Some characteristics of cytochrome f in the cyanobacterium Phormidium laminosum: its sequence and charge properties in the reaction with plastocyanin

AbstractPart of the petCA operon was cloned and the sequence of the cytochrome f gene from the moderately thermophilic cyanobacterium Phormidium laminosum determined. A partial sequence of the petC gene encoding the Rieske iron-sulphur protein was also obtained. The cytochrome f gene encodes a mature protein of 385 residues and a leader sequence of 45 residues. The mature protein contains several acidic or neutral residues corresponding to basic residues in the turnip protein. Some of the latter are thought to be important for the interaction with plastocyanin via its ‘eastern’ face. Many of the corresponding residues on the eastern face of P. laminosum plastocyanin are either basic or neutral instead of acidic. These comparisons suggested that the local charges on P. laminosum cytochrome f that are important for its interaction with the homologous plastocyanin may be negative rather than positive. The importance of acidic groups was confirmed by measuring the rates of reduction of horse heart cytochrome c and P. laminosum and spinach plastocyanins by the cytochrome bf complex isolated from P. laminosum. P. laminosum plastocyanin gave the highest rates, which decreased at high ionic strength, confirming the importance of positive local charges on this protein. When extrapolated to infinite ionic strength the rates observed with the two kinds of plastocyanin were similar, but cytochrome c became unreactive. An optimum was observed in the ionic strength response with P. laminosum plastocyanin

Evaluation of process for sludge particle size reduction

This document evaluates the available technology for K Basin sludge particle size. The results can be used to demonstrate the sensitivity or lack thereof, of K Basin sludge to available reduction processes and TWRS proposed particle acceptance criteria

Alignment-free molecular shape comparison using spectral geometry: the framework

A framework is presented for the calculation of novel alignment-free descriptors of molecular shape. The methods are based on the technique of spectral geometry which has been developed in the field of computer vision where it has shown impressive performance for the comparison of deformable objects such as people and animals. Spectral geometry techniques encode shape by capturing the curvature of the surface of an object into a compact, information-rich representation that is alignment-free while also being invariant to isometric deformations, that is, changes that do not distort distances over the surface. Here, we adapt the technique to the new domain of molecular shape representation. We describe a series of parametrization steps aimed at optimizing the method for this new domain. Our focus here is on demonstrating that the basic approach is able to capture a molecular shape into a compact and information-rich descriptor. We demonstrate improved performance in virtual screening over a more established alignment-free method and impressive performance compared to a more accurate, but much more computationally demanding, alignment-based approach

Small-Scale Vertical Movements of Summer Flounder Relative to Diurnal, Tidal, and Temperature Changes

Observation of animal movements on small spatial scales provides a means to understand how large-scale species distributions are established from individual behavioral decisions. Small-scale vertical movements of 14 Summer Flounder Paralichthys dentatus residing in Chesapeake Bay were observed by using depth data collected with archival tags. A generalized linear mixed model was employed to examine the relationship between these vertical movements and environmental covariates such as tidal state, time of day, lunar phase, and temperature. Vertical movements increased with warming water temperatures, and this pattern was most apparent at night and during rising and falling tides. Fish generally exhibited greater vertical movements at night, but the difference between vertical movements in the day and those at night decreased as fish increased in size. Results from this study fill a void in understanding the small-scale movements of Summer Flounder and could be incorporated into individual-based models to investigate how species distributions develop in response to environmental conditions

Optimal Inverse Design of Magnetic Field Profiles in a Magnetically Shielded Cylinder

Magnetic shields that use both active and passive components to enable the generation of a tailored low-field environment are required for many applications in science, engineering, and medical imaging. Until now, accurate field nulling, or field generation, has only been possible over a small fraction of the overall volume of the shield. This is due to the interaction between the active field-generating components and the surrounding high-permeability passive shielding material. In this paper, we formulate the interaction between an arbitrary static current flow on a cylinder and an exterior closed high-permeability cylinder. We modify the Green’s function for the magnetic vector potential and match boundary conditions on the shield’s interior surface to calculate the total magnetic field generated by the system. We cast this formulation into an inverse optimization problem to design active–passive magnetic field shaping systems that accurately generate any physical static magnetic field in the interior of a closed cylindrical passive shield. We illustrate this method by designing hybrid systems that generate a range of magnetic field profiles to high accuracy over large interior volumes, and simulate them in real-world shields whose passive components have finite permeability, thickness, and axial entry holes. Our optimization procedure can be adapted to design active–passive magnetic field shaping systems that accurately generate any physical user-specified static magnetic field in the interior of a closed cylindrical shield of any length, enabling the development and miniaturization of systems that require accurate magnetic shielding and control

Modeling DNA Structure, Elasticity and Deformations at the Base-pair Level

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid harmonic springs with a non-zero spring length. The competition of these two interactions and the introduction of a simple geometrical constraint leads to a stacked right-handed B-DNA-like conformation. The mapping of the presented model to the Marko-Siggia and the Stack-of-Plates model enables us to optimize the free model parameters so as to reproduce the experimentally known observables such as persistence lengths, mean and mean squared base-pair step parameters. For the optimized model parameters we measured the critical force where the transition from B- to S-DNA occurs to be approximately $140{pN}$. We observe an overstretched S-DNA conformation with highly inclined bases that partially preserves the stacking of successive base-pairs.Comment: 15 pages, 25 figures. submitted to PR

National identity predicts public health support during a global pandemic

Changing collective behaviour and supporting non-pharmaceutical interventions is an important component in mitigating virus transmission during a pandemic. In a large international collaboration (Study 1, N = 49,968 across 67 countries), we investigated self-reported factors associated with public health behaviours (e.g., spatial distancing and stricter hygiene) and endorsed public policy interventions (e.g., closing bars and restaurants) during the early stage of the COVID-19 pandemic (April-May 2020). Respondents who reported identifying more strongly with their nation consistently reported greater engagement in public health behaviours and support for public health policies. Results were similar for representative and non-representative national samples. Study 2 (N = 42 countries) conceptually replicated the central finding using aggregate indices of national identity (obtained using the World Values Survey) and a measure of actual behaviour change during the pandemic (obtained from Google mobility reports). Higher levels of national identification prior to the pandemic predicted lower mobility during the early stage of the pandemic (r = −0.40). We discuss the potential implications of links between national identity, leadership, and public health for managing COVID-19 and future pandemics.publishedVersio