Statistical Analysis of the Loop-Geometry on a Non-Redundant Database of Proteins

The conformations of protein loops from a non-redundant set of 347 proteins with less than 25% sequence homology have been studied in order to clarify the topological variation of protein loops. Loops have been classified in five types (α-α, α-β, β-α, β-links and β-hairpins) depending on the secondary structures that they embrace. Four variables have been used to describe the loop geometry (3 angles and the end-to-end distance between the secondary structures embracing the loop). Loops with well defined geometry are identified by means of the internal dependency between the geometrical variables by application of information-entropy theory. From this it has been deduced that loops formed by less than 10 residues show an intrinsic dependency on the geometric variables that defines the motif shape. In this interval the most stable loops are found for short connections owing to the entropic energy analysed.     

The balancing act of AKT in T cells

The serine/threonine-specific protein kinase AKT is gaining recognition as a major crossroad in numerous cellular signaling pathways through its ability to regulate cell differentiation, proliferation, survival and metabolism. This review focuses on the recent advances in AKT signaling and downstream events in T cells, emphasizing its contrasting role in conventional and regulatory (Treg) Tcell populations. Activation of AKT has been known for many years to be critical in the development and function of conventional Tcells. However, it has just recently been uncovered that AKTexerts an inhibitory effect on Treg generation and suppressor function. These studies have placed AKTat the nexus of Treg development and function, thus opening novel avenues for therapeutic manipulation.     

Internalization of cystatin C in human cell lines

Altered protease activity is considered important for tumour invasion and metastasis, processes in which the cysteine proteases cathepsin B and L are involved. Their natural inhibitor cystatin C is a secreted protein, suggesting that it functions to control extracellular protease activity. Because cystatins added to cell cultures can inhibit polio, herpes simplex and coronavirus replication, which are intracellular processes, the internalization and intracellular regulation of cysteine proteases by cystatin C should be considered. The extension, mechanism and biological importance of this hypothetical process are unknown. We investigated whether internalization of cystatin C occurs in a set of human cell lines. Demonstrated by flow cytometry and confocal microscopy, A-431, MCF-7, MDA-MB-453, MDA-MB-468 and Capan-1 cells internalized fluorophore-conjugated cystatin C when exposed to physiological concentrations (1 microm). During cystatin C incubation, intracellular cystatin C increased after 5 min and accumulated for at least 6 h, reaching four to six times the baseline level. Western blotting showed that the internalized inhibitor was not degraded. It was functionally intact and extracts of cells exposed to cystatin C showed a higher capacity to inhibit papain and cathepsin B than control cells (decrease in enzyme activity of 34% and 37%, respectively). The uptake of labelled cystatin C was inhibited by unlabelled inhibitor, suggesting a specific pathway for the internalization. We conclude that the cysteine protease inhibitor cystatin C is internalized in significant quantities in various cancer cell lines. This is a potentially important physiological phenomenon not previously described for this group of inhibitors.     

Nonmotor Symptoms in LRRK2 G2019S Associated Parkinson’s Disease

Background

Idiopathic Parkinson’s disease (IPD) and LRRK2-associated PD (LRRK2-PD) might be expected to differ clinically since the neuropathological substrate of LRRK2-PD is heterogeneous. The range and severity of extra-nigral nonmotor features associated with LRRK2 mutations is also not well-defined.

Objective

To evaluate the prevalence and time of onset of nonmotor symptoms (NMS) in LRRK2-PD patients.

Methods

The presence of hyposmia and of neuropsychiatric, dysautonomic and sleep disturbances was assessed in 33 LRRK2-G2019S-PD patients by standardized questionnaires and validated scales. Thirty-three IPD patients, matched for age, gender, duration of parkinsonism and disease severity and 33 healthy subjects were also evaluated.

Results

University of Pennsylvania Smell Identification Test (UPSIT) scores in LRRK2-G2019S-PD were higher than those in IPD (23.5±6.8 vs 18.4±6.0; p = 0.002), and hyposmia was less frequent in G2019S carriers than in IPD (39.4% vs 75.8%; p = 0.01). UPSIT scores were significantly higher in females than in males in LRRK2-PD patients (26.9±4.7 vs 19.4±6.8; p<0.01). The frequency of sleep and neuropsychiatric disturbances and of dysautonomic symptoms in LRRK2-G2019S-PD was not significantly different from that in IPD. Hyposmia, depression, constipation and excessive daytime sleepiness, were reported to occur before the onset of classical motor symptoms in more than 40% of LRRK2-PD patients in whom these symptoms were present at the time of examination.

Conclusion

Neuropsychiatric, dysautonomic and sleep disturbances occur as frequently in patients with LRRK2-G2019S-PD as in IPD but smell loss was less frequent in LRRK2-PD. Like in IPD, disturbances such as hyposmia, depression, constipation and excessive daytime sleepiness may antedate the onset of classical motor symptoms in LRRK2-G2019S-PD.     

Brain proteomics identifies potential simvastatin targets in acute phase of stroke in a rat embolic model

Finding an efficient neuroprotectant is of urgent need in the field of stroke research. The goal of this study was to test the effect of acute simvastatin administration after stroke in a rat embolic model and to explore its mechanism of action through brain proteomics. To that end, male Wistar rats were subjected to a Middle Cerebral Arteria Occlusion and simvastatin (20 mg/kg s.c) (n = 11) or vehicle (n = 9) were administered 15 min after. To evaluate the neuroprotective mechanisms of simvastatin, brain homogenates after 48 h were analyzed by two‐dimensional fluorescence Difference in Gel Electrophoresis (DIGE) technology. We confirmed that simvastatin reduced the infarct volume and improved neurological impairment at 48 h after the stroke in this model. Considering our proteomics analysis, 66 spots, which revealed significant differences between groups, were analyzed by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry allowing the identification of 27 proteins. From these results, we suggest that simvastatin protective effect can be partly explained by the attenuation of the oxidative and stress response at blood–brain barrier level after cerebral ischemia. Interestingly, analyzing one of the proteins (HSP75) in plasma from stroke patients who had received simvastatin during the acute phase, we confirmed the results found in the pre‐clinical model.

     

Hydrological extremes modulate nutrient dynamics in mediterranean climate streams across different spatial scales

We studied benthic macroinvertebrate communities upstream and downstream of five small reservoirs (surface release in autumn–winters) (north Spain) to assess the effect of flow regulation on structural and functional characteristics of stream ecosystems. We based our approach on the use of structural metrics (density, biomass, richness and diversity) in combination with two functional diversity indices based on biological and ecological traits: FD_PG index, related to species richness, and FD_Q, which incorporates evenness across taxa. Although water physicochemical parameters were unaffected by the reservoirs during the study period (autumn–winter), macroinvertebrate metrics were lower below the dams, with detritivores (shredders and collector-gatherers) being the most affected. The alder leaf breakdown rate estimated by the litter-bag technique was related to the density, biomass, richness, diversity and FD_PG index of shredders, compromising the ecosystem functioning. The most plausible origin for the observed differences in macroinvertebrate metrics between upstream and downstream reaches was the change of the flow regime caused by the impoundments at downstream sites, leading to droughts in summer in those naturally permanently flowing streams. The observed functional diversity loss might reduce the chances of the community to override natural or man-induced fluctuations in their environment with possible repercussions on important ecosystem functions and services.     

A new exotic bird in Europe: recent spread and potential range of Red‐billed Leiothrix Leiothrix lutea in Catalonia (northeast Iberian Peninsula)

Capsule Following recent introduction in Spain, Red‐billed Leiothrix have the potential to attain a wide distribution in Catalonia and probably in other parts of Europe.

Aim To investigate past, present and potential distribution of this exotic species in Catalonia (northeast Iberian Peninsula).

Methods We collected data on the species’ occurrence over the period 1992–2008 and used information obtained in other regions where it has previously established to produce hypotheses about the ecological processes that affect its population increase and range expansion. We then generated fine‐grained distribution maps covering the entire region for the periods 1992–2001 and 2002–2008, and for the species’ potential range according to its specific habitat requirements.

Results Since being first detected in the wild in the Collserola Park, near the city of Barcelona, Red‐billed Leiothrix have expanded to neighbouring forested areas. The wild population is currently in a phase of exponential growth and, according to our habitat suitability model, the species’ potential distribution in Catalonia might be 36 times greater than at present.

Conclusion Our results suggest that the Red‐billed Leiothrix has the potential to attain a widespread distribution over large regions of Europe in the near future. However, we discuss several factors that might affect these predictions.     

An Optimized Immunohistochemistry Technique Improves NMO-IgG Detection: Study Comparison with Cell-Based Assays

Cell-based assays (CBA) have increased the sensitivity of the neuromyelitis optica (NMO)-IgG/aquaporin-4-antibody detection compared to classical tissue-based indirect assays. We describe the sensitivity of an optimized immunohistochemistry (IHC-o) to detect NMO-IgG/aquaporin-4-antibody in comparison with that of two CBA: an in-house (CBA-ih) and a commercial (CBA-c) assay (Euroimmun, Germany). Coded serum from 103 patients with definite NMO and 122 inflammatory controls were studied by IHC-o, CBA-ih, and CBA-c. IHC-o used the same protocol described to detect antibodies against cell surface antigens. CBA-ih used live cells transfected with the aquaporin-4-M23-isoform. The sensitivity of the IHC-o was 74.8% (95% confidence interval [CI] 65-83) and was similar to that of the CBA-ih 75.7% (95% CI 66-84) and the CBA-c 73.8% (95% CI 64-82). The specificity of the three assays was 100% (95% CI 97-100). Interassay concordance was high, 100 of 103 samples were coincident in all techniques. The optimized immunohistochemistry proves to be as sensitive and specific as the cell-based assays. This assay extends the available tools for NMO-IgG/aquaporin-4-antibody detection.