The BioGRID Interaction Database: 2011 update

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (http://www.thebiogrid.org). BioGRID currently holds 347 966 interactions (170 162 genetic, 177 804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23 000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand curation across multiple metazoan species are underway. The BioGRID houses 48 831 human protein interactions that have been curated from 10 247 publications. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.0 web interface contains new search and display features that enable rapid queries across multiple data types and sources. An automated Interaction Management System (IMS) is used to prioritize, coordinate and track curation across international sites and projects. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions

Influence of Age on Decision Making by Ovipositing Pieris rapae (Lepidoptera: Pieridae).

Due to its effect on the time available for host selection and learning, butterfly age is expected to alter the degree of host specificity and potentially niche breadth. Here, we use the small cabbage white, Pieris rapae L., to test the effect of age on ovipositional specificity and decision-making time. Specifically, we examined the ovipositional behavior of P. rapae 4, 8, and 12 days post-emergence. Females were recorded in thirty-minute trials using leaves of two hosts, mustard leaves, Brassica juncea, and collard greens, Brassica oleracea Acephala group, and the non-host common bean, Phaseolus vulgaris. Subsequently, we measured the duration of drumming events (a proxy for decision-making time) and whether the leaves were accepted or rejected as ovipositional substrates. As would be expected if prior experience influenced ovipositional behavior, we saw a reduction in the duration of drumming events as females aged. In particular, we saw a reduction in duration of drumming events when rejecting the non-host between days 4 and days 8 and 12. We also detected a decrease in drumming time between days 4 and 8 when accepting hosts, but an increase in drumming time between days 8 and 12 when accepting hosts. These results suggest both an increased ability to recognize hosts and an increase in selectivity with age

A Pediatrics Utilization Study in The Netherlands to Identify Active Pharmaceutical Ingredients Suitable for Inkjet Printing on Orodispersible Films

Background: The use of medication in pediatrics, children aged 0-5 years, was explored so as to identify active pharmaceutical ingredients (APIs) suitable for inkjet printing on a plain orodispersible film (ODF) formulation in a pharmacy. Methods: The database IADB.nl, containing pharmacy dispensing data from community pharmacies in the Netherlands, was used to explore medication use in the age group of 0-5 years old, based on the Anatomical Therapeutic Chemical classification code (ATC code). Subsequently, a stepwise approach with four exclusion steps was used to identify the drug candidates for ODF formulation development. Results: there were 612 Active Pharmaceutical Ingredients (APIs) that were dispensed to the target group, mostly antibiotics. Of the APIs, 221 were not registered for pediatrics, but were used off-label. After the exclusion steps, 34 APIs were examined regarding their suitability for inkjet printing. Almost all of the APIs were sparingly water soluble to practically insoluble. Conclusion: Pharmaceutical inkjet printing is a suitable new technique for ODF manufacturing for pediatric application, however the maximal printed dose as found in the literature remained low. From the selected candidates, only montelukast shows a sufficiently high water-solubility to prepare a water-based solution. To achieve higher drug loads per ODF is ambitious, but is theoretically possible by printing multiple layers, using highly water-soluble APIs or highly loaded suspensions

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

Summary: NAViGaTOR is a powerful graphing application for the 2D and 3D visualization of biological networks. NAViGaTOR includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs. Publication-quality images can be rendered through SVG graphics export. NAViGaTOR supports community-developed data formats (PSI-XML, BioPax and GML), is platform-independent and is extensible through a plug-in architecture

Revisiting strategies for breeding anthracnose resistance in lentil: the case with wild species

Non-Peer ReviewedBreeders at the Crop Development Centre (CDC) have up to now only used germplasm resources available in the cultivated lentil to develop new varieties with resistance to diseases. Based on recent studies, the available cultivated germplasm does not offer sufficient genetic variation for resistance to anthracnose and ascochyta diseases. Lentil crop is attacked by two major diseases (anthracnose and ascochyta) that can cause 100% loss in the worst scenarios. Since anthracnose is only a major lentil disease in North America, no work has been done to improve resistance to this disease elsewhere. Wild species of many crops are known to carry many disease resistance genes lacking in the cultivated crop. We began the search for anthracnose resistance in the six wild species of lentil (world collection), of which two can be easily crossed with the cultivated type. Two strains of anthracnose (race 1 and race 2) with varying degrees of virulence were reported. The 2002 field data suggested that some of the Lens ervoides and Lens lamottei accessions exhibited no lesions at all when exposed to the combination of the two anthracnose strains. The cultivated types that show resistance to the less virulent strain were severely affected by anthracnose. In the greenhouse study the wild species were inoculated with the two strains separately and results indicate that no accession is immune to the more virulent type. However, some of the L. ervoides and L. lamottei accessions had good resistance compared to their cultivated counterparts. As a long term strategy, the lentil breeding program at CDC, University of Saskatchewan has a goal of fully utilizing the available resistance sources. However, these two species cannot be easily crossed with the cultivated types using the conventional/manual crossing techniques. A tissue culture procedure involving embryo rescue is used to facilitate crossing. We have been able to successfully rescue some embryos from crosses with Lens ervoides. The hybrid plants produce some fertile seeds which will be evaluated for resistance to both anthracnose and ascochyta. The selected resistant lines will then be backcrossed to the adopted backgrounds in order to deploy resistance genes

Children's Medicines in Tanzania: A National Survey of Administration Practices and Preferences.

The dearth of age-appropriate formulations of many medicines for children poses a major challenge to pediatric therapeutic practice, adherence, and health care delivery worldwide. We provide information on current administration practices of pediatric medicines and describe key stakeholder preferences for new formulation characteristics. We surveyed children aged 6-12 years, parents/caregivers over age 18 with children under age 12, and healthcare workers in 10 regions of Tanzania to determine current pediatric medicine prescription and administration practices as well as preferences for new formulations. Analyses were stratified by setting, pediatric age group, parent/caregiver education, and healthcare worker cadre. Complete data were available for 206 children, 202 parents/caregivers, and 202 healthcare workers. Swallowing oral solid dosage forms whole or crushing/dissolving them and mixing with water were the two most frequently reported methods of administration. Children frequently reported disliking medication taste, and many had vomited doses. Healthcare workers reported medicine availability most significantly influences prescribing practices. Most parents/caregivers and children prefer sweet-tasting medicine. Parents/caregivers and healthcare workers prefer oral liquid dosage forms for young children, and had similar thresholds for the maximum number of oral solid dosage forms children at different ages can take. There are many impediments to acceptable and accurate administration of medicines to children. Current practices are associated with poor tolerability and the potential for under- or over-dosing. Children, parents/caregivers, and healthcare workers in Tanzania have clear preferences for tastes and formulations, which should inform the development, manufacturing, and marketing of pediatric medications for resource-limited settings

Deciphering Network Community Structure by Surprise

The analysis of complex networks permeates all sciences, from biology to sociology. A fundamental, unsolved problem is how to characterize the community structure of a network. Here, using both standard and novel benchmarks, we show that maximization of a simple global parameter, which we call Surprise (S), leads to a very efficient characterization of the community structure of complex synthetic networks. Particularly, S qualitatively outperforms the most commonly used criterion to define communities, Newman and Girvan's modularity (Q). Applying S maximization to real networks often provides natural, well-supported partitions, but also sometimes counterintuitive solutions that expose the limitations of our previous knowledge. These results indicate that it is possible to define an effective global criterion for community structure and open new routes for the understanding of complex networks.Comment: 7 pages, 5 figure

Playing hide and seek with poorly tasting paediatric medicines: do not forget the excipients

The development of paediatric medicines can be challenging since this is a diverse patient population with specific needs. For example, the toxicity of excipients may differ in children compared to adults and children have different taste preferences. Acceptable palatability of oral paediatric medicinal products is of great importance to facilitate patient adherence. This has been recognised by regulatory authorities and so is becoming a key aspect of paediatric pharmaceutical development studies. Many active pharmaceutical ingredients (APIs) have aversive taste characteristics and so it is necessary to utilise taste masking techniques to improve the palatability of paediatric oral formulations. The aim of this review is to provide an overview of different approaches to taste masking APIs in paediatric oral dosage forms, with a focus on the tolerability of excipients used. In addition, where possible, the provision of examples of some marketed products is made

High-throughput, quantitative analyses of genetic interactions in E. coli.

Large-scale genetic interaction studies provide the basis for defining gene function and pathway architecture. Recent advances in the ability to generate double mutants en masse in Saccharomyces cerevisiae have dramatically accelerated the acquisition of genetic interaction information and the biological inferences that follow. Here we describe a method based on F factor-driven conjugation, which allows for high-throughput generation of double mutants in Escherichia coli. This method, termed genetic interaction analysis technology for E. coli (GIANT-coli), permits us to systematically generate and array double-mutant cells on solid media in high-density arrays. We show that colony size provides a robust and quantitative output of cellular fitness and that GIANT-coli can recapitulate known synthetic interactions and identify previously unidentified negative (synthetic sickness or lethality) and positive (suppressive or epistatic) relationships. Finally, we describe a complementary strategy for genome-wide suppressor-mutant identification. Together, these methods permit rapid, large-scale genetic interaction studies in E. coli