Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

<p>Abstract</p> <p>Background</p> <p>Cucumber, <it>Cucumis sativus </it>L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber.</p> <p>Results</p> <p>A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The <it>in silico </it>PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available.</p> <p>Conclusions</p> <p>The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.</p

Parenting Programs for the Prevention of Child Physical Abuse Recurrence: A Systematic Review and Meta-Analysis

Child physical abuse is an issue of global concern. Conservative estimates set global prevalence of this type of maltreatment at 25%, its consequences and cost to society escalating with increasing frequency and severity of episodes. Syntheses of the evidence on parenting programs for reducing rates of physical abuse recidivism have, to date, not been able to establish effectiveness. Paucity of data and inconsistent inclusion criteria in past reviews made meta-analysis often impossible or uninformative. The current systematic review updates prior reviews and overcomes some of the methodological issues they encountered by pooling trial-level data from a well-defined scope of trials of parenting interventions aimed at preventing the re-abuse of children by parents with substantiated or suspected physical abuse history. Randomized controlled trials and rigorous non-randomized designs were sought via nine online databases, two trial registries, several clearinghouses and contact with experts. A total of fourteen studies of variable quality were included in this review, four of which had outcomes that enabled meta-analysis. Overall, this review presents evidence supporting the effectiveness of parenting behavioral programs based on social learning theory for reducing hard markers of child physical abuse recidivism. Meta-analysis found that the absolute risk reduction in risk of recidivism was 11 percentage points less for maltreating parents who undergo parenting programs (RD = -0.11, 95% CI [-0.22, -0.004], p = 0.043, I 2 = 28.9%). However, the pooled effect size was not statistically significant when calculated as a risk ratio (0.76, 95% CI [0.54, 1.07], I 2 = 38.4%). Policy makers and practitioners should be made aware that this intervention method is backed by promising evidence featuring modest yet significant reductions in hard markers of child physical abuse, even though the methodological robustness of these findings should be further explored in future research

Environmental determinants of islet autoimmunity (ENDIA): a pregnancy to early life cohort study in children at-risk of type 1 diabetes

Members of ENDIA Study Group: Peter Baghurst, Simon Barry, Jodie Dodd, Maria Makrides for the University of Adelaide.BACKGROUND The incidence of type 1 diabetes has increased worldwide, particularly in younger children and those with lower genetic susceptibility. These observations suggest factors in the modern environment promote pancreatic islet autoimmunity and destruction of insulin-producing beta cells. The Environmental Determinants of Islet Autoimmunity (ENDIA) Study is investigating candidate environmental exposures and gene-environment interactions that may contribute to the development of islet autoimmunity and type 1 diabetes. METHODS/DESIGN ENDIA is the only prospective pregnancy/birth cohort study in the Southern Hemisphere investigating the determinants of type 1 diabetes in at-risk children. The study will recruit 1,400 unborn infants or infants less than six months of age with a first-degree relative (i.e. mother, father or sibling) with type 1 diabetes, across five Australian states. Pregnant mothers/infants will be followed prospectively from early pregnancy through childhood to investigate relationships between genotype, the development of islet autoimmunity (and subsequently type 1 diabetes), and prenatal and postnatal environmental factors. ENDIA will evaluate the microbiome, nutrition, bodyweight/composition, metabolome-lipidome, insulin resistance, innate and adaptive immune function and viral infections. A systems biology approach will be used to integrate these data. Investigation will be by 3-monthly assessments of the mother during pregnancy, then 3-monthly assessments of the child until 24 months of age and 6-monthly thereafter. The primary outcome measure is persistent islet autoimmunity, defined as the presence of autoantibodies to one or more islet autoantigens on consecutive tests. DISCUSSION Defining gene-environment interactions that initiate and/or promote destruction of the insulin-producing beta cells in early life will inform approaches to primary prevention of type 1 diabetes. The strength of ENDIA is the prospective, comprehensive and frequent systems-wide profiling from early pregnancy through to early childhood, to capture dynamic environmental exposures that may shape the development of islet autoimmunity. TRIAL REGISTRATION Australia New Zealand Clinical Trials Registry ACTRN12613000794707.Megan AS Penno, Jennifer J Couper, Maria E Craig, Peter G Colman, William D Rawlinson, Andrew M Cotterill, Timothy W Jones, Leonard C Harrison and ENDIA Study Grou

Osteotropic Cancers: From Primary Tumor to Bone

Tumour-induced bone disease is a common clinical feature of hematological and metastatic solid cancer. Thus, numerous scientists have gained a better understanding of the mechanisms by which certain tumor types tend to invade specifically the bone. Firstly, Stephen Paget recognized the ‘seed and soil’ hypothesis, stating that cancer cells (the ‘seeds’) can only develop in secondary organs where the microenvironment (the ‘soil’- the bone) is permissive for their growth. Today, this theory has been enlarged to the metastatic process in general, because in order to grow in distant organs, tumor cells need special properties that suit them to those organs. Specifically, in order to metastasize to bone, cancer cells firstly detach from their tissue of origin, subsequently transit through circulation, reside in the bone marrow and acquire a bone cell-like phenotype responsible for bone establishment and invasion. Each step in the metastatic cascade is rich in biological targets and mechanistic pathways, which are summarized in this review