Effect of genetic variation in the MHC Class II DRB region on resistance and susceptibility to Johne’s disease in endangered Indian Jamunapari goats

Evaluation of Single Nucleotide Polymorphisms (SNPs) Associated with Genetic Resistance to Bovine Paratuberculosis in Marchigiana Beef Cattle, an Italian Native Breed

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis (PTB), a widespread chronic enteritis of ruminants. The progression of the infection depends on the containment action of innate and cell-mediated immunity (CMI), and it is related to environmental and genetic factors. In particular, PTB susceptibility seems to be associated with specific genes coding for immune regulators involved in the cell-mediated response during the infection. The aim of this preliminary study was to verify, in Italian beef cattle, an association between MAP infectious status and the presence of single nucleotide polymorphisms (SNPs) in candidate genes. To the best of our knowledge, this is the first investigation conducted on a native beef cattle breed, known as Marchigiana, reared in Central Italy. The present research, based on a longitudinal study, aimed to identify and correlate phenotypic and genetic profiles characteristic of the subjects potentially able to contrast or contain PTB. In a MAP-infected herd, ELISA, IFN-γ tests, qPCR, and cultures were performed at a follow-up, occurring within a period ranging from three to six years, to evaluate the individual state of infection. Animals testing positive for at least one test were considered infected. DNA samples of 112 bovines, with known MAP statuses, were analyzed to verify an association with SNPs in the genes encoding gamma-interferon (BoIFNG), interleukin receptor 10 (IL10RA), interleukin receptor 12 (IL12RB2), and toll-like receptors (TLR1, TLR2, TLR4). Regarding statistical analysis, the differences among target genes and pairs of alleles in the analyzed groups of animals, were evaluated at a significance level of p < 0.05. For IL10RA and for IL12RB2 genes, relevant differences in genotypic frequencies among the considered cattle groups were observed. For all candidate genes studied in this investigation, SNP genotypes already associated with PTB resistance were found more frequently in our population, suggesting potential resistance traits in the Marchigiana breed.

An Offline Image Auditing System for Legacy Meter Reading Systems in Developing Countries: A Machine Learning Approach

The developing countries are challenged with overbilling and underbilling, due to manual meter reading, which results in consumer dissatisfaction and loss of revenue. The existing automated meter reading (AMR) solutions are expensive; hence, sample-based manual snap auditing systems are introduced to control such meter reading inaccuracies. In these systems, the meter reader, besides reading, also collects meter images, which are used to manually audit the meter’s accuracy. Although such systems are inexpensive, they are limited in their ability to be sustainable and ensure 100% accurate meter readings. In this paper, a novel offline optical character recognition (OCR) system-based Snap Audit system is proposed and tested for its efficient and real-time 100% accurate meter reading capabilities. The experimental results on 5,000 real-world instances show that the proposed approach processes an image in 0.05 seconds with 94% accuracy. Moreover, the developed approach is evaluated with four state-of-the-art algorithms: region convolution neural network (RCNN), nanonets, Fast-OCR, and PyTesseract. The results provide evidence that our new system design along with novel approach is more robust and efficient as compared to existing algorithms by 43.6%.

Paratuberculosis: The Hidden Killer of Small Ruminants

Simple Summary

Paratuberculosis is a chronic disease of ruminants and many non-ruminant animals caused by the bacterium Mycobacterium avium subsp. paratuberculosis. Affected animals show diarrhoea, loss of weight, and decreased production performance with consequent economic losses. This bacterium has been detected in some humans suffering from a chronic intestinal disease known as Crohn’s disease (CD) and, therefore, some scientists believe that CD is the human form of paratuberculosis. The disease in small ruminants has been reported in all continents, with goats being more susceptible than sheep. The clinical signs of the disease in goats are not so obvious as often do not show signs of diarrhoea, and the animal may die before being finally diagnosed. In Africa and many developing countries, paratuberculosis is described as a “neglected disease” particularly in small ruminants, which play a vital role in the livelihood of poor communities. This overview attempts to highlight the current research and gaps on this disease in small ruminants to draw more attention for further studies on diagnosis, prevention and control.

Abstract

Paratuberculosis (PTB) is a contagious and chronic enteric disease of ruminants and many non-ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP), and is characterised by diarrhoea and progressive emaciation with consequent serious economic losses due to death, early culling, and reduced productivity. In addition, indirect economic losses may arise from trade restrictions. Besides being a production limiting disease, PTB is a potential zoonosis; MAP has been isolated from Crohn’s disease patients and was associated with other human diseases, such as rheumatoid arthritis, Hashimoto’s thyroiditis, Type 1 diabetes, and multiple sclerosis. Paratuberculosis in sheep and goats may be globally distributed though information on the prevalence and economic impact in many developing countries seem to be scanty. Goats are more susceptible to infection than sheep and both species are likely to develop the clinical disease. Ingestion of feed and water contaminated with faeces of MAP-positive animals is the common route of infection, which then spreads horizontally and vertically. In African countries, PTB has been described as a “neglected disease”, and in small ruminants, which support the livelihood of people in rural areas and poor communities, the disease was rarely reported. Prevention and control of small ruminants’ PTB is difficult because diagnostic assays demonstrate poor sensitivity early in the disease process, in addition to the difficulties in identifying subclinically infected animals. Further studies are needed to provide more insight on molecular epidemiology, transmission, and impact on other animals or humans, socio-economic aspects, prevention and control of small ruminant PTB.

The Paratuberculosis Paradigm Examined: A Review of Host Genetic Resistance and Innate Immune Fitness in Mycobacterium avium subsp. Paratuberculosis Infection

Paratuberculosis, or Johne's Disease (JD) is a debilitating chronic enteritis mainly affecting ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). This organism causes worldwide economic losses to the livestock industry, and is of public health importance due to the potential zoonotic risk between MAP and Crohn's disease (CD) in humans. Without economical treatments, or a vaccine capable of preventing infection without causing cross-reactions with bovine tuberculosis, test-and-cull methods for disease control are imperative. Unfortunately, difficulties in diagnostics and long subclinical stage hinder adequate control and is further complicated by variation in MAP exposure outcome. Interestingly, the majority of infections result in asymptomatic presentation and never progress to clinical disease. One contributing factor is host genetics, where polymorphisms in innate immune genes have been found to influence resistance and susceptibility to disease. Candidate genes identified across studies overlap with those found in CD and tuberculosis including; Solute carrier family 11 member 1 gene (SLC11A1), Nucleotide-binding-oligomerization domain containing gene 2 (NOD2), Major histocompatibility complex type II (MHC-II), and Toll-like receptor (TLR) genes. This review will highlight evidence supporting the vital role of these genes in MAP infection outcome, associated challenges, and implications for the future of JD research.

Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus)

BACKGROUND

The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian species, it is notably different among ruminants due to a chromosomal inversion that splits MHC type II genes into two subregions (IIa, IIb). Recombination rates are reportedly high between these subregions, and a lack of linkage has been documented in domestic ruminants. However, no study has yet examined the degree of linkage between these subregions in a wild ruminant. The white-tailed deer (Odocoileus virginianus), a popular ruminant of the Cervidae family, is habitually plagued by pathogens in its natural environment (e.g. Haemonchus contortus, Elaeophora). Due to the association between MHC haplotypes and disease susceptibility, a deeper understanding of MHC polymorphism and linkage between MHC genes can further aid in this species' successful management. We sequenced MHC-DRB exon 2 (IIa) and MHC-DOB exon 2 (IIb) on the MiSeq platform from an enclosed white-tailed deer population located in Alabama.

RESULTS

We identified 12 new MHC-DRB alleles, and resampled 7 alleles, which along with other published alleles brings the total number of documented alleles in white-tailed deer to 30 for MHC-DRB exon 2. The first examination of MHC-DOB in white-tailed deer found significantly less polymorphism (11 alleles), as was expected of a non-classical MHC gene. While MHC-DRB was found to be under positive, diversifying selection, MHC-DOB was found to be under purifying selection for white-tailed deer. We found no significant linkage disequilibrium between MHC-DRB and MHC-DOB, suggesting that these loci are unlikely to be closely linked.

CONCLUSIONS

Overall, this study identified 12 new MHC-DRB exon 2 alleles and characterized a new, non-classical, MHC II gene (MHC-DOB) for white-tailed deer. We also found a lack of significant linkage between these two loci, which supports previous findings of a chromosomal inversion within the MHC type II gene region in ruminants, and suggests that white-tailed deer may have a recombination hotspot between these MHC regions similar to that found for Bos taurus.

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their association with milk, meat, and reproduction phenotypes. In this regard, causal mutations have been identified in the αS1-casein gene that has a strong effect on milk composition and the PIS locus that is linked to intersexuality and polledness. In recent times, the development of massive parallel sequencing technologies has allowed to build a reference genome for goats as well as to monitor the expression of mRNAs and microRNAs in a broad array of tissues and experimental conditions. Besides, the recent design of a 52K SNP chip is expected to have a broad impact in the analysis of the genetic architecture of traits of economic interest as well as in the study of the population structure of goats at a worldwide scale.

Major histocompatibility complex class II polymorphisms in forest musk deer (Moschus berezovskii) and their probable association with purulent disease

Genes of the major histocompatibility complex (MHC) family are crucial in immune responses because they present pathogenic peptides to T cells. In this study, we analysed the genetic variation in forest musk deer (Moschus berezovskii) MHC II genes and its potential association with musk deer purulent disease. In total, 53 purulent disease-susceptible and 46 purulent disease-resistant individuals were selected for MHC II exon 2 fragment analysis. Among them, 16 DQ alleles and four additional DR alleles were identified, with DQ exon 2 fragments displaying a low level of polymorphism. The nonsynonymous substitutions exceeded the synonymous substitutions in the peptide-binding sites of DQA2, DQB1 and DQB2. Then, 28 MHC II alleles were used to analyse the distribution patterns of purulent disease between the susceptible and resistant groups. Among them, three alleles (DQA1*01, DQA1*02 and DQA2*04) were found to be resistant, and five alleles (DRB3*07, DQA1*03, DQA1*04, DQA2*05 and DQA2*06) were found to increase susceptibility. Additionally, three haplotypes were found to be putatively associated with musk deer purulent disease. However, these three haplotypes were only found in the resistant or susceptible group, and their frequencies were low. The results from our study support a contributory role of MHC II polymorphisms in the development of purulent disease in forest musk deer.

Impact of host genetics on susceptibility and resistance to Mycobacterium avium subspecies Paratuberculosis infection in domestic ruminants

Johne's disease or Paratuberculosis has emerged as major infectious disease of animals in general and domestic livestock in particular on global basis. There have been major initiatives in developed countries for the control of this incurable malady of animals and human beings alike (inflammatory bowel disease or Crohn's disease). Disease has not received similar attention due to inherent complexities of disease, diagnosis and control, in resource poor counties around the world. However, the rich genetic diverstiy of the otherwise low productive animal population offers opportunity for the control of Johne's disease and improve per animal productivity. Present review aims to gather and compile information available on genetics or resistance to Johne's disease and its future exploitation by resource poor countries rich in animal diversity. This review will also help to create awareness and share knowledge and experience on prevalence and opportunities for control of Johne's disease in the livestock population to boost per animal productivity among developing and poor countries of the world. Breeding of animals for disease resistance provides good, safe, effective and cheaper way of controlling Johne's disease in animals, with especial reference to domestic livestock of developing and poor countries. Study will help to establish better understanding of the correlation between host cell factors and resistance to MAP infection which may have ultimately help in the control of Johne's disease in future.