GeneCluster 2.0: an advanced toolset for bioarray analysis

SUMMARY: GeneCluster 2.0 is a software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding classification, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting and k-nearest neighbor algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater. AVAILABILITY: http://www.broad.mit.edu/cancer/software     

The synaptophysin/synaptobrevin interaction critically depends on the cholesterol content

Synaptophysin interacts with synaptobrevin in membranes of adult small synaptic vesicles. The synaptophysin/synaptobrevin complex promotes synaptobrevin to built up functional SNARE complexes thereby modulating synaptic efficiency. Synaptophysin in addition is a cholesterol-binding protein. Depleting the membranous cholesterol content by filipin or beta-methylcyclodextrin (beta-MCD) decreased the solubility of synaptophysin in Triton X-100 with less effects on synaptobrevin. In small synaptic vesicles from rat brain the synaptophysin/synaptobrevin complex was diminished upon beta-MCD treatment as revealed by chemical cross-linking. Mice with a genetic mutation in the Niemann-Pick C1 gene developing a defect in cholesterol sorting showed significantly reduced amounts of the synaptophysin/synaptobrevin complex compared to their homo- or heterozygous littermates. Finally when using primary cultures of mouse hippocampus the synaptophysin/synaptobrevin complex was down-regulated after depleting the endogenous cholesterol content by the HMG-CoA-reductase inhibitor lovastatin. Alternatively, treatment with cholesterol up-regulated the synaptophysin/synaptobrevin interaction in these cultures. These data indicate that the synaptophysin/synaptobrevin interaction critically depends on a high cholesterol content in the membrane of synaptic vesicles. Variations in the availability of cholesterol may promote or impair synaptic efficiency by interfering with this complex.     

DNA markers associated with low Fusarium head blight incidence and narrow flower opening in wheat

Fusarium head blight (FHB) of wheat, caused by Fusarium graminearum, is an important fungal disease in many wheat-growing areas of the world. The objectives of this study were to determine the relationship between width and duration of flower opening and incidence of FHB in wheat, and to identify DNA markers associated with narrow flower opening and low FHB incidence. It was hypothesized that wheat lines whose flowers open briefly and narrowly have a reduced risk of infection. To test the hypothesis, we crossed wheat cultivars Patterson and Goldfield to generate a population of 100 random F₂-derived recombinant inbred lines (RILs). Florets of Patterson open wide; florets of Goldfield tend to stay closed. The population of RILs was characterized for FHB incidence and flower opening width (FOW) and duration in the F_7:9 and F_7:10 generations. Of the 305 simple sequence repeat primer pairs screened on the parents, 79 amplified polymorphic DNA bands. Pooled DNA from each of the two bulks was tested with these 79 SSR primer pairs. Four markers were found to have significant marker-trait association with low FHB incidence and narrow flower opening. The major QTL effect associated with narrow flower opening and low FHB incidence was found between the map interval Xbarc200–Xgwm210, explaining 29% of the phenotypic variation for FHB incidence averaged over six replicated tests in Indiana in 2002 and 2003. This adds credence to the hypothesis that narrow flower opening is responsible for low FHB incidence in this population. Breeding wheat lines for both morphological avoidance, such as narrow flower opening, and physiological resistance to FHB may be valuable in future breeding research to reduce crop production and grain quality losses in wheat due to FHB.Contribution from Purdue University Agricultural Research Programs as Journal Article no. 17451     

Association of a DNA marker with Hessian fly resistance gene H9 in wheat

The Hessian fly [Mayetiola destructor (Say)] is a major pest of wheat (Triticum aestivum L.) and genetic resistance has been used effectively over the past 30 years to protect wheat against serious damage by the fly. To-date, 25 Hessian fly resistance genes, designated H1 to H25, have been identified in wheat. With near-isogenic wheat lines differing for the presence of an individual Hessian fly resistance gene, in conjunction with random amplified polymorphic DNA (RAPD) analysis and denaturing gradient-gel electrophoresis (DGGE), we have identified a DNA marker associated with the H9 resistance gene. The H9 gene confers resistance against biotype L of the Hessian fly, the most virulent biotype. The RAPD marker cosegregates with resistance in a segregating F₂ population, remains associated with H9 resistance in a number of different T. aestivum and T. durum L. genetic backgrounds, and is readily detected by either DGGE or DNA gel-blot hybridization.Purdue University, Agric. Exp. Stn. Journal paper No. 14440     

A resistance-like gene identified by EST mapping and its association with a QTL controlling Fusarium head blight infection on wheat chromosome 3BS.

Fusarium head blight (FHB) is a major disease in the wheat growing regions of the world. A quantitative trait locus (QTL) on the short arm of chromosome 3B controls much of the variation for resistance. The cloning of candidate disease-resistance genes for FHB QTLs on chromosome 3B can provide further elucidation of the mechanisms that control resistance. However, rearrangements and divergence during plant genome evolution often hampers the identification of sequences with similarity to known disease-resistance genes. This study focuses on the use of wheat expressed sequence tags (ESTs) that map to the region on chromosome 3B containing the QTL for FHB resistance and low-stringency BLAST searching to identify sequences with similarity to known disease-resistance genes. One EST rich with leucine repeats and low similarity to a protein kinase domain of the barley Rpg1 gene was identified. Genetic mapping using a Ning894037 x Alondra recombinant inbred (RI) population showed that this EST mapped to the QTL on the short arm of chromosome 3B and may represent a portion of a newly diverged gene contributing to FHB resistance. The EST is a new marker suitable for marker-assisted selection and provides a starting point to begin map-based cloning for chromosome walking and investigate new diverged genes at this locus.     

Paläontologie einer epikontinentalen Lias-Schichtfolge: Oberes Sinemirium bis Oberes Domerium von Empelde bei Hannover

Facies - Es werden zwei Profile beschrieben, die, am südlichen Ortsrand Hannovers gelegen, während Bauarbeiten an einer Trogstrecke und in einer ehemaligen Ziegelei erschlossen waren. Sie...     

Distribution and conservation of mobile elements in the genus Drosophila

Essentially nothing is known of the origin, mode of transmission, and evolution of mobile elements within the genus Drosophila. To better understand the evolutionary history of these mobile elements, we examined the distribution and conservation of homologues to the P, I, gypsy, copia, and F elements in 34 Drosophila species from three subgenera. Probes specific for each element were prepared from D. melanogaster and hybridized to genomic DNA. Filters were washed under conditions of increasing stringency to estimate the similarity between D. melanogaster sequences and their homologues in other species. The I element homologues show the most limited distribution of all elements tested, being restricted to the melanogaster species group. The P elements are found in many members of the subgenus Sophophora but, with the notable exception of D. nasuta, are not found in the other two subgenera. Copia-, gypsy-, and F-element homologues are widespread in the genus, but their similarity to the D. melanogaster probe differs markedly between species. The distribution of copia and P elements and the conservation of the gypsy and P elements is inconsistent with a model that postulates a single ancient origin for each type of element followed by mating-dependent transmission. The data can be explained by horizontal transmission of mobile elements between reproductively isolated species.      

Genotyping-by-sequencing to remap QTL for type II Fusarium head blight and leaf rust resistance in a wheat–tall wheatgrass introgression recombinant inbred population

Fusarium graminearum Schwabe (Fusarium head blight, FHB) and Puccinia triticina Eriks (leaf rust) are two major fungal pathogens posing a continuous threat to the wheat crop; consequently, identifying resistance genes from various sources is always of importance to wheat breeders. We identified tightly linked single nucleotide polymorphism (SNP) markers for the FHB resistance quantitative trait locus (QTL) Qfhs.pur-7EL and the leaf rust resistance locus Lr19 using genotyping-by-sequencing (GBS) in a wheat–tall wheatgrass introgression-derived recombinant inbred line (RIL) population. One thousand and seven hundred high-confidence SNPs were used to conduct the linkage and QTL analysis. Qfhs.pur-7EL was mapped to a 2.9 cM region containing four markers within a 43.6 cM segment of wheatgrass chromosome 7el₂ that was translocated onto wheat chromosome 7DL. Lr19 from 7el₁ was mapped to a 1.21 cM region containing two markers in the same area, in repulsion. Five lines were identified with the resistance-associated SNP alleles for Qfhs.pur-7EL and Lr19 in coupling. Two SNP markers in the Qfhs.pur-7EL region were converted into PCR-based KASP markers. Investigation of the genetic characteristics of the parental lines of this RIL population indicated that they are translocation lines in two different wheat cultivar genetic backgrounds instead of 7E–7D substitution lines in Thatcher wheat background, as previously reported in the literature.