ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform's coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR's flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project - a coordinated effort to drive engagement with training in statistics.

Grafting response to excess boron and expression analysis of genes coding boron transporters in tomato.

Boron (B) is essential for plant growth, however its excess in soil and/or in irrigation water can severely compromise plant growth and yield. The goal of this work was to determine whether grafting onto 'Arnold', a commercial interspecific hybrid (Solanum lycopersicum × S. habrochaites) rootstock, which in a previous study was found to be tolerant to salt stress, could improve tomato (S. lycopersicum L. 'Ikram') tolerance to excess B, and whether this effect is associated with an exclusion mechanism. Non-grafted, self-grafted and grafted plants were hydroponically grown in a greenhouse with B concentration in the nutrient solution of 0.27 (control), 5, 10 and 15 mg·l-1 . A transcription analysis was carried out on SlNIP5 and SlBOR1 genes, which encode putative B transporters. Grafting 'Ikram' onto 'Arnold' rootstock reduced B concentration in leaf tissue of plants exposed to B concentrations of 10-15 mg·l-1 . At high B levels, SlNIP5 was down-regulated in all grafting combinations, while SlBOR1 was down-regulated only in the roots of plants grafted onto 'Arnold'. We conclude that grafting the susceptible tomato cultivar 'Ikram' onto the commercial rootstock 'Arnold' improved tolerance to excess B by reducing expression of genes encoding for B transporters at the root level, thus partially reducing the root uptake of B and its accumulation in the shoot.

Assessing wildfire exposure in the Wildland-Urban Interface area of the mountains of central Argentina.

Wildfires are a major threat to people and property in Wildland Urban Interface (WUI) communities worldwide, but while the patterns of the WUI in North America, Europe and Oceania have been studied before, this is not the case in Latin America. Our goals were to a) map WUI areas in central Argentina, and b) assess wildfire exposure for WUI communities in relation to historic fires, with special emphasis on large fires and estimated burn probability based on an empirical model. We mapped the WUI in the mountains of central Argentina (810,000 ha), after digitizing the location of 276,700 buildings and deriving vegetation maps from satellite imagery. The areas where houses and wildland vegetation intermingle were classified as Intermix WUI (housing density > 6.17 hu/km2 and wildland vegetation cover > 50%), and the areas where wildland vegetation abuts settlements were classified as Interface WUI (housing density > 6.17 hu/km2, wildland vegetation cover < 50%, but within 600 m of a vegetated patch larger than 5 km2). We generated burn probability maps based on historical fire data from 1999 to 2011; as well as from an empirical model of fire frequency. WUI areas occupied 15% of our study area and contained 144,000 buildings (52%). Most WUI area was Intermix WUI, but most WUI buildings were in the Interface WUI. Our findings suggest that central Argentina has a WUI fire problem. WUI areas included most of the buildings exposed to wildfires and most of the buildings located in areas of higher burn probability. Our findings can help focus fire management activities in areas of higher risk, and ultimately provide support for landscape management and planning aimed at reducing wildfire risk in WUI communities.

Intraspecific variability of the essential oil of Calamintha nepeta subsp. nepeta from Southern Italy (Apulia).

The essential oil of 46 spontaneous plants of Calamintha nepeta (L.) Savi subsp. nepeta growing wild in Sud, Italy (Salento, Apulia), were investigated by GC/MS. Fifty-seven components were identified in the oil representing over the 98% of the total oil composition. Four chemotypes were identified: piperitone oxide, piperitenone oxide, piperitone-menthone and pulegone.

Should we treat HCV carriers with normal ALT levels? The '5Ws' dilemma.

Approximately 30% of patients with chronic HCV infection have persistently normal ALT levels. Although formerly referred to as 'healthy' or 'asymptomatic' HCV carriers, and thus historically excluded from antiviral treatment, it has now become clear that the majority of these patients have some degree of histological liver damage that may be significant in up to 20% of cases and might progress towards a more severe degree of liver fibrosis. A significant proportion of patients experience periods of increased serum ALT associated with enhanced disease progression. However, controversies still exist in clinical practice regarding the definition of 'persistent' ALT normality, the virological and histological features of these subjects, the need for liver biopsy, the role of noninvasive tools for the assessment of liver fibrosis, the natural history and the usefulness of antiviral treatment. The advent of new therapeutic options (pegylated interferon plus ribavirin) has shifted treatment targets towards the eradication of underlying infection, with therapy decision based on age, severity of disease and likelihood of response rather than on aminotransferase levels. This review is aimed at approaching the main unresolved issues on this topic, trying to give evidence-based answers to the more frequently asked questions from patients and their physicians.

Inhibition of development, swarming differentiation and virulence factors in Proteus mirabilis by an extract of Lithrea molleoides and its active principle (Z,Z)-5-(trideca-4',7'-dienyl)-resorcinol.

Antibacterial activity of Lithrea molleoides extract against Proteus mirabilis has been previously reported by our group. In the present study, the compound (Z,Z)-5-(trideca-4',7'-dienyl)-resorcinol (1) was isolated as its responsible active principle. The effects of the compound obtained and of L. molleoides extract on P. mirabilis growth and virulence factors were evaluated. Compound 1 showed MIC and MBC values of 4000 µg/ml. It was found that the extract, at four times the MIC, produced complete killing of the uropathogen at 2h from the beginning of the experiment, while the alkylresorcinol, at four times the MIC, produced the same effect after 24 h. Hemolysis was adversely affected in treatments with both products at 8 µg/ml, while hemagglutination was not altered. The whole extract induced complete autoaggregation of P. mirabilis at 2000 µg/ml, while compound 1 at the same concentration did not show this property. Swarming motility was delayed in treatments with the extract and with 1 at 1000 and 8 µg/ml, respectively, at 8h from the beginning of the assay. Complete inhibition of the phenomenon was still observed after 24 h when compound 1 was added at 125 µg/ml. These findings offer the possibility of new classes of antimicrobial medicines to tackle infections caused by P. mirabilis.

Rapid virological response as a predictor of sustained response in HCV-infected patients with persistently normal alanine aminotransferase levels: A multicenter study.

Rapid virological response (RVR) is now considered the strongest predictor of sustained virological response (SVR) in patients with HCV undergoing antiviral treatment, and thus, shorter antiviral treatment for these patients has been suggested. However, no data exist on the predictive value of RVR in HCV carriers with normal ALT values. A total of 137 patients with persistently normal ALT treated with peginterferon alfa 2a and ribavirin were studied. Fifteen patients dropped out early because of side effects, and in 10 patients with HCV-1 treatment was discontinued because of lack of early virological response (EVR). RVR was observed in 68% of the patients (42% patients with HCV-1, 90% HCV-2 and 64% HCV-3). An end-of-treatment response was observed in 86% of the patients (68% HCV-1, 100% HCV-2 and 91% HCV-3). SVR was maintained in 91 patients (46% HCV-1, 97% HCV-2 and 82% HCV-3). Overall, 92% patients with rapid response did obtain HCV eradication vs only 38% of those without rapid response. HCV-1 patients with baseline HCV RNA <400×10(3) IU/mL were more likely to achieve RVR and SVR than those with higher HCV RNA levels. We conclude that patients with genotype 1 and normal ALT who achieve HCV RNA negativity at week 4 may have a higher probability of eradicating their infection. Because of the concomitant favourable demographic and virological features often found in this particular subset of patients, the duration of therapy in these people might be shortened in the case of RVR. Persistently normal alanine aminotransferase levels patients with genotype 2 or 3 have a high chance of achieving SVR, so retesting of HCV RNA during treatment may have no additional practical value in these subjects.

Biochemical characterization of a lipase from olive fruit (Olea europaea L.).

Lipase (triacylglycerol acylhydrolase; EC 3.1.1.3) is the first enzyme of the degradation path of stored triacylglycerols (TAGs). In olive fruits, lipase may determine the increase of free fatty acids (FFAs) which level is an important index of virgin olive oil quality. However, despite the importance of virgin olive oil for nutrition and human health, few studies have been realized on lipase activity in Olea europaea fruits. In order to characterize olive lipase, fruits of the cv. Ogliarola, widely diffused in Salento area (Puglia, Italy), were harvested at four stages of ripening according to their skin colour (green, spotted I, spotted II, purple). Lipase activity was detected in the fatty layer obtained after centrifugation of the olive mesocarp homogenate. The enzyme exhibited a maximum activity at pH 5.0. The addition of calcium in the lipase assay medium leads to an increment of activity, whereas in the presence of copper the activity was reduced by 75%. Furthermore, mesocarp lipase activity increases during olive development but declined at maturity (purple stage). The data represent the first contribution to the biochemical characterization of an olive fruit lipase associated to oil bodies.

Peripheral blood serum markers for apoptosis and liver fibrosis: are they trustworthy indicators of liver realness?

BACKGROUND/AIMS: No reliable serum markers for liver inflammation, apoptosis and fibrosis have been established yet, although a large number have been evaluated. Moreover, it is not clear if a molecule detected and quantified in peripheral vein blood is a really trustworthy marker of the liver condition. To answer to this question, we had the opportunity to study paired serum samples drawn simultaneously during haemodynamic study from the right hepatic vein and from a peripheral vein from patients with hepatitis C virus related cirrhosis. METHODS: The serum levels of transforming growth factor beta-1, tumour necrosis factor-alpha, hyaluronic acid, soluble (s)human leukocyte class I antigens, soluble FAS ligand, and stumour necrosis factor related ligand were assessed in a consecutive series of 15 patients with hepatitis C virus related cirrhosis. RESULTS: No statistically significant differences were found between hepatic vein and peripheral vein levels for the cytokines, substance or soluble molecules evaluated, excepted for shuman leukocyte class I antigens. Instead a strong correlation between hepatic vein and peripheral vein levels was present for: hepatic vein, shuman leukocyte class I antigens, tumour necrosis factor-alpha, soluble FAS ligand and stumour necrosis factor related ligand, but not for transforming growth factor beta-1. CONCLUSIONS: Our results show that peripheral vein measurements seem to reflect the liver compartment in a large majority of cases, but not for all molecules and probably for any liver diseases. Further studies on this line are warranted in particular for new molecules.

Recurrent Intraventricular Hemorrhages Caused by an AVM Detected by Angiography with Initially Normal Angiogram.

Primary intraventricular haemorrhage (PIVH) is an uncommon type of non-traumatic cerebral haemorrhage limited to the ventricular system arising in adults and children, with diverse aetiology and variable course. Vascular malformations account for 34% of PIVH, whereas no cause is found in 21-47%. When a primary intraventricular haemorrhage is detected in a young patient an underlying lesion such as an arteriovenous malformation (AVM) must be ruled out. The diagnosis may be suspected when there is sudden onset of headache, nausea and vomiting with or without a reduced level of consciousness. Nevertheless, even if clinical features suggest the diagnosis of PIVH, cerebral computed tomography (CT) scan is required for confirmation, and magnetic resonance imaging (MRI) and catheter angiography are necessary to establish the aetiology. We describe a case of isolated recurrent intraventricular haemorrhages caused by AVM detected by diagnostic intracranial angiography with no abnormality demonstrated on angiography four years earlier.

CT-Cisternography in Post-Surgical CSF Rhinorrhea. A Report of Two Cases.

Cerebrospinal fluid (CSF) rhinorrhea is a dangerous problem. CSF rhinorrhea implies an abnormal communication between the subarachnoid space and the nasal cavity, with subsequent leakage of CSF through the anterior nasal apertures. requiring surgical repair. Imaging techniques have evolved from conventional cranial radiography to polytomography, thin-section computed tomography (CT) and intrathecal water-soluble iodinated contrast agent-enhanced CT cisternography. We present two cases of post-surgical CSF rhinorrhea in which the best diagnostic findings were obtained by CT cisternography.

Steatosis and portal hypertension.

Non Alcoholic Fatty Liver Disease (NAFLD) is characterized by histologically macrovesicular steatosis in the absence of alcohol consumption. Portal hypertension (PH) is a severe complication of liver cirrhosis leading to a higher risk to develop gastro-esophageal varices, ascites, hepatorenal syndrome, and hepatic encephalopathy. The definition of portal hypertension is based on a pressure measurement. It may be performed directly through portal vein punction or by subtracting the free hepatic venous pressure (FHVP) from the wedged hepatic venous pressure (WHVP). The hepatic venous pressure gradient (HVPG) reflects the degree of PH in the majority of liver diseases. The hepatic vein catheterization with measurement of the HVPG is considered the golden standard for portal pressure evaluation. The mechanisms by which steatosis could induce PH are not fully understood. It is not clear whether the degree of PH differs between patients with viral and alcoholic cirrhosis, and between patients with mild vs severe steatosis, In the majority of the studies subjects with alcoholic cirrhosis were included. Among patients with NASH, the portal hypertensive syndrome appears only in those with advanced cirrhosis. Further, although weight reduction decreases steatosis grade and fibrosis score, it is not clear whether it improves PH in patients with cirrhosis. In contrast, other studies found a correlation between the severity of steatosis and clinical or lab parameters of PH. We can conclude that up to now it is not actually clear whether steatosis in itself might affect portal pressure.

Acute propranolol administration effectively decreases portal pressure in patients with TIPS dysfunction. Transjugular intrahepatic portosystemic shunt.

BACKGROUND AND AIMS: Up to 60% of patients treated with transjugular intrahepatic portosystemic shunt (TIPS) require angioplasty or restenting during the first year of follow up because of TIPS dysfunction (stenosis of the intrahepatic shunt increasing the portal pressure gradient above the 12 mm Hg threshold). We hypothesised that in patients with TIPS stenosis, propranolol administration, by decreasing portal inflow, would markedly decrease portal pressure. PATIENTS AND METHODS: Eighteen patients with TIPS dysfunction were investigated by measuring portal pressure gradient before and after acute propranolol administration (0.2 mg/kg intravenously; n=18). RESULTS: Propranolol markedly reduced the portal pressure gradient (from 16.6 (3.5) to 11.9 (4.8) mm Hg; p<0.0001), cardiac index (-26 (7)%), and heart rate (-18 (7)%) (p<0.0001). Portal pressure gradient decreased to less than 12 mm Hg in nine patients, more frequently in those with moderate dysfunction (portal pressure gradient 16 mm Hg) than in patients with severe dysfunction (portal pressure gradient >16 mm Hg) (8/10 v 1/8; p=0.015). CONCLUSIONS: Propranolol therapy may delay the increase in portal pressure and reduce the need for reintervention in patients with TIPS dysfunction.

What is the utility of selected clinical and endoscopic parameters in predicting the risk of death after caustic ingestion?

BACKGROUND AND STUDY AIMS: Despite the increasing use of early esophagogastroduodenoscopy, the prognostic evaluation and triage of patients who have ingested caustic material is challenging. We evaluated the usefulness of selected clinical and endoscopic parameters in predicting the risk of death after ingestion of caustic substances. PATIENTS AND METHODS: Clinical and endoscopic parameters were obtained from the records of all the patients admitted to our endoscopy unit because of ingestion of caustic material between 1 March 1982 and 30 June 1999. Parameters significantly associated with the risk of death by univariate analysis were entered into a multivariate logistic model. The independent predictors of death by multivariate analysis were used to build a risk score system. RESULTS: Out of 210 patients, 13 underwent emergency surgery (6.2 %) and 25 died (11.9 %). Multivariate analysis identified the following as independent predictors of death: age (10-year intervals; odds ratio [OR] 2.4; 95 % confidence interval 1.4 - 4.1), ingestion of strong acids (OR 7.9; 1.8 - 35.3), white blood cell count at admission > or = 20 000 units/mm3 (OR 6.0; 1.3-28), deep gastric ulcers (OR 9.7; 1.4 - 66.8), and gastric necrosis (OR 20.9; 4.7 - 91.8). The values of the risk score system devised from the results of the multivariate analysis ranged from 1 to 16. No patient scoring < 10 points died and just one of the patients scoring > 14 points survived. CONCLUSION: Age, ingestion of a strong acid, leucocytosis, deep gastric ulcers, and gastric necrosis are predictive of death after caustic ingestion. A risk score system including these predictors may be useful in prognostic evaluation.

Hepatitis C virus RNA quantitation in hepatic veins and peripheral blood in patients with liver cirrhosis: evidence for low level intrahepatic hepatitis C virus replication in advanced liver disease.

BACKGROUND: Very few data exist concerning the level of hepatitis C virus replication within the cirrhotic liver and its relationship to disease severity and progression. AIMS: To quantitate hepatitis C virus RNA in hepatic vein blood and peripheral blood in patients with cirrhosis, to evaluate the correlation of hepatitis C virus levels in paired blood samples, and to compare the results with clinical features. PATIENTS: A series of 25 patients with hepatitis C virus-related liver cirrhosis undergoing hepatic vein catheterization were studied: 11 belonged to Child Pugh class A, 8 to class B and 6 to class C. RESULTS: Hepatitis C virus RNA levels did not differ between hepatic vein blood and peripheral blood (p = 0.26), despite a trend towards higher peripheral hepatitis C virus RNA levels. Hepatitis C virus RNA levels did not differ between patients with genotype 1b and non-1b either in hepatic veins or peripheral blood. Hepatitis C virus loads varied according to the severity of cirrhosis. The patients with more severe liver disease had significantly lower RNA titres than those with less advanced cirrhosis, both in hepatic veins (p = 0.002) and peripheral blood (p = 0.004). No differences in hepatitis C virus load were observed between patients in Child Pugh classes B and C. CONCLUSIONS: The present data show that in patients with cirrhosis hepatitis C virus RNA concentrations do not differ between hepatic blood and peripheral blood and, furthermore, confirm that hepatitis C virus replication is reduced in patients with advanced cirrhosis, compared with patients with less severe liver disease. These findings might indicate that patients with liver cirrhosis maintain an efficient intrahepatic hepatitis C virus replication even in end-stage disease, although hepatitis C virus viraemia decreases according to the severity of liver disease.

Characterization of two Arabidopsis thaliana fructokinases.

Two different fructokinase isoforms of Arabidopsis thaliana have been identified and characterized by non-denaturing electrophoresis followed by activity-staining. The two fructokinases, fructokinase1 (FRK1) and fructokinase2 (FRK2), showed a high specificity for fructose and did not stain when glucose or mannose were used as substrate. Fructose and ATP at high concentrations (above 5 mM) induced a substrate inhibition of the two enzymatic activities. Arabidopsis FRK1 and FRK2 were capable of employing GTP, CTP, UTP and TTP as phosphate donors, although with a significantly lower efficiency than ATP. The two fructokinase activities were also activated by K(+), at around 10-20 mM, and inhibited by ADP and AMP at concentrations above 10 mM. Finally, FRK1 and FRK2 showed a different expression pattern in the plant, with FRK1 being more abundant in the roots and FRK2 in the shoots. The results demonstrate a simple technique that provides important information about fructokinase activities in the plants and which can be useful for the analysis of Arabidopsis mutants.

Purification and characterization of a novel pumpkin short-chain acyl-coenzyme A oxidase with structural similarity to acyl-coenzyme A dehydrogenases.

A novel pumpkin (Cucurbita pepo) short-chain acyl-coenzyme A (CoA) oxidase (ACOX) was purified to homogeneity by hydrophobic-interaction, hydroxyapatite, affinity, and anion-exchange chromatography. The purified enzyme is a tetrameric protein, consisting of apparently identical 47-kD subunits. The protein structure of this oxidase differs from other plant and mammalian ACOXs, but is similar to the protein structure of mammalian mitochondrial acyl-CoA dehydrogenase (ACDH) and the recently identified plant mitochondrial ACDH. Subcellular organelle separation by sucrose density gradient centrifugation revealed that the enzyme is localized in glyoxysomes, whereas no immunoreactive bands of similar molecular weight were detected in mitochondrial fractions. The enzyme selectively catalyzes the oxidation of CoA esters of fatty acids with 4 to 10 carbon atoms, and exhibits the highest activity on C-6 fatty acids. Apparently, the enzyme has no activity on CoA esters of branched-chain or dicarboxylic fatty acids. The enzyme is slightly inhibited by high concentrations of substrate and it is not inhibited by Triton X-100 at concentrations up to 0.5% (v/v). The characteristics of this novel ACOX enzyme are discussed in relation to other ACOXs and ACDHs.

Functional transformation of plant peroxisomes.

Peroxisomes in higher plant cells are known to differentiate into at least three different classes, namely, glyoxysomes, leaf peroxisomes, and unspecialized peroxisomes, depending on the cell types. In germinating fatty seedlings, glyoxysomes that first appear in the etiolated cotyledonary cells are functionally transformed into leaf peroxisomes during greening. Subsequently, the organelles are transformed back into glyoxysomes during senescence of the cotyledons. Flexibility of function is a distinct feature of plant peroxisomes. This article briefly describes recent studies of the regulatory mechanisms involved in the changes of the function of plant peroxisomes.

A novel acyl-CoA oxidase that can oxidize short-chain acyl-CoA in plant peroxisomes.

Short-chain acyl-CoA oxidases are beta-oxidation enzymes that are active on short-chain acyl-CoAs and that appear to be present in higher plant peroxisomes and absent in mammalian peroxisomes. Therefore, plant peroxisomes are capable of performing complete beta-oxidation of acyl-CoA chains, whereas mammalian peroxisomes can perform beta-oxidation of only those acyl-CoA chains that are larger than octanoyl-CoA (C8). In this report, we have shown that a novel acyl-CoA oxidase can oxidize short-chain acyl-CoA in plant peroxisomes. A peroxisomal short-chain acyl-CoA oxidase from Arabidopsis was purified following the expression of the Arabidopsis cDNA in a baculovirus expression system. The purified enzyme was active on butyryl-CoA (C4), hexanoyl-CoA (C6), and octanoyl-CoA (C8). Cell fractionation and immunocytochemical analysis revealed that the short-chain acyl-CoA oxidase is localized in peroxisomes. The expression pattern of the short-chain acyl-CoA oxidase was similar to that of peroxisomal 3-ketoacyl-CoA thiolase, a marker enzyme of fatty acid beta-oxidation, during post-germinative growth. Although the molecular structure and amino acid sequence of the enzyme are similar to those of mammalian mitochondrial acyl-CoA dehydrogenase, the purified enzyme has no activity as acyl-CoA dehydrogenase. These results indicate that the short-chain acyl-CoA oxidases function in fatty acid beta-oxidation in plant peroxisomes, and that by the cooperative action of long- and short-chain acyl-CoA oxidases, plant peroxisomes are capable of performing the complete beta-oxidation of acyl-CoA.