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991.
Johnston R Wang B Nuttall R Doctolero M Edwards P Lü J Vainer M Yue H Wang X Minor J Chan C Lash A Goralski T Parisi M Oliver B Eastman S 《Genome biology》2004,5(3):R19-11
We have constructed a DNA microarray to monitor expression of predicted genes in Drosophila. By using homotypic hybridizations, we show that the array performs reproducibly, that dye effects are minimal, and that array results agree with systematic northern blotting. The array gene list has been extensively annotated and linked-out to other databases. Incyte and the NIH have made the platform available to the community via academic microarray facilities selected by an NIH committee. 相似文献
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995.
Ching Yu Austin Huang Joel Studebaker Anton Yuryev Jianping Huang Kathryn E Scott Jennifer Kuebler Shobha Varde Steven Alfisi Craig A Gelfand Mark Pohl Michael T Boyce-Jacino 《BMC bioinformatics》2004,5(1):1-10
Background
SNP genotyping typically incorporates a review step to ensure that the genotype calls for a particular SNP are correct. For high-throughput genotyping, such as that provided by the GenomeLab SNPstream® instrument from Beckman Coulter, Inc., the manual review used for low-volume genotyping becomes a major bottleneck. The work reported here describes the application of a neural network to automate the review of results.Results
We describe an approach to reviewing the quality of primer extension 2-color fluorescent reactions by clustering optical signals obtained from multiple samples and a single reaction set-up. The method evaluates the quality of the signal clusters from the genotyping results. We developed 64 scores to measure the geometry and position of the signal clusters. The expected signal distribution was represented by a distribution of a 64-component parametric vector obtained by training the two-layer neural network onto a set of 10,968 manually reviewed 2D plots containing the signal clusters.Conclusion
The neural network approach described in this paper may be used with results from the GenomeLab SNPstream instrument for high-throughput SNP genotyping. The overall correlation with manual revision was 0.844. The approach can be applied to a quality review of results from other high-throughput fluorescent-based biochemical assays in a high-throughput mode. 相似文献996.
Anne Purfield Amy Nelson Anita Laoboonchai Kanungnij Congpuong Phillip McDaniel R Scott Miller Kathy Welch Chansuda Wongsrichanalai Steven R Meshnick 《Malaria journal》2004,3(1):1-6
Background
The erythrocyte binding antigen-175 (EBA-175) on Plasmodium falciparum merozoites mediates sialic acid dependent binding to glycophorin A on host erythrocytes and, therefore, plays a crucial role in cell invasion. Dimorphic allele segments have been found in its encoding gene with a 342 bp segment present in FCR-3 strains (F-segment) and a 423 bp segment in CAMP strains (C-segment). Possible associations of the dimorphism with severe malaria have been analysed in a case-control study in northern Ghana.Methods
Blood samples of 289 children with severe malaria and 289 matched parasitaemic but asymptomatic controls were screened for eba- 175 F- and C-segments by nested polymerase chain reaction.Results
In children with severe malaria, prevalences of F-, C- and mixed F-/C-segments were 70%, 19%, and 11%, respectively. The C-segment was found more frequently in severe malaria cases whereas mixed infections were more common in controls. Infection with strains harbouring the C-segment significantly increased the risk of fatal outcome.Conclusion
The results show that the C-segment is associated with fatal outcome in children with severe malaria in northern Ghana, suggesting that it may contribute to the virulence of the parasite. 相似文献997.
Scott?F?Michael Christine?BuckleyEmail author Esteban?Toro Alberto?R?Estrada Shawn?Vincent 《Reproductive biology and endocrinology : RB&E》2004,2(1):6
This study investigates ovulation and egg deposition behaviors in the anuran Eleutherodactylus coqui from Puerto Rico in response to stimulation with gonadotropin and gonadotropin releasing hormones. Five hormones were tested
by injection over a range of doses, including mammalian LHRH, avian LHRH, fish LHRH, D-Ala6, des-Gly10 ethylamide LHRH and
hCG. We report a low level of ovulation and egg deposition in response to all hormones, with the most complete and consistent
results from the non-natural D-Ala6, des-Gly10 ethylamide LHRH derivative. To confirm the viability of eggs produced in this
manner we performed in vitro fertilization experiments that resulted in the development of normal frogs. Reproductive behaviors in E. coqui are apparently not controlled by a mammalian form of LHRH as reported in other common laboratory anuran species. D-Ala6,
des-Gly10 ethylamide LHRH induces ovulation and deposition of mature and fertilizable eggs in E. coqui. 相似文献
998.
Jessica?L.?Dunne Adam?P.?Goobic Scott?T.?Acton Klaus?LeyEmail author 《Biological procedures online》2004,6(1):173-179
Leukocyte endothelial cell interaction is a fundamentally important process in many disease states. Current methods to analyze
such interactions include the parallel-plate flow chamber and intravital microscopy. Here, we present an improvement of the
traditional intravital microscopy that allows leukocyte-endothelial cell interaction to be studied from the time the leukocyte
makes its initial contact with the endothelium until it adheres to or detaches from the endothelium. The leukocyte is tracked
throughout the venular tree with the aid of a motorized stage and the rolling and adhesive behavior is measured off-line.
Because this method can involve human error, methods to automate the tracking procedure have been developed. This novel tracking
method allows for a more detailed examination of leukocyte-endothelial cell interactions.
Published: August 27, 2004. 相似文献
999.
Syka JE Marto JA Bai DL Horning S Senko MW Schwartz JC Ueberheide B Garcia B Busby S Muratore T Shabanowitz J Hunt DF 《Journal of proteome research》2004,3(3):621-626
We describe the design and performance of a prototype high performance hybrid mass spectrometer. This instrument consists of a linear quadrupole ion trap (QLT) coupled to a Fourier transform ion cyclotron resonance mass analyzer (FTMS). This configuration provides rapid and automated MS and MS/MS analyses, similar to the "data dependent scanning" found on standard 3-D Paul traps, but with substantially improved internal scan dynamic range, mass measurement accuracy, mass resolution, and detection limits. Sequence analysis of peptides at the zeptomole level is described. The recently released, commercial version of this instrument operates in the LC/MS mode (1 s/scan) with a mass resolution of 100 000 and is equipped with automatic gain control to provide mass measurement accuracy of 1-2 ppm without internal standard. Methodology is described that uses this instrument to compare the post-translational modifications present on histone H3 isolated from asynchronously growing cells and cells arrested in mitosis. 相似文献
1000.
Wang QT Piotrowska K Ciemerych MA Milenkovic L Scott MP Davis RW Zernicka-Goetz M 《Developmental cell》2004,6(1):133-144
The preimplantation development of the mammalian embryo encompasses a series of critical events: the transition from oocyte to embryo, the first cell divisions, the establishment of cellular contacts, the first lineage differentiation-all the first subtle steps toward a future body plan. Here, we use microarrays to explore gene activity during preimplantation development. We reveal robust and dynamic patterns of stage-specific gene activity that fall into two major phases, one up to the 2-cell stage (oocyte-to-embryo transition) and one after the 4-cell stage (cellular differentiation). The mouse oocyte and early embryo express components of multiple signaling pathways including those downstream of Wnt, BMP, and Notch, indicating that conserved regulators of cell fate and pattern formation are likely to function at the earliest embryonic stages. Overall, these data provide a detailed temporal profile of gene expression that reveals the richness of signaling processes in early mammalian development. 相似文献