Differential expression analysis for sequence count data

High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.     

Chromogranin A and the Tumor Microenvironment

Chromogranin A (CgA) is an acidic glycoprotein belonging to a family of regulated secretory proteins stored in the dense core granules of the adrenal medulla and of many other neuroendocrine cells and neurons. This protein is frequently used as a diagnostic and prognostic serum marker for a range of neuroendocrine tumors. Circulating CgA is also increased in patients with other diseases, including subpopulations of patients with non-neuroendocrine tumors, with important prognostic implications. A growing body of evidence suggests that CgA is more than a diagnostic/prognostic marker for cancer patients. Indeed, results of in vitro experiments and in vivo studies in animal models suggest that this protein and its fragments can affect several elements of the tumor microenvironment, including fibroblasts and endothelial cells. In this article, recent findings implicating CgA as a modulator of the tumor microenvironment and suggesting that abnormal secretion of CgA could play important roles in tumor progression and response to therapy in cancer patients are reviewed and discussed.     

Comparing movement of four butterfly species in experimental grassland strips

In contrast to many studies on the habitat quality of road verges for butterflies in relation to management regimes, little is known about whether road verges also function as corridors linking fragmented grassland habitats. We experimentally compared movements of four model species, two small blues and two medium browns, with one habitat specialist and one habitat generalist in each size and phylogenetic category. A total of 425 individual butterflies were caught and translocated to an experimental arena with three 2 × 30 m grassland strips that approximated road verges; one with adult feeding resources, one sheltered from the wind, and one without food and shelter. Movements in grassland strips were compared to movements in continuous grassland habitat. Results indicated that (1) individuals did not use the low-quality strip, (2) only specialists used strips but not in the same way according to their size and phylogenic category, and (3) strip use could not be predicted from habitat selection. This finding supports the idea that corridors of intermediate quality are the most efficient to promote dispersal rates in fragmented landscapes. Road verges cover 250,000 ha in Sweden, which is nearly the total amount of seminatural grasslands. Our results suggest that, to benefit butterfly dispersal among grassland patches, road verges should be managed to create a more favourable microclimate (e.g. sheltered from wind, high temperatures).     

Analysis of rhamnolipid biosurfactants by methylene blue complexation

Rhamnolipids, produced by Pseudomonas aeruginosa, represent an important group of biosurfactants having various industrial, environmental, and medical applications. Current methods for rhamnolipid quantification involve the use of strong hazardous acids/chemicals, indirect measurement of the concentration of sugar moiety, or require the availability of expensive equipment (HPLC-MS). A safer, easier method that measures the whole rhamnolipid molecules would significantly enhance strain selection, metabolic engineering, and process development for economical rhamnolipid production. A semi-quantitative method was reported earlier to differentiate between the rhamnolipid-producing and non-producing strains using agar plates containing methylene blue and cetyl trimethylammonium bromide (CTAB). In this study, a rapid and simple method for rhamnolipid analysis was developed by systematically investigating the complexation of rhamnolipids and methylene blue, with and without the presence of CTAB. The method relies on measuring the absorbance (at 638 nm) of the rhamnolipid−methylene blue complex that partitions into the chloroform phase. With P. aeruginosa fermentation samples, the applicability of this method was verified by comparison of the analysis results with those obtained from the commonly used anthrone reaction technique.     

A computational algorithm to simulate disorganization of collagen network in injured articular cartilage

Cartilage defects are a known risk factor for osteoarthritis. Estimation of structural changes in these defects could help us to identify high risk defects and thus to identify patients that are susceptible for the onset and progression of osteoarthritis. Here, we present an algorithm combined with computational modeling to simulate the disorganization of collagen fibril network in injured cartilage. Several potential triggers for collagen disorganization were tested in the algorithm following the assumption that disorganization is dependent on the mechanical stimulus of the tissue. We found that tensile tissue stimulus alone was unable to preserve collagen architecture in intact cartilage as collagen network reoriented throughout the cartilage thickness. However, when collagen reorientation was based on both tensile tissue stimulus and tensile collagen fibril strains or stresses, the collagen network architecture was preserved in intact cartilage. Using the same approach, substantial collagen reorientation was predicted locally near the cartilage defect and particularly at the cartilage–bone interface. The developed algorithm was able to predict similar structural findings reported in the literature that are associated with experimentally observed remodeling in articular cartilage. The proposed algorithm, if further validated, could help to predict structural changes in articular cartilage following post-traumatic injury potentially advancing to impaired cartilage function.     

Structural analysis of <Emphasis Type="Italic">N</Emphasis>-/<Emphasis Type="Italic">O</Emphasis>-glycans assembled on proteins in yeasts

Protein glycosylation, the most universal and diverse post-translational modification, can affect protein secretion, stability, and immunogenicity. The structures of glycans attached to proteins are quite diverse among different organisms and even within yeast species. In yeast, protein glycosylation plays key roles in the quality control of secretory proteins, and particularly in maintaining cell wall integrity. Moreover, in pathogenic yeasts, glycans assembled on cell-surface glycoproteins can mediate their interactions with host cells. Thus, a comprehensive understanding of protein glycosylation in various yeast species and defining glycan structure characteristics can provide useful information for their biotechnological and clinical implications. Yeast-specific glycans are a target for glyco-engineering; implementing human-type glycosylation pathways in yeast can aid the production of recombinant glycoproteins with therapeutic potential. The virulenceassociated glycans of pathogenic yeasts could be exploited as novel targets for antifungal agents. Nowadays, several glycomics techniques facilitate the generation of species-and strain-specific glycome profiles and the delineation of modified glycan structures in mutant and engineered yeast cells. Here, we present the protocols employed in our laboratory to investigate the N-and O-glycan chains released from purified glycoproteins or cell wall mannoproteins in several yeast species.     

Residents’ support for wolf and bear conservation: the moderating influence of knowledge

This article examines the combined influence of cognitions (i.e., impact beliefs) and affect (i.e., feelings) on normative beliefs (i.e., support for management options) about wolves and brown bears. Data were obtained from stratified random face-to-face interviews (n = 1,611). The survey was conducted in the Abruzzo Lazio and Molise National Park (central Italy), where people have a long history of coexistence with large carnivores. Knowledge was hypothesized to moderate the relationships of beliefs and feelings on support for management actions. Path analyses supported the role of affect in mediating perceived impact beliefs and support for the protection of large carnivores. Knowledge moderated these relationships in the case of wolves but not brown bears. Residents of the national park had more knowledge about bears than wolves, which might partly explain both the stronger effect that knowledge had on the affective component and its lack of a moderating effect on the bear model. Overall, our findings show the positive attitude of residents toward large carnivores and support the idea of affect being more important than cognition in predicting normative beliefs.     

Abnormal Pelage Color in an Isolated Population of <Emphasis Type="Italic">Alouatta guariba clamitans</Emphasis> Cabrera, 1940 in South Brazil

We located 4 brown howlers (1 adult male, 2 adult females, and 1 juvenile male) showing abnormally lighter pelage in 3 social groups comprising 5, 6, and 9 individuals in a 20 ha-forest fragment in the State of Rio Grande do Sul, Brazil. Two additional groups composed only of normally colored individuals also live in the fragment, which is isolated from nearby fragments by 267–1009 m. They were the only brown howlers with abnormal pelage color out of a total of 386 individuals belonging to 67 groups in 21 fragments in the 5876-ha study area. The isolation of the forest fragment, its high howler density (2.2 individuals⁄ha), and large group size (8.8 ± 2.4 individuals) may decrease the likelihood of successful immigration into the population, leading to an increased probability of inbreeding that may facilitate the expression of rare alleles.