A mRNA landscape of bovine embryos after standard and MAPK-inhibited culture conditions: a comparative analysis

Background

Genes and signalling pathways involved in pluripotency have been studied extensively in mouse and human pre-implantation embryos and embryonic stem (ES) cells. The unsuccessful attempts to generate ES cell lines from other species including cattle suggests that other genes and pathways are involved in maintaining pluripotency in these species. To investigate which genes are involved in bovine pluripotency, expression profiles were generated from morula, blastocyst, trophectoderm and inner cell mass (ICM) samples using microarray analysis. As MAPK inhibition can increase the NANOG/GATA6 ratio in the inner cell mass, additionally blastocysts were cultured in the presence of a MAPK inhibitor and changes in gene expression in the inner cell mass were analysed.

Results

Between morula and blastocyst 3,774 genes were differentially expressed and the largest differences were found in blastocyst up-regulated genes. Gene ontology (GO) analysis shows lipid metabolic process as the term most enriched with genes expressed at higher levels in blastocysts. Genes with higher expression levels in morulae were enriched in the RNA processing GO term. Of the 497 differentially expressed genes comparing ICM and TE, the expression of NANOG, SOX2 and POU5F1 was increased in the ICM confirming their evolutionary preserved role in pluripotency. Several genes implicated to be involved in differentiation or fate determination were also expressed at higher levels in the ICM. Genes expressed at higher levels in the ICM were enriched in the RNA splicing and regulation of gene expression GO term. Although NANOG expression was elevated upon MAPK inhibition, SOX2 and POU5F1 expression showed little increase. Expression of other genes in the MAPK pathway including DUSP4 and SPRY4, or influenced by MAPK inhibition such as IFNT, was down-regulated.

Conclusion

The data obtained from the microarray studies provide further insight in gene expression during bovine embryonic development. They show an expression profile in pluripotent cells that indicates a pluripotent, epiblast-like state. The inability to culture ICM cells as stem cells in the presence of an inhibitor of MAPK activity together with the reported data indicates that MAPK inhibition alone is not sufficient to maintain a pluripotent character in bovine cells.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1448-x) contains supplementary material, which is available to authorized users.     

The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.Key Words: EuReGene, kidney, genome, development, pathophysiology, genetics     

Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data

Background

High-throughput genotype (HTG) data has been used primarily in genome-wide association (GWA) studies; however, GWA results explain only a limited part of the complete genetic variation of traits. In systems genetics, network approaches have been shown to be able to identify pathways and their underlying causal genes to unravel the biological and genetic background of complex diseases and traits, e.g., the Weighted Gene Co-expression Network Analysis (WGCNA) method based on microarray gene expression data. The main objective of this study was to develop a scale-free weighted genetic interaction network method using whole genome HTG data in order to detect biologically relevant pathways and potential genetic biomarkers for complex diseases and traits.

Results

We developed the Weighted Interaction SNP Hub (WISH) network method that uses HTG data to detect genome-wide interactions between single nucleotide polymorphism (SNPs) and its relationship with complex traits. Data dimensionality reduction was achieved by selecting SNPs based on its: 1) degree of genome-wide significance and 2) degree of genetic variation in a population. Network construction was based on pairwise Pearson's correlation between SNP genotypes or the epistatic interaction effect between SNP pairs. To identify modules the Topological Overlap Measure (TOM) was calculated, reflecting the degree of overlap in shared neighbours between SNP pairs. Modules, clusters of highly interconnected SNPs, were defined using a tree-cutting algorithm on the SNP dendrogram created from the dissimilarity TOM (1-TOM). Modules were selected for functional annotation based on their association with the trait of interest, defined by the Genome-wide Module Association Test (GMAT). We successfully tested the established WISH network method using simulated and real SNP interaction data and GWA study results for carcass weight in a pig resource population; this resulted in detecting modules and key functional and biological pathways related to carcass weight.

Conclusions

We developed the WISH network method which is a novel 'systems genetics' approach to study genetic networks underlying complex trait variation. The WISH network method reduces data dimensionality and statistical complexity in associating genotypes with phenotypes in GWA studies and enables researchers to identify biologically relevant pathways and potential genetic biomarkers for any complex trait of interest.

     

Research into the (Cost-) effectiveness of the ketogenic diet among children and adolescents with intractable epilepsy: design of a randomized controlled trial

Background  

Epilepsy is a neurological disorder, characterized by recurrent unprovoked seizures which have a high impact on the individual as well as on society as a whole. In addition to the economic burden, epilepsy imposes a substantial burden on the patients and their surroundings. Patients with uncontrolled epilepsy depend heavily on informal care and on health care professionals. About 30% of patients suffer from drug-resistant epilepsy. The ketogenic diet can be a treatment of last resort, especially for children. The beneficial effect of the ketogenic diet has been proven, but information is lacking about its cost-effectiveness. In the current study we will evaluate the (cost-) effectiveness of the ketogenic diet in children and adolescents with intractable epilepsy.     

Beetles with ‘trochantelli’: phylogeny of Cephenniini (Coleoptera: Staphylinidae: Scydmaeninae) focussing on Neotropical genera

Neotropical genera of Cephenniini characterized by an additional leg ‘segment’ (‘trochantellus’) are revised, and the following new taxa are described: Shyri gen.n. , Shyri pichincha sp.n. (type species of Shyri) (Ecuador), Shyri perversus sp.n. (Ecuador), Shyri quitu sp.n. (Ecuador), Shyri microphthalmus sp.n. (Ecuador), Monstrophennium gen.n. (type species: Cephennium spinicolle Schaufuss), Furcodes gen.n. , Furcodes apicalis sp.n. (type species of Furcodes) (Mexico), Furcodes tutule sp.n. (Honduras), Paracephennium pumilio sp.n. (Costa Rica), Pseudocephennium iwokramanum sp.n. (Guyana), Pseudocephennium trilineatum sp.n. (Guyana), Pseudocephennium araguanum sp.n. (Venezuela), Pseudocephennium maximum sp.n. (Venezuela), Pseudocephennium peruvianum sp.n. (Peru), Pseudocephennium cochabambanum sp.n. (Bolivia), Pseudocephennium saramaccanum sp.n. (Suriname) and Pseudocephennium brokopondonum sp.n. (Suriname). Pseudocephennium spinicolle (Schaufuss) is transferred to Monstrophennium. Cladistic analysis of characters from adult morphology of all genera of Cephenniini and a large outgroup sample from Cyrtoscydmini, Eutheiini, Scydmaenini, Clidicini and Mastigini strongly supported the monophyly of Cephenniini. However, only the Cephennomicrus group comprising nine genera was strongly supported as a monophyletic clade, while only weak support was found for the previously suggested Cephennodes group and Cephennium group. Two alternative hypotheses concerning the phylogeny of Cephenniini are put forward and discussed: (i) the Cephennium group is sister to all remaining Cephenniini; or (ii) the Cephennomicrus group is sister to all remaining Cephenniini. The Neotropical genera with ‘trochantellus’ form a well‐supported clade derived from the ancestral lineage of the Cephennodes group.     

Thwarting of behaviour in different contexts and the gakel-call in the laying hen

Earlier studies have shown that thwarting of feeding behaviour in the laying hen is expressed through a specific vocalisation, the gakel-call. The first aim of this study was to investigate whether the effect of deprivation per se on the occurrence of gakel-calls can be distinguished from the effect of the additional frustration. Frustration is defined as the state of an animal that results from nonreward in the expectancy of reward. The second aim was to investigate whether the occurrence of gakel-calls is restricted to a food context or whether it can be regarded as an expression of frustration in general. For this purpose, 20 hens were deprived of food, water and dustbath. After deprivation at a fixed time, a cue was given and the hens were rewarded with access to food, water or dust during a 15-min session on 4 consecutive days. On the fifth day, they were thwarted in the associated behaviours by blocking the access to these commodities, after the hens had been presented the signal that previously preceded the reward. We then recorded behaviours that might reflect the state of frustration in three 15-min periods. The period "Pre-Frustration" started 15 min before "Frustration". This, in turn, was followed by the period "Post-frustration" in which the hens were rewarded again. Nesting behaviour was thwarted by blocking the access to the nest (Frustration) after a hen had reached the last stage of its prelaying behaviour.In the food, water and dustbath context, deprivation elicited gakel-calls. The additional frustration resulted in a higher number of gakel-calls in all contexts except the food context. However, together with the findings of previous experiments, the results of this study suggest that frustration, in general, is expressed through the gakel-call. Frustration in the nest context elicited more gakel-calls than the other contexts. This latter finding is discussed in the light of the occurrence of the gakel-call under natural circumstances.