Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs

<p>Abstract</p> <p>Background</p> <p>Combining microarray results and biological pathway information will add insight into biological processes. Pathway information is widely available in databases through the internet.</p> <p>Mammalian muscle formation has been previously studied using microarray technology in pigs because these animals are an interesting animal model for muscle formation due to selection for increased muscle mass. Results indicated regulation of the expression of genes involved in proliferation and differentiation of myoblasts, and energy metabolism. The aim of the present study was to analyse microarrays studying myogenesis in pigs. It was necessary to develop methods to search biochemical pathways databases.</p> <p>Results</p> <p>PERL scripts were developed that used the names of the genes on the microarray to search databases. Synonyms of gene names were added to the list by searching the Gene Ontology database. The KEGG database was searched for pathway information using this updated gene list. The KEGG database returned 88 pathways. Most genes were found in a single pathway, but others were found in up to seven pathways. Combining the pathways and the microarray information 21 pathways showed sufficient information content for further analysis. These pathways were related to regulation of several steps in myogenesis and energy metabolism. Pathways regulating myoblast proliferation and muscle fibre formation were described. Furthermore, two networks of pathways describing the formation of the myoblast cytoskeleton and regulation of the energy metabolism during myogenesis were presented.</p> <p>Conclusion</p> <p>Combining microarray results and pathways information available through the internet provide biological insight in how the process of porcine myogenesis is regulated.</p

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits

<p>Abstract</p> <p>Background</p> <p>In a previous screen to identify differentially expressed genes associated with embryonic development, the porcine <it>PNAS-4 </it>gene had been found. Considering differentially expressed genes in early stages of muscle development are potential candidate genes to improve meat quality and production efficiency, we determined how porcine <it>PNAS-4 </it>gene regulates meat production. Therefore, this gene has been sequenced, expression analyzed and associated with meat production traits.</p> <p>Results</p> <p>We cloned the full-length cDNA of porcine <it>PNAS-4 </it>gene encoding a protein of 194 amino acids which was expressed in the Golgi complex. This gene was mapped to chromosome 10, q11–16, in a region of conserved synteny with human chromosome 1 where the human homologous gene was localized. Real-time PCR revealed that <it>PNAS-4 </it>mRNA was widely expressed with highest expression levels in skeletal muscle followed by lymph, liver and other tissues, and showed a down-regulated expression pattern during prenatal development while a up-regulated expression pattern after weaning. Association analysis revealed that allele C of SNP A1813C was prevalent in Chinese indigenous breeds whereas A was dominant allele in Landrace and Large White, and the pigs with homozygous CC had a higher fat content than those of the pigs with other genotypes (<it>P </it>< 0.05).</p> <p>Conclusion</p> <p>Porcine <it>PNAS-4 </it>protein tagged with green fluorescent protein accumulated in the Golgi complex, and its mRNA showed a widespread expression across many tissues and organs in pigs. It may be an important factor affecting the meat production efficiency, because its down-regulated expression pattern during early embryogenesis suggests involvement in increase of muscle fiber number. In addition, the SNP A1813C associated with fat traits might be a genetic marker for molecular-assisted selection in animal breeding.</p

Organoids: a promising new in vitro platform in livestock and veterinary research.

Organoids are self-organizing, self-renewing three-dimensional cellular structures that resemble organs in structure and function. They can be derived from adult stem cells, embryonic stem cells, or induced pluripotent stem cells. They contain most of the relevant cell types with a topology and cell-to-cell interactions resembling that of the in vivo tissue. The widespread and increasing adoption of organoid-based technologies in human biomedical research is testament to their enormous potential in basic, translational- and applied-research. In a similar fashion there appear to be ample possibilities for research applications of organoids from livestock and companion animals. Furthermore, organoids as in vitro models offer a great possibility to reduce the use of experimental animals. Here, we provide an overview of studies on organoids in livestock and companion animal species, with focus on the methods developed for organoids from a variety of tissues/organs from various animal species and on the applications in veterinary research. Current limitations, and ongoing research to address these limitations, are discussed. Further, we elaborate on a number of fields of research in animal nutrition, host-microbe interactions, animal breeding and genomics, and animal biotechnology, in which organoids may have great potential as an in vitro research tool

Therapeutic Effects of Glutamic Acid in Piglets Challenged with Deoxynivalenol

The mycotoxin deoxynivalenol (DON), one of the most common food contaminants, primarily targets the gastrointestinal tract to affect animal and human health. This study was conducted to examine the protective function of glutamic acid on intestinal injury and oxidative stress caused by DON in piglets. Twenty-eight piglets were assigned randomly into 4 dietary treatments (7 pigs/treatment): 1) uncontaminated control diet (NC), 2) NC+DON at 4 mg/kg (DON), 3) NC+2% glutamic acid (GLU), and 4) NC+2% glutamic acid + DON at 4 mg/kg (DG). At day 15, 30 and 37, blood samples were collected to determine serum concentrations of CAT (catalase), T-AOC (total antioxidant capacity), H2O2 (hydrogen peroxide), NO (nitric oxide), MDA (maleic dialdehyde), DAO (diamine oxidase) and D-lactate. Intestinal morphology, and the activation of Akt/mTOR/4EBP1 signal pathway, as well as the concentrations of H2O2, MDA, and DAO in kidney, liver and small intestine, were analyzed at day 37. Results showed that DON significantly (P<0.05) induced oxidative stress in piglets, while this stress was remarkably reduced with glutamic acid supplementation according to the change of oxidative parameters in blood and tissues. Meanwhile, DON caused obvious intestinal injury from microscopic observations and permeability indicators, which was alleviated by glutamic acid supplementation. Moreover, the inhibition of DON on Akt/mTOR/4EBP1 signal pathway was reduced by glutamic acid supplementation. Collectively, these data suggest that glutamic acid may be a useful nutritional regulator for DON-induced damage manifested as oxidative stress, intestinal injury and signaling inhibition

Gene expression patterns in four brain areas associate with quantitative measure of estrous behavior in dairy cows

<p>Abstract</p> <p>Background</p> <p>The decline noticed in several fertility traits of dairy cattle over the past few decades is of major concern. Understanding of the genomic factors underlying fertility, which could have potential applications to improve fertility, is very limited. Here, we aimed to identify and study those genes that associated with a key fertility trait namely estrous behavior, among genes expressed in four bovine brain areas (hippocampus, amygdala, dorsal hypothalamus and ventral hypothalamus), either at the start of estrous cycle, or at mid cycle, or regardless of the phase of cycle.</p> <p>Results</p> <p>An average heat score was calculated for each of 28 primiparous cows in which estrous behavior was recorded for at least two consecutive estrous cycles starting from 30 days post-partum. Gene expression was then measured in brain tissue samples collected from these cows, 14 of which were sacrificed at the start of estrus and 14 around mid cycle. For each brain area, gene expression was modeled as a function of the orthogonally transformed average heat score values using a Bayesian hierarchical mixed model. Genes whose expression patterns showed significant linear or quadratic relationships with heat scores were identified. These included genes expected to be related to estrous behavior as they influence states like socio-sexual behavior, anxiety, stress and feeding motivation (<it>OXT, AVP, POMC, MCHR1</it>), but also genes whose association with estrous behavior is novel and warrants further investigation.</p> <p>Conclusions</p> <p>Several genes were identified whose expression levels in the bovine brain associated with the level of expression of estrous behavior. The genes <it>OXT </it>and <it>AVP </it>play major roles in regulating estrous behavior in dairy cows. Genes related to neurotransmission and neuronal plasticity are also involved in estrous regulation, with several genes and processes expressed in mid-cycle probably contributing to proper expression of estrous behavior in the next estrus. Studying these genes and the processes they control improves our understanding of the genomic regulation of estrous behavior expression.</p

Meta-analysis of Chicken - Salmonella infection experiments.

Chantier qualité GAInternational audienceUNLABELLED: ABSTRACT: BACKGROUND: Chicken meat and eggs can be a source of human zoonotic pathogens, especially Salmonella species. These food items contain a potential hazard for humans. Chickens lines differ in susceptibility for Salmonella and can harbor Salmonella pathogens without showing clinical signs of illness. Many investigations including genomic studies have examined the mechanisms how chickens react to infection. Apart from the innate immune response, many physiological mechanisms and pathways are reported to be involved in the chicken host response to Salmonella infection. The objective of this study was to perform a meta-analysis of diverse experiments to identify general and host specific mechanisms to the Salmonella challenge. RESULTS: Diverse chicken lines differing in susceptibility to Salmonella infection were challenged with different Salmonella serovars at several time points. Various tissues were sampled at different time points post-infection, and resulting host transcriptional differences investigated using different microarray platforms. The meta-analysis was performed with the R-package metaMA to create lists of differentially regulated genes. These gene lists showed many similarities for different chicken breeds and tissues, and also for different Salmonella serovars measured at different times post infection. Functional biological analysis of these differentially expressed gene lists revealed several common mechanisms for the chicken host response to Salmonella infection. The meta-analysis-specific genes (i.e. genes found differentially expressed only in the meta-analysis) confirmed and expanded the biological functional mechanisms. CONCLUSIONS: The meta-analysis combination of heterogeneous expression profiling data provided useful insights into the common metabolic pathways and functions of different chicken lines infected with different Salmonella serovars

The workflow diagram describing the individual steps taken by the software from microarray data to physiological understanding via pathways analysis

<p><b>Copyright information:</b></p><p>Taken from "Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs"</p><p>http://www.biomedcentral.com/1471-213X/7/66</p><p>BMC Developmental Biology 2007;7():66-66.</p><p>Published online 13 Jun 2007</p><p>PMCID:PMC1919358.</p><p></p> Step 1: A PERL script uses a text file with a list of all genes on the microarray to search the Gene Ontology database for synonyms. These Synonyms are added to the gene list. Step 2 uses this updated gene list to search the KEGG pathway database for pathways in which the genes are involved. If one or more pathways were found for a gene the KEGG database returns a list of pathway names for that gene and a link to the reference pathway for each pathway. Both are added to the file. Step 3 combines the results of the microarray and the pathways. All genes of the pathway represented on the microarray have an expression pattern consisting of the expression in the Longissimus muscle at seven time points during gestation. First all genes of the pathway are considered. Secondly, if more than one biochemical path is specified by the pathway (i.e. called subpathways) the individual subpathways are investigated separately. Thirdly, if KEGG-pathways are linked either because the pathway indicates it or because at least one gene is found in two or more pathways, a network of these pathways is constructed. In step 4 the expression patterns of these pathways and networks were analysed for comparable expression patterns that may indicate common regulatory events linking genes in pathways, subpathways, or networks of pathways creating biological understanding of the physiology of the studied processes

The Figure shows an example of the connection of the KEGG pathways Focal adhesion (partial pathway, Green genes) and MAPK signalling (partial pathway, blue genes)

<p><b>Copyright information:</b></p><p>Taken from "Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs"</p><p>http://www.biomedcentral.com/1471-213X/7/66</p><p>BMC Developmental Biology 2007;7():66-66.</p><p>Published online 13 Jun 2007</p><p>PMCID:PMC1919358.</p><p></p> Both biochemical pathways indicate connections to each other (indicated in the boxes) and gene profiles were produced on the microarray