Project description:Background: Epithelial membrane protein 3 (EMP3) was previously reported to be involved in immunological reactions and in tumor as potential suppressor, as well as a candidate gene for cardiac dystrophic calcification (DCC). Given its assumed role in different disorders, we aimed to generate and perform a generalized phenotypic screening of EMP3-knockout mice. Materials and Methods: TaconicArtemis used knockout-targeting strategy and generated knockout mice for EMP3. Large-scale phenotype screens were performed at the German Mouse Clinic (GMC) to obtain a standardized and comprehensive way of phenotype. The phenotype screens involved tests for nearly 320 parameters in different screening areas such as: dysmorphology, behavior, neurology, eye, nociception, energy metabolism, clinical chemistry and hematology, immunology, allergy, steroid metabolism, cardiovascular and lung function and pathology. For DCC, screening was performed in our laboratory using the freeze-thaw injury method. Results: Here, we report on the phenotype of EMP3 knockout. EMP3-KO mice are viable and fertile. Under baseline conditions, an aberrant immunological phenotype was found with nearly 70% penetrance in mutant male mice. Specifically, a lower frequency of T cells and an inverse trend in B cells was observed. Also a higher frequency of B cells was seen in female mutant mice. For all the remaining screening, no genotype-specific differences were found. Also no calcification deposits were found in the EMP3-KO mice as response to injury. In addition we reviewed and discussed the strong role of EMP3 in apoptosis and tumor. Therefore, further analysis of EMP3 as tumor suppressor gene in EMP3-KO mice required investigation under challenging conditions. Conclusion: Large-scale phenotypic screening suggests a role of EMP3 under basal conditions in immunity. Differences in the proportion of various leukocyte subsets from the corresponding wild type were found. Further investigation is ongoing to demonstrate the role of EMP3 as tumor suppressor in a sensitized model. Finally, we excluded the EMP3 gene as candidate gene for DCC on the C57BL/6 genetic background. Thymus and brain of four mutant animals of the EMP3 mutant mice versus a pool of four reference (wildtype) mice; two technical replicates for each mutant mouse including a dye swap experiment - in total 8 chip hybridisations for each of the analysed organs

Project description:Background: Epithelial membrane protein 3 (EMP3) was previously reported to be involved in immunological reactions and in tumor as potential suppressor, as well as a candidate gene for cardiac dystrophic calcification (DCC). Given its assumed role in different disorders, we aimed to generate and perform a generalized phenotypic screening of EMP3-knockout mice. Materials and Methods: TaconicArtemis used knockout-targeting strategy and generated knockout mice for EMP3. Large-scale phenotype screens were performed at the German Mouse Clinic (GMC) to obtain a standardized and comprehensive way of phenotype. The phenotype screens involved tests for nearly 320 parameters in different screening areas such as: dysmorphology, behavior, neurology, eye, nociception, energy metabolism, clinical chemistry and hematology, immunology, allergy, steroid metabolism, cardiovascular and lung function and pathology. For DCC, screening was performed in our laboratory using the freeze-thaw injury method. Results: Here, we report on the phenotype of EMP3 knockout. EMP3-KO mice are viable and fertile. Under baseline conditions, an aberrant immunological phenotype was found with nearly 70% penetrance in mutant male mice. Specifically, a lower frequency of T cells and an inverse trend in B cells was observed. Also a higher frequency of B cells was seen in female mutant mice. For all the remaining screening, no genotype-specific differences were found. Also no calcification deposits were found in the EMP3-KO mice as response to injury. In addition we reviewed and discussed the strong role of EMP3 in apoptosis and tumor. Therefore, further analysis of EMP3 as tumor suppressor gene in EMP3-KO mice required investigation under challenging conditions. Conclusion: Large-scale phenotypic screening suggests a role of EMP3 under basal conditions in immunity. Differences in the proportion of various leukocyte subsets from the corresponding wild type were found. Further investigation is ongoing to demonstrate the role of EMP3 as tumor suppressor in a sensitized model. Finally, we excluded the EMP3 gene as candidate gene for DCC on the C57BL/6 genetic background.

Project description:Background This work focuses on the computational modelling of osteomyelitis, a bone pathology caused by bacteria infection (mostly Staphylococcus aureus). The infection alters the RANK/RANKL/OPG signalling dynamics that regulates osteoblasts and osteoclasts behaviour in bone remodelling, i.e. the resorption and mineralization activity. The infection rapidly leads to severe bone loss, necrosis of the affected portion, and it may even spread to other parts of the body. On the other hand, osteoporosis is not a bacterial infection but similarly is a defective bone pathology arising due to imbalances in the RANK/RANKL/OPG molecular pathway, and due to the progressive weakening of bone structure. Results Since both osteoporosis and osteomyelitis cause loss of bone mass, we focused on comparing the dynamics of these diseases by means of computational models. Firstly, we performed meta-analysis on a gene expression data of normal, osteoporotic and osteomyelitis bone conditions. We mainly focused on RANKL/OPG signalling, the TNF and TNF receptor superfamilies and the NF-kB pathway. Using information from the gene expression data we estimated parameters for a novel model of osteoporosis and of osteomyelitis. Our models could be seen as a hybrid ODE and probabilistic verification modelling framework which aims at investigating the dynamics of the effects of the infection in bone remodelling. Finally we discuss different diagnostic estimators defined by formal verification techniques, in order to assess different bone pathologies (osteopenia, osteoporosis and osteomyelitis) in an effective way. Conclusions We present a modeling framework able to reproduce aspects of the different bone remodeling defective dynamics of osteomyelitis and osteoporosis. We report that the verification-based estimators are meaningful in the light of a feed forward between computational medicine and clinical bioinformatics Model is encoded by Ruby and submitted and curated to BioModels by Ahmad Zyoud

Project description:BackgroundMicroRNAs (miRNA) are 20 approximately 25 nucleotide non-coding RNAs that inhibit the translation of targeted mRNA, and they have been implicated in the development of human malignancies. High grade serous ovarian carcinomas, the most common and lethal subtype of ovarian cancer, can occur sporadically or in the setting of BRCA1/2 syndromes. Little is known regarding the miRNA expression profiles of high grade serous carcinoma in relation to BRCA1/2 status, and compared to normal tubal epithelium, the putative tissue of origin for high grade serous carcinomas.Methodology/principal findingsGlobal miRNA expression profiling was performed on a series of 33 high grade serous carcinomas, characterized with respect to BRCA1/2 status (mutation, epigenetic silencing with loss of expression or normal), and with clinical follow-up, together with 2 low grade serous carcinomas, 2 serous borderline tumors, and 3 normal fallopian tube samples, using miRNA microarrays (328 human miRNA). Unsupervised hierarchical clustering based on miRNA expression profiles showed no clear separation between the groups of carcinomas with different BRCA1/2 status. There were relatively few miRNAs that were differentially expressed between the genotypic subgroups. Comparison of 33 high grade serous carcinomas to 3 normal fallopian tube samples identified several dysregulated miRNAs (false discovery rate <5%), including miR-422b and miR-34c. Quantitative RT-PCR analysis performed on selected miRNAs confirmed the pattern of differential expression shown by microarray analysis. Prognostically, lower level miR-422b and miR-34c in high grade serous carcinomas were both associated with decreased disease-specific survival by Kaplan-Meier analysis (p<0.05).Conclusions/significanceHigh grade serous ovarian carcinomas with and without BRCA1/2 abnormalities demonstrate very similar miRNA expression profiles. High grade serous carcinomas as a group exhibit significant miRNA dysregulation in comparison to tubal epithelium and the levels of miR-34c and miR-422b appear to be prognostically important.

Project description:BackgroundAs central regulators of the gibberellic acid (GA) signaling pathway in plants, DELLA proteins function as growth repressors and affect diverse biological processes. The wheat RHT-B1b and RHT-D1b semi-dwarfing alleles, which encode GA-insensitive DELLA proteins, have been widely adopted in modern wheat varieties to improve lodging tolerance and harvest index. However, the molecular mechanisms by which DELLA modulates these responses in wheat remain largely unknown.ResultsWe identified a tall tetraploid wheat mutant line carrying an induced missense mutation (E529K) in the PFYRE motif of RHT-B1b that partially suppressed the semi-dwarf phenotype. The height-increasing effect of RHT-B1bE529K relative to RHT-B1b (19 cm or 21% increase) was significantly smaller than the effect of RHT-B1a (33 cm or 34% increase) relative to RHT-B1b in the same field experiment. The RHT-B1bE529K mutation was also associated with length increases in coleoptiles, seedling shoots, and stem internodes relative to the RHT-B1b allele. We detected no significant differences in germination rate, seedling root length, tiller number, flag leaf size, spike length, or yield components. Using RNA-seq, we compared gene expression profiles of plants encoding RHT-B1b and RHT-B1bE529K in coleoptile, first leaf, and elongating peduncles. We detected limited overlap among tissues of the genes differentially regulated by the two genotypes, and more genes upregulated (77%) than downregulated (23%) in RHT-B1bE529K relative to RHT-B1b. These results suggest that the wheat DELLA protein affects the transcriptome in a tissue-specific manner and that the mutation mainly eliminates or reduces repression functions of the RHT-B1 protein. Our study identified distinct sets of potential DELLA direct or indirect target genes involved in cell wall and carbohydrate metabolisms, cell cycle/division, and hormone pathways.ConclusionsWe identified the hypomorphic RHT-B1bE529K allele that confers an intermediate plant height and coleoptile elongation. This allele can be useful in rain-fed wheat breeding programs where the strong reduction in height and biomass associated with RHT-B1b has detrimental effects. Transcriptomic characterization of different tissues from the plants encoding RHT-B1bE529K and RHT-B1b provided valuable information for identifying DELLA downstream GA response genes in wheat.

Dataset Information

Genome-wide expression profiling analysis of the Ali35 mutant mouseline carrying a mutation in the Shc2 gene

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets