A rational way to find the appropriate conditions to grow crystal samples for bio-crystallography is to determine the crystallization phase diagram, which allows precise control of the parameters affecting the crystal growth process. First, the nucleation is induced at supersaturated conditions close to the solubility boundary between the nucleation and metastable regions. Then, crystal growth is further achieved in the metastable zone – which is the optimal location for slow and ordered crystal expansion – by modulation of specific physical parameters. Recently, a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant–concentration phase diagrams has been constructed. Here, it is demonstrated that a thorough knowledge of the phase diagram is vital in any crystallization experiment. The relevance of the selection of the starting position and the kinetic pathway undertaken in controlling most of the final properties of the synthesized crystals is shown. The rational crystallization optimization strategies developed and presented here allow tailoring of crystal size and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.

CsCl-type materials have many outstanding characteristics, i.e. simple in structure, ease of synthesis and good stability at room temperature, thus are an excellent choice for designing functional materials. Using high-throughput first-principles calculations, a large number of topological semimetals/metals (TMs) were designed from CsCl-type materials found in crystallographic databases and their crystal and electronic structures have been studied. The CsCl-type TMs in this work show rich topological character, ranging from triple nodal points, type-I nodal lines and critical-type nodal lines, to hybrid nodal lines. The TMs identified show clean topological band structures near the Fermi level, which are suitable for experimental investigations and future applications. This work provides a rich data set of TMs with a CsCl-type structure.

A three-dimensional hydrogen-bonded network based on a rare mok topology has been constructed using an organic molecule synthesized in the solid state. The molecule is obtained using a supramolecular protecting-group strategy that is applied to a solid-state [2+2] photodimerization. The photodimerization affords a novel head-to-head cyclo­butane product. The cyclo­butane possesses tetrahedrally disposed cis-hydrogen-bond donor (phenolic) and cis-hydrogen-bond acceptor (pyridyl) groups. The product self-assembles in the solid state to form a mok network that exhibits twofold interpenetration. The cyclo­butane adopts different conformations to provide combinations of hydrogen-bond donor and acceptor sites to conform to the structural requirements of the mok net.

X-ray imaging of soft materials is often difficult because of the low contrast of the components. This particularly applies to frozen hydrated biological cells where the feature of interest can have a similar density to the surroundings. As a consequence, a high dose is often required to achieve the desired resolution. However, the maximum dose that a specimen can tolerate is limited by radiation damage. Results from 3D coherent diffraction imaging (CDI) of frozen hydrated specimens have given resolutions of ∼80 nm compared with the expected resolution of 10 nm predicted from theoretical considerations for identifying a protein embedded in water. Possible explanations for this include the inapplicability of the dose-fractionation theorem, the difficulty of phase determination, an overall object-size dependence on the required fluence and dose, a low contrast within the biological cell, insufficient exposure, and a variety of practical difficulties such as scattering from surrounding material. A recent article [Villaneuva-Perez et al. (2018), Optica, 5, 450–457] concluded that imaging by Compton scattering gave a large dose advantage compared with CDI because of the object-size dependence for CDI. An object-size dependence would severely limit the applicability of CDI and perhaps related coherence-based methods for structural studies. This article specifically includes the overall object size in the analysis of the fluence and dose requirements for coherent imaging in order to investigate whether there is a dependence on object size. The applicability of the dose-fractionation theorem is also discussed. The analysis is extended to absorption-based imaging and imaging by incoherent scattering (Compton) and fluorescence. This article includes analysis of the dose required for imaging specific low-contrast cellular organelles as well as for protein against water. This article concludes that for both absorption-based and coherent diffraction imaging, the dose-fractionation theorem applies and the required dose is independent of the overall size of the object. For incoherent-imaging methods such as Compton scattering, the required dose depends on the X-ray path length through the specimen. For all three types of imaging, the dependence of fluence and dose on a resolution d goes as 1/d4 when imaging uniform-density voxels. The independence of CDI on object size means that there is no advantage for Compton scattering over coherent-based imaging methods. The most optimistic estimate of achievable resolution is 3 nm for imaging protein molecules in water/ice using lensless imaging methods in the water window. However, the attainable resolution depends on a variety of assumptions including the model for radiation damage as a function of resolution, the efficiency of any phase-retrieval process, the actual contrast of the feature of interest within the cell and the definition of resolution itself. There is insufficient observational information available regarding the most appropriate model for radiation damage in frozen hydrated biological material. It is advocated that, in order to compare theory with experiment, standard methods of reporting results covering parameters such as the feature examined (e.g. which cellular organelle), resolution, contrast, depth of the material (for 2D), estimate of noise and dose should be adopted.

Multi-slice simulations of electron diffraction by three-dimensional protein crystals have indicated that structure solution would be severely impeded by dynamical diffraction, especially when crystals are more than a few unit cells thick. In practice, however, dynamical diffraction turned out to be less of a problem than anticipated on the basis of these simulations. Here it is shown that two scattering phenomena, which are usually omitted from multi-slice simulations, reduce the dynamical effect: solvent scattering reduces the phase differences within the exit beam and inelastic scattering followed by elastic scattering results in diffusion of dynamical scattering out of Bragg peaks. Thus, these independent phenomena provide potential reasons for the apparent discrepancy between theory and practice in protein electron crystallography.

This article presents IMSIM, an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. IMSIM implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm−1]/c[mg ml−1], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample–detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. IMSIM is available as part of the ATSAS software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html).

This article describes rational strategies for the optimization of crystal growth using precise in situ control of the temperature and chemical composition of the crystallization solution through dialysis, to generate crystals of the specific sizes required for different downstream structure determination approaches.

A recent study of dog bones excavated from archaeological sites on the Channel Islands of California has cast new light on the past ecology of the islands and the impact that domestic dogs--brought to the islands by Native Americans more than 6,000 years ago—may have once had on the islands’ animals and ecosystems.

The post Dog bones reveal ecological history of California’s Channel Islands appeared first on Smithsonian Insider.

The Smithsonian’s National Zoo recently acquired Japanese giant salamanders given to the Zoo by the City of Hiroshima Asa Zoological Park. This donation will be the foundation of a new long-term breeding program in the United States and may play an important role in saving amphibians around the globe.

The post Japanese giant salamanders given to the National Zoo by Asa Zoological Park in Hiroshima appeared first on Smithsonian Insider.

The Smithsonian’s National Zoo celebrated the completion of Phase I of Elephant Trails, an innovative and expanded home for Asian elephants, on Sept. 2. Phase […]

The post Elephant Trails exhibition opens at National Zoological Park appeared first on Smithsonian Insider.

On Aug, 31, the Smithsonian’s National Zoo welcomed this year’s second litter of African lion (Panthera leo) cubs. Five-year-old Shera (shown at right) gave birth […]

The post Shera, a 5-year-old lioness at the National Zoological Park appeared first on Smithsonian Insider.

Should global warming cause sea levels to rise as predicted in coming decades, thousands of archaeological sites in coastal areas around the world will be lost to erosion. With no hope of saving all of these sites, three archaeologists—Leslie Reeder of Southern Methodist University, Jon Erlandson of the University of Oregon and Torben Rick from the Smithsonian's National Museum of Natural History—have issued a call to action for scientists to assess the sites most at risk around the world.

The post Scientists issue call to action for archaeological sites threatened by rising seas, urban development appeared first on Smithsonian Insider.

Evidence for a diversified sea-based economy among North American inhabitants dating from 12,200 to 11,400 years ago is emerging from three sites on California's Channel Islands.

The post New archaeological evidence reveals California’s Channel Islands as North America’s earliest seafaring economy appeared first on Smithsonian Insider.

For more than three decades JoGayle Howard dedicated her life and work to reproducing endangered species.

The post JoGayle Howard, National Zoological Park pioneer in reproductive biology, dies appeared first on Smithsonian Insider.

A remarkable 5,000-year-old deposit of bones representing an entire herd of Persian gazelles recently discovered in northeastern Syria is firm evidence, scientists say, of an ancient hunting practice largely responsible for the near extinction of gazelles in this region today.

The post Archaeological evidence confirms mass hunting of gazelles 5,000 years ago appeared first on Smithsonian Insider.

In the United States, natural-gas production from shale rock has increased by more than 700 percent since 2007. Yet scientists still do not fully understand […]

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Geologic mapping is an integral part of exploration and understanding a planetary landscape, because it shows the relationships between geologic units and helps delineate the […]

The post Geologic Mapping of Mars appeared first on Smithsonian Insider.

Olga Kopach, Noemi Esteras, Selina Wray, Dmitri A. Rusakov, and Andrey Y. Abramov

Frontotemporal dementia and parkinsonism (FTDP-17) caused by the 10+16 splice-site mutation in the MAPT provides an established platform to model tau-related dementia in vitro. Human iPSC-derived neurons have been shown to recapitulate the neurodevelopmental profile of tau pathology during in vitro corticogenesis as in the adult human brain. However, the neurophysiological phenotype of these cells has remained unknown, leaving unanswered questions over the functional relevance and the gnostic power of this disease model. Here we used electrophysiology to explore the membrane properties and intrinsic excitability of the generated neurons to find that human cells mature by ~150 days of neurogenesis to become compatible with matured cortical neurons. In earlier FTDP-17, neurons, however, exhibited a depolarized resting membrane potential associated with increased resistance and reduced voltage-gated Na⁺- and K⁺-channel-mediated conductance. The Na_v1.6 protein was reduced in FTDP-17. These led to a reduced cell capability of induced firing and changed action potential waveform in FTDP-17. The revealed neuropathology may thus contribute to the clinicopathological profile of the disease. This sheds new light on the significance of human models of dementia in vitro.

Cambridge, MA -Physicists are capitalizing on a direct connection between the largest cosmic structures and the smallest known objects to use the universe as a […]

The post Scientists are using the universe as a “cosmological collider” appeared first on Smithsonian Insider.

Dr. JoGayle Howard of the Smithsonian's National Zoo discusses her work to breed and study one of the world's most endangered cats, the clouded leopard. More about the National Zoo's work to save clouded leopards: http://nationalzoo.si.edu/SCBI/ReproductiveScience/ConsEn...
http://nationalzoo.si.edu/support/annualappeal/cloudedleo... ... (more info)

The post Meet Our Scientist: Dr. JoGayle Howard of the Smithsonian’s National Zoological Park appeared first on Smithsonian Insider.

Visits to the Smithsonian's National Zoo just became a little bit sweeter with the arrival of a new honeybee colony. With a hive made of glass in the Zoo's Pollinarium and full access to the outdoors, these bees are showing off the wondrous ways of their world.

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Profound ideas don’t need to be complicated. A simple cube made of aluminum tubing, a centerpiece of a new exhibit “Life in One Cubic Foot,” […]

The post From Rochester to Polynesia, a simple cube unveils Earth’s dazzling biological diversity appeared first on Smithsonian Insider.

Using mineralogical data, it is demonstrated that chemical simplicity measured as an amount of Shannon information per atom on average corresponds to higher symmetry measured as an order of the point group of a mineral, which provides a modern formulation of the Fedorov–Groth law.

Yaya Wang
Apr 7, 2020; 133:jcs228072-jcs228072
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Long-term population trends for some North American pollinators -- bees, birds, bats, and other animals and insects that spread pollen so plant fertilization can occur -- are demonstrably downward, says a new report from the National Research Council.

To improve and ensure the efficacy of restoration efforts in the Gulf of Mexico following Deepwater Horizon – the largest oil spill in U.S. history – a new report from the National Academies of Sciences, Engineering, and Medicine recommends a set of best practices for monitoring and evaluating ecological restoration activities.

Over the next five years, the U.S. Department of Defense’s Biological Threat Reduction Program (BTRP) should encourage and be among co-leaders in the federal government’s development of an enduring interagency mechanism to address an array of biological threats – including natural disease outbreaks, accidental releases, and intentional attacks -- to deployed U.S. forces and to the nation itself, says a new report from the National Academies of Sciences, Engineering, and Medicine

Emily Quinn speaks from the TED stage at TEDWomen 2018; Credit: /TED

Part 1 of the TED Radio Hour episode The Biology Of Sex

Artist Emily Quinn is intersex. She's one of over 150 million people in the world who don't fit neatly into the categories of male or female. She explains how biological sex exists on a spectrum.

About Emily Quinn

Emily Quinn is an artist and activist. She worked at Cartoon Network on the Emmy Award winning show, Adventure Time. While there she partnered with interACT and MTV to develop the first intersex main character in television history. She came out publicly as intersex in a PSA alongside the character's debut. She later worked as the Youth Coordinator for interACT: Advocates for Intersex Youth.

As an activist, she speaks about intersex issues before audiences and through her YouTube channel: intersexperiences. As an artist, her most recent projects include a genderless puberty guidebook and a portrait series of intersex people that will be exhibited at medical schools across the U.S. in 2020.

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

Emily Quinn speaks from the TED stage at TEDWomen 2018; Credit: /TED

Part 1 of the TED Radio Hour episode The Biology Of Sex

Artist Emily Quinn is intersex. She's one of over 150 million people in the world who don't fit neatly into the categories of male or female. She explains how biological sex exists on a spectrum.

About Emily Quinn

Emily Quinn is an artist and activist. She worked at Cartoon Network on the Emmy Award winning show, Adventure Time. While there she partnered with interACT and MTV to develop the first intersex main character in television history. She came out publicly as intersex in a PSA alongside the character's debut. She later worked as the Youth Coordinator for interACT: Advocates for Intersex Youth.

As an activist, she speaks about intersex issues before audiences and through her YouTube channel: intersexperiences. As an artist, her most recent projects include a genderless puberty guidebook and a portrait series of intersex people that will be exhibited at medical schools across the U.S. in 2020.

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

Researchers in Berlin have demonstrated that urban wasteland areas can be used as suitable habitats for a range of grassland species. Using simple and cost-effective measures to sow grassland seed mixtures, they found that such areas flourished despite poor soil conditions and high levels of impact from people.

In 1989, researchers dragged a plough harrow across the seafloor of the Peru Basin to recreate some of the effects of deep-sea mining. Twenty-six years later, a new team of researchers returned to the site to assess whether there were any long-term ecological effects. They found that the seabed ecosystem remained disrupted, with significantly fewer suspension feeder species, such as anemones and sea sponges, than in undisturbed areas of seafloor. This suggests that deep-sea mining could cause irreversible changes to marine food webs in highly disturbed areas.

New research has recommended using both ecological and carbon footprints to assess the impact of environmental policies and strategies at a regional level. The combination can provide an evidence-based means of evaluating policies to help achieve environmental targets.

Researchers in Berlin have demonstrated that urban wasteland areas can be used as suitable habitats for a range of grassland species. Using simple and cost-effective measures to sow grassland seed mixtures, they found that such areas flourished despite poor soil conditions and high levels of impact from people.

Producing and consuming food has a significant environmental impact. In the search for a sustainable diet, researchers in Sweden explored a method of food production that does not exceed the level of globally available arable land per capita, and involves raising livestock on pasture or by-products not suitable for humans (the ‘ecological leftovers’ principle). The researchers developed three diets based on this method and evaluated their environmental impact compared with current diets.

A participatory approach to waste management has been tested in Naples, Italy, a city which has experienced ongoing problems with the collection of municipal waste. This study tested a toolkit, which uses stakeholder engagement to improve waste-management decision-making. Residents and other stakeholders supported the use of a technological innovation to develop biomass fuel from municipal waste.

Assessment (ERA), each with different goals. The researchers find that overlaps between the three assessments could be combined to create a more comprehensive form of ERA, usable by regulators and environmental decision makers.

Gendered expectations in marriage are not just bad for women, they are also bad for men, according to a new study by University of Connecticut (UConn) sociologists.

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The environmental benefits of cleaner, more efficient transport may be offset by increasing distances travelled by passengers and goods, according to a new report by the European Environmental Agency (EEA). The report suggests that technology needs to go hand-in-hand with a policy package that improves, avoids and shifts transport emissions.

Khudoleĭ, K. M

Researchers have identified a possible way of reducing the survival rate of the pine processionary moth, a destructive pine forest pest. Including patches of broadleaf trees in pine woodland could trick the caterpillars into pupating in soil that is unsuitable for their survival.

Environmental policies must provide the right incentives for the development of innovative technologies that reduce pollution and mitigate the effects of climate change. A recent study has investigated the characteristics of policies that are likely to encourage green innovation and concluded that those that are stringent, predictable and flexible are the most effective.

To assess the impact on ecosystems of chemical contamination in aquatic environments, scientists need to measure not only the concentration of the contaminants, but also the extent to which they can disrupt biological processes at a cellular level in plants and animals and at an ecosystem level. According to a new study, considering these complex inter-relationships in combination will help improve the ecological status of waterways, in line with Water Framework Directive (WFD) commitments.

Climate change will substantially increase the severity and length of droughts in Europe by the end of the century, according to new research. The study showed that some European countries could experience a reduction in river flow of up to 80% by the 2080s.

Belgrad, Daniel, author

Establishing ecological networks across national boundaries is recognised as essential to supporting biodiversity. New research in Germany has indicated that these networks could be improved through greater exchange of knowledge and better links with land planning.

A recent study has developed a mapping system to show the impact on habitats and species caused by construction projects, such as dams, near Natura 2000 conservation areas. Using a Greek case study, the system was able to identify risks from a dam construction project to species including otters, toads and tortoises.

Solar panels are attractive to aquatic insects because they reflect light in a similar way to water, indicates recent research. This has ecological implications, especially if insects lay eggs on the panels. However, if panels are surrounded by white borders and divided by white grids, they are considerably less attractive to the insects.

Human activities can have a multitude of different effects on rivers and streams, and it is difficult identify those that have the biggest impact on aquatic populations. A newly developed method for assessing ecological degradation in waterways helps deal with this problem and could provide crucial information for water managers charged with tackling the root causes of degradation.

The concept of the Ecological Footprint can be used to illustrate the balance between the use of a natural resource or an ecological service and its availability. According to a new study, the Ecological Footprint could be valuable as an indicator to help track progress towards the goals of the Convention on Biological Diversity.