Assessment of histogenesis and proliferative potential in cytologic specimens of human brain tumors. Value of immunocytochemistry and nucleolar organizer regions.

The value of immunocytochemistry and nucleolar organizer regions (NORs) for the histogenetic identification and the estimation of the proliferative potential of brain tumors was assessed by the investigation of imprint smears of 51 neurosurgical tumor specimens. A panel of five monoclonal antibodies was used to cover a broad range of immunohistochemical markers. For the assessment of NORs, a silver staining technique (AgNOR) was used. NORs were enumerated and measured by means of an interactive image analysis system. The immunocytochemical results were similar for the smears and paraffin-embedded sections for 95.6% of the investigations performed and for 76.2% of the cases. Glial fibrillary acidic protein (GFAP) was positive in 9 of 17 tumors of glial origin, but was negative in 9 metastatic tumors. Vimentin was positive in 10 of 10 and fibronectin in 9 of 10 meningiomas investigated. The number of NORs increased steadily with the increasing grade of malignancy. Especially in glioblastomas, the number of NORs per cell exhibited a wide range, which might reflect the heterogeneity of these neoplasms. Metastases revealed a higher number of NORs per cell than did glioblastomas. In the cytologic differential diagnosis of these tumors, an absence of GFAP expression combined with a high NOR count is suggestive of a metastatic tumor.     

Occupancy modelling as a new approach to assess supranational trends using opportunistic data: a pilot study for the damselfly Calopteryx splendens

There is limited information available on changes in biodiversity at the European scale, because there is a lack of data from standardised monitoring for most species groups. However, a great number of observations made without a standardised field protocol is available in many countries for many species. Such opportunistic data offer an alternative source of information, but unfortunately such data suffer from non-standardised observation effort and geographical bias. Here we describe a new approach to compiling supranational trends using opportunistic data which adjusts for these two major imperfections. The non-standardised observation effort is dealt with by occupancy modelling, and the unequal geographical distribution of sites by a weighting procedure. The damselfly Calopteryx splendens was chosen as our test species. The data were collected from five countries (Ireland, Great Britain, the Netherlands, Belgium and France), covering the period 1990–2008. We used occupancy models to estimate the annual number of occupied 1 × 1 km sites per country. Occupancy models use presence-absence data, account for imperfect detection of species, and thereby correct for between-year variability in observation effort. The occupancy models were run per country in a Bayesian mode of inference using JAGS. The occupancy estimates per country were then aggregated to assess the supranational trend in the number of occupied 1 × 1 km². To adjust for the unequal geographical distribution of surveyed sites, we weighted the countries according to the number of sites surveyed and the range of the species per country. The distribution of C. splendens has increased significantly in the combined five countries. Our trial demonstrated that a supranational trend in distribution can be derived from opportunistic data, while adjusting for observation effort and geographical bias. This opens new perspectives for international monitoring of biodiversity.     

A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Overwintering locations and hosts for onion thrips (Thysanoptera: Thripidae) in the onion cropping ecosystem in New York

Identifying locations where onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae), overwinter and subsequently disperse is important for designing control strategies. In upstate New York from 2003 through 2006, potential overwintering sites in the commercial onion, Allium cepa L., cropping system were investigated early in the spring before onion seedling emergence and again late in the season after onions were harvested. Onion thrips adults were sampled directly from the soil and indirectly from the soil by using emergence cages. Sampling locations included onion field interiors and edges and areas outside of these fields, including woods. Host material sampled included onion culls; volunteer onions, which sprout from cull onions left behind after harvest; and weeds. Onion thrips adults were found in all sections of onion fields and in locations outside of onion fields, with the fewest emerging from woods. Emergence began in early May and extended into June. Peak emergence occurred during the last half of May, at which time 50-75% of the population had emerged. Adults colonized volunteer onions as early as late March and as late as mid-November. No adults were found overwintering in onion cull piles. Adults also colonized several weed species, especially pigweed, Amaranthus hybridis L., and lambsquarters, Chenopodium album L., late in the fall. Our results indicate that onion thrips adults overwinter in the soil within and near onion fields and that they probably colonize volunteer onion plants before subsequent generations infest the onion crop in the spring. Volunteer onions and weeds also provide onion thrips with a host after onions are harvested. Consequently, onion thrips management strategies should include tactics that reduce volunteer onion and weed abundance.     

On the possibility of oral treatment with protein solutions

Experiments on animals showed that native proteins may diffuse into the blood flow after oral administration of diluted protein solutions. An in vitro study led us to hypothesize that treatment with diluted solutions is accompanied by a decrease in the rate of protein proteolysis and accelerated protein diffusion through the intestinal mucosa.     

Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis

Introduction  

The vast difference in the abundance of different proteins in biological samples limits the determination of the complete proteome of a cell type, requiring fractionation of proteins and peptides before MS analysis.