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Large-scale Screening (large-scale + screening)
Selected AbstractsLarge-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA libraryGENES TO CELLS, Issue 3 2000Da-Qiao Ding Background Intracellular localization is an important part of the characterization of a gene product. In an attempt to search for genes based on the intracellular localization of their products, we constructed a green fluorescent protein (GFP)-fusion genomic DNA library of S. pombe. Results We constructed the S. pombe GFP-fusion genomic DNA library by fusing, in all three reading frames, random fragments of genomic DNA to the 5, end of the GFP gene in such a way that expression of potential GFP-fusion proteins would be under the control of the own promoters contained in the genomic DNA fragments. Fission yeast cells were transformed with this plasmid library, and microscopic screening of 49 845 transformants yielded 6954 transformants which exhibited GFP fluorescence, of which 728 transformants showed fluorescence localized to distinct intracellular structures such as the nucleus, the nuclear membrane, and cytoskeletal structures. Plasmids were isolated from 516 of these transformants, and a determination of their DNA sequences identified 250 independent genes. The intracellular localizations of the 250 GFP-fusion constructs was categorized as an image database; using this database, DNA sequences can be searched for based on the localizations of their products. Conclusions A number of new intracellular structural components were found in this library. The library of GFP-fusion constructs also provides useful fluorescent markers for various intracellular structures and cellular activities, which can be readily used for microscopic observation in living cells. [source] Large-scale screening of Arabidopsis circadian clock mutants by a high-throughput real-time bioluminescence monitoring systemTHE PLANT JOURNAL, Issue 1 2004Kiyoshi Onai Summary Using a high-throughput real-time bioluminescence monitoring system, we screened large numbers of Arabidopsis thaliana mutants for extensively altered circadian rhythms. We constructed reporter genes by fusing a promoter of an Arabidopsis flowering-time gene , either GIGANTEA (GI) or FLOWERING LOCUS T (FT) , to a modified firefly luciferase gene (LUC+), and we transferred the fusion gene (PGI::LUC+ or PFT::LUC+) into the Arabidopsis genome. After mutagenesis with ethyl methanesulfonate, 50 000 M2 seedlings carrying the PGI::LUC+ and 50 000 carrying PFT::LUC+ were screened their bioluminescence rhythms. We isolated six arrhythmic (AR) mutants and 29 other mutants that showed more than 3 h difference in the period length or phase of rhythms compared with the wild-type strains. The shortest period length was 16 h, the longest 27 h. Five of the six AR mutants carrying PGI::LUC+ showed arrhythmia in bioluminescence rhythms in both constant light and constant dark. These five AR mutants also showed arrhythmia in leaf movement rhythms in constant light. Genetic analysis revealed that each of the five AR mutants carried a recessive mutation in a nuclear gene and the mutations belonged to three complementation groups, and at least one of which was mapped on a novel locus. Our results suggest that the three loci identified here may contain central clock or clock-related genes, at least one of which may be a novel. [source] SAFE biopsy: A validated method for large-scale staging of liver fibrosis in chronic hepatitis C,HEPATOLOGY, Issue 6 2009Giada Sebastiani The staging of liver fibrosis is pivotal for defining the prognosis and indications for therapy in hepatitis C. Although liver biopsy remains the gold standard, several noninvasive methods are under evaluation for clinical use. The aim of this study was to validate the recently described sequential algorithm for fibrosis evaluation (SAFE) biopsy, which detects significant fibrosis (,F2 by METAVIR) and cirrhosis (F4) by combining the AST-to-platelet ratio index and Fibrotest-Fibrosure, thereby limiting liver biopsy to cases not adequately classifiable by noninvasive markers. Hepatitis C virus (HCV) patients (2035) were enrolled in nine locations in Europe and the United States. The diagnostic accuracy of SAFE biopsy versus histology, which is the gold standard, was investigated. The reduction in the need for liver biopsies achieved with SAFE biopsy was also assessed. SAFE biopsy identified significant fibrosis with 90.1% accuracy (area under the receiver operating characteristic curve = 0.89; 95% confidence interval, 0.87-0.90) and reduced by 46.5% the number of liver biopsies needed. SAFE biopsy had 92.5% accuracy (area under the receiver operating characteristic curve = 0.92; 95% confidence interval, 0.89-0.94) for the detection of cirrhosis, obviating 81.5% of liver biopsies. A third algorithm identified significant fibrosis and cirrhosis simultaneously with high accuracy and a 36% reduction in the need for liver biopsy. The patient's age and body mass index influenced the performance of SAFE biopsy, which was improved with adjusted Fibrotest-Fibrosure cutoffs. Two hundred two cases (9.9%) had discordant results for significant fibrosis with SAFE biopsy versus histology, whereas 153 cases (7.5%) were discordant for cirrhosis detection; 71 of the former cases and 56 of the latter cases had a Fibroscan measurement within 2 months of histological evaluation. Fibroscan confirmed SAFE biopsy findings in 83.1% and 75%, respectively. Conclusion: SAFE biopsy is a rational and validated method for staging liver fibrosis in hepatitis C with a marked reduction in the need for liver biopsy. It is an attractive tool for large-scale screening of HCV carriers. (HEPATOLOGY 2009.) [source] Transcriptional changes in insulin- and lipid metabolism-related genes in the hippocampus of olfactory bulbectomized miceJOURNAL OF NEUROSCIENCE RESEARCH, Issue 14 2008Peter Gass Abstract Affymetrix chips were used to perform a hypothesis-free large-scale screening of transcripts in the hippocampus of olfactory bulbectomized mice, an established animal model of depression. Because only 11 transcripts were significantly changed, the statistically subsequent 25 transcripts below the significance level were additionally included in a first round of qRT-PCR evaluations. Furthermore, all 36 genes were then tested for mutual interactions or interactions with other molecules in a physiological context using PathwayArchitect software. Thirty of them were displayed in a network interacting with at least one partner molecule from the list or with other partner molecules known from the literature. All partner molecules from the most prominent 10 molecules of this network were then identified and put together into a new list. On those grounds, the hypothesis was made that metabolic network components of the insulin signaling pathway are perturbed in the disease. This pathway was subsequently tested by a second round of qRT-PCR, adding also a few additional candidate molecules belonging to this pathway. It turned out that the key target,FABP7,fell into the group of transcripts not significantly regulated within the chip data, and another key target,IRS1,did not show up in the chip experiments at all. In conclusion, our data reveal a problem with adhering to statistical significances in microarray experiments, insofar as molecules important for the disease may fall into the range of statistical noise. This approach may also be useful to find new targets for pharmacotherapy in affective disorders. © 2008 Wiley-Liss, Inc. [source] 4143: The German Mouse Clinic: recent findings from the Eye ScreenACTA OPHTHALMOLOGICA, Issue 2010O PUK Purpose The purpose of this study was the large-scale screening of different mouse mutant lines in order to detect novel models for eye disorders. Methods The eyes of the mouse mutants were analyzed by slit lamp biomicroscopy, funduscopy, laser interference biometry, optokinetic drum, and histology. Results In the past 12 months, 46 mouse mutant lines were investigated in the primary Eye Screen of the German Mouse Clinic (GMC). These included Csemp1 and Aey69 that exhibited irregular eye development. All tested mice of the mutant line Csemp1 unexpectedly showed white fundus flecks and significantly reduced axial eye lengths. Moreover, we additionally found strong opacities in a least a portion of the Csemp1 mutant lenses. Aey69 mice are severely microphthalmic due to a yet undefined ENU-induced mutation. The rudimentary eyes completely lack ocular structures as iris or lens. Further significant irregularities in fat metabolism, immunology, and behaviour were detected in the GMC-wide primary screen. Linkage studies mapped the mutated site on chromosome 3 within a 0.78 Mb spanning region between the flanking microsatellite markers D3Mit188 and D3Mit76. Among the 34 positional candidate genes, Tnrc4 (elav-like family member 3) and Selenbp1 (selenium binding protein 1) are expressed in the eye. Sequencing studies in order to detect the causative mutation of Aey69 are in process. Conclusion Two novel mouse models for microphthalmia were detected in the primary Eye Screen of the GMC. These mutant lines will provide further insights into molecular mechanisms behind this kind of eye disease. [source] NOVEL MITOCHONDRIAL DNA MUTATIONS ASSOCIATED WITH CHINESE FAMILIAL HYPERTROPHIC CARDIOMYOPATHYCLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, Issue 9 2009Yan-Ling Wei SUMMARY 1Hypertrophic cardiomyopathy (HCM) is a genetic disorder that has a complex set of symptoms and potentially devastating consequences. Increasing evidence indicates that mitochondrial DNA (mtDNA) mutations are responsible for the development of HCM, but the mtDNA mutations appear to differ considerably among different populations and regions. 2In the present study, three families with HCM were found and investigated: one in Shandong province and two in the Chongqing region of China. The entire mtDNA genome from the 18 affected and 66 unaffected family members was sequenced directly and the mtDNA mutations were determined. 3The frequency of haplogroup M10 was significantly higher in family members with HCM (HCM group) than in unaffected family members (normal group). Three mtDNA mutations were found with a significantly higher frequency in affected individuals than in unaffected family individuals, namely G7697A in the cytochrome c oxidase subunit II gene (P < 0.0001; odds ratio (OR) 227.5; 95% confidence interval (CI) 23.6,2194.8) and T12477C (P = 0.0037; OR 5.6; 95% CI 1.8,17.6) and G13135A in the NADH dehydrogenase 5 gene (P < 0.0001; OR 26.0; 95% CI 6.9,98.3), suggesting that these mutations are probably associated with susceptibility to HCM. In addition, mitochondrial Complex I activity was markedly decreased in the HCM group, suggesting that these mutations most likely affect mitochondrial respiratory function. 4In conclusion, the results of the present study imply that mtDNA mutations G7697A, T12477C and G13135A are genetic factors that indicate a susceptibility to HCM and that could be used for the large-scale screening of genetic markers as well as the early diagnosis of HCM. [source] | |||||||||||||