Redox-sensitive DNA Binding by Homodimeric Methanosarcina Acetivorans MsvR is Modulated by Cysteine Residues

Background: Methanoarchaea are among the strictest known anaerobes, yet they can survive exposure to oxygen. The mechanisms by which they sense and respond to oxidizing conditions are unknown. MsvR is a transcription regulatory protein unique to the methanoarchaea. Initially identified and characterized in the methanogen Methanothermobacter thermautotrophicus (Mth), MthMsvR displays differential DNA binding under either oxidizing or reducing conditions. Since MthMsvR regulates a potential oxidative stress operon in M. thermautotrophicus, it was hypothesized that the MsvR family of proteins were redox-sensitive transcription regulators. Results: An MsvR homologue from the methanogen Methanosarcina acetivorans, MaMsvR, was overexpressed and purified. The two MsvR proteins bound the same DNA sequence motif found upstream of all known MsvR encoding genes, but unlike MthMsvR, MaMsvR did not bind the promoters of select genes involved in the oxidative stress response. Unlike MthMsvR that bound DNA under both non-reducing and reducing conditions, MaMsvR bound DNA only under reducing conditions. MaMsvR appeared as a dimer in gel filtration chromatography analysis and site-directed mutagenesis suggested that conserved cysteine residues within the V4R domain were involved in conformational rearrangements that impact DNA binding. Conclusions: Results presented herein suggest that homodimeric MaMsvR acts as a transcriptional repressor by binding Ma PmsvR under non-reducing conditions. Changing redox conditions promote conformational changes that abrogate binding to Ma PmsvR which likely leads to de-repression

Assessing Vulnerability of Fish in the U.S. Marine Aquarium Trade

The trade in coral reef fishes for aquariums encompasses over 1,800 species from over 40 exporting countries, yet the population status for most traded species is unknown and unevaluated. At the same time, these coral reef fishes face a growing number of threats and often occur in jurisdictions with limited management capacity and data. In response, we assess vulnerability to overfishing for 72 coral reef fishes popular in the aquarium trade for the United States – the top importer – from the top exporting countries (Indonesia and the Philippines). We use a data-limited assessment approach: productivity susceptibility analysis (PSA). PSA estimates relative vulnerability of species by assessing their biological productivity and susceptibility to overfishing. The most and least vulnerable stocks were differentiated by attributes related to the reproductive biology (e.g., breeding strategy, recruitment pattern, and fecundity), appropriateness, for an average home aquarium, ease of capture (e.g., schooling and aggregation), and rates of natural mortality. Our analysis identifies several of the most and least vulnerable species popular in the aquarium fish trade. The species that ranked as least vulnerable to overcollection were Gobiodon okinawae, Nemateleotris magnifica, Gobiodon acicularis, Salarias fasciatus, Ptereleotris zebra, Gobiodon citrinus, Pseudocheilinus hexataenia, Chaetodon lunula, Nemateleotris decora, and Halichoeres chrysus. In contrast, the ten most vulnerable species were Chromileptes altivelis, Plectorhinchus chaetodonoides, Pterapogon kauderni, Premnas biaculeatus, Echidna nebulosa, Centropyge bicolor, Zebrasoma veliferum, Pomacanthus semicirculatus, Zebrasoma scopas, and Thalassoma lunare. In a data-limited context, we suggest how these vulnerability rankings can help guide future efforts for reducing vulnerability risk. In particular, species that are relatively high-vulnerability are prime targets for research and aquaculture efforts, increased monitoring of collection and exports, species-specific stock assessments, and voluntary reductions by retailers and consumers to avoid overexploitation

New Directions in Conservation for the National Wildlife Refuge System

The National Wildlife Refuge System Improvement Act of 1997 includes the nation’s broadest statutory commitment to ecosystem protection: to “ensure that the biological integrity, diversity, and environmental health of the system are maintained.” The act also directs the US Fish and Wildlife Service (FWS) to expand the scope of conservation monitoring, assessment, and management beyond refuge boundaries to encompass surrounding landscapes. The act thus gives the FWS a leadership role in developing research and management partnerships with other agencies, organizations, and neighboring landowners. Increasing research capacity and scientific expertise, and strengthening institutional resolve to limit activities that impede the attainment of this directive, are challenges for the FWS. Success requires reexamination of existing priorities, refocused training, the acquisition of new funding and technical expertise, and creative application of those new skills to meet the law’s broad mandat

Development and testing of a fiber/multianode photomultiplier system for use on FiberGLAST

A scintillating fiber detector is currently being studied for the NASA Gamma-Ray Large Area Space Telescope (GLAST) mission. This detector utilizes modules composed of a thin converter sheet followed by an x, y plane of scintillating fibers to examine the shower of particles created by high energy gamma-rays interacting in the converter material. The detector is composed of a tracker with 90 such modular planes and a calorimeter with 36 planes. The two major component of this detector are the scintillating fibers and their associated photodetectors. Here we present current status of development and test result of both of these. The Hamamatsu R5900-00-M64 multianode photomultiplier tube (MAPMT) is the baseline readout device. A characterization of this device has been performed including noise, cross- talk, gain variation, vibration, and thermal/vacuum test. A prototype fiber/MAPMT system has been tested at the Center for Advanced Microstructures and Devices at Louisiana State University with a photon beam and preliminary results are presented

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.ResultsIn this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations.ConclusionsOverall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches

Prime Focus Spectrograph (PFS): the metrology camera system

The Prime Focus Spectrograph (PFS) is a new optical/near-infrared multi-fiber spectrograph designed for the prime focus of the 8.2m Subaru telescope. PFS will cover a 1.3 degree diameter field with 2394 fibers to complement the imaging capabilities of Hyper SuprimeCam. To retain high throughput, the final positioning accuracy between the fibers and observing targets of PFS is required to be less than 10 µ m. The metrology camera system (MCS) serves as the optical encoder of the fiber positioners for configuring of fibers. The MCS locates at the Cassegrain focus of the Subaru telescope to cover the whole focal plane with one 50M pixel CMOS sensor. The information from MCS will be fed into the fiber positioner control system for closed loop control. The MCS was delivered to Subaru Observatory in Apr. 2018 and it had two engineering runs in Oct. 2018 and Aug. 2019. The 1st engineering run concluded that the original mirror supports need to be improved to provide better image quality. The newly designed mirror supports were installed before the 2nd engineering run. The 2nd engineering run result shows that the MCS overall position accuracy is better than 4μm and the image processing time is less than 4 seconds. The MCS is ready for the system integration with other PFS components

Prime Focus Spectrograph (PFS) for the Subaru Telescope: Overview, recent progress, and future perspectives

PFS (Prime Focus Spectrograph), a next generation facility instrument on the 8.2-meter Subaru Telescope, is a very wide-field, massively multiplexed, optical and near-infrared spectrograph. Exploiting the Subaru prime focus, 2394 reconfigurable fibers will be distributed over the 1.3 deg field of view. The spectrograph has been designed with 3 arms of blue, red, and near-infrared cameras to simultaneously observe spectra from 380nm to 1260nm in one exposure at a resolution of ~1.6-2.7A. An international collaboration is developing this instrument under the initiative of Kavli IPMU. The project is now going into the construction phase aiming at undertaking system integration in 2017-2018 and subsequently carrying out engineering operations in 2018-2019. This article gives an overview of the instrument, current project status and future paths forward.Comment: 17 pages, 10 figures. Proceeding of SPIE Astronomical Telescopes and Instrumentation 201

Toward community standards and software for whole-cell modeling

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML. Results: Our analysis revealed several challenges to representing WC models using the current standards. Conclusion: We, therefore, propose several new WC modeling standards, software, and databases. Significance:We anticipate that these new standards and software will enable more comprehensive models

BioSimulators: a central registry of simulation engines and services for recommending specific tools

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations