Bioscience Horizons - current issue

Editorial

2009-05-19

Measuring interdisciplinary research: analysis of co-authorship for research staff at the University of York

Bellanca, L. — 2009-05-19

Collaboration allows researchers to combine the strength of different disciplines to undertake research that neither could do individually. Scientific collaboration can be examined by analysing patterns of co-authorship of papers in publication databases (e.g. Web of Science) using methods from Social Network Analysis. In this project, I describe three networks consisting of researchers in the Biology and Chemistry Departments at the University of York to investigate degree, degree distribution, key brokers and preference of researchers for collaborating within or outside their own research field. Clustering (or transitivity) was used to describe whether collaboration is more likely if two researchers have a collaborator in common. To introduce a control and realize the significance of the results produced, a network consisting of 98 researchers from the Chemistry and Biology departments was produced and compared with a distribution of 1000 ER random graphs for degree, transitivity and betweenness. We find that researchers in the Department of Biology (50 researchers) have fewer collaborations with their departmental colleagues than those in the Department of Chemistry (45 researchers): the average number of links each researcher had with others in the Biology collaboration network was 2.6, the corresponding values for Chemistry were 4.8 links per researcher. We also find that researchers within the Chemistry department were more likely than their colleagues in Biology to collaborate with another researcher if they had a collaborator in common. One aim of the study was to characterize the extent of interdisciplinary research within the Department of Biology. Staff in the Biology department were categorized into distinct research foci, indicating the discipline of the researcher. There were many links from the Bioinformatics and Mathematics, and Biophysics and Biochemistry foci, to other foci, implying that staff within these foci were interdisciplinary in their research—indicative of their role in providing techniques or tools that are applicable across discipline boundaries. This sort of analysis provides quantitative evidence to understand the social patterns of scientific collaboration and may be a useful tool in the development of strategies to promote interdisciplinary research within research institutions.

Therapeutic drug monitoring: an e-learning resource

Samani, K. — 2009-05-19

The main aim of this project was to produce an interactive e-learning resource explaining the pharmacokinetic principles related to therapeutic drug monitoring (TDM). The target audience for the resource were scientists at Manchester Royal Infirmary and the intended learning outcome for the users was to improve their understanding of the pharmacology behind the results they generate. The null hypothesis stated that the resource would not cause a significant improvement in the users' understanding of pharmacokinetics. The ADDIE Instructional Design Model was applied to the learning situation. A pre-project questionnaire allowed for a needs analysis to be conducted, determining the current level of knowledge. Design and development involved production of project plans and storyboards and the entire resource was produced using Opus Professional. The resource was distributed via compact discs, along with pre- and post-resource questionnaires to permit analysis. Knowledge was compared before and after using the resource to establish the effectiveness of the resource, and the functionality of the resource was evaluated. The needs questionnaire results outlined the existing level of knowledge as being varied and provided suggestions for possible concepts to include in the resource. A more precise and accurate definition of TDM, why it is carried out, and the pharmacokinetic parameters were apparent in the post-resource questionnaire results. Confidence in the understanding and interpretation of data produce was not significantly improved (Wilcoxon matched pairs signed ranks test, n = 14, P = 0.13), while confidence in the understanding of pharmacokinetic parameters was significantly improved (Wilcoxon matched pairs signed ranks test, n = 16, P = 0.01). About 81% of the audience found the resource very helpful to understanding TDM and all of the users found it either easy to use or very easy to use. The post-resource results showed that confidence in the understanding of pharmacokinetics was improved, indicating that the learning outcomes of the user were achieved thus allowing the null hypothesis to be rejected. However, confidence in understanding the data generated was not improved, suggesting a possible aspect to be developed if the project was to be repeated. Functionality of the resource was successful as users found the resource easy to use and navigate.

The effects of riparian habitat quality and biological water quality on the European Otter (Lutra lutra) in Devon

Bedford, S. J. — 2009-05-19

After a period of decline, European Otter (Lutra lutra) populations are showing signs of recovery throughout the UK. Populations in Devon are thought to be almost fully recovered, although exact numbers are unknown; however, there are still rivers within Devon that do not appear to support Otter populations. The aim of this research was to determine the relationship between environmental condition and the presence of Otters by comparing the quality of riparian habitat of rivers with and without evidence of Otters. The research was undertaken in four rivers in Devon, the Rivers Culm, Ken, Coly and Otter: the first two being river stretches with no documented evidence of Otter populations, and the latter two having documented evidence of Otter populations. Along each of the rivers, 10 sections of 50 m were sampled. In each section, the riparian habitat quality was recorded using the Qualitat del Bosc de Riberia index. The biological water quality was determined by calculating Biological Monitoring Water Party scores, and water chemical concentrations were obtained from Environment Agency data. The riparian habitat quality and biological water quality were found to be of significantly lower quality in the river stretches that did not have evidence of Otter populations when compared with those with Otter populations. The chemical water quality was correlated to biological water quality: the quality being worse in the rivers without evidence of Otter populations. The results of this research suggest that rivers with no evidence of Otter populations are generally of worse riparian quality than those supporting Otter populations.

Optimization of MALDI tissue imaging and correlation with immunohistochemistry in rat kidney sections

Gregson, C. — 2009-05-19

Cancer is responsible for approximately 6.7 million deaths and 10.9 million newly diagnosed cases worldwide per year. Currently, the definitive diagnosis of a tissue or cell sample is determined by molecular pathology and histochemical techniques, which assess tumour type, grade and stage. This information also allows for the diagnosis, prognosis and available treatment options to be established. In addition, immunohistochemistry (IHC) in combination with histochemistry is used to determine the surgical margin status of tumours, which can be correlated to the likelihood of recurrence. Matrix-assisted laser desorption/ionization (MALDI) imaging is a mass spectrometry profiling technique, which can be used to simultaneously identify multiple species within a tissue section. The array format of the acquisition allows for the creation of an image that is viewed in a similar way to an IHC section. MALDI imaging could potentially provide an alternative diagnostic assay that could be used to provide cancer prognosis. To assess the suitability of MALDI imaging for this application, sample preparation and MALDI imaging methodology were developed using _2u-globulin as an example protein. This protein is known to be preferably expressed in the kidneys of male rats allowing a proof-of-principle study to be performed comparing the expression levels and localization between male and female rat kidney sections. The expression of _2u-globulin was localized to the cortex region of the kidney, with the levels of _2u-globulin shown to be significantly higher in the male than the female kidney sections. These findings were validated by comparison with IHC data. The proof-of-principle study therefore demonstrated that MALDI imaging could be a potential alternative to current molecular pathology and histochemical techniques for the determination of tumour type, grade and stage as well as the determination of surgical margin status.

Patterns of genetic diversity in populations of two bat species (Sturnira ludovici and Artibeus toltecus) in Cusuco National Park, Honduras

Asher, C. — 2009-05-19

Habitat loss, disturbance and fragmentation are thought to be major threats to many species, particularly those in habitats that are already rare. In this study, we examined whether habitat disturbance, primarily due to the cultivation of coffee, has had a major impact on populations of two species of bats in a Honduran cloud forest, using genetic diversity as a measure of population health. Bats were selected as the study species because they play a major role in seed dispersal within the tropics. I compared the genetic diversity of two frugivorous bat species, Sturnira ludovici and Artibeus toltecus, between two localities within Cusuco National Park; a buffer zone in which some human activity, including coffee plantations, is allowed, and the core zone in which no disturbance is permitted. Genetic diversity was assessed using intersimple sequence repeats, a technique similar to random amplification of polymorphic DNA (RAPD). I also measured various habitat variables including foliage height diversity (FHD), fruit availability, canopy cover, aspect of slope and angle of slope in the two sites. I found that FHD and fruit availability differed significantly between the two localities, with the buffer zone having higher values for both. Despite these differences in habitat, we found no significant differences in the level of genetic diversity between the two locations for either bat species. This may be because effective population sizes of the bats do not differ significantly between the sites, because of a lag between disturbance and population decline or because migration is sufficiently frequent to homogenize allele frequencies between the localities.

Study of small mammal populations within two Barn owl corridors at Folly Farm

Keene, A. — 2009-05-19

This study examines small mammal populations present within Barn owl corridors on Folly Farm, an Avon Wildlife Trust Reserve located near the village of Bishop Sutton in Bath and North East Somerset. Two corridors were chosen, the primary difference between the two sites being only one has undergone management (grazing). The focus of this study was the Microtus agrestis (Short-tailed field vole) population, the most frequently taken prey item by Barn owls. Apodemus sylvaticus (Wood mice) and Sorex araneus (Common shrew) populations are also discussed as they are frequently taken. Using Longworth live traps, 600 trap-nights data were collected from three sessions in November 2006, February and March 2007. Although M. agrestis was the most abundant species in both corridors, they were more prevalent in the un-grazed corridor (comprising 19 of the 31 individuals). In the corridor that had undergone management, fewer M. agrestis were captured (eight), although a higher species diversity and richness was recorded. Unusually for a grassland habitat, there were nearly as many A. sylvaticus as there were M. agrestis (seven compared with eight) in the grazed corridor. Some small mammal species not usually found in grassland habitats were captured; explanations for these seemingly anomalous results are discussed. Differences in population characteristics between the two corridors are discussed including: sex ratio, weights, seasonal variation and age structure. Pellet analysis from the nearby pair of Barn owls showed that they were preferentially hunting M. agrestis; the pellet data largely mirrored findings of the trapping data.

Pre- and post-copulatory mate choice in Platygryllus primiformis: cryptic female choice and sexual conflict

Parker, D. — 2009-05-19

The effect of sexual conflict upon mating systems is a controversial topic. The aim of this study was to determine whether post-copulatory choice by females (spermatophore removal) reinforces pre-copulatory choice with respect to male body size and fighting ability, and whether such post-copulatory female choice is influenced by post-copulatory mate guarding by males using Platygryllus primiformis (Orthoptera: Gryllidae; Gryllinae). A no-choice test was used to determine the attractiveness of males and spermatophore attachment time was recorded as a measure of cryptic female choice. Females maintained a pre-copulatory mate choice for large males that were more successful in fighting, shown by a shorter latency to copulation. Larger, males that were more successful in fighting were also preferred by post-copulatory cryptic female choice, shown by a longer spermatophore attachment time, reinforcing pre-copulatory mate choice. Males attempted to counter this selection by guarding females, which increased their spermatophore attachment time. Interestingly, spermatophore attachment time increased similarly for all sizes of male as a result of mate guarding, meaning that females maintained their original choice.

The anti-proliferative effect of different tomato varieties on the human colon adenocarcinoma cells

Saunders, C. — 2009-05-19

Epidemiological evidence suggests that diets rich in fruit and vegetables protect against the development of colon cancer, primarily due to their high levels of polyphenols, in particular a group known as flavonoids. Tomatoes contain significant amounts of the glycosides of the flavonoids quercetin and naringenin. Both quercetin and naringenin have been shown to exert anti-proliferative effects on colon cancer cells, although the effects of whole tomato polyphenol extracts are unclear. The aim of this study was to determine the effect of three tomato varieties, with differing levels of flavonoids and total phenolics, on the proliferation of human colon adenocarcinoma cells. We show that all three varieties were able to significantly inhibit the growth of colon cancer cells, although this activity was found not to be linked to the levels of the flavonoids rutin and naringenin in the tomatoes, but rather to their total phenolic content. We show that the mechanism of growth inhibition was linked to the effects of tomato phenolics on the cell cycle, in that exposure of cells to the tomato extract induced a reduction in the percentage of cells in the S-phase, i.e. those actively synthesizing DNA. These data indicate that tomatoes may help to prevent colon cancer but that their flavonoid content does not appear to determine the magnitude of their biological effect.

Human attitudes towards animals in relation to species similarity to humans: a multivariate approach

Batt, S. — 2009-05-19

Human attitudes towards animals are becoming of increasing importance in the areas of conservation and welfare. It has long been taken for granted that our attitudes are influenced by the degree of biological or behavioural similarity between a given species and ourselves. This research investigates whether there is a link between bio-behavioural similarity to humans and preferences for animal species that are obtained when subjects view a set of 40 pictures illustrating a wide diversity of animals. Extensive data regarding the natural history, behaviour and physiology of 40 species of animals from a wide range of taxonomic groups were collected. Bio-behavioural similarity between animal species and humans was formed on the basis of multidimensional analyses, including factors such as size, weight and lifespan among the physical attributes, and reproductive strategy, parental investment and social organization among the behavioural traits. It was found that a clear relationship between similarity and preference exists, suggesting that humans are predisposed to liking species on the basis of shared bio-behavioural traits. These results imply that efforts made in the conservation and welfare of species may be biased more by anthropocentric views than has been previously recognized. It may be important for a new approach to be taken when it comes to determining the targets of conservation.

Characterizing chloroplast sensor kinase

Ibrahim, I. M. — 2009-05-19

In higher plants and green algae, photosynthesis takes place within specialized sub-cellular organelles called chloroplasts. Chloroplasts were once prokaryotes and evolved by endosymbiosis from cyanobacteria. They contain a semi-autonomous genetic system that encodes for core proteins of photosynthetic reaction centres in the energy-transducing membrane known as the chloroplast thylakoid. The photosynthetic apparatus in the thylakoid membrane makes use of excitation energy from sunlight to remove four electrons and protons from two water molecules. The electrons transfer them to the electron acceptor ferredoxin and NADP⁺, respectively. In this system, plastoquinone acts as a mobile electron and proton carrier between Photosystem I and Photosystem II in reduction–oxidation or ‘redox’ reactions. A balanced redox state in the chloroplast is important for efficient energy conversion. However, the slightest error could lead to photo-inactivation as well as DNA mutation. Therefore, photosynthetic enzymes that are involved in photosynthesis are tightly regulated. In this study we analyse the mechanism of redox regulation involved in chloroplast gene expression that requires chloroplast sensor kinase (CSK). CSK is a bacterial-like histidine kinase that functions as a two-component system. Such simple but effective signalling transduction is abundant in prokaryotes, but found less widely in eukaryotic cells. CSK is encoded by the nuclear genomes of all higher plants examined, and the CSK proteins are targeted to chloroplasts where they function as a redox sensor. Through the cloning process, the result expressed the full-length CSK and the putative sensor domain (GAF domain) into a pGEX-6P-2 plasmid containing a GST tag. The construction was over-expressed into Escherichia coli cells. From bioinformatics study, it was found that in higher plants CSK is a modified histidine kinase, whereas in diatoms and red algae it is a typical histidine kinase.

Can ESR be used to assess the levels of oxidative stress in fat-loaded human hepatocytes and hepatic stellate cells?

Wetherill, L. F. — 2009-05-19

Non-alcoholic fatty liver disease (NAFLD) is a growing clinical problem, which manifests itself particularly in obese subjects who may have the metabolic syndrome. A two-hit hypothesis for the pathogenesis of the disease has been proposed. The first hit is the development of insulin resistance leading to fat accumulation specifically in the liver. The second hit involves oxidative damage to the liver when intracellular triglyceride is metabolized by beta-oxidation in the mitochondria to produce harmful reactive oxygen species (ROS) and their hydroperoxide by-products. An in vitro model for NAFLD along with a method to detect the levels of oxidative stress would be useful for testing this hypothesis. Such a model would also allow investigation of the ability of antioxidants such as selenium to prevent oxidative damage. This study aimed to develop a method for assessing the levels of oxidative stress in cultured fat-loaded human hepatocytes (C3A cells) and hepatic stellate cells (LX-2 cells) using electron spin resonance with the spin trap 1-hydroxy-2,2,6,6-tetramethyl-4-oxopiperidine (TEMPONE-H). Cells were fat-loaded with either LPON (lactate, pyruvate, octanoate and NH₄⁺) or oleate. Initial experiments showed that the culture media alone generated free radicals but this was minimal when Dulbecco's phosphate-buffered saline was used as the TEMPONE-H carrier. It proved difficult to detect the free radical production by cells cultured in the basal state; however, when marked oxidative stress was induced in the cells by adding tertiary butyl hydroperoxide (t-BuOOH), free radical production by cells could be identified. Pre-treating cells with selenium, to induce the synthesis of selenoenzymes with antioxidant action, protected cells from the harmful effects of t-BuOOH. This supported selenium's role as an antioxidant, which may have the potential to prevent the onset of non-alcoholic steato-hepatitis. The human vascular endothelial cell line EAhy926 also accumulates lipid as triglyceride when pre-treated with oleate but not with LPON. This suggests that the use of LPON rather than oleate may be a more appropriate model of NAFLD.

Differential localization of two plant homologues of Rab5 GTPases in the secretory pathway

Lee, H. — 2009-05-19

Rab5 GTPases are key regulators of vesicular transport. Known plant Rab5 homologues ARA6 and RHA1 have been assigned to the endocytic and/or biosynthetic vesicular trafficking pathway, but conflicting reports in the literature justify further work on these two GTPases. In this project, binary vectors for Agrobacterium-mediated plant transformation were constructed to drive expression in tobacco leaf epidermis of GTP-trapped mutants of ARA6-green fluorescent protein (GFP) and Venus-RHA1. Confocal laser scanning microscopy revealed key differences in the subcellular localization of the two fluorescently tagged GTPase mutants. When present in the GTP-locked configuration ARA6-GFP is primarily found associated with the tonoplast, whereas Venus-RHA1 is significantly cytosolic. Co-expression of the two fluorescently tagged mutant GTPases with the Golgi markers ST-YFP and ST-CFP, respectively, suggest that neither ARA6 nor RHA1 mutants are mis-targeted to the Golgi apparatus and moreover, they do not show any significant colocalization with each other. The results are consistent with the notion that they differ in their roles within the endocytic and biosynthetic vesicular pathway. A future focus to continue this project would be to use GFP-tagged ARA7, the third plant Rab5 homologue, to verify if the high sequence homology between RHA1 and ARA7 warrants overlapping redundant functions or not.

Viral evasion of interferon stimulated genes

Short, J. A.L. — 2009-05-19

Viruses and their hosts since the dawn of time have been battling for supremacy. In recent years, the ‘Interferon Gateway’ encompassing interferon-alpha and -beta (IFN-/β) expression, signalling and antiviral responses, has been uncovered. IFN-/β are cytokines that co-ordinate the innate and adaptive immune responses to eliminate virus infections from the host. Interferon Stimulated Gene (ISG) products, such as protein kinase R, can prevent the translation of viral and cellular mRNAs to limit viral replication and can also initiate apoptosis if the cell is overwhelmed. In order to replicate, viruses have evolved viral evasion proteins that are able to target all aspects of the host response through a variety of sophisticated mechanisms. Viral evasion proteins can encode cellular domains to interact directly with ISGs and neutralize their function, hijack cellular pathways or degrade antiviral components. The high mutation rates associated with viral replication ensure that viruses will continue to adapt to our defences, but equally the viral evasion proteins are novel drug targets for eliminating or managing virus infections.