A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164\ua0Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models

The Efficacy of Trastuzumab in Animal Models of Breast Cancer:A Systematic Review and Meta-Analysis

BACKGROUND:Breast cancer is the most frequent cancers and is the second leading cause of cancer death among women. Trastuzumab is an effective treatment, the first monoclonal antibody directed against the human epidermal growth factor receptor 2 (HER2). To inform the development of other effective treatments we report summary estimates of efficacy of trastuzumab on survival and tumour volume in animal models of breast cancer. METHODS:We searched PubMed and EMBASE systematically to identify publications testing trastuzumab in animal models of breast cancer. Data describing tumour volume, median survival and animal features were extracted and we assessed quality using a 12-item checklist. We analysed the impact of study design and quality and evidence for publication bias. RESULTS:We included data from 83 studies reporting 169 experiments using 2076 mice. Trastuzumab treatment caused a substantial reduction in tumour growth, with tumours in treated animals growing to 32.6% of the volume of tumours in control animals (95%CI 27.8%-38.2%). Median survival was prolonged by a factor of 1.45 (1.30-1.62). Many study design and quality features accounted for between-study heterogeneity and we found evidence suggesting publication bias. CONCLUSION:We have found trastuzumab to be effective in animal breast cancer models across a range of experimental circumstances. However the presence of publication bias and a low prevalence of measures to reduce bias provide a focus for future improvements in preclinical breast cancer research

Quantitative analysis of genetic variability in floral and germinative characteristics of meadowfoam (Limnanthes alba) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Science at Massey University

Genetic and physiological aspects of flowering, seeding, seed shattering and dormancy of meadowfoam have been studied to provide information on the new crop meadowfoam, and to assist in its domestication and early breeding. Two hundred and fifty-nine plants were chosen randomly to form an unbiased sample representing the germplasm of eight divergent meadowfoam accessions, which had been intermated to form a composite. Thirteen characters associated with flowering and seeding were involved. Both principal components and clustering proved to be efficient analyses which maximized the discrimination of differences amongst plants in this segregating population. These procedures recognized 190 phenotypes within this germplasm. A high level of significant genotypic variance in all characters was found. Moreover, environmental variances were generally lower in size, so that most characters had high heritability (h2 > 0.800). Early seed set was an exception, with heritability of only 0.446. The results showed that meadowfoam should respond well to selection. A special feature of this germplasm analysis was the use of cluster analysis, to define "natural" groups. This involved truncating the cluster dendrogram on the basis of minimum F-probability of amongst-cluster to within cluster mean-squares. Further refinement was based on the maximum genotypic variance (σG2), phenotypic variance (σP2) and heritability (h2), at or near the original truncation. Another innovation was the use of principal components analysis to identify patterns of fresh flowers, total flowers and seed set. Variability in floral initiation, general flowering time or seed set was randomly distribution, which indicated that the base population was panmictic: one large segregating gamodeme. This pattern analysis was superior to regressions (over time), because there were few time-nodes, and it avoided the need to find optimum functions. Next, germination and dormancy of this gene-pool were studied, requiring extensive use of the Richards functions and MANOVA. These analyses provided better discrimination amongst treatments than did the univariate character "final germination level". Dormancy-breaking for meadowfoam was found to be possible by using KNO3 and/or GA4+7 in darkness at 10/5°C, without prechilling. This special test assesses whole-seed germinative maturity; the difference between this and standard germination provides an estimate of dormancy. The results indicated that biosynthesis of GAs and/or sensitivity to GAs were probably involved in meadowfoam germination. A representative sample gene-pool for study of seed development was established using principal components, giving eight half-sib lines. Harvest ripeness (decline in seed moisture to 12.5%) was compared with seed growth (dry mass), and line differences were found. Standard and special germination tests showed that primary dormancy developed in seeds before they were harvest ripe. Dormancy varied in the eight lines. ABA content was assayed by ELISA, and principal components and cluster analyses followed using ABA peak measurements (peak height, width and time reaching peak). There were four ABA groups for the eight lines. However, a clear link between ABA pattern and dormancy breaking was not established. Difference in sensitivity to ABA may explain why this was the case. The results indicated the presence of considerable genotypic variation, allowing estimates of heritability for the development traits. Although the contrast of variance from Ŷ (regression) with pooled σ2Ŷ was novel, it conformed with biological expectation, and compared well with results from wheat. Heritability was high for harvest-ripe seed mass (0.9238), showing a strong genetic control. In contrast, seed moisture heritability was low (0.3292), indicating considerable environmental influence. Heritability of germinative maturity (dormancy-breaking test on 5 weeks storage seed) was very high (0.9437), indicating that this is a credible measure of true physiological maturity. The heritability of dormancy-breaking was also high (0.9306) after 5 weeks storage. Conversely, after 15 weeks storage, both germinative maturity and dormancy-breaking heritability were low. This indicated that prolonged storage effects were more environmental than genetic. The general levels of genetic influences (variances and heritabilities) indicate that there is much potential for changing (domesticating) meadowfoam in these characters

Scar‐Degrading Endothelial Cells as a Treatment for Advanced Liver Fibrosis

Abstract Deposition of extracellular matrix (ECM) in the liver is an important feature of liver cirrhosis. Recovery from liver cirrhosis is physiologically challenging, partially due to the ECM in scar tissue showing resistance to cell‐mediated degradation by secreted matrix metalloproteinases (MMPs). Here, a cell‐mediated ECM‐degradation screening system (CEDSS) in vitro is constructed for high‐throughput searching for cells with tremendous degradation ability. ECM‐degrading liver sinusoidal endothelial cells (dLSECs) are screened using CEDSS, which exhibit 17 times the ability to degrade collagen when compared to other cells. The degradation ability of dLSECs is mediated by the upregulation of MMP9. In particular, mRNA expression of MMP9 shows an 833‐fold increase in dLSECs compared to normal endothelial cells (nLSECs), and MMP9 is regulated by transcription factor c‐Fos. In vivo, single intrasplenic injection of dLSECs alleviates advanced liver fibrosis in mice, while intraperitoneal administration of liver‐targeting peptide‐modified dLSECs shows enhanced fibrosis‐targeting effects. Degradative human umbilical vein endothelial cells (dHUVECs) prove their enhanced potential of clinical translation. Together, these results highlight the potential of ECM‐degrading endothelial cells in alleviating advanced liver fibrosis, thus providing remarkable insights in the development of ECM‐targeting therapeutics

Additional file 8: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Sequenced cDNA’s used to verify the gene models.Fasta formatted predicted protein sequences of 550 bidirectionally sequenced expressed sequence tag clones from A. chinensis var. chinensis used in evaluating manually annotated gene models of Red5. (FASTA 220 kb

Additional file 6: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Revised ‘Hongyang’ genes omitted from the manually edited gene set. Average RNA-Seq read coverage of the 1069 KIR V2 models perfectly aligned to the Red5 genome without a protein match in the Red5 gene set. (XLSX 114 kb

Additional file 3: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Comparison of predicted paired end distance to genome.Heatmaps of alignment distance scores for the alignment of the read pairs from the 9Kb long-insert mate-paired-end (LIMP) library to each of the 29 chromosomes within the Red5 whole genome assembly and. Individual chromosome plots were prepared using hagfish_blockplot from the software program ‘hagfish’ ( https://github.com/mfiers/hagfish/ ). Individual images were cropped for height (not length) then cut and pasted into a table format for easier viewing. Each image depicted the entire length of the chromosome but all images are of standard length irrespective of chromosome length. Green regions indicate mate pairs aligning to the whole genome sequence within the expected distance of the library. Black indicates regions without mate pair alignment. Pinkish-red indicates regions where the distance between mated paired end reads is shorter (assembly compression relative to physical genome) or longer (assembly expansion relative to physical genome). (PPTX 432 kb

Additional file 1: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Map back rates to the Red5 genome sequence.Summary of the numbers of input reads reads that align to the RED5 genome construction (XLSX 10 kb