VSGdb: a database for trypanosome variant surface glycoproteins,a large and diverse family of coiled coil proteins

Background  

Trypanosomes are coated with a variant surface glycoprotein (VSG) that is so densely packed that it physically protects underlying proteins from effectors of the host immune system. Periodically cells expressing a distinct VSG arise in a population and thereby evade immunity. The main structural feature of VSGs are two long α-helices that form a coiled coil, and sets of relatively unstructured loops that are distal to the plasma membrane and contain most or all of the protective epitopes. The primary structure of different VSGs is highly variable, typically displaying only ~20% identity with each other. The genome has nearly 2000 VSG genes, which are located in subtelomeres. Only one VSG gene is expressed at a time, and switching between VSGs primarily involves gene conversion events. The archive of silent VSGs undergoes diversifying evolution rapidly, also involving gene conversion. The VSG family is a paradigm for α helical coiled coil structures, epitope variation and GPI-anchor signals. At the DNA level, the genes are a paradigm for diversifying evolutionary processes and for the role of subtelomeres and recombination mechanisms in generation of diversity in multigene families. To enable ready availability of VSG sequences for addressing these general questions, and trypanosome-specific questions, we have created VSGdb, a database of all known sequences.     

SAM68 is a physiological regulator of SMN2 splicing in spinal muscular atrophy

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by loss of motor neurons in patients with null mutations in the SMN1 gene. The almost identical SMN2 gene is unable to compensate for this deficiency because of the skipping of exon 7 during pre–messenger RNA (mRNA) processing. Although several splicing factors can modulate SMN2 splicing in vitro, the physiological regulators of this disease-causing event are unknown. We found that knockout of the splicing factor SAM68 partially rescued body weight and viability of SMAΔ7 mice. Ablation of SAM68 function promoted SMN2 splicing and expression in SMAΔ7 mice, correlating with amelioration of SMA-related defects in motor neurons and skeletal muscles. Mechanistically, SAM68 binds to SMN2 pre-mRNA, favoring recruitment of the splicing repressor hnRNP A1 and interfering with that of U2AF65 at the 3′ splice site of exon 7. These findings identify SAM68 as the first physiological regulator of SMN2 splicing in an SMA mouse model.     

Long-chain polyunsaturated fatty acids profile in plasma phospholipids of hyperphenylalaninemic children on unrestricted diet

IntroductionThe aim of the present study was to examine whether hyperphenylalaninemic children on unrestricted diet (MHP) may exhibit a different LCPUFA profile from PKU or healthy children in plasma phospholipids.Patients and methodsForty-five MHP children (age 9–14 years) were age and sex matched with 45 PKU and 45 healthy children. Fatty acids were determined and expressed as % of total fatty acids.ResultsMHP children showed docosahexaenoic acid (DHA) levels higher than PKU children (mean difference, 0.2%; 95% confidence interval, 0.02%–0.38%), although difference was not significant after correction for multiple comparisons, and lower levels than healthy children (?0.8%; ?1.01% to ?0.59%). Concentration of n-3 PUFA was higher in MHP than PKU children (0.6%; 0.4% to 0.8%),ConclusionsThe results suggest that low DHA levels in plasma phospholipids not only are evident in PKU but also may occur in MHP children, who are on unrestricted diet, as compared to healthy children.     

Selection of thrombin-binding aptamers by using computational approach for aptasensor application

The possibility of introducing a computationally assisted method to study aptamer-protein interaction was evaluated with the aim of streamlining the screening and selection of new aptamers. Starting from information on the 15-mer (5'-GGTTGGTGTGGTTGG-3') thrombin binding aptamer (TBA), a library of mutated DNA sequences (994 elements) was generated and screened using shapegauss a shape-based scoring function from openeye software to generate computationally derived binding scores. The TBA and three other mutated oligonucleotides, selected on the basis of their binding score (best, medium, worst), were incorporated into surface plasmon resonance (SPR) biosensors. By reducing the ionic strength (binding buffer, 50 mM TrisHCl pH 7.4, 140 mM NaCl, 1mM MgCl?, diluted 1:50) in order to match the simulated condition, the analytical performances of the four oligonucleotide sequences were compared using signal amplitude, sensitivity (slope), linearity (R2) and reproducibility (CVav %). The experimental results were in agreement with the simulation findings.     

Natural daucane sesquiterpenes with antiproliferative and proapoptotic activity against human tumor cells

Plants of the genera Ferula and Ferulago are known for their complex content in bioactive secondary metabolites such as coumarins, phenylpropanoids, and sesquiterpenes. We used the ground parts of Ferula communis subsp. communis, Ferula glauca subsp. glauca and Ferulago campestris as natural sources for the isolation of four coumarins (CU-1 to CU-4), two phenylpropanoids (PE-1 and PE-2), one polyacetylene (PA-1) and 16 daucane esters (DE-1 to DE-16). The cytotoxic activity of the isolated compounds was evaluated against a panel of seven human tumor cell lines. Fourteen of the daucane derivatives showed antiproliferative activity at least against one of the human tumor cell lines tested, four compounds (DE-5, DE-8, DE-11, and DE-16) were active against all the tested cell lines. Among them DE-11 was the most cytotoxic compound against HeLa (4.4 ± 0.7 μM), A549 (2.8 ± 1.4 μM), HL-60 (2.6 ± 0.4 μM), K562 (26.5 ± 6.0 μM) RS 4;11 (1.7 ± 0.3 μM) and SEM (2.4 ± 0.1 μM) cell lines, while DE-8 was the most active against Jurkat (3.3 ± 0.8 μM). Preliminary structure-activity relationship suggests that the most active compounds in the daucane series present the trans fusion of the penta- and hepta-atomic cycles, and lipophylic ester groups linked to position 6. Isomeric derivatives such as DE-8 and DE-9 or DE-3, DE-4, and DE-5 exhibited significant differences in their IC(50) supporting that the β orientation for the ester group in the position 2 enhances the cytotoxic activity. Furthermore, the pro-apoptotic effect of the most active compounds evaluated in Jurkat cell line showed that these compounds are able to induce apoptosis in a time and concentration-dependent manner. Our findings suggest the potential role of daucane derivatives as models for the development of proapoptotic compounds.     

An unexpected evolution of symptomatic mild middle cerebral artery (MCA) stenosis: asymptomatic occlusion

Background  

The intracranial localization of large artery disease is recognized as the main cause of ischemic stroke in the world, considering all countries, although its global burden is widely underestimated. Indeed it has been reported more frequently in Asians and African-American people, but the finding of intracranial stenosis as a cause of ischemic stroke is relatively common also in Caucasians. The prognosis of patients with stroke due to intracranial steno-occlusion is strictly dependent on the time of recanalization. Moreover, the course of the vessel involvement is highly dynamic in both directions, improvement or worsening, although several data are derived from the atherosclerotic subtype, compared to other causes.     

Molecular pathways involved in the cyclic activity of frog (Pelophylax esculentus) Harderian gland: Influence of temperature and testosterone

The Harderian gland of Pelophylax esculentus (previously: Rana esculenta) shows seasonal secretory activity changes. Specifically, the secretory activity reaches a maximum during the hottest months, i.e., July and August, drops in September and slowly increases from October onwards. Expressions of P-CaMKII, P-ERK1 and P-Akt1 correlate well with gland secretory activity; i.e., they peak immediately before the hottest part of the year (maximum secretory activity). When the gland activity declines, kinase expressions drop and remain low until February. Experiments of thermal manipulation indicate that high temperature induces the activation of CaMKII, ERK1 and Akt1, and at low temperatures, Akt1 expression decreases. Experiments of chemical castration indicate that the Harderian gland of Cyproterone acetate-treated frogs shows lower Akt1 activity as compared to controls, but the CaMKII and ERK1 activities remain unchanged. Furthermore, in a period of resumed gland activity (October–December) we observed the highest expression of PCNA, a mitotic marker. Immediately after the proliferative phase, we found the highest expression of caspase 3, an enzyme that plays a key role in apoptosis. In combination, the results suggest the following: 1) CaMKII, ERK1, and Akt1 modulate the annual secretory activity of the frog Harderian gland; 2) CaMKII and ERK1 activities are regulated by temperature, whereas both temperature and testosterone likely play a central role in Akt1 regulation; and 3) proliferation and apoptosis occur to restore and balance, respectively, an adequate cell number, which is essential to gland function.     

Evaluating the effects of climate change on tree species abundance and distribution in the Italian peninsula

Question: What is the effect of climate change on tree species abundance and distribution in the Italian peninsula? Location: Italian peninsula. Methods: Regression tree analysis, Random Forest, generalized additive model and geostatistical methods were compared to identify the best model for quantifying the effect of climate change on tree species distribution and abundance. Future potential species distribution, richness, local colonization, local extinction and species turnover were modelled according to two scenarios (A2 and B1) for 2050 and 2080. Results: Robust Random Forest proved to be the best statistical model to predict the potential distribution of tree species abundance. Climate change could lead to a shift in tree species distribution towards higher altitudes and a reduction of forest cover. Pinus sylvestris and Tilia cordata may be considered at risk of local extinction, while the other species could find potential suitable areas at the cost of a rearrangement of forest community composition and increasing competition. Conclusions: Geographical and topographical regional characteristics can have a noticeable influence on the impact of predicted climate change on forest ecosystems within the Mediterranean basin. It would be highly beneficial to create a standardized and harmonized European forest inventory in order to evaluate, at high resolution, the effect of climate change on forest ecosystems, identify regional differences and develop specific adaptive management strategies and plans.