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Reference Database (reference + database)
Selected AbstractsAnalysis of phosphatase and tensin homolog tumor suppressor interacting proteins by in vitro and in silico proteomicsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 5 2005David K. Crockett Abstract The phosphatase and tensin homolog (PTEN) tumor suppressor is a multifunctional protein deregulated in many types of cancer. To date, a comprehensive documentation of PTEN interacting proteins has not been performed. The goal of our study was to characterize the PTEN interactome using affinity pull-down and tandem mass spectrometry (MS/MS). Wild-type PTEN cDNA was inserted into pTRC-His2 vector to create a 6-His tagged protein, which was expressed in Escherichia coli. Lysate from a human lymphoma cell line was used in pull-down assays, utilizing affinity for nickel-agarose beads. Bound proteins were eluted with imidazole, digested and analyzed on an LCQ DecaXP ion trap mass spectrometer. The nickel affinity pull-down efficiency was evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis. Acquired data were searched against the NCBI nr.fasta nonredundant protein database using the SEQUEST algorithm and screened using INTERACT and ProteinProphet. All experiments were performed in duplicate with 6-His- lacZ serving as control. A total of 79 proteins were identified in the wild-type 6-His-PTEN pull-down by MS/MS. We further validated a subset of the proteins present in the PTEN interactome by performing immunoprecipitation using an anti-PTEN antibody and establishing the presence of the proteins in the immunocomplex by Western blot analysis. A search of published PTEN interactions was also performed using Online Mendelian Inheritance in Man, Human Protein Reference Database, the IntAct Project database, and PubMed. This in silico analysis confirmed 42 out of 79 (53%) of the proteins identified by MS/MS. The remaining 37 proteins represent probable PTEN interactions not previously documented in public databases or reported in the literature. These results highlight the value of combining both in vitro biochemical approaches with in silico analyses for a comprehensive study of protein-protein interactions. [source] Evaluation of Uncertainties Associated with Geocoding TechniquesCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 3 2004Hassan A. Karimi Geocoded data play a major role in numerous engineering applications such as transportation and environmental studies where geospatial information systems (GIS) are used for spatial modeling and analysis as they contain spatial information (e.g., latitude and longitude) about objects. The information that a GIS produces is impacted by the quality of the geocoded data (e.g., coordinates) stored in its database. To make appropriate and reasonable decisions using geocoded data, it is important to understand the sources of uncertainty in geocoding. There are two major sources of uncertainty in geocoding, one related to the database that is used as a reference data set to geocode objects and one related to the interpolation technique used. Factors such as completeness, correctness, consistency, currency, and accuracy of the data in the reference database contribute to the uncertainty of the former whereas the specific logic and assumptions used in an interpolation technique contribute to the latter. The primary purpose of this article is to understand uncertainties associated with interpolation techniques used for geocoding. In doing so, three geocoding algorithms were used and tested and the results were compared with the data collected by the Global Positioning System (GPS). The result of the overall comparison indicated no significant differences between the three algorithms. [source] An integrated map of the murine hippocampal proteome based upon five mouse strainsELECTROPHORESIS, Issue 13 2006Daniela D. Pollak Abstract With the advent of proteomics technologies it is possible to simultaneously demonstrate the expression of hundreds of proteins. The information offered by proteomics provides context-based understanding of cellular protein networks and has been proven to be a valuable approach in neuroscience studies. The mouse hippocampus has been a major target of analysis in the search for molecular correlates to neuronal information storage. Although human and rat hippocampal samples have been successfully subjected to proteomic profiling, no elaborate analysis providing the fundamental experimental basis for protein-expression studies in the mouse hippocampus has been carried out as yet. This led us to construct a master map generated from the individual hippocampal proteomes of five different mouse strains. A proteomic approach, based upon 2-DE coupled to MS (MALDI-TOF/TOF) has been chosen in an attempt to establish a comprehensive reference database of proteins expressed in the mouse hippocampus. 469 individual proteins, represented by 1156 spots displaying various functional states of the respective gene products were identified. Proteomic profiling of the hippocampus, a brain region with a pivotal role for neuronal information processing and storage may provide insight into the characteristics of proteins serving this highly sophisticated function. [source] The relative sensitivity of four benthic invertebrates to metals in spiked-sediment exposures and application to contaminated field sedimentENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 4 2003Danielle Milani Abstract The relative sensitivity of four benthic invertebrates (Hyalella azteca, Chironomus riparius, Hexagenia spp., and Tubifex tubifex) was determined for Cd, Cu, and Ni in water-only and in spiked-sediment exposures. Survival (median lethal concentrations [LC50s] and the concentrations estimated to be lethal to 25% of test organisms [LC25s]), and endpoints for growth and reproduction (mean inhibitory concentrations [IC25s]) were compared. The sensitivities differed depending on the species and metal, although some trends emerged. In water-only exposures, H. azteca is the most sensitive species to cadmium and nickel, with mean LC50s of 0.013 and 3.6 mg/L, respectively; C. riparius is the most sensitive species to copper, with a mean LC50 of 0.043 mg/L. In the spiked-sediment exposures, the order in decreasing sensitivity to copper is Hyalella = Hexagenia < Chironomus < Tubifex for survival and growth/reproduction. For cadmium, the order in decreasing sensitivity is Hyalella = Chironomus < Hexagenia < Tubifex, and for nickel is Hyalella , Hexagenia < Chironomus < Tubifex. Chironomus riparius and Hexagenia spp. survival can be used to distinguish between toxicity caused by different metals. Species test responses in field-collected sediment (Collingwood Harbour, ON, Canada) were examined in an attempt to determine the causative agent of toxicity throughout, using the established species sensitivities. Sediment toxicity was categorized first by comparing species responses to those established for a reference database. Test responses in the field-collected sediment do not support causality by Cu, a suspected toxicant based on comparison of sediment chemistry with sediment quality guidelines. [source] Accuracy of Very Low Pretest Probability Estimates for Pulmonary Embolism Using the Method of Attribute Matching Compared with the Wells ScoreACADEMIC EMERGENCY MEDICINE, Issue 2 2010Jeffrey A. Kline MD Abstract Objectives:, Attribute matching matches an explicit clinical profile of a patient to a reference database to estimate the numeric value for the pretest probability of an acute disease. The authors tested the accuracy of this method for forecasting a very low probability of venous thromboembolism (VTE) in symptomatic emergency department (ED) patients. Methods:, The authors performed a secondary analysis of five data sets from 15 hospitals in three countries. All patients had data collected at the time of clinical evaluation for suspected pulmonary embolism (PE). The criterion standard to exclude VTE required no evidence of PE or deep venous thrombosis (DVT) within 45 days of enrollment. To estimate pretest probabilities, a computer program selected, from a large reference database of patients previously evaluated for PE, patients who matched 10 predictor variables recorded for each current test patient. The authors compared the outcome frequency of having VTE [VTE(+)] in patients with a pretest probability estimate of <2.5% by attribute matching, compared with a value of 0 from the Wells score. Results:, The five data sets included 10,734 patients, and 747 (7.0%, 95% confidence interval [CI] = 6.5% to 7.5%) were VTE(+) within 45 days. The pretest probability estimate for PE was <2.5% in 2,975 of 10,734 (27.7%) patients, and within this subset, the observed frequency of VTE(+) was 48 of 2,975 (1.6%, 95% CI = 1.2% to 2.1%). The lowest possible Wells score (0) was observed in 3,412 (31.7%) patients, and within this subset, the observed frequency of VTE(+) was 79 of 3,412 (2.3%, 95% CI = 1.8% to 2.9%) patients. Conclusions:, Attribute matching categorizes over one-quarter of patients tested for PE as having a pretest probability of <2.5%, and the observed rate of VTE within 45 days in this subset was <2.5%. ACADEMIC EMERGENCY MEDICINE 2010; 17:133,141 © 2010 by the Society for Academic Emergency Medicine [source] Molecular sexing and sources of CHD1-Z/W sequence variation in Hawaiian birdsMOLECULAR ECOLOGY RESOURCES, Issue 4 2006SUSAN I. JARVI Abstract Sequence information from 28 CHD1 gene fragments reveals that a primary source of variability in CHD1-W genes is a variable intron microsatellite; a single-codon deletion was found in the 3, exon in one species. Sequence variation of CHD1-Z genes was detected in males that altered polymerase chain reaction (PCR) fragment length. Three sets of CHD1-based primers were evaluated for sex determination in 12 endemic and 8 alien Hawaiian species, including one of the last po'o-uli. Combined, these primers provide a reliable means of sex determination in most species (including the po'o-uli), and have produced a valuable reference database for future expanded population-level studies. [source] Neuronal gene expression correlates of Parkinson's disease with dementia,MOVEMENT DISORDERS, Issue 11 2008Chelsea Stamper BS Abstract Dementia is a common disabling complication in patients with Parkinson's disease (PD). The underlying molecular causes of Parkinson's disease with dementia (PDD) are poorly understood. To identify candidate genes and molecular pathways involved in PDD, we have performed whole genome expression profiling of susceptible cortical neuronal populations. Results show significant differences in expression of 162 genes (P < 0.01) between PD patients who are cognitively normal (PD-CogNL) and controls. In contrast, there were 556 genes (P < 0.01) significantly altered in PDD compared to either healthy controls or to PD-CogNL cases. These results are consistent with increased cortical pathology in PDD relative to PD-CogNL and identify underlying molecular changes associated with the increased pathology of PDD. Lastly, we have identified expression differences in 69 genes in PD cortical neurons that occur before the onset of dementia and that are exacerbated upon the development of dementia, suggesting that they may be relevant presymptomatic contributors to the onset of dementia in PD. These results provide new insights into the cortical molecular changes associated with PDD and provide a highly useful reference database for researchers interested in PDD. © 2008 Movement Disorder Society [source] | |||||||||||||