Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription

BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a powerful tool for genome-wide transcription studies. Unlike microarrays, it has the ability to detect novel forms of RNA such as alternatively spliced and antisense transcripts, without the need for prior knowledge of their existence. One limitation of using SAGE on an organism with a complex genome and lacking detailed sequence information, such as the hexaploid bread wheat Triticum aestivum, is accurate annotation of the tags generated. Without accurate annotation it is impossible to fully understand the dynamic processes involved in such complex polyploid organisms. Hence we have developed and utilised novel procedures to characterise, in detail, SAGE tags generated from the whole grain transcriptome of hexaploid wheat. RESULTS: Examination of 71,930 Long SAGE tags generated from six libraries derived from two wheat genotypes grown under two different conditions suggested that SAGE is a reliable and reproducible technique for use in studying the hexaploid wheat transcriptome. However, our results also showed that in poorly annotated and/or poorly sequenced genomes, such as hexaploid wheat, considerably more information can be extracted from SAGE data by carrying out a systematic analysis of both perfect and "fuzzy" (partially matched) tags. This detailed analysis of the SAGE data shows first that while there is evidence of alternative polyadenylation this appears to occur exclusively within the 3' untranslated regions. Secondly, we found no strong evidence for widespread alternative splicing in the developing wheat grain transcriptome. However, analysis of our SAGE data shows that antisense transcripts are probably widespread within the transcriptome and appear to be derived from numerous locations within the genome. Examination of antisense transcripts showing sequence similarity to the Puroindoline a and Puroindoline b genes suggests that such antisense transcripts might have a role in the regulation of gene expression. CONCLUSION: Our results indicate that the detailed analysis of transcriptome data, such as SAGE tags, is essential to understand fully the factors that regulate gene expression and that such analysis of the wheat grain transcriptome reveals that antisense transcripts maybe widespread and hence probably play a significant role in the regulation of gene expression during grain development

Elucidating the genetic basis of antioxidant status in lettuce (Lactuca sativa).

A diet rich in phytonutrients from fruit and vegetables has been acknowledged to afford protection against a range of human diseases, but many of the most popular vegetables are low in phytonutrients. Wild relatives of crops may contain allelic variation for genes determining the concentrations of these beneficial phytonutrients, and therefore understanding the genetic basis of this variation is important for breeding efforts to enhance nutritional quality. In this study, lettuce recombinant inbred lines, generated from a cross between wild and cultivated lettuce (Lactuca serriola and Lactuca sativa, respectively), were analysed for antioxidant (AO) potential and important phytonutrients including carotenoids, chlorophyll and phenolic compounds. When grown in two environments, 96 quantitative trait loci (QTL) were identified for these nutritional traits: 4 for AO potential, 2 for carotenoid content, 3 for total chlorophyll content and 87 for individual phenolic compounds (two per compound on average). Most often, the L. serriola alleles conferred an increase in total AOs and metabolites. Candidate genes underlying these QTL were identified by BLASTn searches; in several cases, these had functions suggesting involvement in phytonutrient biosynthetic pathways. Analysis of a QTL on linkage group 3, which accounted for >30% of the variation in AO potential, revealed several candidate genes encoding multiple MYB transcription factors which regulate flavonoid biosynthesis and flavanone 3-hydroxylase, an enzyme involved in the biosynthesis of the flavonoids quercetin and kaempferol, which are known to have powerful AO activity. Follow-up quantitative RT-PCR of these candidates revealed that 5 out of 10 genes investigated were significantly differentially expressed between the wild and cultivated parents, providing further evidence of their potential involvement in determining the contrasting phenotypes. These results offer exciting opportunities to improve the nutritional content and health benefits of lettuce through marker-assisted breeding

Planck-LFI: Design and Performance of the 4 Kelvin Reference Load Unit

The LFI radiometers use a pseudo-correlation design where the signal from the sky is continuously compared with a stable reference signal, provided by a cryogenic reference load system. The reference unit is composed by small pyramidal horns, one for each radiometer, 22 in total, facing small absorbing targets, made of a commercial resin ECCOSORB CR (TM), cooled to approximately 4.5 K. Horns and targets are separated by a small gap to allow thermal decoupling. Target and horn design is optimized for each of the LFI bands, centered at 70, 44 and 30 GHz. Pyramidal horns are either machined inside the radiometer 20K module or connected via external electro-formed bended waveguides. The requirement of high stability of the reference signal imposed a careful design for the radiometric and thermal properties of the loads. Materials used for the manufacturing have been characterized for thermal, RF and mechanical properties. We describe in this paper the design and the performance of the reference system.Comment: This is an author-created, un-copyedited version of an article accepted for publication in JINST. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at [10.1088/1748-0221/4/12/T12006]. 14 pages, 34 figure

Further investigation of confirmed urinary tract infection (UTI) in children under five years: a systematic review.

Background: Further investigation of confirmed UTI in children aims to prevent renal scarring and future complications. Methods: We conducted a systematic review to determine the most effective approach to the further investigation of confirmed urinary tract infection (UTI) in children under five years of age. Results: 73 studies were included. Many studies had methodological limitations or were poorly reported. Effectiveness of further investigations: One study found that routine imaging did not lead to a reduction in recurrent UTIs or renal scarring. Diagnostic accuracy: The studies do not support the use of less invasive tests such as ultrasound as an alternative to renal scintigraphy, either to rule out infection of the upper urinary tract (LR- = 0.57, 95%CI: 0.47, 0.68) and thus to exclude patients from further investigation or to detect renal scarring (LR+ = 3.5, 95% CI: 2.5, 4.8). None of the tests investigated can accurately predict the development of renal scarring. The available evidence supports the consideration of contrast-enhanced ultrasound techniques for detecting vesico-ureteric reflux (VUR), as an alternative to micturating cystourethrography (MCUG) (LR+ = 14.1, 95% CI: 9.5, 20.8; LR- = 0.20, 95%CI: 0.13, 0.29); these techniques have the advantage of not requiring exposure to ionising radiation. Conclusion: There is no evidence to support the clinical effectiveness of routine investigation of children with confirmed UTI. Primary research on the effectiveness, in terms of improved patient outcome, of testing at all stages in the investigation of confirmed urinary tract infection is urgently required

Pituitary gland abscess in a horse subsequent to head trauma

A 5‐year‐old Thoroughbred gelding with recent history of head trauma presented with multiple facial swellings, bilateral mucopurulent nasal discharge, neck pain, inappetence and depression. On computed tomographic examination, lesions within the pituitary fossa and structures adjacent to the right guttural pouch were identified. Soft tissue swelling was seen in the dorsal aspect of the right guttural pouch surrounding several cranial nerves, with fluid‐like material in the dependent portions of the right guttural pouch. A CSF sample revealed mild mixed pleocytosis and increased protein concentration. The horse had concurrent periapical disease of the 209‐cheek tooth and mild left sinusitis. The horse's demeanour deteriorated requiring euthanasia. Post‐mortem examination revealed a pituitary gland abscess

Assessment of Magnetic Resonance Imaging Artefacts Caused By Equine Anaesthesia Equipment:A Cadaver Study

Acquisition of magnetic resonance images of the equine limb is still sometimes conducted under general anaesthesia. Despite low-field systems allow the use of standard anaesthetic equipment, possible interferences of the extensive electronic componentry of advanced anaesthetic machines on image quality is unknown. This prospective, blinded, cadaver study investigated the effects of 7 standardised conditions [Tafonius positioned as in clinical cases, Tafonius on the boundaries of the controlled area, anaesthetic monitoring only, Mallard anaesthetic machine, Bird ventilator, complete electronic silence in the room (negative control), source of electronic interference (positive control)] on image quality through the acquisition of 78 sequences using a 0.31T equine MRI scanner. Images were graded with a 4-point scoring system, where 1 denoted absence of artefacts and 4 major artefacts requiring repetition in a clinical setting. A lack of STIR fat suppression was commonly reported (16/26). Ordinal logistic regression showed no statistically significant differences in image quality between the negative control and either the non-Tafonius or the Tafonius groups (p = 0.535 and p = 0.881, respectively), and with the use of Tafonius compared to the other anaesthetic machines (p = 0.578). The only statistically significant differences in scores were observed between the positive control and the non-Tafonius (p = 0.006) and the Tafonius groups (p = 0.017). Our findings suggest that anaesthetic machines and monitoring do not appear to affect MRI scan quality and support the use of Tafonius during acquisition of images with a 0.31T MRI system in a clinical context

How does study quality affect the results of a diagnostic meta-analysis?

Background: The use of systematic literature review to inform evidence based practice in diagnostics is rapidly expanding. Although the primary diagnostic literature is extensive, studies are often of low methodological quality or poorly reported. There has been no rigorously evaluated, evidence based tool to assess the methodological quality of diagnostic studies. The primary objective of this study was to determine the extent to which variations in the quality of primary studies impact the results of a diagnostic meta-analysis and whether this differs with diagnostic test type. A secondary objective was to contribute to the evaluation of QUADAS, an evidence-based tool for the assessment of quality in diagnostic accuracy studies. Methods: This study was conducted as part of large systematic review of tests used in the diagnosis and further investigation of urinary tract infection (UTI) in children. All studies included in this review were assessed using QUADAS, an evidence-based tool for the assessment of quality in systematic reviews of diagnostic accuracy studies. The impact of individual components of QUADAS on a summary measure of diagnostic accuracy was investigated using regression analysis. The review divided the diagnosis and further investigation of UTI into the following three clinical stages: diagnosis of UTI, localisation of infection, and further investigation of the UTI. Each stage used different types of diagnostic test, which were considered to involve different quality concerns. Results: Many of the studies included in our review were poorly reported. The proportion of QUADAS items fulfilled was similar for studies in different sections of the review. However, as might be expected, the individual items fulfilled differed between the three clinical stages. Regression analysis found that different items showed a strong association with test performance for the different tests evaluated. These differences were observed both within and between the three clinical stages assessed by the review. The results of regression analyses were also affected by whether or not a weighting (by sample size) was applied. Our analysis was severely limited by the completeness of reporting and the differences between the index tests evaluated and the reference standards used to confirm diagnoses in the primary studies. Few tests were evaluated by sufficient studies to allow meaningful use of meta-analytic pooling and investigation of heterogeneity. This meant that further analysis to investigate heterogeneity could only be undertaken using a subset of studies, and that the findings are open to various interpretations. Conclusion: Further work is needed to investigate the influence of methodological quality on the results of diagnostic meta-analyses. Large data sets of well-reported primary studies are needed to address this question. Without significant improvements in the completeness of reporting of primary studies, progress in this area will be limited

I teatri a Venezia nel 1868

In 1868 the theatrical context in Venice was affected by local abut also statal economic situation, due by the development of the new Italian State, formed after the Peace of Vienna that, signed on 23 October 1866, marked the end of the Third War of Independence and the annexation of Venice to the unitary state. Venice therefore became less important for theatrical production, and the city was no longer among the capitals of theatre and music, as it could have been considered until in the first half of 19th century. A new trend throughout Europe was moreover the 'grand opera', while in Venice the dominant show was still the traditional musical opera, in addition to opera and 'opera buffa', created by great Italian composers. The theatres active in 1868 in the city are La Fenice, Teatro San Benedetto then called Rossini, Teatro Apollo, Teatro Malibran and Teatro San Samuele. Through the reviews of the Gazzetta di Venezia and documents such as sketches of the scene made by famous set designers, that interesting moment is reconstructed