Cryo-electron tomography (cryo-ET) enables molecular-resolution 3D imaging of complex biological specimens such as viral particles, cellular sections and, in some cases, whole cells. This enables the structural characterization of molecules in their near-native environments, without the need for purification or separation, thereby preserving biological information such as conformational states and spatial relationships between different molecular species. Subtomogram averaging is an image-processing workflow that allows users to leverage cryo-ET data to identify and localize target molecules, determine high-resolution structures of repeating molecular species and classify different conformational states. Here, STOPGAP, an open-source package for subtomogram averaging that is designed to provide users with fine control over each of these steps, is described. In providing detailed descriptions of the image-processing algorithms that STOPGAP uses, this manuscript is also intended to serve as a technical resource to users as well as for further community-driven software development.

Crystal polymorphism serves as a strategy to study the conformational flexibility of proteins. However, the relationship between protein crystal packing and protein conformation often remains elusive. In this study, two distinct crystal forms of a green fluorescent protein variant, NowGFP, are compared: a previously identified monoclinic form (space group C2) and a newly discovered ortho­rhombic form (space group P212121). Comparative analysis reveals that both crystal forms exhibit nearly identical linear assemblies of NowGFP molecules interconnected through similar crystal contacts. However, a notable difference lies in the stacking of these assemblies: parallel in the monoclinic form and perpendicular in the orthorhombic form. This distinct mode of stacking leads to different crystal contacts and induces structural alteration in one of the two molecules within the asymmetric unit of the orthorhombic crystal form. This new conformational state captured by orthorhombic crystal packing exhibits two unique features: a conformational shift of the β-barrel scaffold and a restriction of pH-dependent shifts of the key residue Lys61, which is crucial for the pH-dependent spectral shift of this protein. These findings demonstrate a clear connection between crystal packing and alternative conformational states of proteins, providing insights into how structural variations influence the function of fluorescent proteins.

Bacterial ABC toxin complexes (Tcs) comprise three core proteins: TcA, TcB and TcC. The TcA protein forms a pentameric assembly that attaches to the surface of target cells and penetrates the cell membrane. The TcB and TcC proteins assemble as a heterodimeric TcB–TcC subcomplex that makes a hollow shell. This TcB–TcC subcomplex self-cleaves and encapsulates within the shell a cytotoxic `cargo' encoded by the C-terminal region of the TcC protein. Here, we describe the structure of a previously uncharacterized TcC protein from Yersinia entomophaga, encoded by a gene at a distant genomic location from the genes encoding the rest of the toxin complex, in complex with the TcB protein. When encapsulated within the TcB–TcC shell, the C-terminal toxin adopts an unfolded and disordered state, with limited areas of local order stabilized by the chaperone-like inner surface of the shell. We also determined the structure of the toxin cargo alone and show that when not encapsulated within the shell, it adopts an ADP-ribosyltransferase fold most similar to the catalytic domain of the SpvB toxin from Salmonella typhimurium. Our structural analysis points to a likely mechanism whereby the toxin acts directly on actin, modifying it in a way that prevents normal polymerization.

X-ray and neutron crystallography, as well as cryogenic electron microscopy (cryo-EM), are the most common methods to obtain atomic structures of biological macromolecules. A feature they all have in common is that, at typical resolutions, the experimental data need to be supplemented by empirical restraints, ensuring that the final structure is chemically reasonable. The restraints are accurate for amino acids and nucleic acids, but often less accurate for substrates, inhibitors, small-molecule ligands and metal sites, for which experimental data are scarce or empirical potentials are harder to formulate. This can be solved using quantum mechanical calculations for a small but interesting part of the structure. Such an approach, called quantum refinement, has been shown to improve structures locally, allow the determination of the protonation and oxidation states of ligands and metals, and discriminate between different interpretations of the structure. Here, we present a new implementation of quantum refinement interfacing the widely used structure-refinement software Phenix and the freely available quantum mechanical software ORCA. Through application to manganese superoxide dismutase and V- and Fe-nitro­genase, we show that the approach works effectively for X-ray and neutron crystal structures, that old results can be reproduced and structural discrimination can be performed. We discuss how the weight factor between the experimental data and the empirical restraints should be selected and how quantum mechanical quality measures such as strain energies should be calculated. We also present an application of quantum refinement to cryo-EM data for particulate methane monooxygenase and show that this may be the method of choice for metal sites in such structures because no accurate empirical restraints are currently available for metals.

In recent decades, sustained theoretical and software developments have clearly established that representation analysis and magnetic symmetry groups are complementary concepts that should be used together in the investigation and description of magnetic structures. Historically, they were considered alternative approaches, but currently, magnetic space groups and magnetic superspace groups can be routinely used together with representation analysis, aided by state-of-the-art software tools. After exploring the historical antagonism between these two approaches, we emphasize the significant advancements made in understanding and formally describing magnetic structures by embracing their combined use.

The pair angle distribution function (PADF) is a three- and four-atom correlation function that characterizes the local angular structure of disordered materials, particles or nanocrystalline materials. The PADF can be measured using X-ray or electron fluctuation diffraction data, which can be collected by scanning or flowing a structurally disordered sample through a focused beam. It is a natural generalization of established pair distribution methods, which do not provide angular information. The software package pypadf provides tools to calculate the PADF from fluctuation diffraction data. The package includes tools for calculating the intensity correlation function, which is a necessary step in the PADF calculation and also the basis for other fluctuation scattering analysis techniques.

Predicting crystal symmetry simply from chemical composition has remained challenging. Several machine-learning approaches can be employed, but the predictive value of popular crystallographic databases is relatively modest due to the paucity of data and uneven distribution across the 230 space groups. In this work, virtually all crystallographic information available to science has been compiled and used to train and test multiple machine-learning models. Composition-driven random-forest classification relying on a large set of descriptors showed the best performance. The predictive models for crystal system, Bravais lattice, point group and space group of inorganic compounds are made publicly available as easy-to-use software downloadable from https://gitlab.com/vishsoft/cosy.

Coherent diffractive imaging with X-ray free-electron lasers could enable structural studies of macromolecules at room temperature. This type of experiment could provide a means to study structural dynamics on the femtosecond timescale. However, the diffraction from a single protein is weak compared with the incoherent scattering from background sources, which negatively affects the reconstruction analysis. This work evaluates the effects of the presence of background on the analysis pipeline. Background measurements from the European X-ray Free-Electron Laser were combined with simulated diffraction patterns and treated by a standard reconstruction procedure, including orientation recovery with the expand, maximize and compress algorithm and 3D phase retrieval. Background scattering did have an adverse effect on the estimated resolution of the reconstructed density maps. Still, the reconstructions generally worked when the signal-to-background ratio was 0.6 or better, in the momentum transfer shell of the highest reconstructed resolution. The results also suggest that the signal-to-background requirement increases at higher resolution. This study gives an indication of what is possible at current setups at X-ray free-electron lasers with regards to expected background strength and establishes a target for experimental optimization of the background.

The Pathfinding Partnerships Award from CO-LABS recognizes impactful, collaborative research projects organized by four or more research entities, including federal labs, in Colorado. This year, the Wildfire Research (WiRē) team received this award for their support of evidence-based community wildfire education to help communities live with wildfire. 

Actor Dwayne Johnson (L) and Simone Alexandra Johnson attend the People's Choice Awards 2017 at Microsoft Theater on January 18, 2017 in Los Angeles, California. ; Credit: Christopher Polk

When Dwayne "The Rock" Johnson debuted his Hollywood persona in World Wrestling Entertainment in 2003, he was two years removed from his first successful protagonist role in "The Scorpion King" and on the heels of more film success with roles in "The Rundown" and "Walking Tall." 

Little did anyone foresee that "Hollywood" Rock would buoy the overall representation for Asian and Pacific Islanders in popular film for the next 20 years.

Last week, the USC Annenberg Inclusion Initiative released a report documenting the prevalence of Asian and Pacific Islanders both on-and off-screen across the top-grossing films each year from 2007 to 2019.  Of the 1,300 films examined, only 44 featured API actors playing lead roles, nearly a third of which were played by Johnson. 

The report offers more staggering statistics:

• In 2019, over a quarter of API characters in the top-grossing films died. Most died by drowning, explosions, stabbing or suicides

• Of the over 51,000 speaking characters in the 1,300 films examined, only 6% were Asian, Asian American or Native Hawaiian/Pacific Islanders

• Only 50 of the 1,447 directors in the 1,300 films examined were of API heritage.

• In 2019, 67% of API characters played stereotyped roles

The release of this report comes at a time of rising anti-Asian hate crimes nationally, and the authors of the report believe the portrayal of Asian and Pacific Islanders in mass media contributes to that. Today on FilmWeek, we delve into the study's findings and discuss the history of API filmmakers and actors in Hollywood.

Guests: 

Nancy Wang Yuen, professor of sociology at Biola University in La Mirada; she is co-author of “The Prevalence and Portrayal of Asian and Pacific Islanders Across 1,300 Popular Films”; she tweets @nancywyeun

Justin Chang, film critic for the Los Angeles Times and NPR’s Fresh Air; he tweets @JustinCChang

This content is from Southern California Public Radio. View the original story at SCPR.org.

Dryden Gold Corp. (DRY:TSXV; DRYGF:OTCQB) has announced its participation in three significant mining investment conferences scheduled for November 2024. Read more about the company's plans to showcase major project updates and connect with global investors at these key events.

A rollercoaster that once sat on the Funtown Pier in Seaside Heights, N.J., rests in the ocean on Wednesday, Oct. 31, 2012 after the pier was washed away by superstorm Sandy.; Credit: Julio Cortez/AP

When Hurricane Sandy swept up the eastern seaboard in 2012, it left a trail of damage from Florida to Maine. Subways were inundated in New York City. Hurricane-force winds tore across New Jersey. Blizzard conditions walloped Appalachia.

The hurricane — also known as Superstorm Sandy — caused an estimated $70 billion in damages in the U.S., mostly from flooding. And while scientists have long believed that some of the carnage was attributable to a warming climate, it's been unclear just how much of a role human-caused warming played in the storm's impacts. New research, published Tuesday in the journal Nature Communications, puts a dollar amount on some of those damages and it's a startling figure.

Using flood maps and sea-level rise measurements, researchers found that human-induced sea-level rise caused an estimated $8 billion in excess flooding damage during Hurricane Sandy and affected an additional 70,000 people.

"I often hear people say when we're trying to help them adapt to increasing coastal flooding, 'Well, it's not going to happen in my lifetime, the sea-level rise won't happen in my lifetime,'" said Philip Orton, a co-author of the study from the Stevens Institute of Technology in New Jersey. "But it's already happening to people. It's already here."

Sea levels at the tip of Manhattan have risen about 8 inches since 1950, according to the National Oceanic and Atmospheric Administration. Estimates range for how much additional sea-level rise is likely to occur, but on average, the expectation is that by mid-century water levels could rise by more than a foot in New York City, compared to the year 2000.

In worst case scenarios, in which humanity does not significantly cut its climate-warming greenhouse gas emissions and the world's ice sheets rapidly melt, sea levels could rise by more than 6 feet by the end of the century, putting hundreds of millions of people at risk worldwide.

Higher water levels mean more areas are susceptible to flooding, storm surge and other problems associated with hurricanes, as well as more chronic flooding from high tides.

The Biden administration has made addressing climate change one of its top priorities. It's proposed a major reconfiguration of the nation's energy and transportation sectors to cut the country's outsized contribution to global warming, with the goal of making the U.S. carbon neutral by the year 2050. Accomplishing that feat will require major federal investments and likely bipartisan support. It's unclear if the administration will be able to procure the latter.

The new study, which joins a growing body of broader attribution science, aims to quantify the cost of inaction and business as usual. Similar studies found that climate change fueled the strength of Hurricane Harvey, increased the risk of Australia's recent unprecedented fire season and contributed to a record-breaking heatwave in Europe.

Scientists have debated whether Hurricane Sandy was made more intense by a warming climate, but it's difficult to know. Generally, there's agreement in the scientific community that hotter global temperatures and warmer ocean waters will lead to more rapid intensification of hurricanes.

Quantifying exactly how much those climatic differences affected a storm like Sandy is difficult. That's why Orton and the team of researchers focused their efforts on sea-level rise, where there's a bevvy of good data. They used that data to model the impacts of Hurricane Sandy in a world without climate change and found the estimated $8 billion difference.

"Increasingly we have the tools to simulate these events and study and quantify the impact of climate change on people's lives," Orton said. "People's lives were dramatically changed by Hurricane Sandy and a lot of them don't realize it had to do with climate change at all."

This content is from Southern California Public Radio. View the original story at SCPR.org.

RealtyAnalytix Advisors, LLC announces the introduction of Catawba Industrial Commons, a multi-tenant industrial campus offering the most attractive, affordable and functional manufacturing, distribution and warehousing space in the Greater Catawba County region.

While every mode of transportation in the U.S. will be affected as the climate changes, potentially the greatest impact on transportation systems will be flooding of roads, railways, transit systems, and airport runways in coastal areas because of rising sea levels and surges brought on by more intense storms, says a new report from the National Research Council.

The call for expanding undergraduates’ access to research experiences in science, technology, engineering, and mathematics (STEM) raises questions about their use and potential to increase students’ interest and persistence in these disciplines.

Federal agencies or other organizations responsible for sponsoring research or collecting data on technology and the workforce should establish a multidisciplinary research program that addresses unanswered questions related to the impact of changing technology on the nature of work and U.S. national economy, says a new report by the National Academies of Sciences, Engineering, and Medicine.

NASA’s large strategic missions like the Hubble Space Telescope, the Curiosity rover on Mars, and the Terra Earth observation satellite are essential to maintaining the United States’ global leadership in space exploration and should continue to be a primary component of a balanced space science program that includes large, medium, and smaller missions, says a new report by the National Academies of Sciences, Engineering, and Medicine.

Although NASA has made progress toward the overall space exploration science priorities recommended in a 2011 decadal survey by the National Academies of Sciences, Engineering, and Medicine, the space agency should raise the priority of scientific research that addresses the risks and unknowns of human space exploration.

NASA, the National Oceanic and Atmospheric Administration (NOAA), and the United States Geological Survey (USGS) should implement a coordinated approach for their space-based environmental observations to further advance Earth science and applications for the next decade, says a new report by the National Academies of Sciences, Engineering, and Medicine.

The Gulf Research Program (GRP) of the National Academies of Sciences, Engineering, and Medicine today announced 11 grant awards totaling $341,283 to assist in the recovery of Gulf Coast scientific research efforts impacted by hurricanes Harvey and Irma.

Introducing drone operations into the nation’s airspace can provide substantial benefits to society, such as preventing derailments, inspecting cell phone towers, delivering medical devices to patients in cardiac distress, and assisting firefighters, says a new congressionally mandated report by the National Academies of Sciences, Engineering, and Medicine.

The Gulf Research Program (GRP) of the National Academies of Sciences, Engineering, and Medicine today announced 11 grant awards totaling $287,565 to assist in the recovery of Gulf of Mexico region scientific research efforts impacted by hurricanes Harvey and Irma.

The current process for planetary protection policy development is inadequate to respond to increasingly complex solar system exploration missions, says a new report from the National Academies of Sciences, Engineering, and Medicine.

A new report from the National Academies of Sciences, Engineering, and Medicine examines the effects and efficacy of using dispersants in marine oil spill response.

We tend to think of the process of seeing as fairly objective — that our eyes are similar to cameras, neutrally taking in light and turning it into pictures. But research has shown that biases buried beneath our awareness can powerfully shape how we see.

NASA, NSF, and NOAA have made substantial progress in implementing the programs recommended in the 2013 decadal survey on solar and space physics (heliophysics) despite a challenging budgetary landscape, says a new midterm assessment from the National Academies of Sciences, Engineering, and Medicine.

Rwanda’s Human Resources for Health (HRH) Program – funded in part by the U.S. President’s Emergency Plan for AIDS Relief (PEPFAR) from 2012 to 2017 – more than tripled the country’s physician specialist workforce and produced major increases in the numbers and qualifications of nurses and midwives, says a new report from the National Academies of Sciences, Engineering, and Medicine.

As wildfires tear across the Western U.S., officials are confronting the challenge of evacuating and sheltering people in the middle of a pandemic.

In my nearly 20 years at SpaceX, I have experienced hundreds of Falcon launches and test firings. As such, my level of anxiety prior to these events had been waning until, of course, Saturday, May 30, 2020. On that day, and for days leading up to it, my heart was in my throat.

The COVID-19 pandemic has shone a harsh light on the consequences of chronic underinvestment in public health, and the limited recognition of its role. Unless there is a crisis, it is not always obvious that public health is “always on,” working quietly in the background on chronic disease prevention, vital statistics, sanitation, safe water, safe food, occupational diseases and injury, and infection control.

In 2010 a group of researchers conducted an experiment in which they pretended to be students, emailing 6,500 professors in nearly 90 academic fields at 259 universities with a request to discuss research before applying for a doctoral program. The text of the messages was identical, but the sender’s name was varied to signal race and gender, such as Brad Anderson, Latoya Brown, and Mei Chen.

Using nuclear propulsion technologies to support a human mission to Mars in 2039 will require NASA to pursue an aggressive and urgent technology development program, says a new report from the National Academies of Sciences, Engineering, and Medicine.

The U.S. Department of Energy (DOE) and private industry should invest now in order to have an operational fusion pilot plant in the 2035-2040 time frame, says Bringing Fusion to the U.S. Grid, a new report from the National Academies of Sciences, Engineering, and Medicine.

Preliminary evidence indicates that the COVID 19 pandemic has negatively affected the well-being of women in academic STEMM fields in a range of areas, including productivity, work-life boundary control, networking and community building, and mental well-being, says a new report from the National Academies of Sciences, Engineering, and Medicine.

Research continues to reveal more about the nature and impacts of implicit bias — something hidden from our direct awareness that causes tangible damage in many spheres of life, even for the very young.

A new decadal survey presents a visionary plan for the fields of astronomy and astrophysics, identifying scientific priorities and opportunities, and recommending an ambitious program of investment to strengthen the profession and achieve new capabilities.

The U.S. should undertake a new research program to better understand the potential risks and benefits of ocean-based interventions to remove or sequester carbon dioxide from the atmosphere and learn how these methods could be used to mitigate the impacts of climate change.

Even before the COVID-19 pandemic, many older Americans experienced social isolation or loneliness, which can impact both mental and physical health. Carla Perissinotto, a geriatrician who served on a National Academies study committee that examined the topic, reflected on her patients’ experiences during the pandemic and what we’ve learned.

The National Academies of Sciences, Engineering, and Medicine released a final report today reviewing the second draft of a U.S. Department of Veterans Affairs (VA) monograph, The Economic Impact and Cost Effectiveness of Service Dogs for Veterans with Post Traumatic Stress Disorder, which assesses the economic impact and cost-effectiveness of programs involving trained service dogs or emotional support dogs and veterans with post-traumatic stress disorder (PTSD).

A new report from the Intergovernmental Panel on Climate Change (IPCC) warns the increasingly numerous and widespread impacts of climate change may soon overcome our ability to adapt, unless action is taken to reduce emissions.

Rapid advances in small satellite technology and associated launch and production capabilities have transformed the space industry. A new report recommends ways the government can partner with commercial entities to enhance national missions and make transformative science advancements.

A new report examines how the U.S. Department of Defense can increase the capacity of historically Black colleges and universities (HBCUs) and other minority institutions to conduct defense and national security research.

Automated research workflows — which integrate computation, laboratory automation, and tools from artificial intelligence — have the potential to increase the speed of research activities and accelerate scientific discovery. A new report recommends ways to advance their development.

To meet its diversity and inclusion goals for competed mission leadership, NASA should invest in STEM career pathways, partner with historically Black colleges and universities and minority-serving institutions, and expand training and mentorship opportunities, among other actions.

A range of ‘climate-smart’ farming practices have the potential to lower greenhouse gas emissions from agriculture and help sequester carbon dioxide emitted by other parts of the economy. A recent webinar explored how to expand use of these practices.

EPA should conduct an ecological risk assessment of ultraviolet filters used in sunscreens, given the evidence that aquatic ecosystems in the U.S. and possibly endangered species are exposed to these UV filters, and given the importance of these ingredients in skin cancer prevention.

For decades the National Academies have provided objective, expert advice to help the nation understand issues related to maternal and reproductive health, unintended pregnancy, prenatal care, racial and ethnic disparities in health care, and abortion.

With renewed attention on mining gold at both new and historical sites in Virginia, the state’s regulations and practices should be updated to protect against the potential environmental and health impacts of gold mining — though the risk of adverse impacts cannot be eliminated completely, says a new report.

The National Institute of Standards and Technology’s facilities should be modernized to ensure that the agency can continue to deliver measurement science and standards that advance U.S. innovation and competitiveness on national technology priorities. Substandard facilities brought about through lack of investment have created ongoing problems that affect research.