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

Perioperative melatonin secretion in patients undergoing coronary artery bypass grafting.

UNLABELLED: Melatonin, a neurohormone, plays an important role in adjusting the "biological clock" in humans. We sought to describe perioperative patterns of melatonin secretion in patients undergoing coronary artery bypass grafting surgery with cardiopulmonary bypass (CPB). After IRB approval and written informed consent, 12 male patients scheduled for elective coronary artery bypass grafting under hypothermic CPB were enrolled in the study. During anesthesia, patients' eyes were carefully covered to prevent light effects. Blood samples were taken at specific time points during surgery, every 3 h in the immediate postoperative period, and for 24 h from 6:00 PM of Postoperative Day 2 until 6:00 PM of Postoperative Day 3. Plasma melatonin and cortisol concentrations were measured by radioimmunoassay and enzyme-linked immunosorbent assay, respectively. During surgery, plasma melatonin concentrations were below the minimum sensitivity concentration, yet small concentrations, without circadian variation, were detected during the immediate postoperative period. During Postoperative Days 2 and 3, circadian secretion patterns of melatonin were present in 10 patients and showed an inverse correlation with light intensity (r = 0.480; P < 0.01). Plasma cortisol concentrations in the immediate postoperative period were significantly larger than those before the induction of anesthesia (P < 0.01). Only three patients regained circadian secretion of cortisol. We concluded that melatonin and cortisol secretion was disrupted during cardiac surgery with CPB and in the immediate postoperative period. However, circadian rhythms of melatonin were present in most patients from Postoperative Day 2. Only 30% of the patients regained circadian rhythm of cortisol secretion. IMPLICATIONS: Melatonin is a hormone that plays an important role in adjusting the biological clock in humans and that regulates secretion of various other hormones. We studied melatonin secretion in patients undergoing cardiac surgery with cardiopulmonary bypass. Melatonin secretion was disturbed during and immediately after surgery but had recovered a circadian rhythm 24 h later, raising the question of whether melatonin should be supplemented before cardiac surgery

Crop growth models for the -omics era: the EU-SPICY project

The prediction of phenotypic responses from genetic and environmental information is an area of active research in genetics, physiology and statistics. Rapidly increasing amounts of phenotypic information become available as a consequence of high throughput phenotyping techniques, while more and cheaper genotypic data follow from the development of new genotyping platforms. , A wide array of -omics data can be generated linking genotype and phenotype. Continuous monitoring of environmental conditions has become an accessible option. This wealth of data requires a drastic rethinking of the traditional quantitative genetic approach to modeling phenotypic variation in terms of genetic and environmental differences. Where in the past a single phenotypic trait was partitioned in a genetic and environmental component by analysis of variance techniques, nowadays we desire to model multiple, interrelated and often time dependent, phenotypic traits as a function of genes (QTLs) and environmental inputs, while we would like to include transcription information as well. The EU project 'Smart tools for Prediction and Improvement of Crop Yield' (KBBE-2008-211347), or SPICY, aims at the development of genotype-to-phenotype models that fully integrate genetic, genomic, physiological and environmental information to achieve accurate phenotypic predictions across a wide variety of genetic and environmental configurations. Pepper (Capsicum annuum) is chosen as the model crop, because of the availability of genetically characterized populations and of generic models for continuous crop growth and greenhouse production. In the presentation the objectives and structure of SPICY as well as its philosophy will be discussed

Treatment algorithm in patients with ovarian cancer

Most ovarian cancer patients are diagnosed only at advanced stages when survival outcomes are worse, and when therapeutic decisions might prove challenging. The fundamental treatment for women with ovarian cancer includes debulking surgery whenever possible and appropriate systemic therapy (chemotherapy, targeted and antiangiogenic agents). In the last few years, knowledge about histological and molecular characteristics of ovarian cancer subtypes and stages has increased considerably. This has enabled the development and improvement of several options for the diagnosis and treatment of ovarian cancer in a patient-tailored approach. Accordingly, therapeutic decisions are guided by the characteristics of the patient and the tumour, especially the molecular features of the cancer subtype and disease stage. Particularly relevant are the advances in early genetic testing of germline and somatic mutations involved in DNA repair, and the clinical development of targeted agents. In order to implement the best individual medical strategies, in this article, we present an algorithm of treatment options, including recently developed targeted agents, for primary and recurrent ovarian cancer patients in Belgium

Alternative therapies in controlling oral malodour: a systematic review.

peer reviewedIs there a role for alternative therapies in controlling intra-oral halitosis? Treatments other than tongue cleaning and anti-halitosis products containing zinc, chlorhexidine and cetylpyridinium chloride were considered as alternative therapies. Four databases were searched (PubMed, EMBASE, Web of Science and The Cochrane Library). Inclusion criteria were: examination of alternative halitosis therapies, study population with oral malodour, a (negative or positive) control group and evaluation of breath odour via organoleptic and/or instrumental assessment. Data were extracted for descriptive analysis. The screening of 7656 titles led to the inclusion of 26 articles. Analysis showed heterogeneity concerning the population of interest (from cysteine-induced to genuine halitosis), the examined treatment and the reported outcomes. This made a meta-analysis impossible. Essential oils, fluoride-containing products and herbal substances were the most studied. Results varied enormously and none of the active ingredients had an unambiguously positive effect on the malodour. The risk of bias was assessed as high in all articles. Given the fact that little evidence was found for each of the investigated treatments, it could be concluded that there is currently insufficient evidence that alternative therapies are of added value in the treatment of halitosis.Clinical relevanceScientific rationale:Halitosis is a common problem causing social isolation. Out of embarrassment, patients search the internet, leading to many questions about alternative solutions (e.g. oil pulling, herbs). This is the first systematic review on these alternative therapies.Principal findings: Results varied among studies. Some promising results were found for fluoride-containing toothpastes and probiotics. For other products (such as herbal and antibacterial products and essential oils) results were inconsistent. Long-term follow-up studies on these products are scarce. Moreover, the quality of the studies was poor.Practical implications:No clear evidence was found to support a certain alternative anti-halitosis therapy

Physiological and transcriptomic evidence for a close coupling between chloroplast ontogeny and cell cycle progression in the pennate diatom <i>Seminavis robusta</i>

Despite the growing interest in diatom genomics, detailed time series of gene expression in relation to key cellular processes are still lacking. Here, we investigated the relationships between the cell cycle and chloroplast development in the pennate diatom Seminavis robusta. This diatom possesses two chloroplasts with a well-orchestrated developmental cycle, common to many pennate diatoms. By assessing the effects of induced cell cycle arrest with microscopy and flow cytometry, we found that division and reorganization of the chloroplasts are initiated only after S-phase progression. Next, we quantified the expression of the S. robusta FtsZ homolog to address the division status of chloroplasts during synchronized growth and monitored microscopically their dynamics in relation to nuclear division and silicon deposition. We show that chloroplasts divide and relocate during the S/G2 phase, after which a girdle band is deposited to accommodate cell growth. Synchronized cultures of two genotypes were subsequently used for a cDNA-amplified fragment length polymorphism-based genome-wide transcript profiling, in which 917 reproducibly modulated transcripts were identified. We observed that genes involved in pigment biosynthesis and coding for light-harvesting proteins were up-regulated during G2/M phase and cell separation. Light and cell cycle progression were both found to affect fucoxanthin-chlorophyll a/c-binding protein expression and accumulation of fucoxanthin cell content. Because chloroplasts elongate at the stage of cytokinesis, cell cycle-modulated photosynthetic gene expression and synthesis of pigments in concert with cell division might balance chloroplast growth, which confirms that chloroplast biogenesis in S. robusta is tightly regulated

olaparib maintenance therapy in patients pts with platinum sensitive relapsed psr ovarian cancer oc and stable disease sd following platinum based chemotherapy

n/