Daniel P. Taylor

Quantitative method for the assignment of hinge and shear mechanism in protein domain movements

Motivation: A popular method for classification of protein domain movements apportions them into two main types: those with a ‘hinge’ mechanism and those with a ‘shear’ mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term ‘shear’ is often interpreted to mean a relative translation of the domains. Results: Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms. Availability and implementation: Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/. Contact: sjh@cmp.uea.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.

Classification of domain movements in proteins using dynamic contact graphs.

A new method for the classification of domain movements in proteins is described and applied to 1822 pairs of structures from the Protein Data Bank that represent a domain movement in two-domain proteins. The method is based on changes in contacts between residues from the two domains in moving from one conformation to the other. We argue that there are five types of elemental contact changes and that these relate to five model domain movements called: “free”, “open-closed”, “anchored”, “sliding-twist”, and “see-saw.” A directed graph is introduced called the “Dynamic Contact Graph” which represents the contact changes in a domain movement. In many cases a graph, or part of a graph, provides a clear visual metaphor for the movement it represents and is a motif that can be easily recognised. The Dynamic Contact Graphs are often comprised of disconnected subgraphs indicating independent regions which may play different roles in the domain movement. The Dynamic Contact Graph for each domain movement is decomposed into elemental Dynamic Contact Graphs, those that represent elemental contact changes, allowing us to count the number of instances of each type of elemental contact change in the domain movement. This naturally leads to sixteen classes into which the 1822 domain movements are classified.

Production of omega-3 enriched tilapia through the dietary use of algae meal or fish oil: Improved nutrient value of fillet and offal

The goal of this project was to increase the nutrient value of fillets, by-product muscle, and offal of aquacultured tilapia. A diet that includes seafood with a high omega-3 (n-3) fatty acid content, more specifically eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are known to have numerous health benefits for consumers. Improved nutrient value of the offal may also attract new market opportunities for the aquaculture industry. Tilapia were cultured on different experimental feeds that contained various levels of n-3 fatty acids from either fish oil (FO) or algae meal (AM) that were used to replace corn oil. The experimental diets included a control (corn oil 6.3%), FO1%, FO3%, FO5%, AM1.75%, AM5.26%, and AM8.77%. All diets were formulated to be isocaloric, isonitrogenous, and isolipid. Three hundred and fifty tilapia with an initial mean weight of 158±2 g were cultured in a recirculating aquaculture system (seven diets replicated at the tank level, 14 tanks, 25 fish per tank). For all of the production performance data, no differences (P>0.05) were observed between the experimental groups which included survival (overall mean ± standard error, 99.4±0.3%), growth per week (45.4±1.0 g/wk), food conversion ratio (1.32±0.03), fillet yield (44.4±0.2%), hepatosomatic index (1.61±0.02), viscerosomatic index (2.86±0.06), and mesenteric fat index (0.97±0.04). Fillet and rib meat tissues were collected at weeks four and eight, and liver and mesenteric fat tissues were collected at week eight. Fatty acids were extracted, methylated and identified with gas chromatography–mass spectrometry. All tissues had improved fatty acid profiles (higher n-3, lower n-6, n-6:n-3) with increasing levels of FO and AM in the diet. For example, the best diet for significantly (P<0.05) improving the lipid profile in tilapia fillets at week eight was diet AM8.77%. In the fillet, total n-3 was increased (control versus AM8.77%) from 151.2±19.0 to 438.7±14.2 mg per 4 ounce (113 g) serving and n-6:n-3 ratio was improved from 5.19±0.76 to 1.29±0.03.

Adsorptive performance of granular activated carbon in aquaculture and aquaria: a simplified method

ABSTRACT A principle concern for aquaculturists and aquarium hobbyists is the control and removal of dissolved organic matter. Granular activated carbon is a well-established medium for the adsorption of dissolved organic substances associated with these issues. The selection of activated carbon for aquaria and aquaculture is not well established due to innate heterogeneity of these waters. The means to completely characterize adsorption between carbon sources are generally not available to end users provided their level of expertise and/or resources at their disposal. This study introduces a relatively simple method for characterizing activated carbon quality and filter performance utilizing readily available and relatively safe indicator compounds to test adsorptive capabilities between different sources of granular activated carbon. Methylene blue and a commercial mix of humic and tannic substances were used to comparatively test adsorptive performance between two filter groups (i.e., sources of granular activated carbon) by tracking spectral absorbance with nonlinear regression statistics and validating removal trends against mature aquaculture water. Greater adsorptive capacities were consistently observed in one filter group throughout the indicator testing battery. Similar findings were observed between the two indicator tests, thereby confirming the method. This method can be adopted by commercial aquaculture operations or aquarists to assist in comparatively screening particular types, particle sizes, and sources of granular activated carbon for specific water quality and engineering requirements.