Towards a lightweight generic computational grid framework for biological research

Background: An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology. Results: In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: http://igrid-ext.cryst.bbk.ac.uk/portal_guide/. Conclusion: This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project

Expanding the librarian role: integration into the faculty narrative

Current academic expectations for evaluation, promotion, and even tenure, have created an environment that places more emphasis on the ability of faculty to demonstrate their impacts on a scholarly level. Although many faculty would agree on specific indicators of impact such as publications and citations, these two gauges may not necessarily be exhaustive, and the increasing multitude of tools potentially used to locate and identify them may be unknown to faculty. this paper will provide information on the needs of academic faculty in reporting the scope and breadth of their scholarly activities, and how leveraging the knowledge, practices, and skill-sets of librarians helps to achieve the desired outcomes

Enzyme hydrolysis of cassava peels : treatment by amylolytic and cellulolytic enzymes

Cassava peels provide a cheap non-food biomass waste that can be hydrolyzed to simple sugars as a useful feedstock. Unlike most crop wastes, they have high starch content as well as lignocellulose. In this study, an enzymatic treatment of cassava peels by various concentrations of amylase and glucoamylase is considered. Steam explosion pre-treatments reduced rate and yield of hydrolysis. Milled peels suspended at 10% w/v yielded a maximum reducing sugar of 0.41 g (as glucose) per gram of peels. HPLC analysis showed that levels of soluble oligosaccharides remained low throughout. A pretreatment with amylase at 95 °C slightly increased rates although final yield was the same. Additional treatment with cellulolytic enzymes increases the total hydrolysis yield to 0.61 g (as glucose) per gram of peels representing 91% of the carbohydrate in cassava peels

Brucella 'HOOF-Prints': strain typing by multi-locus analysis of variable number tandem repeats (VNTRs)

BACKGROUND: Currently, there are very few tools available for subtyping Brucella isolates for epidemiological trace-back. Subtyping is difficult because of the genetic homogeneity within the genus. Sequencing of the genomes from three Brucella species has facilitated the search for DNA sequence variability. Recently, hypervariability among short tandem repeat sequences has been exploited for strain-typing of several bacterial pathogens. RESULTS: An eight-base pair tandem repeat sequence was discovered in nine genomic loci of the B. abortus genome. Eight loci were hypervariable among the three Brucella species. A PCR-based method was developed to identify the number of repeat units (alleles) at each locus, generating strain-specific fingerprints. None of the loci exhibited species- or biovar-specific alleles. Sometimes, a species or biovar contained a specific allele at one or more loci, but the allele also occurred in other species or biovars. The technique successfully differentiated the type strains for all Brucella species and biovars, among unrelated B. abortus biovar 1 field isolates in cattle, and among B. abortus strains isolated from bison and elk. Isolates from the same herd or from short-term in vitro passage exhibited little or no variability in fingerprint pattern. Sometimes, isolates from an animal would have multiple alleles at a locus, possibly from mixed infections in enzootic areas, residual disease from incomplete depopulation of an infected herd or molecular evolution within the strain. Therefore, a mixed population or a pool of colonies from each animal and/or tissue was tested. CONCLUSION: This paper describes a new method for fingerprinting Brucella isolates based on multi-locus characterization of a variable number, eight-base pair, tandem repeat. We have named this technique "HOOF-Prints" for Hypervariable Octameric Oligonucleotide Finger-Prints. The technique is highly discriminatory among Brucella species, among previously characterized Brucella strains, and among unrelated field isolates that could not be differentiated by classical methods. The method is rapid and the results are reproducible. HOOF-Printing will be most useful as a follow-up test after identification by established methods since we did not find species-specific or biovar-specific alleles. Nonetheless, this technology provides a significant advancement in brucellosis epidemiology, and consequently, will help to eliminate this disease worldwide

Development of a Value-Added Database of Evaluated Systematic Reviews in Veterinary Medicine: DVM Evidence

Objectives: This presentation will describe the development of the Database of Veterinary Medicine Evidence (DVM Evidence). The database was created by collecting, annotating, and evaluating systematic reviews and meta-analyses of relevance to veterinary medicine. Methods: The process includes four steps, similar to conducting a systematic review: identification, selection, appraisal, and data abstraction. Identification includes searching bibliographic databases (MEDLINE, Cab Abstracts, and more), grey literature, and expert selected list of conference proceedings and journal titles. The selection and appraisal process was completed independently by 2 team members, with disagreements settled by consensus. The appraisal process utilized AMSTAR and PRISMA. The data abstraction form includes citation, review question, inclusion criteria, topic, resources searched, and list of included primary studies. The database will be open access and browsable by species, specialty area, and type of study as well as searchable by keywords, author(s), journal titles, and year. Collaboration will be sought with librarians, researchers, and veterinarians to add in various perspectives. Results: A pilot group of 20 studies was selected by the team’s systematic review expert based on criteria designed to facilitate training team members in appraisal, coding, and testing the coding form. The coding form which incorporates AMSTAR, PRISMA, and custom questions, was developed in Qualtrics, a subscription based survey tool. Although initially the survey format of Qualtrics had some promise as a tool for the coding form, several issues were found during the pilot phase. The team decided to build a custom form that provides more flexibility with importing and exporting data to and from the database, and more control in the desired outcome of the resource. The team chose MySQL for the database management system, and PHP as the scripting language, because these software are supported by the library IT department, powerful and flexible enough to accomplish the tasks, and common enough for others to adapt them as the database evolves and personnel change occurs. Graduate students, selected for their expertise with MySQL and PHP, created the database and public interfaces with design input from team members. During each step of the process, the team considered needs of potential external evaluators. Conclusions: Developing a systematic review database of this complexity takes a team with a variety of skills, strategic planning, and frequent checkpoints along the way. The next step will focus on the usability of the custom made form and the search interface with external evaluators

Kinetics of enzyme-catalysed de-symmetrisation of prochiral substrates : product enantiomeric excess is not always constant

The kinetics of enzymatic desymmetrisation were analysed for the most common kinetic mechanisms: ternary complex ordered (prochiral ketone reduction); ping-pong second (ketone amination, diol esterification, desymmetrisation in the second half reaction); ping-pong first (diol ester hydrolysis) and ping-pong both (prochiral diacids). For plausible values of enzyme kinetic parameters, the product enantiomeric excess (ee) can decline substantially as the reaction proceeds to high conversion. For example, an ee of 0.95 at the start of the reaction can decline to less than 0.5 at 95% of equilibrium conversion, but for different enzyme properties it will remain almost unchanged. For most mechanisms a single function of multiple enzyme rate constants (which can be termed ee decline parameter, eeDP) accounts for the major effect on the tendency for the ee to decline. For some mechanisms, the concentrations or ratios of the starting materials have an important influence on the fall in ee. For the application of enzymatic desymmetrisation it is important to study if and how the product ee declines at high conversion

Thermodynamic favorability of end products of anaerobic glucose metabolism

The eQuilibrator component contribution method allows calculation of the overall Gibbs energy changes for conversion of glucose to a wide range of final products in the absence of other oxidants. Values are presented for all possible combinations of products with up to three carbons and selected others. The most negative Gibbs energy change is for the formation of graphite and water (-499 kJ mol-1) followed by CH4 and CO2 (-430 kJ mol-1), the observed final products of anaerobic digestion. Other favored products (with various combinations having Gibbs energy changes between-300 and-367 kJ mol-1) are short-chain alkanes, fatty acids, dicarboxylic acids, and even hexane and benzene. The most familiar products, lactate and ethanol + CO2, are less favored (Gibbs energy changes of-206 and-265 kJ mol-1 respectively). The values presented offer an interesting perspective on observed metabolism and its evolutionary origins as well as on cells engineered for biotechnological purposes

Extensive counter-ion interactions seen at the surface of subtilisin in an aqueous medium

The extent of protein and counter-ion interactions in solution is still far from being fully described and understood. In low dielectric media there is documented evidence that counter-ions do bind and affect enzymatic activity. However, published crystal structures of macromolecules of biological interest in aqueous solution often do not report the presence of any counter-ions on the surface. The extent of counter-ion interactions within subtilisin in an aqueous medium has been investigated crystallographically using CsCl soak and X-ray wavelength optimised anomalous diffraction at the Cs K-edge. Ten Cs+, as well as six Cl- sites, have been clearly identified, revealing that in aqueous salt solutions ions can bind at defined points around the protein surface. The counter-ions do not generally interact with formal charges on the protein; formally neutral oxygens, mostly backbone carbonyls, mostly coordinate the Cs+ ions. The Cl- ion sites are also found likely to be near positive charges on the protein surface. The presence of counter-ions substantially changes the protein surface electrical charge. The surface charge distribution on a protein is commonly discussed in relation to enzyme function. The correct identification of counter-ions associated with a protein surface is necessary for a proper understanding of an enzyme's function

Estimation of flattening coefficient for absorption and circular dichroism using simulation

The absorbance and circular dichroism (CD) of suspensions is lower than if the same amount of chromophore were uniformly distributed throughout the medium. Several mathematical treatments of this absorption flattening phenomenon have been presented using various assumptions and approximations. This article demonstrates an alternative simulation approach that allows relaxation of assumptions. On current desktop computers, the algorithm runs quickly with enough particles and light paths considered to get answers that are usually accurate to better than 3%. Results from the simulation agree with the most popular analytical model for 0.01 volume fraction of particles, showing that the extent of flattening depends mainly on the absorbance through a particle diameter. Unlike previous models, the simulation can show that flattening is significantly lower when volume fraction increases to 0.1 but is higher when the particles have a size distribution. The simulation can predict the slope of the nearly linear relationship between flattening of CD and the absorbance of the suspension. This provides a method to correct experimental CD data where volume fraction and particle size are known