Protein secondary structure: Entropy, correlations and prediction

Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities of primary structure and secondary structure sequences, and the local inter-sequence mutual information density. We find that the important inter-sequence interactions are short ranged, that correlations between neighboring amino acids are essentially uninformative, and that only 1/4 of the total information needed to determine the secondary structure is available from local inter-sequence correlations. Since the remaining information must come from non-local interactions, this observation supports the view that the majority of most proteins fold via a cooperative process where secondary and tertiary structure form concurrently. To provide a more direct comparison to existing secondary structure prediction methods, we construct a simple hidden Markov model (HMM) of the sequences. This HMM achieves a prediction accuracy comparable to other single sequence secondary structure prediction algorithms, and can extract almost all of the inter-sequence mutual information. This suggests that these algorithms are almost optimal, and that we should not expect a dramatic improvement in prediction accuracy. However, local correlations between secondary and primary structure are probably of under-appreciated importance in many tertiary structure prediction methods, such as threading.Comment: 8 pages, 5 figure

Detection of benzimidazole carbamates and amino metabolites in liver by surface plasmon resonance-biosensor

This research was funded by the Irish Department of Agriculture, Fisheries and Food under the Food Institutional Research Measure as part of the National Development Plan (Project 05/R&D/TN/355)peer-reviewedTwo surface plasmon resonance (SPR) biosensor screening assays were developed and validated to detect 11 benzimidazole carbamate (BZT) and four amino-benzimidazole veterinary drug residues in liver tissue. The assays used polyclonal antibodies, raised in sheep, to detect BZTs and amino-benzimidazoles. A modified Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) extraction method was developed to isolate benzimidazole carbamate residues. Liver samples were extracted using an acetonitrile extraction method. BZTs were purified by dispersive solid phase extraction (d-SPE) using C18 sorbent. Residues of amino-benzimidazoles were effectively cleaned-up using a simple cyclohexane defatting step. The assays were validated in accordance with the performance criteria described in 2002/657/EC. The BZT assay limit of detection was calculated to be 32 μg kg−1, the detection capability (CCβ) was determined to be 50 μg kg−1 and the mean recovery of analytes was in the range 77–132%. The amino-benzimidazole assay limit of detection was determined to be 41 μg kg−1, the CCβ was determined to be 75 μg kg−1 and analyte recovery was in the range 103–116%. Biosensor assay performance was tested by analysing liver tissue from animals treated with benzimidazole drugs and comparing the results with an ultra high performance liquid chromatography tandem mass spectrometry (UHPLC–MS/MS) confirmatory method. All non-compliant samples were identified using the biosensor assays.Department of Agriculture, Food and the Marin

Computer-Based Instruction and Cognitive Load

Following cognitive load theory, we used a computer-based software training paradigm to determining the optimal number of steps or information chunks to present before practice opportunities. Results demonstrating that the size of information chunks presented and the type of practice used individually influenced participants\u27 ability to effectively learn via computer-based instruction. These findings contribute to the literature by showing the importance of practice and optimal segment sizes for learning via a computer

Frequency and surface dependence of the mechanical loss in fused silica

We have compiled measurements of the mechanical loss in fused silica from samples spanning a wide range of geometries and resonant frequency in order to model the known variation of the loss with frequency and surface-to-volume ratio. This improved understanding of the mechanical loss has contributed significantly to the design of advanced interferometric gravitational wave detectors, which require ultra-low loss materials for their test mass mirrors.Comment: 5 pages, 3 figure but 5 figure file

Examining the Effects of Gender and Presentation Mode on Learning from a Multimedia Presentation

  Visual presentation modes in multimedia learning include pictures, video, and animations. Research also reveals cognitive differences between males and females (Halpern, 2004). Which one of the presentation modes is more effective? Can one of these presentation modes be more effective for a specific gender? This study aimed to investigate the role of gender and presentation mode in multimedia learning. Participants were 72 university students randomly assigned to one of the two different versions of a computer-based multimedia program (narration with animation vs. narration with static images). A 2 × 2 factorial design is created by crossing gender and presentation mode (animation vs. static image). Dependent measures consisted of a transfer and a comprehension test. The results showed a significant modality by gender interaction on the comprehension test. Females performed better studying animations, whereas males performed better studying static pictures. The results are interpreted in light of multimedia learning principles and studies in the area of gender differences in learning. The important contribution of this study is the suggestion that individual differences such as gender should be considered in multimedia learning