Centromere sequence and dynamics in Dictyostelium discoideum

Centromeres play a pivotal role in the life of a eukaryote cell, perform an essential and conserved function, but this has not led to a standard centromere structure. It remains currently unclear, how the centromeric function is achieved by widely differing structures. Since centromeres are often large and consist mainly of repetitive sequences they have only been analyzed in great detail in a handful of organisms. The genome of Dictyostelium discoideum, a valuable model organism, was described a few years ago but its centromere organization remained largely unclear. Using available sequence information we reconstructed the putative centromere organization in three of the six chromosomes of D. discoideum. They mainly consist of one type of transposons that is confined to centromeric regions. Centromeres are dynamic due to transposon integration, but an optimal centromere size seems to exist in D. discoideum. One centromere probably has expanded recently, whereas another underwent major rearrangements

Transcriptome analysis of the sex pheromone gland of the noctuid moth Heliothis virescens

<p>Abstract</p> <p>Background</p> <p>The chemical components of sex pheromones have been determined for more than a thousand moth species, but so far only a handful of genes encoding enzymes responsible for the biosynthesis of these compounds have been identified. For understanding the evolution of moth sexual communication, it is essential to know which genes are involved in the production of specific pheromone components and what controls the variation in their relative frequencies in the pheromone blend. We used a transcriptomic approach to characterize the pheromone gland of the Noctuid moth <it>Heliothis virescens</it>, an important agricultural pest, in order to obtain substantial general sequence information and to identify a range of candidate genes involved in the pheromone biosynthetic pathway.</p> <p>Results</p> <p>To facilitate identifying sets of genes involved in a broad range of processes and to capture rare transcripts, we developed our majority of ESTs from a normalized cDNA library of <it>Heliothis virescens </it>pheromone glands (PG). Combining these with a non-normalized library yielded a total of 17,233 ESTs, which assembled into 2,082 contigs and 6,228 singletons. Using BLAST searches of the NR and Swissprot databases we were able to identify a large number of putative unique gene elements (unigenes), which we compared to those derived from previous transcriptomic surveys of the larval stage of <it>Heliothis virescens</it>. The distribution of unigenes among GO Biological Process functional groups shows an overall similarity between PG and larval transcriptomes, but with distinct enrichment of specific pathways in the PG. In addition, we identified a large number of candidate genes in the pheromone biosynthetic pathways.</p> <p>Conclusion</p> <p>These data constitute one of the first large-scale EST-projects for Noctuidae, a much-needed resource for exploring these pest species. Our analysis shows a surprisingly complex transcriptome and we identified a large number of potential pheromone biosynthetic pathway and immune-related genes that can be applied to population and systematic studies of <it>Heliothis virescens </it>and other Noctuidae.</p

Origin of land plants: Do conjugating green algae hold the key?

<p>Abstract</p> <p>Background</p> <p>The terrestrial habitat was colonized by the ancestors of modern land plants about 500 to 470 million years ago. Today it is widely accepted that land plants (embryophytes) evolved from streptophyte algae, also referred to as charophycean algae. The streptophyte algae are a paraphyletic group of green algae, ranging from unicellular flagellates to morphologically complex forms such as the stoneworts (Charales). For a better understanding of the evolution of land plants, it is of prime importance to identify the streptophyte algae that are the sister-group to the embryophytes. The Charales, the Coleochaetales or more recently the Zygnematales have been considered to be the sister group of the embryophytes However, despite many years of phylogenetic studies, this question has not been resolved and remains controversial.</p> <p>Results</p> <p>Here, we use a large data set of nuclear-encoded genes (129 proteins) from 40 green plant taxa (Viridiplantae) including 21 embryophytes and six streptophyte algae, representing all major streptophyte algal lineages, to investigate the phylogenetic relationships of streptophyte algae and embryophytes. Our phylogenetic analyses indicate that either the Zygnematales or a clade consisting of the Zygnematales and the Coleochaetales are the sister group to embryophytes.</p> <p>Conclusions</p> <p>Our analyses support the notion that the Charales are not the closest living relatives of embryophytes. Instead, the Zygnematales or a clade consisting of Zygnematales and Coleochaetales are most likely the sister group of embryophytes. Although this result is in agreement with a previously published phylogenetic study of chloroplast genomes, additional data are needed to confirm this conclusion. A Zygnematales/embryophyte sister group relationship has important implications for early land plant evolution. If substantiated, it should allow us to address important questions regarding the primary adaptations of viridiplants during the conquest of land. Clearly, the biology of the Zygnematales will receive renewed interest in the future.</p

Selenoprotein H is an essential regulator of redox homeostasis that cooperates with p53 in development and tumorigenesis

Selenium, an essential micronutrient known for its cancer prevention properties, is incorporated into a class of selenocysteine-containing proteins (selenoproteins). Selenoprotein H (SepH) is a recently identified nucleolar oxidoreductase whose function is not well understood. Here we report that seph is an essential gene regulating organ development in zebrafish. Metabolite profiling by targeted LC-MS/MS demonstrated that SepH deficiency impairs redox balance by reducing the levels of ascorbate and methionine, while increasing methionine sulfoxide. Transcriptome analysis revealed that SepH deficiency induces an inflammatory response and activates the p53 pathway. Consequently, loss of seph renders larvae susceptible to oxidative stress and DNA damage. Finally, we demonstrate that seph interacts with p53 deficiency in adulthood to accelerate gastrointestinal tumor development. Overall, our findings establish that seph regulates redox homeostasis and suppresses DNA damage. We hypothesize that SepH deficiency may contribute to the increased cancer risk observed in cohorts with low selenium levels.National Cancer Institute (U.S.) (Grant R01 DK090311)National Cancer Institute (U.S.) (Grant R24OD017870

Heavy Ion Testing at the Galactic Cosmic Ray Energy Peak

A 1 GeV/u Fe-56 ion beam allows for true 90deg tilt irradiations of various microelectronic components and reveals relevant upset trends for an abundant element at the GCR flux energy peak

Fitness Benefits of Systemic Acquired Resistance During Hyaloperonospora parasitica Infection in Arabidopsis thaliana

We investigated the fitness benefits of systemic acquired resistance (SAR) in Arabidopsis thaliana using a mutational and transformational genetic approach. Genetic lines were designed to differ in the genes determining resistance signaling in a common genetic background. Two mutant lines (cpr1 and cpr5) constitutively activate SAR at different points in SAR signaling, and one mutant line (npr1) has impaired SAR. The transgenic line (NPR1-H) has enhanced resistance when SAR is activated, but SAR is still inducible similarly to wild type. The fitness benefits were also investigated under two nutrient levels to test theories that preventing pathogen damage and realized resistance benefits may be affected by nutrient availability. Under low-nutrient conditions and treatment with the pathogenic oomycete, Hyaloperonospora parasitica, wild type had a higher fitness than the mutant that could not activate SAR, demonstrating that normal inducible SAR is beneficial in these conditions; this result, however, was not found under high-nutrient conditions. The mutants with constitutive SAR all failed to show a fitness benefit in comparison to wild type under a H. parasitica pathogen treatment, suggesting that SAR is induced to prevent an excessive fitness cost

Data from: Pinpointing genes underlying annual/perennial transitions with comparative genomics

Background: Transitions between perennial and an annual life history occur often in plant lineages, but the genes that control whether a plant is an annual or perennial are largely unknown. To identify genes that confer differences between annuals and perennials we compared the gene content of four pairs of sister lineages (Arabidopsis thaliana/Arabidopsis lyrata, Arabis montbretiana/Arabis alpina, Arabis verna/Aubrieta parviflora and Draba nemorosa/Draba hispanica) in the Brassicaceae in which each pair contains one annual and one perennial, plus one extra annual species (Capsella rubella). Results: After sorting all genes in all nine species into gene families, we identified five families in which well-annotated genes are present in the perennials A. lyrata and A. alpina, but are not present in any of the annual species. For the eleven genes in perennials in these families, an orthologous pseudogene or otherwise highly diverged gene was found in the syntenic region of the annual species in six cases. The five candidate families identified encode: a kinase, an oxidoreductase, a lactoylglutathione lyase, a F-box protein and a zinc finger protein. By comparing the active gene in the perennial to the pseudogene or heavily altered gene in the annual, dN and dS were calculated. The low dN/dS values in one kinase suggest that it became pseudogenized more recently, while the other kinase, F-box, oxidoreductase and zinc-finger became pseudogenized closer to the divergence between the annual-perennial pair. Conclusions: We identified five gene families that may be involved in the life history switch from perennial to annual. Considering the dN and dS data and whether syntenic pseudogenes were found and the potential functions of the genes, the F-box family is considered the most promising candidate for future functional studies to determine if it affects life history

Natural Variation in MAM Within and Between Populations of Arabidopsis lyrata Determines Glucosinolate Phenotype

The genetic variation that underlies the glucosinolate phenotype of Arabidopsis lyrata ssp. petraea was investigated between and within populations. A candidate glucosinolate biosynthetic locus (MAM, containing methylthioalkylmalate synthase genes) was mapped in A. lyrata to a location on linkage group 6 corresponding to the homologous location for MAM in A. thaliana. In A. thaliana MAM is responsible for side chain elongation in aliphatic glucosinolates, and the MAM phenotype can be characterized by the ratios of long- to short-chain glucosinolates. A quantitative trait loci (QTL) analysis of glucosinolate ratios in an A. lyrata interpopulation cross found one QTL at MAM. Additional QTL were identified for total indolic glucosinolates and for the ratio of aliphatic to indolic glucosinolates. MAM was then used as the candidate gene for a within-population cosegregation analysis in a natural A. lyrata population from Germany. Extensive variation in microsatellite markers at MAM was found and this variation cosegregated with the same glucosinolate ratios as in the QTL study. The combined results indicate that both between- and within-population genetic variation in the MAM region determines phenotypic variation in glucosinolate side chains in A. lyrata