Project description:The pathogen and host factors that contribute to the establishment of foot-and-mouth disease virus (FMDV) persistence are currently not understood. Using primary bovine soft palate multilayers in combination with RNA sequencing, we analyzed the transcriptional responses during acute and persistent FMDV infection.
Project description:We report for the first time movement of Correia Repeat Enclosed Elements, through inversion of the element at its chromosomal location. Analysis of Ion Torrent generated genome sequence data from Neisseria gonorrhoeae strain NCCP11945 passaged for 8 weeks in the laboratory under standard conditions and stress conditions revealed a total of 37 inversions: 24 were exclusively seen in the stressed sample; 7 in the control sample; and the remaining 3 were seen in both samples. These inversions have the capability to alter gene expression in N. gonorrhoeae through the previously determined activities of the sequence features of these elements. In addition, the locations of predicted non-coding RNAs were investigated to identify potential associations with CREE. Associations varied between strains, as did the number of each element identified. The analysis indicates a role for CREE in disrupting ancestral regulatory networks, including non-coding RNAs. RNA-Seq was used to examine expression changes related to Correia repeats in the strain
Project description:In order to determine whether dis-regulation of a genetic pathway could explain the increased apoptosis of parp-2-/- double positive thymocytes, the gene expression profiles in double positive thymocytes derived from wild-type and parp-2-/- mice were analysed using Affymetrix oligonucleotide chips (mouse genome 430 2.0).
Project description:Non-nutritive sweeteners represent an ingredient class that directly affects human health, via the development of inflammatory processes that promote chronic diseases related to microbiota dysbiosis. Several in vitro tests were conducted in the static GIS1 simulator. The aim of the study was to highlight the effect of sweeteners on the microbiota pattern of healthy individuals, associated with any alteration in the metabolomic response, through the production of organic acids and ammonium. The immediate effect of the in vitro treatment and the influence of the specific sweetener type on the occurrence of dysbiosis were evaluated by determining the biomarkers of the microbiota response. The presence of the steviol reduced the ammonium level (minimum of 410 mg/L), while the addition of cyclamate and saccharin caused a decrease in the number of microorganisms, in addition to lowering the total quantity of synthesized short-chain fatty acids (SCFAs). The bifidobacteria appeared to decrease below 102 genomes/mL in all the analyzed samples at the end of the in vitro simulation period. Barring the in vitro treatment of steviol, all the sweeteners tested exerted a negative influence on the fermentative profile, resulting in a decline in the fermentative processes, a rise in the colonic pH, and uniformity of the SCFA ratio.
Project description:Holm oak (Quercus ilex) is considered one of the major structural elements of the Mediterranean forests and the agrosilvopastoral Spanish “dehesa”, representing an outstanding example of ecological and socio-economic sustainability of forest ecosystems. The exotic pathogen Phytophthora cinnamomi is one of the most aggressive of woody species, and together drought is considered one of the main drivers of holm oak decline. The effect and responses of P. cinnamomi inoculation has been studied on the offspring of mother trees growing in declined and non-declined areas of two Andalusian populations (Cordoba and Huelva). Damage symptoms, mortality, and chlorophyll fluorescence have been evaluated in seedlings inoculated under humid and drought conditions. The effect and responses depended on the population, being more accused in Huelva than in Cordoba population. An integrative proteomic and metabolomic analysis revealed the involvement of different metabolic pathways in response to the pathogen in both populations, such as amino acid metabolism pathways in Huelva, and terpenoids and flavonoids biosynthesis in Cordoba. However, a differential response was not observed between seedlings inoculated under humid and drought conditions. A protective mechanism of the photosynthetic apparatus is launched in response to defective photosynthetic activity in inoculated plants, which seems to be more efficient in the Cordoba population. In addition, enzymes and metabolites of the phenylpropanoid and flavonoid biosynthesis pathways may confer higher resistance to Cordoba population. Some of these enzymes are proposed as markers of resilience, among which glyoxalase I, glutathione reductase, thioredoxin reductase, and cinnamyl alcohol dehydrogenase are candidates.
Project description:Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. MicroRNAs are small nucleatides that function as regulators of gene expression in almost any biological process. However, few microRNAs are reported to have a role in the pathological process of OPLL. Therefore, we performed high-throughput microRNA sequencing and transcriptome sequencing of primary OPLL and PLL cells in order to decipher the interacting network of microRNAs in OPLL. MRNA and microRNA profiles were done using primary culture cells of human ossification of the posterior longitudinal ligament (OPLL) tissue and normal posterior longitudinal ligament (PLL) tissue.
Project description:Variation in methotrexate (MTX) efficacy represents a significant barrier to early and effective disease control in the treatment of autoimmune arthritis. We hypothesize that the utilization of metabolomic techniques will allow for an improved understanding of the biochemical basis for the pharmacological activity of MTX, and can promote the identification and evaluation of novel molecular biomarkers of MTX response. In this work, erythroblastoid cells were exposed to MTX at the physiologic concentration of 1,000 nM and analyzed using three metabolomic platforms to give a broad spectrum of cellular metabolites. MTX pharmacological activity, defined as cellular growth inhibition, was associated with an altered cellular metabolomic profile based on the analysis of 724 identified metabolites. By discriminant analysis, MTX treatment was associated with increases in ketoisovaleric acid, fructose, galactose, and 2-deoxycytidine, and corresponding reductions in 2-deoxyuridine, phosphatidylinositol 32:0, orotic acid, and inosine monophosphate. Inclusion of data from analysis of folate metabolism in combination with chemometric and metabolic network analysis demonstrated that MTX treatment is associated with dysregulated folate metabolism and nucleotide biosynthesis, which is in line with its known mechanism of action. However, MTX treatment was also associated with alterations in a diversity of metabolites, including intermediates of amino acid, carbohydrate, and lipid metabolism. Collectively, these findings support a robust metabolic response following exposure to physiologic concentrations of MTX. They also identify various metabolic intermediates that are associated with the pharmacological activity of MTX, and are, therefore, potential molecular biomarker candidates in future preclinical and clinical studies of MTX efficacy in autoimmune arthritis.
Project description:Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. Recently, disorders of metabolism are thought to be the center of many diseases such as OPLL. Advanced glycation end product (AGE) are accumulated in many extracellular matrixes such as ligament fibers, and it can functions as cellular signal through its receptor (RAGE), contributing to various events such as atherosclerosis or oxidative stress. However, its role in OPLL formation is not yet known. Therefore, we performed high-through-put RNA sequencing on primary posterior longitudinal ligament cells treated with different doses of AGEs (1µM, 5µM and negative control), with or without BMP2 (1µM). mRNA profiles of Primary human posterior longitudinal ligament cells stimulated with various stimuli (Control, 1µM AGE-BSA, 5µM AGE-BSA, 1µM AGE-BSA with BMP2, 5µM AGE-BSA with BMP2) were generated by deep sequencing on Ion Proton
Project description:The goal of this study was to compare the transcriptome between wild type strain of Listeria monocytogenes and delete nmlR mutant strain of L. monocytogenes using NGS. Method: Duplicate samples of rRNA depleted RNA from wild type and mutants were used to study transcriptomes by ion torrent platform. Transcriptomes of wild type and nmlR mutant were compared by EDGE-pro program. Result: Differential expression by EDGE-pro showed 74 genes with differential expressions between wild type and nmlR null mutant (46 genes were negatively regluated and 28 genes were positively regulated by NmlR). rRNA-depleted RNA samples from stationary phase wilde type and nmlR null mutant cultures were used to compare transcriptomes. Some affected genes from RNAseq result were selected for confirmation by quantitative reverse transcriptase PCR.
Project description:MicroRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. To this purpose, different measurement platforms to determine their RNA abundance levels in biological samples have been developed. In this study, we have systematically compared 12 commercially available microRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from homologous microRNA family members. We developed novel quality metrics in order to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, quantitative performance, and specificity. The results indicate that each method has its strengths and weaknesses, which helps guiding informed selection of a quantitative microRNA gene expression platform in function of particular study goals.