Project description:The LH surge induces panoply of events that are essential for ovulation and corpus luteum formation. The transcriptional responses to the LH surge of pre-ovulatory granulosa cells are complex and still poorly understood. In the present study, a genome wide bovine oligo array was used to determine how the gene expression profiles of granulosa cells are modulated by the LH surge. Granulosa cells from three different statuses were used (1) 2 h before the induction of the LH surge, (2) 6 h and (3) 22 h after the LH surge to assess the short and long term effects of this hormone on follicle differentiation. The results obtained were a list of differentially expressed transcripts for each granulosa cell group. To provide a comprehensive understanding of the processes at play, biological annotations were used to reveal the different functions of transcripts, confirming that the LH surge acts in a temporal manner. The pre-LH group is involved in typical tasks such as cell division, development and proliferation, while the short response of the LH surge included features such as response to stimulus, vascularisation and lipid synthesis, which are indicative of cells preparing for ovulation. The late response of granulosa cells revealed terms associated with protein localization and intra-cellular transport corresponding to the future secretion task that will be required for the transformation of granulosa cells into corpus luteum. Overall, results described in this study provide new insights into the different transcriptional steps that granulosa cells go through during ovulation and before luteinization. Three biological granulosa cells samples: 2 h pre-LH vs. 6 h post-LH vs. 22 h post-LH. Biological replicates: 3 with a technical dye-swap replicates (Dy 547 and Dy 647) for each biological replicate. Hybridizations were performed in a loop design for a total a 9 hybridizations.
Project description:Water is a fundamental resource for living things, which is why its control is necessary. The widespread use of pesticides for agricultural and non-agricultural purposes has resulted in the presence of their residues in surface water and groundwater resources. Their presence in water is regulated through different directives, such as the Groundwater Directive, the Drinking Water Directive, and the Water Framework Directive, modified later several times, setting a maximum concentration of 0.1 µg.L-1 for individual pesticides and their degradation products, and 0.5 µg.L-1 for total pesticide residues present in a sample. There are different kinds of pesticides (e.g., organophosphorus and organochlorine pesticides, triazines, chloroacetamides, triazoles, (thio)carbamates) that have diverse chemical structures. Their determination and monitoring in a single analytical procedure are possible through multiresidue methods. In this study, 53 pesticides belonging to different chemical classes and their metabolites were selected based on their local occurrence and investigated in surface water and groundwater from agricultural areas susceptible to pesticide contamination. The methodology consisted of a classical solid-phase extraction (SPE) for the purification and enrichment of the pesticides, with a subsequent analysis in multidimensional gas chromatography coupled to mass spectrometry (GC×GC-MS). The quantification method was validated according to the Eurachem Guide in terms of linearity, precision, accuracy, limit of detection, and limit of quantification. After validation, the method was applied to 34 real-world water samples, and the results were compared with those obtained by a GC-QMS routine method.
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:BackgroundUrinary organic acids are water-soluble intermediates and end products of the metabolism of amino acids, carbohydrates, lipids, and a number of other metabolic processes. In the hereditary diseases known as organic acidurias, an enzyme or co-factor defect in a metabolic pathway leads to the accumulation and increased excretion of one or more of these acidic metabolites. Gas chromatography is the most commonly-used technology to separate and identify these metabolites. In this report the analytical conditions for the determination of methylmalonic acid using a gas chromatography/flame ionization detector (GC-FID) are studied with the aim to establish a method to analyze organic acids in human urine.MethodsStudies included the GC-FID method development, the conditions of the derivatization (trimethylsilylation) reaction, and the stability of the methylmalonic acid standard solution and trimethylsilyl derivatives during storage. Also, a systematic comparison between GC-FID and gas chromatography/mass spectrometry (GC-MS) was performed.ResultsThe highest resolution and sensitivity were obtained at 60 °C with a 30 min reaction time. Standard solutions and derivatized samples were stable for 7 days at 4-8 °C. Relative standard deviations of within-day and day-to-day assay results were less than 5%. Methylmalonic acid was detected in thirty human urine samples by the proposed GC-FID, and the results were compared with gold standard technique GC-MS. The correlation coefficient between GC-MS and GC-FID was obtained with R(2)= 0.997.ConclusionThe developed method was applied to the quantitative analysis of methylmalonic acid in urine from hospitalized children with methylmalonic acidemia. With this method we aim to support pediatric clinics in Iran and assist in clinical diagnostics.
Project description:Sample multiplexed scRNA-seq is a promising strategy to overcome current barriers in high cost and potential technical variations by multiple scRNA-seq tests. In this study, we developed a highly efficienct novel sample barcode labeling method using DNA-encoded Lipid Nanoparticles ('Nanocoding') that could label cells with minimal dependence on their type or sample conditions. This method provids a roubust and general protocol for sample barcoding and multiplexing in scRNA-seq. We demonstrated the performance of Nanocoding through three scRNA-seq studies, which include: 1. mouse spleen cells mix (one dataset including 6 mouse spleen tissues samples); 2. HeLa-mouse Stromal Vascular Fraction(SVF) cells mix (one dataset containing mixed HeLa cell and SVF cell); 3. Aged-Young SVF cells mix (one dataset containing two SVF samples) tests. These studies showcased the biomodal distribution of barcode counts in different models with high signal-to-background ratio, as well as pan-cell labeling activity for efficient and accurate sample-multiplexing. By using Nanocoding, we profiled obsity and age related change in lipid metabolism associated genes or inflammatory related features, in various cell types from spleen or adipose tissues.
Project description:As seized drug casework becomes increasingly complex due to the continued prevalence of emerging drugs, laboratories are often looking for new analytical approaches including developing methods for the analysis of specific compounds classes. Recent efforts have focused on the development of targeted gas chromatography mass spectrometry (GC-MS) confirmation methods to compliment the information-rich screening results produced by techniques like direct analysis in real time mass spectrometry (DART-MS). In this work, a method for the confirmation of synthetic opioids and related compounds was developed and evaluated. An 11-component test solution was used to develop a method that focused on minimizing overlapping retention time acceptance windows and understanding the influence of instrument parameters on reproducibility and sensitivity. Investigated settings included column type, flow rate, temperature program, inlet temperature, source temperature, and tune type. Using a DB-200 column, a 35-min temperature ramped method was created. It was evaluated against a suite of 222 synthetic opioids and related compounds, and successfully differentiated all but four compound pairs based on nonoverlapping retention time acceptance windows or objectively different mass spectra. Compared to a general confirmatory method used in casework, the targeted method was up to 25 times more sensitive and provided at least a two-fold increase in retention time differences. Analysis of extracts from actual case samples successfully demonstrated utility of the method and showed no instance of carryover, although the high polarity column required wider retention time windows than other columns.
Project description:To address challenges associated with the increased prevalence of novel psychoactive substances (NPSs), laboratories often adopt new techniques or new methods with the goal of obtaining more detailed chemical information with a higher level of confidence. To demonstrate how new methods applied to existing techniques can be a viable approach, a targeted gas chromatography mass spectrometry (GC-MS) method for synthetic cathinones was developed. To create the method, a range of GC-MS parameters were first investigated using a seven-component test solution with the goal of minimizing compounds with overlapping acceptance windows by maximizing retention time differences within a reasonable runtime. Once developed, the targeted method was evaluated through several studies and was compared to a general GC-MS confirmatory method. The method produced a twofold increase in retention time differences of the test solution compounds with a 3.83-min shorter runtime than the general method. Limitations of the method were also studied by analyzing an additional forty-eight cathinones to identify instances where definitive compound identification may not be possible due to overlapping acceptance windows and mass spectra. Thirty-eight pairs of compounds had retention times differences of less than 2% and, of those thirty-eight, one pair had indistinguishable mass spectra. A set of case samples were also analyzed using the method to evaluate suitability for casework. An increase in split ratio was required to obtain acceptable sensitivity. The development of this method is part of a larger project to measure benefits and drawbacks of different drug chemistry workflows.
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:Aberrant miRNA expression has been related to the development of human germ cell tumors, but little is known about effect of ELF-EMFs on miRNA expression. ELF-EMFs may epigenetically modify cells, which may account for the adverse effects of ELF-EMFs on the male reproductive system. To identify miRNAs that were differentially expressed between the sham and ELF-EMF exposure groups, we performed an Affymetrix microarray analysis to establish the miRNA expression profiles. Mouse spermatocyte-derived GC-2 cells were intermittently exposed to a 50 Hz ELF-EMF for 72 h (5 min on/10 min off) at magnetic field intensities of 1 mT and 3 mT. miRNA expression was profiled using Affymetrix Mouse Genechip miRNA 3.0 arrays.