Next-generation sequencing to generate interactome datasets

Next-generation sequencing has not been applied to protein-protein interactome network mapping so far because the association between the members of each interacting pair would not be maintained in en masse sequencing. We describe a massively parallel interactome-mapping pipeline, Stitch-seq, that combines PCR stitching with next-generation sequencing and used it to generate a new human interactome dataset. Stitch-seq is applicable to various interaction assays and should help expand interactome network mapping.     

Revision of the central Mediterranean xerothermic cliff vegetation

Questions

What are the syntaxonomic and synchorological patterns of the xerothermic chasmophytic vegetation in the central part of the Mediterranean Basin? What are the diagnostic species of the high‐rank syntaxa of Asplenietalia glandulosi, Onosmetalia frutescentis and Centaureo dalmaticae‐Campanuletalia pyramidalis?

Location

Mediterranean coastal and subcoastal areas of southern France, Italy, Malta, Slovenia, Croatia, Bosnia and Herzegovina, Montenegro, Albania and of mainland Greece.

Methods

The data set of 1,261 published relevés was analysed using hierarchical clustering (Flexible Beta method), involving a series of data transformations. Indicator species analysis was used to select the best dendrogram solution and identify diagnostic taxa of the main clusters. The dendrogram was interpreted from a syntaxonomic point of view, using nomenclatural type relevés as a basis. The NMDS ordination was performed in order to visualize the floristic relationships among associations and high‐rank syntaxa. MRPP was used to test for differences among alliances.

Results

The classification revealed four main clusters of relevés representing the chasmophytic vegetation of southern France, Sardinia and the northwestern part of Italy (Asplenienalia glandulosi/Asplenietalia glandulosi), the southwestern part of Italy and Malta (Tinguarrenalia siculae/Asplenietalia glandulosi), the Adriatic Basin area (Centaureo dalmaticae‐Campanuletalia pyramidalis) and the southern Balkans (Onosmetalia frutescentis). The NMDS ordination confirmed the overall pattern, while MRPP showed significant differences among the alliances of the above‐mentioned orders and suborders. The lists of diagnostic taxa of the high‐rank syntaxa were revised according to a supra‐national perspective.

Conclusions

The new syntaxonomic scheme provides a comprehensive overview of the chasmophytic vegetation of the central part of the Mediterranean Basin. This scheme mostly matches the recently published EuroVegChecklist, but also exhibits important novelties concerning the syntaxonomic position of some alliances (Dianthion rupicolae, Centaureion pentadactyli, Arenarion bertolonii and Caro‐Aurinion), and the floristic and chorological relationships among high‐rank syntaxa, with new revised sets of diagnostic taxa. This revision might be useful for further small‐scale phytosociological studies.

     

Hydrogen sulphide-related thiol metabolism and nutrigenetics in relation to hypertension in an elderly population

Hydrogen sulphide (H₂S) is a gaseous signalling molecule that regulates blood flow and pressure. It is synthesised from cysteine via cystathionine β-synthase and cystathionine γ-lyase. We examined whether thiol precursors of H₂S, transsulphuration pathway gene variants (CBS-844ins68 and CTH-G1364T) and key B-vitamin cofactors might be critical determinants of hypertension in an elderly Australian population. An elderly Australian retirement village population (n = 228; age 65–96 years, 91 males and 137 females) was assessed for the prevalence of two transsulphuration pathway–related variant genes associated with cysteine synthesis and hence H₂S production. Thiols were determined by HPLC, genotypes by PCR and dietary intake by food frequency questionnaire. Homocysteine levels were statistically higher in the hypertensive phenotype (p = 0.0399), but there was no difference for cysteine or glutathione. Using nominal logistic regression, cysteine, CTH-G1364T genotype, dietary synthetic folate and vitamin B₆ predicted clinical phenotype (determined as above/below 140/90 mm Hg) and then only in female subjects (p = 0.0239, 0.0178, 0.0249 and 0.0371, respectively). Least-squares regression supports cysteine being highly inversely predictive of diastolic blood pressure: p and r ² values <0.0001 and 0.082; 0.0409 and 0.046; and <0.0001 and 0.113 for all subjects, males and females, respectively. Additionally, CTH-G1364T genotype predicts diastolic blood pressure in males (p = 0.0217; r ² = 0.083), but contrasts with observations for females. Overall, analyses, including stepwise regression, suggest cysteine, dietary natural and synthetic folate, vitamins B₆ and B₁₂, and both genetic variants (CTH-C1364T and CBS-844ins68) are all aetiologically relevant in the regulation of blood pressure. Hydrogen sulphide is a vasorelaxant gasotransmitter with characteristics similar to nitric oxide. Cysteine and the G1364T and 844ins68 variants of the cystathionine γ-lyase and cystathionine β-synthase genes, respectively, are the biological determinants of H₂S synthesis, and all three are shown here to influence the hypertensive phenotype. Additionally, B-vitamin cofactors for these three enzymes may also be important determinants of blood pressure.     

Skeletal Manifestations of Hydatid Disease in Serbia: Demographic Distribution,Site Involvement,Radiological Findings,and Complications

Although Serbia is recognized as an endemic country for echinococcosis, no information about precise incidence in humans has been available. The aim of this study was to investigate the skeletal manifestations of hydatid disease in Serbia. This retrospective study was conducted by reviewing the medical database of Institute for Pathology (Faculty of Medicine in Belgrade), a reference institution for bone pathology in Serbia. We reported a total of 41 patients with bone cystic echinococcosis (CE) during the study period. The mean age of 41 patients was 40.9±18.8 years. In 39% of patients, the fracture line was the only visible radiological sign, followed by cyst and tumefaction. The spine was the most commonly involved skeletal site (55.8%), followed by the femur (18.6%), pelvis (13.9%), humerus (7.0%), rib (2.3%), and tibia (2.3%). Pain was the symptom in 41.5% of patients, while some patients demonstrated complications such as paraplegia (22.0%), pathologic fracture (48.8%), and scoliosis (9.8%). The pathological fracture most frequently affected the spine (75.0%) followed by the femur (20.0%) and tibia (5.0%). However, 19.5% of patients didn''t develop any complication or symptom. In this study, we showed that bone CE is not uncommon in Serbian population. As reported in the literature, therapy of bone CE is controversial and its results are poor. In order to improve the therapy outcome, early diagnosis, before symptoms and complications occur, can be contributive.     

Tree mineral nutrition is deteriorating in Europe

The response of forest ecosystems to increased atmospheric CO₂ is constrained by nutrient availability. It is thus crucial to account for nutrient limitation when studying the forest response to climate change. The objectives of this study were to describe the nutritional status of the main European tree species, to identify growth‐limiting nutrients and to assess changes in tree nutrition during the past two decades. We analysed the foliar nutrition data collected during 1992–2009 on the intensive forest monitoring plots of the ICP Forests programme. Of the 22 significant temporal trends that were observed in foliar nutrient concentrations, 20 were decreasing and two were increasing. Some of these trends were alarming, among which the foliar P concentration in F. sylvatica, Q. Petraea and P. sylvestris that significantly deteriorated during 1992–2009. In Q. Petraea and P. sylvestris, the decrease in foliar P concentration was more pronounced on plots with low foliar P status, meaning that trees with latent P deficiency could become deficient in the near future. Increased tree productivity, possibly resulting from high N deposition and from the global increase in atmospheric CO₂, has led to higher nutrient demand by trees. As the soil nutrient supply was not always sufficient to meet the demands of faster growing trees, this could partly explain the deterioration of tree mineral nutrition. The results suggest that when evaluating forest carbon storage capacity and when planning to reduce CO₂ emissions by increasing use of wood biomass for bioenergy, it is crucial that nutrient limitations for forest growth are considered.