A Method for Photoinitating Protein Folding in a Nondenaturing Environment

The early kinetic events of protein folding are an important part of the folding pathway, yet our understanding towards the process is limited. Information from the study of these early events can allow us to distinguish between the various models that have been proposed to describe the folding of a protein in real time. Unlike “typical” chemical kinetics with well-defined initial and final states, the initial state of a denatured protein is relatively ill-defined. This uncertainty introduces ambiguity in the interpretation of the experimental data on the early events in protein folding. Toward developing a unified theory of protein folding, it is necessary to begin the observation of the refolding process from a well-defined initial state, trigger folding as rapidly as possible, and to follow the protein in real time as it samples its conformational space over its highly complex free-energy landscape

Diamondback Terrapin Bycatch Reduction Strategies for Commercial and Recreational Blue Crab Fisheries

Diamondback terrapin (Malaclemys terrapin) is considered a keystone species for its influence on community structure of tidal marshes. Terrapins exhibit strong habitat and nest site fidelity, and have relatively small home ranges (\u3c 2 km), so that sub-populations tend to be spatially discrete. Terrapins rely on open water, wetlands, and adjacent uplands at various stages of their life-cycle, so the quality and connectivity of these habitat patches is critical to population persistence. Terrapin is listed in Virginia as a species of Very High Conservation Need based on threats due to nest predation and drowning of adults in crab pots. Terrapin population declines, reduced growth, and changes in sex ratios have been directly attributed to bycatch mortality in commercial crab pots. Our overall project goal was to characterize essential terrapin habitats toward development of bycatch reduction strategies for managing commercial and recreational blue crab fisheries. In a pilot study area surrounding the mouth of the York River, Virginia, our approach was to 1) geospatially define suitable terrapin habitat based on natural features, 2) integrate spatial datasets to develop a Vulnerability Index of terrapin habitats and define potential resource conflict areas where crab pots correspond to essential terrapin habitat, and 3) conduct terrapin and crab pot counts in habitats with varying suitability to test predictions. Suitable terrapin habitat (full connectivity among habitat metrics) accounted for over 50% of all terrapin observations, and another 45% of observations occurred in areas where only one habitat metric was absent. In 96% of these cases, the absent metric was SAV presence. In contrast, full habitat connectivity was determined for only 5% of areas where terrapins were absent. Within the pilot study area during a two year retrieval program, 2872 derelict pots were removed. Of these, 22% were within shallow waters (≤ 2 m) where terrapins typically reside. Of the suitable terrapin habitat (70km2 ), 21% (15 km2 ) was considered vulnerable to crabbing pressures (10% highly and 11% moderately vulnerable). Approximately 15% of the study area was considered to be potential resource conflict areas for terrapin and crabbing. Candidate zones for the targeted application of blue crab fishery management actions to reduce terrapin bycatch include the Severn River, Perrin River, Guinea Marshes, and south of Gwynn Island. The integration of spatial information on terrapin habitat and crabbing pressure in a single framework will allow managers to identify areas where terrapins are most likely to encounter threats and target conservation efforts in those areas. In resource conflict areas, there are several management options that can be used in combination 1) Require use of bycatch reduction devices (BRDs) on commercial & recreational crab pots 2) Avoid particular habitats (e.g. small tidal creeks) or establish fishing exclusion zones 3) Educate – design public education programs to • promote the voluntary use of BRDs, and • communicate to recreational boaters the ramifications of severing buoy lines of active crab pots 4) Promote proper use of gear (e.g. retrieving pots regularly to minimize terrapin mortality). With further refinement to improve the predictability of terrapin occupancy, the terrapin habitat vulnerability model is transferable to all coastal areas where diamondback terrapins occur and where blue crabs are commercially and recreationally fished—from southern New England to Texas

The LCLS-II Photoinjector Laser Infrastructure

This paper presents a comprehensive technical overview of the Linac Coherent Light Source II (LCLS-II) photoinjector laser system, its first and foremost component. The LCLS-II photoinjector laser system serves as an upgrade to the original LCLS at SLAC National Accelerator Laboratory. This advanced laser system generates high-quality laser beams to power the LCLS-II, contributing to the instrument's unprecedented brightness, precision, and flexibility. Our discussion extends to the various subsystems that comprise the photoinjector, including the photocathode laser, laser heater, and beam transport systems. Lastly, we draw attention to the ongoing research and development infrastructure underway to enhance the functionality and efficiency of the LCLS-II, and similar X-ray free-electron laser facilities around the world, thereby contributing to the future of laser technology and its applications.Comment: Submitted to High Power Laser Science and Engineerin

Overview of Spirit Microscopic Imager Results

This paper provides an overview of Mars Exploration Rover Spirit Microscopic Imager (MI) operations and the calibration, processing, and analysis of MI data. The focus of this overview is on the last five Earth years (2005-2010) of Spirit's mission in Gusev crater, supplementing the previous overview of the first 450 sols of the Spirit MI investigation. Updates to radiometric calibration using in-flight data and improvements in high-level processing are summarized. Released data products are described, and a table of MI observations, including target/feature names and associated data sets, is appended. The MI observed natural and disturbed exposures of rocks and soils as well as magnets and other rover hardware. These hand-lens-scale observations have provided key constraints on interpretations of the formation and geologic history of features, rocks, and soils examined by Spirit. MI images complement observations by other Spirit instruments, and together show that impact and volcanic processes have dominated the origin and evolution of the rocks in Gusev crater, with aqueous activity indicated by the presence of silica-rich rocks and sulfate-rich soils. The textures of some of the silica-rich rocks are similar to terrestrial hot spring deposits, and observations of subsurface cemented layers indicate recent aqueous mobilization of sulfates in places. Wind action has recently modified soils and abraded many of the rocks imaged by the MI, as observed at other Mars landing sites. Plain Language Summary The Microscopic Imager (MI) on NASA's Spirit rover returned the highest-resolution images of the Martian surface available at the time of the 2004-2010 mission. Designed to survive 90 Mars days (sols) and search for evidence of water in the past, Spirit returned data for 2210 sols, far exceeding all expectations. This paper summarizes the scientific insights gleaned from the thousands of MI images acquired during the last 5years of the mission, supplementing the summary of the first 450 sols of the Spirit MI investigation published previously (Herkenhoff et al., ). Along with data from the other instruments on Spirit, MI images guided the scientific interpretation of the geologic history of the rocks and soils observed in Gusev crater on Mars. We conclude that the geologic history of the area explored by Spirit has been dominated by impacts and volcanism, and that water, perhaps very hot water, was involved in the evolution of some of the rocks and soils. More recently, winds have moved soil particles and abraded rocks, as observed elsewhere on Mars. These results have improved our understanding of Mars' history and informed planning of future missions to Mars.National Aeronautics and Space AdministrationPublic domain articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

The Science Performance of JWST as Characterized in Commissioning

This paper characterizes the actual science performance of the James Webb Space Telescope (JWST), as determined from the six month commissioning period. We summarize the performance of the spacecraft, telescope, science instruments, and ground system, with an emphasis on differences from pre-launch expectations. Commissioning has made clear that JWST is fully capable of achieving the discoveries for which it was built. Moreover, almost across the board, the science performance of JWST is better than expected; in most cases, JWST will go deeper faster than expected. The telescope and instrument suite have demonstrated the sensitivity, stability, image quality, and spectral range that are necessary to transform our understanding of the cosmos through observations spanning from near-earth asteroids to the most distant galaxies.Comment: 5th version as accepted to PASP; 31 pages, 18 figures; https://iopscience.iop.org/article/10.1088/1538-3873/acb29

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.The workshop was supported by funding to RCSB PDB by the National Science Foundation (DBI 1338415); PDBe by the Wellcome Trust (104948); PDBj by JST-NBDC; BMRB by the National Institute of General Medical Sciences (GM109046); D3R by the National Institute of General Medical Sciences (GM111528); registration fees from industrial participants; and tax-deductible donations to the wwPDB Foundation by the Genentech Foundation and the Bristol-Myers Squibb Foundation.This is the final version of the article. It first appeared from Cell Press via https://doi.org//10.1016/j.str.2016.02.01