growth in terms of plant height by 27.4% compared to positive control under Cd stress. The same treatment improved shoot vitamin C (ascorbic acid) contents by 35% and functioning of antioxidant enzymes catalase and phenyl ammonia lyase by 16% and 51%, respectively and the levels of malondialdehyde and hydrogen peroxide decreased by 57% and 42%, respectively with the application of 20 mg/L CaONPs and 2% of FM. The gas exchange parameters such as stomata conductance and leaf net transpiration rate were improved due to FM mediated better availability of water. The FM improved soil nutrient contents and friendly biota culminating in good yields. Overall, 2% FM and 20 mg/L CaONPs proved as the best treatment to reduce cadmium toxicity. The growth, yield, and crop performance in terms of physiological and biochemical attributes can be improved by the application of CaONPs and FM under the heavy metal stress.
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