Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP.

BACKGROUND: Transcriptomics is being increasingly applied to generate new insight into the interactions between plants and their pathogens. For the wheat yellow (stripe) rust pathogen (Puccinia striiformis f. sp. tritici, Pst) RNA-based sequencing (RNA-Seq) has proved particularly valuable, overcoming the barriers associated with its obligate biotrophic nature. This includes the application of RNA-Seq approaches to study Pst and wheat gene expression dynamics over time and the Pst population composition through the use of a novel RNA-Seq based surveillance approach called "field pathogenomics". As a dual RNA-Seq approach, the field pathogenomics technique also provides gene expression data from the host, giving new insight into host responses. However, this has created a wealth of data for interrogation. RESULTS: Here, we used the field pathogenomics approach to generate 538 new RNA-Seq datasets from Pst-infected field wheat samples, doubling the amount of transcriptomics data available for this important pathosystem. We then analysed these datasets alongside 66 RNA-Seq datasets from four Pst infection time-courses and 420 Pst-infected plant field and laboratory samples that were publicly available. A database of gene expression values for Pst and wheat was generated for each of these 1024 RNA-Seq datasets and incorporated into the development of the rust expression browser ( http://www.rust-expression.com ). This enables for the first time simultaneous 'point-and-click' access to gene expression profiles for Pst and its wheat host and represents the largest database of processed RNA-Seq datasets available for any of the three Puccinia wheat rust pathogens. We also demonstrated the utility of the browser through investigation of expression of putative Pst virulence genes over time and examined the host plants response to Pst infection. CONCLUSIONS: The rust expression browser offers immense value to the wider community, facilitating data sharing and transparency and the underlying database can be continually expanded as more datasets become publicly available.

Sensitivity and specificity of the Geriatric Anxiety Inventory and the Hospital Anxiety and Depression Scale in the detection of anxiety disorders in older people with chronic obstructive pulmonary disease.

BACKGROUND: Anxiety and depression are prevalent in patients with chronic obstructive pulmonary disease (COPD). This study evaluates the sensitivity and specificity of two self-administered anxiety rating scales in older people with COPD. The Geriatric Anxiety Inventory (GAI) and the Hospital Anxiety and Depression Scale (HADS) are established useful screening tools but they have not been previously validated in this population. METHODS: Older people with COPD completed the GAI and the HADS along with a structured diagnostic psychiatric interview, the Mini International Neuropsychiatric Interview (MINI). The outcomes of both rating scales were compared against the diagnosis of anxiety disorders based on the MINI. Receiver operating characteristic (ROC) curves were used to identify the optimal diagnostic cut points for each scale. RESULTS: Fourteen (25.5%) of the 55 participants, were diagnosed with an anxiety disorder. Mean GAI and HADS-anxiety subscale scores were significantly higher in subjects with an anxiety disorder than those without the diagnosis (p = 0.002 and 0.005 respectively). Both scales demonstrated moderate diagnostic value (area under the ROC curve was 0.83 for GAI and 0.79 for HADS). Optimal cut points were ≥3 (GAI) and ≥4 (HADS-anxiety subscale). At these cut-points, the GAI had a sensitivity of 85.7%, specificity of 78.0% and the HADS had a sensitivity of 78.6%, specificity 70.7%. CONCLUSION: Our results support the use of the GAI and HADS as screening instruments for anxiety disorders in older people with COPD. The optimal cut points in this population were lower than previously recommended for both rating scales. The results of this study should be replicated before these cut points can be recommended for general use in older people with COPD.

Detection of tetrahydrobiopterin by LC-MS/MS in plasma from multiple species.

BACKGROUND: Tetrahydrobiopterin (BH4) is a naturally occurring pteridine and cofactor for a variety of enzymes, including phenylalanine-4-hydroxylase, nitric oxide synthetase and glyceryl ether monooxygenase. BH4 is readily oxidized to dihydrobiopterin and biopterin (B), however only BH4 can provide proper cofactor functions. BH4 is the active ingredient in Kuvan™ for the treatment of phenylketonuria. In order to measure BH4 in plasma from nonclinical and clinical samples with good accuracy, precision, sensitivity and robustness, an LC-MS/MS method was validated. To overcome the oxidation of BH4 in postcollection plasma, the approach was to measure the concentration of BH4 indirectly by measuring B concentration and applying an oxidation conversion ratio. Different endogenous levels of BH4 are determined in human, monkey, dog, rabbit, rat and mouse plasma. Furthermore, the conversion ratio of BH4 to B for each species is different and determined empirically. Plasma is transferred into cryogenic vials containing 0.1% dithioerythritol to prevent oxidation of BH4. The samples are then extracted and oxidized under basic conditions. B is measured with LC-MS/MS using negative ion mode. RESULTS: The method is accurate, and precise to within 15%. The lower limit of quantitation in matrix is 5, 50 or 100 ng/ml, depending on the species endogenous levels of BH4. The pharmacokinetics of a single oral dose at three concentrations of BH4 administered to C57BL/6 mice is presented. In this mouse study, the T(1/2) of BH4 in plasma was approximately 1.2 h. CONCLUSION: The validated LC-MS/MS method to determine plasma BH4 concentration described herein has been used to support many nonclinical and clinical toxicokinetic and pharmacokinetic studies. BH4 is sensitive to oxidation and has a complicated biology. The method successfully supported the approval of Kuvan for the treatment of phenylketonuria.