Many biologists are now routinely seeking to determine the three-dimensional structures of their proteins of choice, illustrating the importance of this knowledge, but also of the simplification and streamlining of structure-determination processes. Despite the fact that most software packages offer simple pipelines, for the non-expert navigating the outputs and understanding the key aspects can be daunting. Here, the structure determination of the type IV pili (TFP) protein PilA1 from Clostridioides difficile is used to illustrate the different steps involved, the key decision criteria and important considerations when using the most common pipelines and software. Molecular-replacement pipelines within CCP4i2 are presented to illustrate the more commonly used processes. Previous knowledge of the biology and structure of TFP pilins, particularly the presence of a long, N-terminal α-helix required for pilus formation, allowed informed decisions to be made during the structure-determination strategy. The PilA1 structure was finally successfully determined using ARCIMBOLDO and the ab initio MR strategy used is described.

The performance of automated protein model building usually decreases with resolution, mainly owing to the lower information content of the experimental data. This calls for a more elaborate use of the available structural information about macromolecules. Here, a new method is presented that uses structural homologues to improve the quality of protein models automatically constructed using ARP/wARP. The method uses local structural similarity between deposited models and the model being built, and results in longer main-chain fragments that in turn can be more reliably docked to the protein sequence. The application of the homology-based model extension method to the example of a CFA synthase at 2.7 Å resolution resulted in a more complete model with almost all of the residues correctly built and docked to the sequence. The method was also evaluated on 1493 molecular-replacement solutions at a resolution of 4.0 Å and better that were submitted to the ARP/wARP web service for model building. A significant improvement in the completeness and sequence coverage of the built models has been observed.

Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.

Model quality assessment programs estimate the quality of protein models and can be used to estimate local error in protein models. ProQ3D is the most recent and most accurate version of our software. Here, it is demonstrated that it is possible to use local error estimates to substantially increase the quality of the models for molecular replacement (MR). Adjusting the B factors using ProQ3D improved the log-likelihood gain (LLG) score by over 50% on average, resulting in significantly more successful models in MR compared with not using error estimates. On a data set of 431 homology models to address difficult MR targets, models with error estimates from ProQ3D received an LLG of >50 for almost half of the models 209/431 (48.5%), compared with 175/431 (40.6%) for the previous version, ProQ2, and only 74/431 (17.2%) for models with no error estimates, clearly demonstrating the added value of using error estimates to enable MR for more targets. ProQ3D is available from http://proq3.bioinfo.se/ both as a server and as a standalone download.

A new report from the National Research Council recommends best practices that law enforcement agencies and courts should follow to improve the likelihood that eyewitness identifications used in criminal cases will be accurate.

There is no substitute for dramatic reductions in greenhouse gas emissions to mitigate the negative consequences of climate change, a National Research Council committee concluded in a two-volume evaluation of proposed climate-intervention techniques.

Conducting clinical investigations of mitochondrial replacement techniques (MRT) in humans is ethically permissible as long as significant conditions and principles are met, says a new report from the National Academies of Sciences, Engineering, and Medicine.

The U.S. DRIVE Partnership – a government-industry partnership that fosters the development of precompetitive and innovative technologies for clean and efficient light-duty vehicles – has made significant progress in many technical areas including advanced combustion technologies, durability and cost of hydrogen fuel cells, and electric drive systems such as motors, power electronics, and batteries, says a new report by the National Academies of Sciences, Engineering, and Medicine.

Despite progress in recent decades, more than 10,000 alcohol-impaired driving fatalities occur each year in the U.S. To address this persistent problem, stakeholders -- from transportation systems to alcohol retailers to law enforcement -- should work together to implement policies and systems to eliminate these preventable deaths, says a new report from the National Academies of Sciences, Engineering, and Medicine.

NAS President Marcia McNutt delivered the commencement address to Boston University graduates on May 19, where she discussed trust in science and evidence, and the importance of making informed decisions.

A new report from the National Academies of Sciences, Engineering, and Medicine says that enhancements to the geodetic infrastructure are needed to answer important questions about sea level rise, water resources, geological hazards, and more over the next decade.

A new study finds that a quarter of fish products labelled as ‘cod’ or ‘haddock’ in Dublin, Ireland, are in fact completely different species of fish. This indicates that fish consumers are being misled by inaccurate labels, which could compromise sustainable fishing and consumption efforts.

Important factors in the creation and maintenance of effective Environmental Enforcement Networks (EENs) have been shared by the International Network on Environment Compliance and Enforcement (INECE), one of the first EENs to emerge. By disseminating these ‘lessons learned’ the INECE hopes to facilitate the creation of effective EENs in emerging networks, such as those in Eastern Africa, Western Africa and South America.

How environmental agencies can best engage with, and reap the benefits of, Environmental Enforcement Networks (EENs) has been identified in new research. The study used questionnaires and interviews with senior figures from eight environment agencies, spanning seven countries, to identify the key themes of, and ways of improving engagement with, EENs, to extract the maximum benefits. The input was then used to perform a SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis of engaging with EENs, from which options for improved engagement could be developed.

Technological advances in European cement production could reduce energy consumption by up to 10% and CO2 emissions by 4%, according to a new analysis. The research suggests that initial costs of some of the pending technological improvements could be recouped in as little as a year.

Regardless of how well-designed environmental legislation is, for it to be effective it must be properly enforced. This study explored the enforcement practices of several environmental agencies, recommending that strategies are chosen based on regulatory context and environmental risk.

Ireland’s Environmental Protection Agency (EPA) established the Network for Ireland’s Environmental Compliance and Enforcement (NIECE) over 10 years ago to ensure an effective, integrated, national approach to the enforcement of environmental legislation, as presented in a recent conference paper and a report from the EPA.

Administrative sanctions against environmental crime, such as fines, are generally easier and cheaper to implement than criminal punishment methods, such as prison sentences. This study explored enforcement methods for environmental crime in four Western European areas: Flanders (Belgium), Germany, the Netherlands and the UK. Based on their findings, the authors say it is most cost-effective — and may increase deterrence — to use both forms of enforcement.

Soil stabilisation and the process of strengthening the physical properties of soil is fundamental to the construction process of infrastructure such as roads, runways and earth dams. Many chemical additives currently used in soil stabilisation are associated with adverse environmental effects and this study examines the use of biopolymers, such as xanthan gum and guar gum, as more sustainable alternatives. The researchers have run a series of laboratory experiments to evaluate the viability of these two types of biopolymers for use as additives for collapsible soil stabilisation, and found that both could be used in place of conventional additives to improve soil strength, permeability and collapse potential.

Marine protected areas (MPAs) in which fishing is prohibited contain substantially more fish, including commercially valuable species, than either partially protected or unenforced MPAs, according to a recent survey of rocky reef fish in the Mediterranean Sea. This suggests that MPAs need to be highly protected to offer the best chance of recovery for fish stocks, say the researchers.

Wildlife laws are important to protect animals from harmful human activity, and are largely enforced by state authorities, but occasionally by non-governmental organisations (NGOs). By reviewing academic literature and government legislation, this study explored the different perspectives and ideologies of NGOs and how they enforce wildlife law in practice, focusing on the UK and the US. The study concludes that environmental NGOs are vital for the effective policing of wildlife legislation.

A new study has analysed marine litter on beaches across the UK, indicating that the fishing industry is responsible for large quantities of marine rubbish. The researchers recommend a combination of better enforcement of regulations covering waste disposal, and incentives for fishing vessels to reduce marine litter.

The prominent role of EU countries in the international trade of reptiles for pets, including many rare and illegally traded species, is highlighted in a recent study. The researchers call for better enforcement and tighter legislation to control the trade, which is a major threat to global biodiversity. In particular the researchers appeal for legislation to be passed for species protected in their native range countries, which can currently be freely traded in the EU if they are not subject to international trade conventions such as CITES.

New figures on how much titanium dioxide nanomaterial (TiO2-NM) could be released into the environment from photocatalytic cement — a new type of self-cleaning cement — are presented in a recent study. Based on experimental test results, the researchers estimate that between 0.015% and 0.033% of photocatalytic cement’s TiO2-NM content could potentially escape over several years of cement use, depending on the level of cement porosity. The study could help inform environmental risk assessment of TiO2-NM, as well as safer design of nano-products (i.e. commercialised products incorporating nanomaterials).

SUFFOLK– As Tropical Storm Michael approaches, the Virginia Department of Transportation (VDOT) Hampton Roads District stands ready to respond to...

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FREDERICKSBURG , Va. – An additional evening of work is required this week for an ongoing pin replacement on the Robert O. Norris Bridge, and...

FREDERICKSBURG , Va. – An additional evening of work is required this week for an ongoing pin replacement on the Robert O. Norris Bridge, and...

MANTUA – Glenbrook Road between Little River Turnpike (Route 236) and Denise Lane will be closed to through traffic from 9 a.m. Monday, Oct. 29 to 5...

FAIRFAX – Due to weather delays, the closure of Popes Head Road (Route 654) between Colchester Road (Route 612) and Fairfax County Parkway (Route...

LYNCHBURG – Motorists who use Odd Fellows Road from the US 29 Business Lynchburg Expressway to access the Main Post Office, Division of Motor Vehicles or other businesses/organizations in the immediate area will need to use alternate routes beginning Monday, October 8. The bridge on Odd Fellows Road over the railroad will be closed for approximately one year beginning that date for replacement.

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The retiring three-term Republican will leave behind many legacies, including a strong anti-environment record.

Cement made from 'fly ash', a byproduct from coal-fired power plants, has a remarkably lower carbon footprint, recycles industrial waste, and is more durable.

Switching out some surprisingly toxic household products for cleaner, greener alternatives can help save your health, money and the planet.

The software giant is expected to unveil its first tablet computer.

A USGBC report highlights green building advancements made in all 50 states.

Sorry to see 100-watt bulbs disappear from stores because they were energy hogs? LED bulbs will roughly match the 100-watters for size and brightness, but their

Although several manufacturers have plans to release long-lasting, energy-sipping LED A-Line bulbs that replace the near-obsolete 100-watt incandescent, Osram S