A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis

Introduction  

The vast difference in the abundance of different proteins in biological samples limits the determination of the complete proteome of a cell type, requiring fractionation of proteins and peptides before MS analysis.     

A screening tool to identify older people at risk of adverse health outcomes at the time of hospital admission

The proportional increase of the ageing population results in an ever growing percentage of elderly among hospitalised patients. Older patients have complex medical, social and psychological problems that could benefit from coordinated care or case management. Identification of high-risk older adults is mandatory to initiate a liaison geriatric management program. A simple screening tool is presented to identify older people at the time of admission who are at increased risk of adverse health outcomes. The instrument was validated during a period of 6 months when all (n = 618) older adults (> 70 year) hospitalised in non-geriatric departments of a general hospital were screened. This "Variable Indicative of Placement risk" (VIP) shows a good sensitivity (81%) and specificity (86%) and has a high Negative Predictive Value (97%). Furthermore, it shows a significant positive correlation with the length of stay (p < 0.001). The questionnaire turned out to be a very useful tool in the emergency department as well as in other wards because it probes premorbid frailty components with three simple questions. Due to its simplicity a nurse without geriatric training can complete it. Patients who are not at risk of an adverse outcome are easily recognised. A positive score indicates loss of functional independence and a risk of increased length of stay. Further geriatric assessment and intervention seem then appropriate.     

Gibberellin-like substances and indole type auxins in developing grains of normal- and high-lysine genotypes of barley

Changes in gibberellin-like activity and content of indole type auxins were investigated during grain development of the two high-lysine barley (Hordeum vulgare L.) genotypes Sv 73608 and Risø 1508, and their corresponding normal cultivars Mona and Bomi. A peak in gibberellin-like activity was found in developing grains of the normal cultivars about 18 days after anthesis, whereas the grains of the high-lysine genotypes showed a two to five times higher maximum about 3–4 days later. The auxin content of the cultivar Bomi showed a maximum between the 22nd and the 29th day after anthesis, whereas, throughout their development the grains of the mutant Risø 1508 exhibited only about ¹/10 of the maximum level of auxin found in the grains of Bomi. The normal cultivar Mona also displayed higher contents of auxin than the high-lysine genotypes Sv 73608, particularly at the later stages of grain growth, but the differences in concentration were considerable smaller than for the pair ‘Bomi’—‘Risø 1508’. It is suggested that auxins play an important role in the development of barley grains.     

Genome‐wide expression reveals multiple systemic effects associated with detection of anticoagulant poisons in bobcats (Lynx rufus)

Anticoagulant rodenticides (ARs) are indiscriminate toxicants that threaten nontarget predatory and scavenger species through secondary poisoning. Accumulating evidence suggests that AR exposure may have disruptive sublethal consequences on individuals that can affect fitness. We evaluated AR‐related effects on genome‐wide expression patterns in a population of bobcats in southern California. We identify differential expression of genes involved in xenobiotic metabolism, endoplasmic reticulum stress response, epithelial integrity and both adaptive and innate immune function. Further, we find that differential expression of immune‐related genes may be attributable to AR‐related effects on leucocyte differentiation. Collectively, our results provide an unprecedented understanding of the sublethal effects of AR exposure on a wild carnivore. These findings highlight potential detrimental effects of ARs on a wide variety of species worldwide that may consume poisoned rodents and indicate the need to investigate gene expression effects of other toxicants added to natural environments by humans.