Enrichment of ultraconserved elements among genomic imbalances causing mental delay and congenital anomalies

Background

In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required.

Results

We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms.

Conclusions

The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.     

Topological change of Andean plant–pollinator networks along an altitudinal gradient

Pollination interaction networks exhibit structural regularities across a wide range of natural environments. Long-tailed degree distribution, nestedness, and modularity are the most prevalent topological patterns found in most bipartite networks analyzed up to day. In this work we evaluate the variation of these topological properties along an altitudinal gradient. To this end, we examined four plant–pollinator networks from the Chilean Andes at 33°S, in range from 1800 to 3600 m elevation. Our results indicate that network topology is strongly and systematically affected by elevation. At increasing altitude, the number of potential visitors per plant decreased, and species’ degree distributions are closer to random expectations. On the other hand, the nested structure of mutualistic interactions systematically decreased with elevation, and network modularity was significantly higher than random expectations over the entire altitudinal range. In addition, at increasing elevations the pollination networks were organized in fewer and more strongly connected modules. Our results suggest that the severe abiotic conditions found at increased elevations translate into less organized pollination networks.     

The length of vesicular stomatitis virus particles dictates a need for actin assembly during clathrin-dependent endocytosis

Microbial pathogens exploit the clathrin endocytic machinery to enter host cells. Vesicular stomatitis virus (VSV), an enveloped virus with bullet-shaped virions that measure 70 x 200 nm, enters cells by clathrin-dependent endocytosis. We showed previously that VSV particles exceed the capacity of typical clathrin-coated vesicles and instead enter through endocytic carriers that acquire a partial clathrin coat and require local actin filament assembly to complete vesicle budding and internalization. To understand why the actin system is required for VSV uptake, we compared the internalization mechanisms of VSV and its shorter (75 nm long) defective interfering particle, DI-T. By imaging the uptake of individual particles into live cells, we found that, as with parental virions, DI-T enters via the clathrin endocytic pathway. Unlike VSV, DI-T internalization occurs through complete clathrin-coated vesicles and does not require actin polymerization. Since VSV and DI-T particles display similar surface densities of the same attachment glycoprotein, we conclude that the physical properties of the particle dictate whether a virus-containing clathrin pit engages the actin system. We suggest that the elongated shape of a VSV particle prevents full enclosure by the clathrin coat and that stalling of coat assembly triggers recruitment of the actin machinery to finish the internalization process. Since some enveloped viruses have pleomorphic particle shapes and sizes, our work suggests that they may use altered modes of endocytic uptake. More generally, our findings show the importance of cargo geometry for specifying cellular entry modes, even when the receptor recognition properties of a ligand are maintained.     

The role of nurse plants in the establishment of shrub seedlings in the semi-arid subtropical Andes

In the nurse plant syndrome, or nurse association, seedlings (beneficiaries) are associated with adult shrubs/trees (benefactors). This phenomenon has been documented in several regions of the planet. Abiotic stress amelioration (one mechanism of facilitation) is one of the causes of this association. Most of the studies addressing the nurse syndrome have been conducted on spatial scales of a few hectares and have focused on only one or a few species. Moreover, there is an almost complete lack of studies addressing the incidence and characteristics of the nurse phenomenon in the arid Andes of South America. We undertook a first approximation to the study of facilitation in these ecosystems. The study was conducted at local and regional scales and involved the assessment of the spatial distribution of juveniles (seedlings and saplings) of 51 populations of 16 shrub and 12 cactus species in relation to shrub cover at 20 localities of the Prepuna (subtropical Andes of Bolivia and Argentina, 20–26°S). In terms of spatial distribution, the juveniles of most of the populations of shrubs studied were distributed both under the shrubs and in open spaces, thereby showing an apparent indifference to microhabitat. Globose and opuntioid cacti were preferentially distributed below the canopies of shrubs and were usually more associated with the dominant shrub species, which stood out as better potential nurses. The pattern was consistent throughout the region, including the more mesic and arid localities. The fact that Prepuna woody species are capable of establishing in open spaces would confer this region a greater resilience. Our findings further suggest that community dynamics in arid and semi-arid environments are more variable than previously thought.     

Instability of copronecrophagous beetle assemblages (Coleoptera: Scarabaeinae) in a mountainous tropical landscape of Mexico

We analyzed changes over time in species composition and functional guild structure (temporal beta diversity) for natural assemblages and those modified by humans in a fragmented, tropical mountain landscape. The assemblages belong to cloud forests (the original vegetation type), secondary forests, traditional shaded coffee plantations, commercial shaded coffee plantations, and a cattle pasture. Copronecrophagous beetles, subfamily Scarabaeinae (Insecta: Coleoptera: Scarabaeidae), were used as the indicator group. This group has been used in previous studies and other tropical forests and has been found to be a good indicator of the effects of anthropogenic change. For each assemblage, we compared samples that were collected several years apart. Changes were found in species composition, order of abundance, and in the proportion that a given species is present in the different functional groups. The changes that occurred between samplings affected the less abundant species in the cloud forest and in the pasture. In the other vegetation types, both abundant and less abundant species were affected. Their order of abundance and proportion in the different guilds also changed. This study shows that, although landscape richness remains relatively constant, richness at the local level (alpha diversity) changes notably even over short lapses of time. This could be a characteristic of landscapes with intermediate degrees of disturbance (such as those that have been partially modified for human use), where assemblage composition is very fluid.     

Histopathological alterations, EROD activity, CYP1A protein and biliary metabolites in gilthead seabream Sparus aurata exposed to benzo(a)pyrene

This study compared for seabream, Sparus aurata exposed to benzo(a)pyrene-B(a)P-, the response of molecular cytochrome P450 1A (CYP1A) and cellular histopathology biomarkers. Male gilthead seabream, Sparus aurata specimens were exposed for 20 days via water to a series of high B(a)P concentrations. CYP1A was assessed by measuring enzymatic activity (EROD) and CYP1A protein content, and cellular responses were evaluated by routine histopathological methods. In addition, biliary metabolites were measured in order to verify that B(a)P was absorbed and metabolised. Histological lesions, both in liver and gills, increased in parallel to B(a)P concentrations, with the majority of changes representing rather non-specific alterations. Hepatic EROD and CYP1A proteins data showed a concentration-dependent induction, while in the gills, EROD activity but not CYP1A proteins showed a non-monotonous dose response, with a maximum induction level at 200 microg B(a)P.L-1 and decreasing levels thereafter. The findings provide evidence that short-term, high dose exposure of fish can result in significant uptake and metabolism of the lipophilic B(a)P, and in pronounced pathological damage of absorptive epithelia and internal organs.     

Synthesis and characterization of pyrrolidine derivatives as potent agonists of the human melanocortin-4 receptor

A series of trans-4-phenylpyrrolidine-3-carboxamides were synthesized and characterized as potent ligands of the human melanocortin-4 receptor. Interestingly, a pair of diastereoisomers 20f-1 and 20f-2 displayed potent functional agonist and antagonist activity, respectively. Thus, the 3S,4R-compound 20f-1 possessed a K(i) of 11nM and an EC(50) of 24nM, while its 3R,4S-isomer 20f-2 exhibited a K(i) of 8.6 and an IC(50) of 65nM. Both compounds were highly selective over other melanocortin receptor subtypes. The MC4R agonist 20f-1 also demonstrated efficacy in diet-induced obese rats.     

Nitric oxide production by haemocytes from Mytilus galloprovincialis shows seasonal variations

Nitric oxide (NO) has been identified as an important physiological modulator, with evidence of its role as a signalling molecule throughout the whole phylogenetic scale. In marine molluscs, it intervenes in processes related to the immune function of haemocytes. The presented results indicate that basal NO production by haemocytes of Mytilus galloprovincialis shows seasonal variations, with summer values statistically higher than those of winter. The presence of IL-2 increased NO production in winter. In summer, incubating the haemocytes with TNF-alpha for 6h slightly increased NO production. LPS, TGF-beta1 or PDGF did not induce significant effects on NO production by the haemocytes. Immunoblotting experiments detected two proteins that bind to vertebrate iNOS and eNOS antibodies, with different seasonal expression: the protein that binds to anti-iNOS antibody was expressed throughout the year, whereas the anti-eNOS antibody bound with a protein that was only detected in winter. IL-2 is suggested to start a signalling system dependent on the seasonal presence of winter protein. Such a system would activate the enzyme, thus favouring the higher NO production detected in winter.     

Implication of PKC in the seasonal variation of the immune response of the hemocytes of Mytilus galloprovincialis Lmk. and its role in interleukin-2-induced nitric oxide synthesis

The hemocytes are the cells responsible for the immune response in marine mollusks. The role of NO in processes related to the activation of the hemocytes has turned out evident over the late years. In the case of the mussel Mytilus galloprovincialis Lmk., hemocyte NO basal production varies throughout the year, showing a maximum in summer and a minimum in winter. IL-2 reverts the low winter NO basal production through a process mediated by cAMP-dependent protein kinase and by an apparent side effect of protein kinase C. The seasonal variation of NO production in the presence of the PKC inhibitor bisindolylmaleimide (BSM) allows suggesting a model in which PKC would modulate the activity of the enzymes responsible for nitric oxide production.