Enhanced genome assembly and a new official gene set for Tribolium castaneum

Background. The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. Results. Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. Conclusions. The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis

H2AX phosphorylation screen of cells from radiosensitive cancer patients reveals a novel DNA double-strand break repair cellular phenotype

BACKGROUND: About 1-5% of cancer patients suffer from significant normal tissue reactions as a result of radiotherapy (RT). It is not possible at this time to predict how most patients' normal tissues will respond to RT. DNA repair dysfunction is implicated in sensitivity to RT particularly in genes that mediate the repair of DNA double-strand breaks (DSBs). Phosphorylation of histone H2AX (phosphorylated molecules are known as gammaH2AX) occurs rapidly in response to DNA DSBs, and, among its other roles, contributes to repair protein recruitment to these damaged sites. Mammalian cell lines have also been crucial in facilitating the successful cloning of many DNA DSB repair genes; yet, very few mutant cell lines exist for non-syndromic clinical radiosensitivity (RS).\ud \ud METHODS: Here, we survey DNA DSB induction and repair in whole cells from RS patients, as revealed by gammaH2AX foci assays, as potential predictive markers of clinical radiation response.\ud \ud RESULTS: With one exception, both DNA focus induction and repair in cell lines from RS patients were comparable with controls. Using gammaH2AX foci assays, we identified a RS cancer patient cell line with a novel ionising radiation-induced DNA DSB repair defect; these data were confirmed by an independent DNA DSB repair assay.\ud \ud CONCLUSION: gammaH2AX focus measurement has limited scope as a pre-RT predictive assay in lymphoblast cell lines from RT patients; however, the assay can successfully identify novel DNA DSB repair-defective patient cell lines, thus potentially facilitating the discovery of novel constitutional contributions to clinical RS

Factors affecting the survival ability in lambs in the period till weaning

В 1963 г в Сельскохозяйственной опытной станции Пучнев, а в 1964 г. в Сельскохозяйственной опытной станции Желязна анализировали влияние селекционных факторов на выживальную способность ягнят. Исследования охватывали соответственно 453 и 1080 ягнят в отдельных стадах. В обоих стадах установлено существенное влияние веса тела после рождения на выживаемость, а жлияние типа родов было подтвержвено статистически в одном стаде. Влияние пола ягненка на выживаемость не было доказано, установлено лишь, что среди наиболее легких и наиболее тяжелых ягнят чаще родятся мертвые ягнята или чаще падают после родов баранчики, чем овечки. На основании проводимых только в овчарне Желязна наблюдений были установлены четкие разницы в проценте падежей между группами потомства после отдельных баранов. При средней для стада составляющей 9,47%, в группе с наименьшими потерями участие падежей составляло 2,27%, а в самой плохой группе в этом отношении оно составляло 20,87%. Это указывает на возможность ведения отбора на указанный признак.The effect of breeding factors on the survival ability was analyzed in 1985 at the Agricultural Experiment Station Puczniew and in 1984 at the Agricultural Experiment Station Żelazna. The analysis comprised 453 and 1080 lambs in suitable flocks. In both flocks a significant effect of the body weight after birth on the survival was found and the effect of this birth type was statistically confirmed in one flock. The lamb sex effect on the survival has not been proved, although it has been found that among the lightest and heaviest lambs more frequent stillbirths and/or deaths of born ram-lambs than ewe-lambs took place. The observations, which were performed at Żelazna only, proved significant differences in the per cent of losses between progeny groups after particular rams. For the mean for flock amounting to 9.47 % in the group of the least losses this difference was 2.27 .% and in the worst group - 20.87 %. This would suggest to possibility of selection for this trait