Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum

BACKGROUND: Stagonospora nodorum, a fungal ascomycete in the class dothideomycetes, is a damaging pathogen of wheat. It is a model for necrotrophic fungi that cause necrotic symptoms via the interaction of multiple effector proteins with cultivar-specific receptors. A draft genome sequence and annotation was published in 2007. A second-pass gene prediction using a training set of 795 fully EST-supported genes predicted a total of 10762 version 2 nuclear-encoded genes, with an additional 5354 less reliable version 1 genes also retained. RESULTS: In this study, we subjected soluble mycelial proteins to proteolysis followed by 2D LC MALDI-MS/MS. Comparison of the detected peptides with the gene models validated 2134 genes. 62% of these genes (1324) were not supported by prior EST evidence. Of the 2134 validated genes, all but 188 were version 2 annotations. Statistical analysis of the validated gene models revealed a preponderance of cytoplasmic and nuclear localised proteins, and proteins with intracellularassociated GO terms. These statistical associations are consistent with the source of the peptides used in the study. Comparison with a 6-frame translation of the S. nodorum genome assembly confirmed 905 existing gene annotations (including 119 not previously confirmed) and provided evidence supporting 144 genes with coding exon frameshift modifications, 604 genes with extensions of coding exons into annotated introns or untranslated regions (UTRs), 3 new gene annotations which were supported by tblastn to NR, and 44 potential new genes residing within un-assembled regions of the genome. CONCLUSION: We conclude that 2D LC MALDI-MS/MS is a powerful, rapid and economical tool to aid in the annotation of fungal genomic assemblies

An unusual presentation of a Gastrointestinal stromal tumour (GIST)

<p>Abstract</p> <p>Background</p> <p>Gastrointestinal stromal tumours (GIST) are rare tumours, now more frequently identified with the new imaging modalities like computerised tomography (CT) and magnetic resonance imaging (MRI). We report a rare presentation of a GIST with an unusual diagnostic workup in a multidisciplinary setting leading to a definitive diagnosis and treatment.</p> <p>Case presentation</p> <p>A 55-year-old lady was admitted under the general surgeons, with 3-day history of abdominal pain, three-week history of loss of appetite and weight. The patient was sequentially investigated with ultrasonography, computerised tomography and finally selective angiogram in a multidisciplinary setting. The selective angiogram showed a GIST with intratumour bleed, leading to successful surgical excision and being recurrence free at 22 month follow up.</p> <p>Conclusion</p> <p>Clinical presentation of these tumours can be varied and gastrointestinal bleeding is the commonest mode described in the literature. The clinician needs to be aware of much more rare presentations of the GIST including an intra tumour bleed. A structured multidisciplinary approach would lead to successful diagnosis and treatment.</p

The role of urinary kininogen in the regulation of kinin generation

The role of urinary kininogen in the regulation of kinin generation. The kallikrein-kininogen-kinin system has been postulated to play a role in the regulation of blood pressure and modulation of renal salt and water transport. The activity of this system has usually been determined by measurements of urinary kallikrein excretion. However, urinary kallikrein rarely correlates with simultaneously measured urinary kinins. To further evaluate the factors influencing urinary kinin excretion, we evaluated the role of urinary kininogen in this system. Urines were analyzed from normal subjects and individuals with untreated essential hypertension and end-stage renal disease. Intact urinary kininogen was significantly correlated with urinary kinins in normal subjects (r = 0.65, P = 0.003) and essential hypertensives (r = 0.52, P = 0.026). In both essential hypertension and end-stage renal disease, urinary kinins were significantly decreased (8.00 ± 1.93, 0.90 ± 0.18, P < 0.05, respectively) compared to controls (23.73 ± 5.20). In essential hypertensives, the reduction in urinary kinins was paralleled by a reduction in intact kininogen with a normal excretion of kallikrein. In end-stage renal disease, the reduction in kinins was paralleled by a reduction in kallikrein with a normal excretion of intact kininogen. This data suggests that kininogen may be an important determinant of urinary kinin excretion in various disease states

Proteomic identification of extracellular proteins regulated by the Gna1 Gα subunit in Stagonospora nodorum

The fungus Stagonospora nodorum is the causal agent of stagonospora nodorum blotch (syn.leaf and glume blotch) disease of wheat. The Gna1-encoded Ga protein is an important signaltransduction component in the fungus, which is required for full pathogenicity, sporulationand extracellular depolymerase production. In this study, we sought to gaina better understanding of defects associated with the gna1 mutant by using twodimensionalgel electrophoresis to analyse the extracellular proteome for differences tothe wildtype. Mass spectrometry analysis of altered abundant protein spots and peptidematching to the Stagonospora nodorum genome database have led to the identification ofgenes implicated in cell wall degradation, proteolysis, RNA hydrolysis and aromatic compoundmetabolism. In addition, quantitative RT-PCR has demonstrated that some of theencoding genes showed differential expression throughout host infection. Implicationsof these proteins and their corresponding genes in fungal virulence are discussed.The fungus Stagonospora nodorum is the causal agent of stagonospora nodorum blotch (syn. leaf and glume blotch) disease of wheat. The Gna1-encoded Gα protein is an important signal transduction component in the fungus, which is required for full pathogenicity, sporulation and extracellular depolymerase production. In this study, we sought to gain a better understanding of defects associated with the gna1 mutant by using two-dimensional gel electrophoresis to analyse the extracellular proteome for differences to the wildtype. Mass spectrometry analysis of altered abundant protein spots and peptide matching to the Stagonospora nodorum genome database have led to the identification of genes implicated in cell wall degradation, proteolysis, RNA hydrolysis and aromatic compound metabolism. In addition, quantitative RT-PCR has demonstrated that some of the encoding genes showed differential expression throughout host infection. Implications of these proteins and their corresponding genes in fungal virulence are discussed

Noninvasive imaging of focal atherosclerotic lesions using fluorescence molecular tomography

Insights into the etiology of stroke and myocardial infarction suggest that rupture of unstable atherosclerotic plaque is the precipitating event. Clinicians lack tools to detect lesion instability early enough to intervene, and are often left to manage patients empirically, or worse, after plaque rupture. Noninvasive imaging of the molecular events signaling prerupture plaque progression has the potential to reduce the morbidity and mortality associated with myocardial infarction and stroke by allowing early intervention. Here, we demonstrate proof-of-principle in vivo molecular imaging of C-type natriuretic peptide receptor in focal atherosclerotic lesions in the femoral arteries of New Zealand white rabbits using a custom built fiber-based, fluorescence molecular tomography (FMT) system. Longitudinal imaging showed changes in the fluorescence signal intensity as the plaque progressed in the air-desiccated vessel compared to the uninjured vessel, which was validated by ex vivo tissue studies. In summary, we demonstrate the potential of FMT for noninvasive detection of molecular events leading to unstable lesions heralding plaque rupture

Increased platelet expression of FcGammaRIIa and its potential impact on platelet reactivity in patients with end stage renal disease

<p>Abstract</p> <p>Background</p> <p>Increased platelet reactivity has been implicated in cardiovascular disease – the major cause of death in patients with end stage renal disease (ESRD). FcGammaRIIA is a component of glycoprotein VI and Ib-IX-V that mediate activation of platelets by collagen and von Willebrand factor. To determine whether expression of FcGammaRIIA impacts platelet reactivity we quantified its expression and platelet reactivity in 33 patients with ESRD who were undergoing hemodialysis.</p> <p>Methods</p> <p>Blood samples were obtained from patients immediately before hemodialysis and before administration of heparin. Platelet expression of FcGammaRIIA and the activation of platelets in response to low concentrations of convulxin (1 ng/ml, selected to mimic effects of collagen), thrombin (1 nM), adenosine diphosphate (ADP, 0.2 uM), or platelet activating factor (PAF, 1 nM) were determined with the use of flow cytometry in samples of whole blood anticoagulated with corn trypsin inhibitor (a specific inhibitor of Factor XIIa).</p> <p>Results</p> <p>Patients were stratified with respect to the median expression of FcGammaRIIA. Patients with high platelet expression of FcGammaRIIA exhibited 3-fold greater platelet reactivity compared with that in those with low expression in response to convulxin (p < 0.01) and 2-fold greater activation in response to thrombin, ADP, and PAF (p < 0.05 for each). For each agonist, expression of FcGammaRIIA correlated modestly but positively with platelet reactivity. The strongest correlation was with thrombin-induced activation (r = 0.6, p < 0.001).</p> <p>Conclusion</p> <p>Increased platelet reactivity in response to low concentrations of diverse agonists is associated with high expression of FcGammaRIIA and may contribute to an increased risk of thrombosis in patients with ESRD.</p

Difference in Brain Densities Between Chronic Alcoholic and Normal Control Patients.

The densities of the brains of 11 chronic alcoholics were compared with those of 11 age-matched normal control subjects. Densities were determined from the density numbers generated by computerized tomography at three levels of the brain-the highest level of the lateral ventricles and the next two higher levels-with adjustments made to control for possible artifacts in the data. The advantage of the dominant hemisphere over the nondominant hemisphere was lessened in alcoholic

A diagnostic instrument to help field graders evaluate active trachoma

Funding: Production of prototypes and the final design was supported by The Fred Hollows Foundation.The SAFE strategy (Surgery for trichiasis, mass treatment with Antibiotics to clear ocular Chlamydia trachomatis infection, and Facial cleanliness and Environmental improvement to reduce transmission) is being used to eliminate trachoma as a public health problem. Decisions on whether or not to implement the A, F, and E components of SAFE are made on the basis of the prevalence of trachomatous inflammation—follicular (TF) in 1–9-year-olds. TF has a precise definition: at least five follicles, each of which is at least 0.5-mm diameter, in the central part of the upper tarsal conjunctiva. Determining whether a follicle has a diameter ≥0.5mm is difficult using magnifying loupes alone. We have developed an ultra-low-cost solution: a follicle size guide that takes the form of a durable printed adhesive sticker which can be fixed to graders’ thumb nails for direct size comparison. This tool will be made available to health ministries free of charge. It is anticipated to simplify grader training, increase grader trainee pass rates, and prevent in-service diagnostic drift after training is complete.Publisher PDFPeer reviewe

Yours ever (well, maybe): Studies and signposts in letter writing

Electronic mail and other digital communications technologies seemingly threaten to end the era of handwritten and typed letters, now affectionately seen as part of snail mail. In this essay, I analyze a group of popular and scholarly studies about letter writing-including examples of pundits critiquing the use of e-mail, etiquette manuals advising why the handwritten letter still possesses value, historians and literary scholars studying the role of letters in the past and what it tells us about our present attitudes about digital communications technologies, and futurists predicting how we will function as personal archivists maintaining every document including e-mail. These are useful guideposts for archivists, providing both a sense of the present and the past in the role, value and nature of letters and their successors. They also provide insights into how such documents should be studied, expanding our gaze beyond the particular letters, to the tools used to create them and the traditions dictating their form and function. We also can discern a role for archivists, both for contributing to the literature about documents and in using these studies and commentaries, suggesting not a new disciplinary realm but opportunities for new interdisciplinary work. Examining a documentary form makes us more sensitive to both the innovations and traditions as it shifts from the analog to the digital; we can learn not to be caught up in hysteria or nostalgia about one form over another and archivists can learn about what they might expect in their labors to document society and its institutions. At one time, paper was part of an innovative technology, with roles very similar to the Internet and e-mail today. It may be that the shifts are far less revolutionary than is often assumed. Reading such works also suggests, finally, that archivists ought to rethink how they view their own knowledge and how it is constructed and used. © 2010 Springer Science+Business Media B.V