Project description:Male Fischer 344 rats aged 4 months (young, n=10), 14 months (mid-aged, n=10), and 24 months (aged, n=10) were trained sequentially on two tasks: Morris Spatial Water Maze (SWM) and Object Memory Task (OMT). The training/testing sequence lasted 7 d, and hippocampal tissue was collected 24 hr later. Training and testing occured on each day except for days 2 and 3 of the 7 d sequence. (01/10/05: Series was updated to correct mislabeling of all sample signal values within the Young Treatment Group) Keywords = bioinformatics Keywords = gene expression Keywords = memory Keywords = synaptic plasticity Keywords = myelin Keywords = inflamation Keywords = aging Keywords: repeat sample
Project description:We examined the CLL cells transcriptome data of six patients who fail to clear their leukemia cells and develop progressive disease on venetoclax therapy. Methods: CLL cells were collected prior to venetoclax therapy (Sample Collection 1 (SC1)) and then more than 1 year later (Sample Collection 2 (SC2)). Negative isolation of CLL cells to ≥95% purity was performed prior to RNA isolation.
Project description:We compared the proteome of primary SqCLC tumor tissue between patients with ER (< 10 months) vs. LR (> 30 months) following surgery. iTRAQ-based quantitative 2D LC-MS/MS proteomics were performed on 20 SqCLC tumor samples (10 ER, 10 LR) using a matched pair design in which each ER tumor sample was paired and analyzed together with a LR tumor sample matched based on similar patient clinicopathologic features, including gender, smoking history, age and TNM status.
Project description:Biomolecules preserved in dental pulp are increasingly being used to identify individuals in the context of forensics and archaeology. Despite the vast amount of research into host and pathogen DNA, the potential use of physiologically informative proteins preserved in dental pulp has rarely been studied. Here, we hypothesized that pregnancy specific proteins circulating in the blood could be identified from the dental pulp of postpartum individuals and this was investigated using 8 human third molars extracted from 4 postpartum and 3 control individuals during clinical treatment. A total of 885 proteins were identified from these 8 dental pulp samples using liquid chromatography coupled tandem mass spectrometry, whose gene ontology compositions were similar to previous studies. However, despite our hypothesis, pregnancy specific proteins were not identified from the dental pulp of postpartum individuals (n = 5, 4–12 months postpartum). Although the dental pulp proteomes obtained from three individuals postpartum ≤6 months were distinct from those of other individuals by principal component analysis, their driving proteins were less evident. Although our hypothesis was not supported, sample collection, protein extraction, and mass spectrometry analysis could be improved to explore the forensic application of detecting pregnancy specific proteins in dental pulp.
Project description:Venoms of N. naja and D. russelii individuals of various developmental stages, including neonates (<30 days), juveniles (between 1 to 12 months), and mature individuals (>36 months), were sampled with permission from the state forest department of Karnataka. 226 individuals and 9 clutches were examined, including periodic venom collection (every three months) from the same N. naja and D. russelii juvenile individuals to track ontogenetic changes across time. Freshly collected venoms were flash-frozen in liquid nitrogen, lyophilised and stored at -80° C. Venoms were fractionated using RP-HPLC and SDS-PAGE and subjected to tandem mass spectrometry for toxin identification. The relative abundance of each toxin family were estimated and compared across different developmental stages.
Project description:This expanded access study will assess the efficacy and safety of intravenous (IV) bevacizumab in combination with chemotherapy regimens as first-line treatment of metastatic cancer of the colon or rectum. The anticipated median time on study treatment is approximately 10 months, and the target sample size is 40 individuals.
Project description:The purpose of this study was to analyze the transcriptional effects induced by glatiramer acetate treatment (GA; Copaxone, 20 mg injected subcutaneously once daily) in blood monocytes of patients with relapsing-remitting form of multiple sclerosis (MS). By using Affymetrix DNA microarrays, we obtained genome-wide expression profiles of monocytes from 8 MS patients within the first two months of GA administration. EDTA blood samples were taken from all patients immediately before first and second GA injection as well as after 1 week, 1 month and 2 months. Total RNA of CD14+ monocytes isolated by magnetic-activated cell sorting (MACS) from each sample was extracted, labeled and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays to quantify the mRNA levels. This GEO entry provides the U133 Plus 2.0 microarray data.
Project description:Mice are the most commonly used preclinical animal model, but protein analytics of murine cerebrospinal fluid (CSF) remains challenging because of low CSF volume (often <10 µl) and frequent blood contaminations. We developed an improved CSF sampling method that allows routine collection of increased volumes (20-30 µl) of pure CSF from individual mice, enabling multiple protein analytical assays from a single sample. Here, we have analysed the CSF of 3, 6, and 12 months old wild-type mice. Additionally, we collected murine CSF of the same mice at 3 and 6 months of age to compare repeated and single CSF sampling. Furthermore, we analysed human CSF samples as a reference.
Project description:Male Fischer 344 rats aged 4 months (young, n=10), 14 months (mid-aged, n=10), and 24 months (aged, n=10) were trained sequentially on two tasks: Morris Spatial Water Maze (SWM) and Object Memory Task (OMT). The training/testing sequence lasted 7 d, and hippocampal tissue was collected 24 hr later. Training and testing occured on each day except for days 2 and 3 of the 7 d sequence. (01/10/05: Series was updated to correct mislabeling of all sample signal values within the Young Treatment Group)
Project description:Molecular mechanisms that influence susceptibility to multiple sclerosis are poorly understood. We conducted a gene expression study in healthy subjects that subsequently developed the disease. Gene expression profiles (HG U133A and A2, Affymetrix, 22,215 transcripts) of peripheral blood mononuclear cells were analyzed in 9 healthy subjects (mean age 19.8+1.1 years) up to 9 years (mean 5.1±1.2 years) before onset of MS (MS to be, MS2b), 11 age-, gender-, and origin-matched subjects that remained MS-free (MSf), and 31 clinically isolated syndrome (CIS) patients. Most informative genes (p<0.05) and significant biological processes were compared. 1051 genes (611 up-regulated, 440 down-regulated) were significantly different between MS2b and MSf subjects. MS2b signature was characterized by down-regulation of the nuclear receptor (NR) family genes including NR subfamily 4 group A member1 (NR4A1, p=0.01), member 3 (NR4A3, p=0.01), NR subfamily 2 group F member 2 (NR2F1, p=0.03) and vitamin D receptor (VDR, p=0.02), all known to be involved in T-cell regulation by apoptosis. Comparison between MS2b and CIS operating networks demonstrated evolution of the altered NR dependent apoptosis regulation. Decreased NR4A1 expression was verified at the mRNA and protein level in an independent cohort of 20 relapsing-remitting MS patients. The identified MS trait is associated with suppressed transcription of NR networks that leads to altered apoptosis of activated T cells and the development of clinical disease. MS2b subjects have already an ongoing process that eventually will lead to clinical disease and our finding are of importance as they suggest the possibility of early detection and prevention of MS. Keywords: disease state analysis Blood samples of healthy subjects that later developed MS (MS-to-be, MS2b, N=9) were identified and used for gene expression study. For each sample of MS2b subject, a sample of an age and gender matched subject that remained MS-free (MSf, N=11) was randomly selected. A cohort of 31 CIS patients who gave blood sample for gene expression analysis within 3 months of the onset of their first neurological event, was used for comparison with the MS2b gene expression signature. For establishment of the CIS gene expression signature, microarray data from 13 age- and sex- matched healthy subjects were used.