Assessment and communication of the toxicological risk of consuming shrimp in the EU

The numbers of alerts from the EU's Rapid Alert System for Food and Feed (RASFF) related to crustacean products were compared to numbers of mainstream media stories related to health concerns. An internet search of "farmed shrimp" was also conducted and the content of the websites assessed for subject matter and balance. The study found that the absolute number of RASFF alerts has fallen considerably since legislation controlling testing of food being traded into and within the EU was introduced in 2002 and tracked increasing stringency of EU procedures. There were 1512 alerts from 1980 to 2015 with 44.0% and 21.2% of alerts attributed to farmed and wild shrimp respectively. There were large numbers of alerts reporting antibiotic residues in wild shrimp, which raised questions about the source of the contamination, and natural occurrence of the antimicrobial residues was considered. The number of mainstream media stories closely followed the number of alerts, but 91.2% of media articles concerning the health aspects were concerned with consumption of farmed shrimp. The internet search revealed a much more negative view of farmed shrimp compared to the mainstream media. It is suggested that the internet generally follows an historic negative narrative on farmed seafood, often with little validation which narrows the discourse on seafood production rather than empowering consumers. According to the risk assessment of RASFF data, it was concluded that farmed shrimp does not possess any more risk than wild seafood choices but producers have not been able to communicate the benefits of farmed produce to the consumer

De Novo Enzyme Design Using Rosetta3

The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for a variety of chemical reactions, and in principle can be applied to any arbitrary chemical reaction of interest, The process has four stages: 1) choice of a catalytic mechanism and corresponding minimal model active site, 2) identification of sites in a set of scaffold proteins where this minimal active site can be realized, 3) optimization of the identities of the surrounding residues for stabilizing interactions with the transition state and primary catalytic residues, and 4) evaluation and ranking the resulting designed sequences. Stages two through four of this process can be carried out with the Rosetta package, while stage one needs to be done externally. Here, we demonstrate how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction

Modeling Symmetric Macromolecular Structures in Rosetta3

Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta

Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements. Foldit Standalone was built from the ground up with a custom rendering and event engine, configurable visualizations and interactions driven by Rosetta. Foldit Standalone contains, among other features: electron density and contact map visualizations, multiple sequence alignment tools for template-based modeling, rigid body transformation controls, RosettaScripts support and an embedded Lua interpreter

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

The prediction of changes in protein stability and structure resulting from single amino acid substitutions is both a fundamental test of macromolecular modeling methodology and an important current problem as high throughput sequencing reveals sequence polymorphisms at an increasing rate. In principle, given the structure of a wild-type protein and a point mutation whose effects are to be predicted, an accurate method should recapitulate both the structural changes and the change in the folding-free energy. Here, we explore the performance of protocols which sample an increasing diversity of conformations. We find that surprisingly similar performances in predicting changes in stability are achieved using protocols that involve very different amounts of conformational sampling, provided that the resolution of the force field is matched to the resolution of the sampling method. Methods involving backbone sampling can in some cases closely recapitulate the structural changes accompanying mutations but not surprisingly tend to do more harm than good in cases where structural changes are negligible. Analysis of the outliers in the stability change calculations suggests areas needing particular improvement; these include the balance between desolvation and the formation of favorable buried polar interactions, and unfolded state modeling

1992: Abilene Christian College Bible Lectures - Full Text

CORINTH REVISITED: Studies in I Corinthians Being the Abilene Christian University Annual Bible Lectures 1992 Published by ACU PRESS 1634 Campus Court Abilene, Texas 7960

De Novo Enzyme Design Using Rosetta3

The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for a variety of chemical reactions, and in principle can be applied to any arbitrary chemical reaction of interest, The process has four stages: 1) choice of a catalytic mechanism and corresponding minimal model active site, 2) identification of sites in a set of scaffold proteins where this minimal active site can be realized, 3) optimization of the identities of the surrounding residues for stabilizing interactions with the transition state and primary catalytic residues, and 4) evaluation and ranking the resulting designed sequences. Stages two through four of this process can be carried out with the Rosetta package, while stage one needs to be done externally. Here, we demonstrate how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu

The Head-On Collision of Two Equal Mass Black Holes Peter Anninos

We study the head-on collision of two equal mass, nonrotating black holes. Various initial configurations are investigated, including holes which are initially surrounded by a common apparent horizon to holes that are separated by about $20M$, where $M$ is the mass of a single black hole. We have extracted both $\ell = 2$ and $\ell=4$ gravitational waveforms resulting from the collision. The normal modes of the final black hole dominate the spectrum in all cases studied. The total energy radiated is computed using several independent methods, and is typically less than $0.002 M$. We also discuss an analytic approach to estimate the total gravitational radiation emitted in the collision by generalizing point particle dynamics to account for the finite size and internal dynamics of the two black holes. The effects of the tidal deformations of the horizons are analysed using the membrane paradigm of black holes. We find excellent agreement between the numerical results and the analytic estimates.Comment: 33 pages, NCSA 94-048, WUGRAV-94-

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling capabilities is hampering the wider adoption of computational methods by non-experts. RosettaScripts is an XML-like language for specifying modeling tasks in the Rosetta framework. RosettaScripts provides access to protocol-level functionalities, such as rigid-body docking and sequence redesign, and allows fast testing and deployment of complex protocols without need for modifying or recompiling the underlying C++ code. We illustrate these capabilities with RosettaScripts protocols for the stabilization of proteins, the generation of computationally constrained libraries for experimental selection of higher-affinity binding proteins, loop remodeling, small-molecule ligand docking, design of ligand-binding proteins, and specificity redesign in DNA-binding proteins