Sequence Capture and Next Generation Resequencing of the MHC Region Highlights Potential Transplantation Determinants in HLA Identical Haematopoietic Stem Cell Transplantation

How cells coordinate the immune system activities is important for potentially life-saving organ or stem cell transplantations. Polymorphic immunoregulatory genes, many of them located in the human major histocompatibility complex, impact the process and assure the proper execution of tolerance-versus-activity mechanisms. In haematopoietic stem cell transplantation, on the basis of fully human leukocyte antigen (HLA)-matched donor–recipient pairs, adverse effects like graft versus leukaemia and graft versus host are observed and difficult to handle. So far, high-resolution HLA typing was performed with Sanger sequencing, but for methodological reasons information on additional immunocompetent major histocompatibility complex loci has not been revealed. Now, we have used microarray sequence capture and targeted enrichment combined with next generation pyrosequencing for 3.5 million base pair human major histocompatibility complex resequencing in a clinical transplant setting and describe 3025 variant single nucleotide polymorphisms, insertions and deletions among recipient and donor in a single sequencing experiment. Taken together, the presented data show that sequence capture and massively parallel pyrosequencing can be used as a new tool for risk assessment in the setting of allogeneic stem cell transplantation

Chrysomelidial in the Opisthonotal Glands of the Oribatid Mite, Oribotritia berlesei

Gas chromatographic–mass spectrometric analyses of whole body extracts of Oribotritia berlesei, a large-sized soil-dwelling oribatid mite, revealed a consistent chemical pattern of ten components, probably originating from the well-developed opisthonotal glands. The three major components of the extract were the iridoid monoterpene, (3S,8S)-chrysomelidial (about 45% of the extract), the unsaturated hydrocarbon 6,9-heptadecadiene, and the diterpene β-springene (the latter two, each about 20–25% of the extract). The remaining minor components (together about 10% of the extract) included a series of hydrocarbons (tridecene, tridecane, pentadecene, pentadecane, 8-heptadecene, and heptadecane) and the tentatively identified 9,17-octadecadienal. In contrast, analysis of juveniles showed only two compounds, namely a 2:1 mixture of (3S,8S)-chrysomelidial and its epimer, epi-chrysomelidial (3S,8R-chrysomelidial). Unexpectedly, neither adult nor juvenile secretions contained the so-called astigmatid compounds, which are considered characteristic of secretions of oribatids above moderately derived Mixonomata. The chrysomelidials, as well as β-springene and octadecadienal, are newly identified compounds in the opisthonotal glands of oribatid mites and have chemotaxonomic potential for this group. This is the first instance of finding chrysomelidials outside the Coleoptera

How Do Honeybees Attract Nestmates Using Waggle Dances in Dark and Noisy Hives?

It is well known that honeybees share information related to food sources with nestmates using a dance language that is representative of symbolic communication among non-primates. Some honeybee species engage in visually apparent behavior, walking in a figure-eight pattern inside their dark hives. It has been suggested that sounds play an important role in this dance language, even though a variety of wing vibration sounds are produced by honeybee behaviors in hives. It has been shown that dances emit sounds primarily at about 250–300 Hz, which is in the same frequency range as honeybees' flight sounds. Thus the exact mechanism whereby honeybees attract nestmates using waggle dances in such a dark and noisy hive is as yet unclear. In this study, we used a flight simulator in which honeybees were attached to a torque meter in order to analyze the component of bees' orienting response caused only by sounds, and not by odor or by vibrations sensed by their legs. We showed using single sound localization that honeybees preferred sounds around 265 Hz. Furthermore, according to sound discrimination tests using sounds of the same frequency, honeybees preferred rhythmic sounds. Our results demonstrate that frequency and rhythmic components play a complementary role in localizing dance sounds. Dance sounds were presumably developed to share information in a dark and noisy environment

The genome of the emerging barley pathogen Ramularia collo-cygni

Background Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph

Acute high-dose X-radiation-induced genomic changes in A549 cells

Accidents with ionizing radiation often involve single, acute high-dose exposures that can lead to acute radiation syndrome and late effects such as carcinogenesis. To study such effects at the cellular level, we investigated acute ionizing radiation-induced chromosomal aberrations in A549 adenocarcinoma cells at the genome-wide level by exposing the cells to an acute dose of 6 Gy 240 kV X rays. One sham-irradiated clone and four surviving irradiated clones were recovered by minimal dilution and further expanded and analyzed by chromosome painting and tiling-path array CGH, with the nonirradiated clone 0 serving as the control. Acute X-ray exposure induced specific translocations and changes in modal chromosome number in the four irradiated clones. Array CGH disclosed unique and recurrent genomic changes, predominantly losses, and revealed that the fragile sites FRA3B and FRA16D were preferential regions of genomic alterations in all irradiated clones, which is likely related to radioresistant S-phase progression and genomic stress. Furthermore, clone 4 displayed an increased radiosensitivity at doses >5 Gy. Pairwise comparisons of the gene expression patterns of all irradiated clones to the sham-irradiated clone 0 revealed an enrichment of the Gene Ontology term "M Phase" (P = 6.2 x 10(-7)) in the set of differentially expressed genes of clone 4 but not in those of clones 1-3. Ionizing radiation-induced genomic changes and fragile site expression highlight the capacity of a single acute radiation exposure to affect the genome of exposed cells by inflicting genomic stress