Comparative analysis of diversity based on morphoagronomic traits and molecular markers in durum wheat under heat stress

The objectives of this study were to compare the application and utility of sequence-related amplified polymorphism (SRAP) and target region amplification polymorphism (TRAP) techniques for the analysis of genetic diversity among durum wheat genotypes under heat stress and to compare genetic diversity estimated using molecular markers with morpho-agronomic performance under heat stress. Six durum wheat genotypes were used in this study. They were evaluated phenotypically for heat tolerance. The dendrogram generated from standardized morpho-agronomic data separated the six durum wheat genotypes into three main groups. The dendrogram generated from the standardized morpho-agronomic data separated the six durum wheat genotypes into three clusters, which diverged at similarity index of 0.72. The dendrogram based on SRAP markers differed from that based on TRAP markers. The combined dendrogram (SRAP, TRAP and morpho-agronomic data) agrees better with the grouping of these durum wheat genotypes depending on pedigree and the dendrogram generated by morpho-agronomic data alone.Key words: Durum wheat, genetic diversity, heat tolerance, morpho-agronomic, sequence-related amplified polymorphism (SRAP) markers, target region amplification polymorphism (TRAP) markers

Modulation of ATP/ADP Concentration at the Endothelial Cell Surface by Flow: Effect of Cell Topography

Determining how flow affects the concentration of the adenine nucleotides ATP and ADP at the vascular endothelial cell (EC) surface is essential for understanding flow-induced mobilization of intracellular calcium. Previously, mathematical models were formulated to describe the ATP/ADP concentration at the EC surface; however, all previous models assumed the endothelium to be flat. In the present study we investigate the effect of surface undulations on ATP/ADP concentration at the EC surface. The results demonstrate that under certain geometric and flow conditions, the ATP + ADP concentration at the EC surface is considerably lower for a wavy cell surface than for a flat surface. Because ECs in regions of disturbed arterial flow are expected to have larger undulations than cells in non-disturbed flow zones, our findings suggest that ECs in regions of flow disturbance would exhibit lower ATP + ADP concentrations at their surfaces, which may lead to impaired calcium signaling. If validated experimentally, the present results may contribute to our understanding of endothelial cell dysfunction observed in regions of disturbed flow

Intra-abdominal pectus bar migration – a rare clinical entity: case report

We present the case of a 20-year-old male who underwent successful surgical correction of pectus excavatum with the Highly Modified Ravitch Repair (HMRR). At 29 months the attempted operative removal of the Ravitch bar was unsuccessful despite the impression of adequate bar location on chest x-ray. Subsequent imaging with computed tomography was unclear in determining whether the bar was supra or infra-diaphragmatic due to the tissue distortion subsequent to initial surgery. Video assisted thoracoscopic surgery (VATS) successfully retrieved the bar and revealed that it was not in the thorax, but had migrated to the intra-abdominal bare area of the liver, with no evidence of associated diaphragmatic defect or hernia. Intra-abdominal pectus bar migration is a rare clinical entity, and safe removal can be facilitated by the use of the VATS technique

Trends and inequalities in short-term acute myocardial infarction case fatality in Scotland, 1988-2004

<p>Abstract</p> <p>Background</p> <p>There have been substantial declines in ischemic heart disease in Scotland, partly due to decreases in acute myocardial infarction (AMI) incidence and case fatality (CF). Despite this, Scotland's IHD mortality rates are among the worst in Europe. We examine trends in socioeconomic inequalities in short-term CF after a first AMI event and their associations with age, sex, and geography.</p> <p>Methods</p> <p>We used linked hospital discharge and death records covering the Scottish population (5.1 million). Between 1988 and 2004, 178,781 of 372,349 patients with a first AMI died on the day of the event (Day0 CF) and 34,198 died within 28 days after surviving the day of their AMI (Day1-27 CF).</p> <p>Results</p> <p>Age-standardized Day0 CF at 30+ years decreased from 51% in 1988-90 to 41% in 2003-04. Day1-27 CF decreased from 29% to 18% over that period. Socioeconomic inequalities in Day0 CF existed for both sexes and persisted over time. The odds of case fatality for men aged 30-59 living in the most deprived areas in 2000-04 were 1.7 (95%CI: 1.3-2.2) times as high as in the least deprived areas and 1.9 (1.1-3.2) times as high for women. There was little evidence of socioeconomic inequality in Day1-27 CF in men or women. After adjustment for socioeconomic deprivation, significant geographic variation still remained for both CF definitions.</p> <p>Conclusions</p> <p>A high proportion of AMI incidents in Scotland result in death on the day of the first event; many of these are sudden cardiac deaths. Short-term CF has improved, perhaps reflecting treatment advances and reductions in first AMI severity. However, persistent socioeconomic and geographic inequalities suggest these improvements are not uniform across all population groups, emphasizing the need for population-wide primary prevention.</p

Genomic epidemiology and population structure of Neisseria gonorrhoeae from remote highly endemic Western Australian populations

Background: Neisseria gonorrhoeae causes gonorrhoea, the second most commonly notified sexually transmitted infection in Australia. One of the highest notification rates of gonorrhoea is found in the remote regions of Western Australia (WA). Unlike isolates from the major Australian population centres, the remote community isolates have low rates of antimicrobial resistance (AMR). Population structure and whole-genome comparison of 59 isolates from the Western Australian N. gonorrhoeae collection were used to investigate relatedness of isolates cultured in the metropolitan and remote areas. Core genome phylogeny, multilocus sequencing typing (MLST), N. gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) in addition to hierarchical clustering of sequences were used to characterize the isolates. Results: Population structure analysis of the 59 isolates together with 72 isolates from an international collection, revealed six population groups suggesting that N. gonorrhoeae is a weakly clonal species. Two distinct population groups, Aus1 and Aus2, represented 63% of WA isolates and were mostly composed of the remote community isolates that carried no chromosomal AMR genotypes. In contrast, the Western Australian metropolitan isolates were frequently multi-drug resistant and belonged to population groups found in the international database, suggesting international transmission of the isolates. Conclusions: Our study suggests that the population structure of N. gonorrhoeae is distinct between the communities in remote and metropolitan WA. Given the high rate of AMR in metropolitan regions, ongoing surveillance is essential to ensure the enduring efficacy of the empiric gonorrhoea treatment in remote WA

The genetic organisation of prokaryotic two-component system signalling pathways

<p>Abstract</p> <p>Background</p> <p>Two-component systems (TCSs) are modular and diverse signalling pathways, involving a stimulus-responsive transfer of phosphoryl groups from transmitter to partner receiver domains. TCS gene and domain organisation are both potentially informative regarding biological function, interaction partnerships and molecular mechanisms. However, there is currently little understanding of the relationships between domain architecture, gene organisation and TCS pathway structure.</p> <p>Results</p> <p>Here we classify the gene and domain organisation of TCS gene loci from 1405 prokaryotic replicons (>40,000 TCS proteins). We find that 200 bp is the most appropriate distance cut-off for defining whether two TCS genes are functionally linked. More than 90% of all TCS gene loci encode just one or two transmitter and/or receiver domains, however numerous other geometries exist, often with large numbers of encoded TCS domains. Such information provides insights into the distribution of TCS domains between genes, and within genes. As expected, the organisation of TCS genes and domains is affected by phylogeny, and plasmid-encoded TCS exhibit differences in organisation from their chromosomally-encoded counterparts.</p> <p>Conclusions</p> <p>We provide here an overview of the genomic and genetic organisation of TCS domains, as a resource for further research. We also propose novel metrics that build upon TCS gene/domain organisation data and allow comparisons between genomic complements of TCSs. In particular, '<it>percentage orphaned TCS genes</it>' (or 'Dissemination') and '<it>percentage of complex loci</it>' (or 'Sophistication') appear to be useful discriminators, and to reflect mechanistic aspects of TCS organisation not captured by existing metrics.</p

Cancer during Adolescence: Negative and Positive Consequences Reported Three and Four Years after Diagnosis

Persons diagnosed with cancer during adolescence have reported negative and positive cancer-related consequences two years after diagnosis. The overall aim was to longitudinally describe negative and positive cancer-related consequences reported by the same persons three and four years after diagnosis. A secondary aim was to explore whether reports of using vs. not using certain coping strategies shortly after diagnosis are related to reporting or not reporting certain consequences four years after diagnosis. Thirty-two participants answered questions about coping strategies shortly after diagnosis and negative and positive consequences three and four years after diagnosis. Answers about consequences were analysed with content analysis, potential relations between coping strategies and consequences were analysed by Fisher's exact test. The great majority reported negative and positive consequences three and four years after diagnosis and the findings indicate stability over time with regard to perceived consequences during the extended phase of survival. Findings reveal a potential relation between seeking information shortly after diagnosis and reporting a more positive view of life four years after diagnosis and not using fighting spirit shortly after diagnosis and not reporting good self-esteem and good relations four years after diagnosis. It is concluded that concomitant negative and positive cancer-related consequences appear stable over time in the extended phase of survival and that dialectical forces of negative and positive as well as distress and growth often go hand-in-hand after a trauma such as cancer during adolescence

Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology

Background: Switchgrass (Panicum virgatum L.) is a C4 perennial grass and widely popular as an important bioenergy crop. To accelerate the pace of developing high yielding switchgrass cultivars adapted to diverse environmental niches, the generation of genomic resources for this plant is necessary. The large genome size and polyploid nature of switchgrass makes whole genome sequencing a daunting task even with current technologies. Exploring the transcriptional landscape using next generation sequencing technologies provides a viable alternative to whole genome sequencing in switchgrass. Principal Findings: Switchgrass cDNA libraries from germinating seedlings, emerging tillers, flowers, and dormant seeds were sequenced using Roche 454 GS-FLX Titanium technology, generating 980,000 reads with an average read length of 367 bp. De novo assembly generated 243,600 contigs with an average length of 535 bp. Using the foxtail millet genome as a reference greatly improved the assembly and annotation of switchgrass ESTs. Comparative analysis of the 454-derived switchgrass EST reads with other sequenced monocots including Brachypodium, sorghum, rice and maize indicated a 70– 80 % overlap. RPKM analysis demonstrated unique transcriptional signatures of the four tissues analyzed in this study. More than 24,000 ESTs were identified in the dormant seed library. In silico analysis indicated that there are more than 2000 EST-SSRs in this collection. Expression of several orphan ESTs was confirmed by RT-PCR. Significance: We estimate that about 90 % of the switchgrass gene space has been covered in this analysis. This study nearl

Millets across Eurasia: chronology and context of early records of the genera Panicum and Setaria from archaeological sites in the Old World

We have collated and reviewed published records of the genera Panicum and Setaria (Poaceae), including the domesticated millets Panicum miliaceum L. (broomcorn millet) and Setaria italica (L.) P. Beauv. (foxtail millet) in pre-5000 cal b.c. sites across the Old World. Details of these sites, which span China, central-eastern Europe including the Caucasus, Iran, Syria and Egypt, are presented with associated calibrated radiocarbon dates. Forty-one sites have records of Panicum (P. miliaceum, P. cf. miliaceum, Panicum sp., Panicum type, P. capillare (?) and P. turgidum) and 33 of Setaria (S. italica, S. viridis, S. viridis/verticillata, Setaria sp., Setaria type). We identify problems of taphonomy, identification criteria and reporting, and inference of domesticated/wild and crop/weed status of finds. Both broomcorn and foxtail millet occur in northern China prior to 5000 cal b.c.; P. miliaceum occurs contemporaneously in Europe, but its significance is unclear. Further work is needed to resolve the above issues before the status of these taxa in this period can be fully evaluated