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

Clinical and Serological Characterization of Orf-Induced Immunobullous Disease

Importance: Ecthyma contagiosum, or orf, is a viral zoonotic infection caused by Poxviridae. Although human orf infection is considered to follow a self-limited course, various immunological reactions may be triggered, including immunobullous diseases. In the majority of the latter cases, the antigenic target remained enigmatic. Objective: To characterize the predominant autoantigen in orf-induced immunobullous disease and further describe this clinical entity. Design, Setting, and Participants: This multicenter case series sought to provide detailed clinical, histopathological and immunological characteristics of a patient with orf-induced pemphigoid. Based on this index patient, serological analyses were conducted of 4 additional patients with previously reported orf-induced immunobullous disease. Immunoblotting with extracellular matrix and a recently established indirect immunofluorescence assay for detection of serum anti-laminin 332 IgG were performed. Exposures: The disease course and clinical characteristics of orf-induced immunobullous disease were observed. Main Outcomes and Measures: Orf-induced immunobullous disease is primarily characterized by anti-laminin 332 autoantibodies, predominant skin involvement, and a self-limiting course. The study provides further details on epidemiological, clinical, immunopathological, diagnostic, and therapeutic aspects of orf-induced immunobullous disease. Results: In all 5 patients, IgG1 and/or IgG3 autoantibodies against laminin 332 were identified. The α3, β3, and γ2 chains were recognized in 2, 4, and 1 patient(s), respectively. Conclusions and Relevance: In this case series, laminin 332, a well-known target antigen in mucous membrane pemphigoid, was a major autoantigen in orf-induced immunobullous disease, even though predominant mucosal lesions were lacking in this autoimmune blistering disease. Orf-induced anti-laminin 332 pemphigoid is proposed as distinct clinical entity

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

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

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

Clinical and Serological Characterization of Orf-Induced Immunobullous Disease

Importance: Ecthyma contagiosum, or orf, is a viral zoonotic infection caused by Poxviridae. Although human orf infection is considered to follow a self-limited course, various immunological reactions may be triggered, including immunobullous diseases. In the majority of the latter cases, the antigenic target remained enigmatic. Objective: To characterize the predominant autoantigen in orf-induced immunobullous disease and further describe this clinical entity. Design, Setting, and Participants: This multicenter case series sought to provide detailed clinical, histopathological and immunological characteristics of a patient with orf-induced pemphigoid. Based on this index patient, serological analyses were conducted of 4 additional patients with previously reported orf-induced immunobullous disease. Immunoblotting with extracellular matrix and a recently established indirect immunofluorescence assay for detection of serum anti-laminin 332 IgG were performed. Exposures: The disease course and clinical characteristics of orf-induced immunobullous disease were observed. Main Outcomes and Measures: Orf-induced immunobullous disease is primarily characterized by anti-laminin 332 autoantibodies, predominant skin involvement, and a self-limiting course. The study provides further details on epidemiological, clinical, immunopathological, diagnostic, and therapeutic aspects of orf-induced immunobullous disease. Results: In all 5 patients, IgG1 and/or IgG3 autoantibodies against laminin 332 were identified. The α3, β3, and γ2 chains were recognized in 2, 4, and 1 patient(s), respectively. Conclusions and Relevance: In this case series, laminin 332, a well-known target antigen in mucous membrane pemphigoid, was a major autoantigen in orf-induced immunobullous disease, even though predominant mucosal lesions were lacking in this autoimmune blistering disease. Orf-induced anti-laminin 332 pemphigoid is proposed as distinct clinical entity.