Distribution,functional impact,and origin mechanisms of copy number variation in the barley genome

Background

There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys.

Results

A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley.

Conclusions

We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.     

Indiscelio: A new genus of Scelionidae (Platygastroidea) from India

A new scelionine genus Indiscelio Veenakumari, Popovici and Talamas is described from India with type species Indiscelio aulon Veenakumari, Popovici and Talamas. Both sexes are described and imaged. Affinities with morphologically similar genera are discussed.     

Early transposable element insertion in intron 9 of the Hsf4 gene results in autosomal recessive cataracts in lop11 and ldis1 mice

Lens opacity 11 (lop11) is an autosomal recessive mouse cataract mutation that arose spontaneously in the RIIIS/J strain. At 3 weeks of age mice exhibit total cataracts with vacuoles. The lop11 locus was mapped to mouse chromosome 8. Analysis of the mouse genome for the lop11 critical region identified Hsf4 as a candidate gene. Molecular evaluation of Hsf4 revealed an early transposable element (ETn) in intron 9 inserted 61 bp upstream of the intron/exon junction. The same mutation was also identified in a previously mapped cataract mutant, ldis1. The ETn insertion altered splicing and expression of the Hsf4 gene, resulting in the truncated Hsf4 protein. In humans, mutations in HSF4 have been associated with both autosomal dominant and recessive cataracts. The lop11 mouse is an excellent resource for evaluating the role of Hsf4 in transparency of the lens.     

Molecular characterisation of the <Emphasis Type="Italic">STRUBBELIG-RECEPTOR FAMILY</Emphasis> of genes encoding putative leucine-rich repeat receptor-like kinases in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Background  

Receptor-like kinases are a prominent class of surface receptors that regulate many aspects of the plant life cycle. Despite recent advances the function of most receptor-like kinases remains elusive. Therefore, it is paramount to investigate these receptors. The task is complicated by the fact that receptor-like kinases belong to a large monophyletic family with many sub-clades. In general, functional analysis of gene family members by reverse genetics is often obscured by several issues, such as redundancy, subtle or difficult to detect phenotypes in mutants, or by decision problems regarding suitable biological and biochemical assays. Therefore, in many cases additional strategies have to be employed to allow inference of hypotheses regarding gene function.     

Revision of the Paridris nephtaspecies group (Hymenoptera, Platygastroidea, Platygastridae)

The Paridris nephta group is revised (Hymenoptera: Platygastridae). Fifteen species are described, 14 of which are new: Paridris atroxTalamas, sp. n.(Yunnan Province, China), Paridris bununTalamas, sp. n.(Taiwan), Paridris ferusTalamas, sp. n.(Thailand), Paridris kagemonoTalamas, sp. n.(Japan), Paridris minatorTalamas, sp. n.(Laos, Thailand), Paridris mystaxTalamas, sp. n.(Laos, Thailand), Paridris nephta(Kozlov) (Japan, North Korea, South Korea, Far Eastern Russia), Paridris nilakaTalamas, sp. n.(Thailand), Paridris reptilisTalamas, sp. n.(Taiwan), Paridris rugulosusTalamas, sp. n.(Laos, Vietnam), Paridris solarisTalamas, sp. n.(Laos, Thailand, Vietnam), Paridris teresTalamas, sp. n.(Vietnam), Paridris toketokiTalamas, sp. n.(Taiwan), Paridris verrucosusTalamas, sp. n.(Guangdong Province, China), Paridris yakTalamas, sp. n.(Thailand).     

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation

Background

Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity.

Results

To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine.

Conclusion

This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from ftp://ftpmips.gsf.de/plants/apollo_webservice.     

Genetic pattern of the HLA system: HLA A, B, C, DR, and DQ antigens in Mexican patients with parenchymal brain cysticercosis

The distribution of HLA class I and class II determinants was investigated in 48 patients with parenchymal neurocysticercosis and in 295 healthy controls of the same ethnic group, the Mexican Mestizo population. Two antigens, A28 and DQw2, showed significantly differences in frequency between patients and controls; HLA A28 was increased (39.6% versus 15.6%; pc = 0.008), and HLA DQw2 was decreased (4.2% versus 31.7%; pc = 0.004) in neurocysticercosis patients. The relative risk for developing the disease in HLA A28 positive individuals was 3.55. Our results show that the major histocompatibility complex plays some role in the susceptibility and resistance to parenchymal neurocysticercosis, but the HLA genetic background of patients with neurocysticercosis does not seem to influence the severity of inflammatory response against cysticerci, nor is the disease sex related.     

A novel series of IKKβ inhibitors part I: Initial SAR studies of a HTS hit

A novel series of (E)-1-((2-(1-methyl-1H-imidazol-5-yl) quinolin-4-yl) methylene) thiosemicarbazides was discovered as potent inhibitors of IKKβ. In this Letter we document our early efforts at optimization of the quinoline core, the imidazole and the semithiocarbazone moiety. Most potency gains came from substitution around the 6- and 7-positions of the quinoline ring. Replacement of the semithiocarbazone with a semicarbazone decreased potency but led to some measurable exposure.