The use of general and specific combining abilities in a context of gene expression relevant to plant breeding

Many common traits are believed to be a composite reflection of multiple genetic and environmental factors. Recent advances suggest that subtle variations in the regulation of gene expression may contribute to quantitative traits. The nature of sequence variation affecting the regulation of gene expression either in cis (that is, affecting the expression of only one of the two alleles in a heterozygous diploid) or in trans (that is, affecting the expression of both alleles in a heterozygous diploid) is a key and usually unknown feature for the breeders. If the change in expression acts entirely in cis, then the structural gene can be treated as a candidate gene and a potential target for marker-assisted selection. Therefore, gene surveys for cis-regulatory variation are a first step in identifying potential targets for marker-assisted breeding. Here, we discuss in detail the ¿genome-wide analysis of allele-specific expression differences¿ (GASED) approach. The GASED approach was developed to screen for cis-regulatory variation on a genome-wide scale. In GASED, mRNA abundance is treated as if it were a quantitative phenotypic response variable, whose genetic between-F1 hybrid variance is partitioned into additive and non-additive components. In plant breeding, this partitioning of the genetic variance is well known in the context of estimation of general and specific combining abilities for diallel crossing schemes. We demonstrate the GASED method using Arabidopsis thaliana data. The method can be used to screen for cis-regulatory variation in any crop species for which diallel crossing schemes are appropriate and genomic tools are available

Cost-effectiveness of management strategies for acute urethritis in the developing world.

OBJECTIVE: To recommend a cost-effective approach for the management of acute male urethritis in the developing world, based on the findings of a theoretical study. METHODS: A model was developed to assess the cost-effectiveness of three urethritis management strategies in a theoretical cohort of 1000 men with urethral syndrome. (1) All patients were treated with cefixime and doxycycline for gonococcal urethritis (GU) and nongonococcal urethritis (NGU), respectively, as recommended by WHO. (2) All patients were treated with doxycycline for NGU; treatment with cefixime was based on the result of direct microscopy of a urethral smear. (3) All patients were treated with cotrimoxazole or kanamycin for GU and doxycycline for NGU. Cefixime was kept for patients not responding to the first GU treatment. Strategy costs included consultations, laboratory diagnosis (where applicable) and drugs. The outcome was the rate of patients cured of urethritis. Cost-effectiveness was measured in terms of cost per cured urethritis. RESULTS: Strategy costs in our model depended largely on drug costs. The first strategy was confirmed as the most effective but also the most expensive approach. Cefixime should cost no more than US$1.5 for the strategy to be the most cost-effective. The second strategy saved money and drugs but proved a valuable alternative only when laboratory performance was optimal. The third strategy with cotrimoxazole was the least expensive but a low follow-up visit rate, poor treatment compliance or lower drug efficacy limited effectiveness. Maximizing compliance by replacing cotrimoxazole with single-dose kanamycin had the single greatest impact on the effectiveness of the third strategy. CONCLUSION: Our model suggested that a cost-effective approach would be to treat gonorrhoea with a single-dose antibiotic selected from locally available products that cost no more than US$ 1.5

Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)

Genetic markers based on single nucleotide polymorphisms (SNPs) are in increasing demand for genome mapping and fingerprinting of breeding populations in crop plants. Recent advances in high-throughput sequencing provide the opportunity for whole-genome resequencing and identification of allelic variants by mapping the reads to a reference genome. However, for many species, such as pepper (Capsicum annuum), a reference genome sequence is not yet available. To this end, we sequenced the C. annuum cv. "Yolo Wonder" transcriptome using Roche 454 pyrosequencing and assembled de novo 23,748 isotigs and 60,370 singletons. Mapping of 10,886,425 reads obtained by the Illumina GA II sequencing of C. annuum cv. "Criollo de Morclos 334" to the "Yolo Wonder" transcriptome allowed for SNP identification. By setting a threshold value that allows selecting reliable SNPs with minimal loss of information, 11,849 reliable SNPs spread across 5919 isotigs were identified. In addition, 853 single sequence repeats were obtained. This information has been made available online

'You can't just hit a button’: an ethnographic study of strategies to repurpose data from advanced clinical information systems for clinical process improvement

Background Current policies encourage healthcare institutions to acquire clinical information systems (CIS) so that captured data can be used for secondary purposes, including clinical process improvement. Such policies do not account for the extra work required to repurpose data for uses other than direct clinical care, making their implementation problematic. This paper aims to analyze the strategies employed by clinical units to use data effectively for both direct clinical care and clinical process improvement. Methods Ethnographic methods were employed. A total of 54 contextual interviews with health professionals spanning various disciplines and 18 hours of observation were carried out in 5 intensive care units in England using an advanced CIS. Case studies of how the extra work was achieved in each unit were derived from the data and then compared. Results We found that extra work is required to repurpose CIS data for clinical process improvement. Health professionals must enter data not required for clinical care and manipulation of this data into a machine-readable form is often necessary. Ambiguity over who should be responsible for this extra work hindered CIS data usage for clinical process improvement. We describe 11 strategies employed by units to accommodate this extra work, distributing it across roles. Seven of these motivated data entry by health professionals and four addressed the machine readability of data. Many of the strategies relied heavily on the skill and leadership of local clinical customizers. Conclusions To realize the expected clinical process improvements by the use of CIS data, clinical leaders and policy makers need to recognize and support the redistribution of the extra work that is involved in data repurposing. Adequate time, funding, and appropriate motivation are needed to enable units to acquire and deliver the necessary skills in CIS customization

Electronic patient record use during ward rounds: a qualitative study of interaction between medical staff

INTRODUCTION: Electronic patient records are becoming more common in critical care. As their design and implementation are optimized for single users rather than for groups, we aimed to understand the differences in interaction between members of a multidisciplinary team during ward rounds using an electronic, as opposed to paper, patient medical record. METHODS: A qualitative study of morning ward rounds of an intensive care unit that triangulates data from video-based interaction analysis, observation, and interviews. RESULTS: Our analysis demonstrates several difficulties the ward round team faced when interacting with each other using the electronic record compared with the paper one. The physical setup of the technology may impede the consultant's ability to lead the ward round and may prevent other clinical staff from contributing to discussions. CONCLUSIONS: We discuss technical and social solutions for minimizing the impact of introducing an electronic patient record, emphasizing the need to balance both. We note that awareness of the effects of technology can enable ward-round teams to adapt their formations and information sources to facilitate multidisciplinary communication during the ward round