Radiation damage is the most fundamental limitation for achieving high resolution in electron cryo-microscopy (cryo-EM) of biological samples. The effects of radiation damage are reduced by liquid-helium cooling, although the use of liquid helium is more challenging than that of liquid nitrogen. To date, the benefits of liquid-nitrogen and liquid-helium cooling for single-particle cryo-EM have not been compared quantitatively. With recent technical and computational advances in cryo-EM image recording and processing, such a comparison now seems timely. This study aims to evaluate the relative merits of liquid-helium cooling in present-day single-particle analysis, taking advantage of direct electron detectors. Two data sets for recombinant mouse heavy-chain apoferritin cooled with liquid-nitrogen or liquid-helium to 85 or 17 K were collected, processed and compared. No improvement in terms of resolution or Coulomb potential map quality was found for liquid-helium cooling. Interestingly, beam-induced motion was found to be significantly higher with liquid-helium cooling, especially within the most valuable first few frames of an exposure, thus counteracting any potential benefit of better cryoprotection that liquid-helium cooling may offer for single-particle cryo-EM.

Single-particle electron cryo-microscopy (cryoEM) has undergone a `resolution revolution' that makes it possible to characterize megadalton (MDa) complexes at atomic resolution without crystals. To fully exploit the new opportunities in molecular microscopy, new procedures for the cloning, expression and purification of macromolecular complexes need to be explored. Macromolecular assemblies are often unstable, and invasive construct design or inadequate purification conditions and sample-preparation methods can result in disassembly or denaturation. The structure of the 2.6 MDa yeast fatty acid synthase (FAS) has been studied by electron microscopy since the 1960s. Here, a new, streamlined protocol for the rapid production of purified yeast FAS for structure determination by high-resolution cryoEM is reported. Together with a companion protocol for preparing cryoEM specimens on a hydrophilized graphene layer, the new protocol yielded a 3.1 Å resolution map of yeast FAS from 15 000 automatically picked particles within a day. The high map quality enabled a complete atomic model of an intact fungal FAS to be built.

Although microscopes and image-analysis software for electron cryomicroscopy (cryo-EM) have improved dramatically in recent years, specimen-preparation methods have lagged behind. Most strategies still rely on blotting microscope grids with paper to produce a thin film of solution suitable for vitrification. This approach loses more than 99.9% of the applied sample and requires several seconds, leading to problematic air–water interface interactions for macromolecules in the resulting thin film of solution and complicating time-resolved studies. Recently developed self-wicking EM grids allow the use of small volumes of sample, with nanowires on the grid bars removing excess solution to produce a thin film within tens of milliseconds from sample application to freezing. Here, a simple cryo-EM specimen-preparation device that uses components from an ultrasonic humidifier to transfer protein solution onto a self-wicking EM grid is presented. The device is controlled by a Raspberry Pi single-board computer and all components are either widely available or can be manufactured by online services, allowing the device to be constructed in laboratories that specialize in cryo-EM rather than instrument design. The simple open-source design permits the straightforward customization of the instrument for specialized experiments.

The composition of occupied and unoccupied electronic states in the vicinity of Fermi energies is vital for all materials and relates to their physical, chemical and mechanical properties. This work demonstrates how the combination of resonant and non-resonant X-ray emission spectroscopies supplemented with theoretical modelling allows for quantitative analysis of electronic states in 5d transition metal and metal-oxide materials. Application of X-rays provides element selectivity that, in combination with the penetrating properties of hard X-rays, allows determination of the composition of electronic states under working conditions, i.e. non-vacuum environment. Tungsten metal and tungsten oxide are evaluated to show the capability to simultaneously assess composition of around-band-gap electronic states as well as the character and magnitude of the crystal field splitting.

This article describes a high-efficiency experimental configuration for a self-referenced lattice comparator with a `brush beam' of synchrotron radiation from a bending magnet and two linear position-sensitive photon-counting-type X-ray detectors. The efficiency is more than ten times greater compared with the `pencil-beam' configuration and a pair of zero-dimensional detectors. A solution for correcting the systematic deviation of d-spacing measurements caused by the horizontal non-uniformity of the brush beam is provided. Also, the use of photon-counting-type one-dimensional detectors not only improves the spatial resolution of the measurements remarkably but can also adjust the sample's attitude angles easily.

Serial crystallography, at both synchrotron and X-ray free-electron laser light sources, is becoming increasingly popular. However, the tools in the majority of crystallization laboratories are focused on producing large single crystals by vapour diffusion that fit the cryo-cooled paradigm of modern synchrotron crystallography. This paper presents several case studies and some ideas and strategies on how to perform the conversion from a single crystal grown by vapour diffusion to the many thousands of micro-crystals required for modern serial crystallography grown by batch crystallization. These case studies aim to show (i) how vapour diffusion conditions can be converted into batch by optimizing the length of time crystals take to appear; (ii) how an understanding of the crystallization phase diagram can act as a guide when designing batch crystallization protocols; and (iii) an accessible methodology when attempting to scale batch conditions to larger volumes. These methods are needed to minimize the sample preparation gap between standard rotation crystallography and dedicated serial laboratories, ultimately making serial crystallography more accessible to all crystallographers.

Because researchers do not understand the formation mechanism of cocrystals, the preparation of cocrystals is mostly done by trial and error. This study focuses on the cocrystal formation mechanism to improve the efficiency of cocrystal preparation.

A calculation procedure for X-ray total scattering and the pair distribution function from a crystalline structural model is presented. It allows one to easily and precisely deal with diffraction-angle-dependent parameters such as the atomic form factor and the resolution of the optics.

A detailed theoretical and experimental comparison of dark-field electron holography (DFEH) and high-resolution X-ray diffraction (HRXRD) is performed. Both techniques are being applied to measure elastic strain in an array of transistors and the role of the geometric phase is emphasized.

Describing a species is a serious undertaking. In the case of T. acutus, Coats and his collaborators documented its microscopic life cycle, conducted extensive DNA analysis and unearthed scientific papers dating back to 1873—when parasitic dinoflagellates were first noted by German scientist Ernst Haeckel.

The post Introducing the parasitic dinoflagellate: Tintinnophagus acutus appeared first on Smithsonian Insider.

One such parasite lurks in Chesapeake Bay: an invasive barnacle that hijacks a mud crab’s reproductive system and impregnates it with parasite larvae—even if the crab is male.

The post Undersea parasite turns male mud crabs female appeared first on Smithsonian Insider.

A newly-discovered species of ant supports a controversial theory of species formation. The ant, known to live only under a single eucalyptus tree on the […]

The post Deadbeat ant species branched off as parasite inside its own colony appeared first on Smithsonian Insider.

Have you ever had a pet that seemed just a little bit crazy or odd? Can you be sure that it was in control of […]

The post Crazy eyes and mind control – the power of parasites appeared first on Smithsonian Insider.

The odds of being attacked and castrated by a variety of parasitic flatworms increases for marine horn snails the farther they are found from the […]

The post Parasitic flatworms flout global biodiversity patterns appeared first on Smithsonian Insider.

Through sheer coincidence, two Smithsonian researchers at the National Zoological Park have discovered that 18 percent of the white-tailed deer population in the Eastern United […]

The post Smithsonian study reveals white-tailed deer in eastern U.S. are infected with a malaria parasite appeared first on Smithsonian Insider.

A one-cubic-foot approach to studying biodiversity as showcased in the new Biocube exhibit at the Smithsonian’s National Museum of Natural History has led to the […]

The post New parasitic crab species discovered during Smithsonian Biocube work in Solomon Islands appeared first on Smithsonian Insider.

Fat, toxic and nocturnal, cane toads (Rhinella marina) are abundant today in Hawaii, even though they are South American natives. Released on the Hawaiian Islands […]

The post Two invasive species have Hawaiian reunion after 80-year separation appeared first on Smithsonian Insider.

Aline A. Alves, Heloisa B. Gabriel, Maria J. R. Bezerra, Wanderley de Souza, Sue Vaughan, Narcisa L. Cunha-e-Silva, and Jack D. Sunter

Eukaryotic flagella are complex microtubule based organelles and in many organisms there are extra-axonemal structures present, including the outer dense fibres of mammalian sperm and the paraflagellar rod (PFR) of trypanosomes. Flagellum assembly is a complex process occurring across three main compartments, the cytoplasm, the transition fibre-transition zone, and the flagellum. It begins with translation of protein components, followed by their sorting and trafficking into the flagellum, transport to the assembly site and then incorporation. Flagella are formed from over 500 proteins; the principles governing axonemal component assembly are relatively clear. However, the coordination and sites of extra-axonemal structure assembly processes are less clear.

We have discovered two cytoplasmic proteins in T. brucei that are required for PFR formation, PFR assembly factors 1 and 2. Deletion of either PFR-AF1 or PFR-AF2 dramatically disrupted PFR formation and caused a reduction in the amount of major PFR proteins. The presence of cytoplasmic factors required for PFR formation aligns with the concept of processes occurring across multiple compartments to facilitate axoneme assembly and this is likely a common theme for extra-axonemal structure assembly.

Under the anomalous transmission condition in the Bragg mode, X-ray interference fringes were observed between two beams with different hyperbolic trajectories in a very weakly bent plane-parallel perfect crystal with negative strain gradient. The origin of the fringes was analysed based on the dynamical theory of diffraction for a distorted crystal. In the reflected beam from the entrance surface, the interference fringes were observed between once- and twice-reflected beams from the back surface. In the transmitted beam from the back surface, the interference fringes were observed between the direct beam and once-reflected beam from the entrance surface. In the emitted beam from the lateral surface, the interference fringes were observed between the beams after different numbers of reflections in the crystal. The multiply reflected beams were formed by a combined result of long propagation length along the beam direction with large divergence of the refracted beams when the strain gradient was negative. The period of these interference fringes was sensitive to very weak strain, of the order of 10−7.

Mark Torchin, a marine ecologist at the Smithsonian Tropical Research Institute (STRI) in Panama, talks about how he studies the parasites of invasive marine animals such as snails. Much of his research focuses on biological invasions and the dynamics between the host, the parasites and the surrounding ecosystem.

The post Meet our Scientist–Mark Torchin tracks invasive marine species and their parasites in Panama appeared first on Smithsonian Insider.

 This film depicts the Onward Brass Band parading through the French Quarter of New Orleans and picking up second liners along the way. The […]

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“Parallax Gap” transforms the Renwick Gallery’s Bettie Rubenstein Grand Salon into a visual puzzle. This immersive, site-specific installation explores examples of interplay between craft and […]

The post About the Renwick’s “Parallax Gap” appeared first on Smithsonian Insider.

Zebra mussels in the Great Lakes, lionfish in the Atlantic and pythons in the Everglades: Large creatures like these generally draw the spotlight when talking […]

The post DNA is trusty new weapon for detecting slime nets and other invasive marine parasites appeared first on Smithsonian Insider.

The Earth’s changing climate could cause the extinction of up to a third of its parasite species by 2070, according to a global analysis reported […]

The post Study shows parasites may be among earliest victims of climate change appeared first on Smithsonian Insider.

Aline A. Alves
Apr 15, 2020; 0:jcs.242271v1-jcs.242271
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Many wild southern sea otters in California are infected with the parasite Toxoplasma gondii, yet the infection is fatal for only a fraction of sea otters, which has long puzzled the scientific community. A National Science Foundation-funded study identifies the parasite's specific strains that are killing southern sea otters, tracing them back to a bobcat and feral domestic cats from nearby watersheds. The study marks the first time a genetic link has been clearly established between the Toxoplasma strains in felid hosts and parasites causing fatal disease in marine wildlife. The study's results highlight how infectious agents like Toxoplasma can spread from cat feces on land to the sea, leading to detrimental impacts on marine wildlife.

Image credit: Trina Wood/UC Davis

One of the nation’s largest surveys of crime victims is likely undercounting incidences of rape and sexual assault, making it difficult to ensure that adequate law enforcement resources and support services are available for victims, says a new report by the National Research Council.

Young adults ages 18-26 should be viewed as a separate subpopulation in policy and research, because they are in a critical period of development when successes or failures could strongly affect the trajectories of their lives, says a new report from the Institute of Medicine and National Research Council.

While the U.S. Department of Veterans Affairs (VA) provides mental health care of comparable or superior quality to care provided in private and non-VA public sectors, accessibility and quality of services vary across the VA health system, leaving a substantial unmet need for mental health services among veterans of the recent wars in Afghanistan and Iraq, says a new congressionally mandated report from the National Academies of Sciences, Engineering, and Medicine.

We urge the U.S. Department of Homeland Security to immediately stop separating migrant children from their families, based on the body of scientific evidence that underscores the potential for lifelong, harmful consequences for these children and based on human rights considerations.

Chemical separations — which are used to divide chemical mixtures into their distinct elements — are critical in providing many of the foods and services needed to maintain our quality of life.

Engineering is emerging as an important topic in K-12 education in the U.S., and is being incorporated into education standards, instructional materials, and assessments.

World War II veterans Pyotr Vorobyev (left), 90, and Pavel Yeroshenko, 94, attend a performance in Minsk by the 120th Rogachev Guards Mechanized Brigade of the Belarusian Armed Forces ahead of the 75th anniversary of the victory in World War II. Belarus is raising eyebrows — and concerns — by going ahead with a mass military parade marking the anniversary on Saturday.; Credit: Natalia Fedosenko/TASS

With the coronavirus forcing much of Europe to tone down public celebrations this week marking the 75th anniversary of the end of World War II, the small nation of Belarus is raising eyebrows — and concerns — by going ahead with a mass military parade in the capital Minsk on Saturday.

The move reflects the business-as-usual approach of the country's longtime president, Alexander Lukashenko — a former Soviet collective farm director leading what the U.S. once dubbed the last dictatorship in Europe.

As the coronavirus has raced across the globe, Lukashenko has dismissed the pandemic as mass "psychosis" — a disease easily cured with a bit of vodka, a hot sauna or time spent playing hockey or doing farm work on one of country's legendary Soviet-designed tractors.

The country's soccer league still competes. Belarus' schools opened after a short delay. And annual Victory Day celebrations will go on.

The government "simply cannot cancel the parade," the Belarusian leader said in a Cabinet meeting this week. "It's an emotional, deeply ideological event."

In a rare concession to at least some social distancing measures, Lukashenko has urged Belarusian men to spend time with their families, rather than their mistresses. But behind the theatrics sits a wily politician who plays to his base in the country's towns and villages, analysts say.

"Lukashenko prioritizes combating panic rather than combating the pandemic," Artyom Shraibman, a Minsk-based political analyst with Sense Analytics, tells NPR. "He downplays the threat, and of course he's very concerned about [the] state of [the] economy."

Shraibman notes similar echoes coming out of the Trump White House.

Belarus has reported over 21,000 suspected coronavirus cases and more than 120 deaths — comparatively low in the global count, but one of the fastest-growing infection rates in Europe, the World Health Organization says.

Amid the growing crisis, Belarusian civil society is rallying to fix what Lukashenko will not. With many Belarusians now self-isolating by choice, even the country's health ministry has endorsed some public distancing measures over Lukashenko's advice.

Volunteers have raised money to buy personal protective gear for hospitals. Restaurants have donated food. Hotels provide rooms pro bono to medical workers. Private businesses have raised funds.

"People who normally don't talk to each other are working together to help," says Andrej Stryzhak of #ByCovid19, a group of volunteer activists leading crowdfunded efforts to equip health workers across the country. "It's been magical and I don't use that word lightly."

Stryzhak says many are bracing for the aftershocks of Saturday's Victory parade, where attendance isn't required but there are reports of pay bonuses given to those who show up.

"We believe in statistics. And the experts and doctors tell us that if there's a crowd, then expect a new spike in cases a week or two later," says Stryzhak. "Belarus isn't Mars," he adds, noting that the country is as susceptible to the virus as any other.

Meanwhile, Lukashenko's contrarian approach has also fueled a rift with Belarus' big brother to the east. Russia has embraced lockdowns amid its own soaring coronavirus infection rates.

This week, the Belarusian leader ordered the expulsion of a journalist from Russia's Channel 1 state television network after it aired a report criticizing Lukashenko for risking lives and ignoring the pandemic.

"Leave us alone and don't count your chickens before they hatch," said Lukashenko. "Later we'll sit and find out who was right."

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

The last two decades have seen a series of new construction waste policies management in Hong Kong. One of the most significant is an offsite construction waste sorting (CWS) programme which, since its implementation in 2006, has separated 5.11 million tonnes of construction waste into different materials. The researchers suggest that the study provides an important reference for other countries working to minimise construction waste.

In a new study, Spanish researchers describe a method specifically designed for measuring and characterising noise from building sites. They claim the method could help shape future policy related to noise pollution caused by the construction industry and provide important information to help reduce construction noise.

In a previous blog post, Notifications from MATLAB, I showed how Amazon's Notification system (AWS SNS) can be used from MATLAB service can be used to easily send information between endpoints in a distributed system, be they applications or people.... read more >>

Insights from a recent Italian study could help local authorities across Europe improve their rates of separate waste collection for recycling. The researchers found higher rates of separate waste collection in municipalities with high-quality governmental institutions for waste collection, non-mountainous terrain and higher income levels. Separating household waste into streams, such as glass or food, for re-use and recycling helps free up resources for a circular economy. Good-quality institutions are the main driver of separate waste collection and can overcome barriers such as low economic prosperity.

“Create a separate user profile with minimal privileges for work-only use. Close all work-related windows, applications, files, and documents when not in use. Do not use work email addresses to sign up for unauthorised, free tools. Grant access to your employees to corporate network only though a company-approved VPN with multi-factor authentication,” the advisory states.

It is possible to balance agricultural production with improved biodiversity on farmland, according to researchers. A new study suggests using a combination of land sharing techniques, which enhance biodiversity on existing farmland, with land separation techniques, which designate separate areas for conservation and farmland production.

A drug used to treat parasite infections at fish farms can contaminate the surrounding environment and threaten local wildlife, a new study shows. Following a week-long treatment at a Norwegian salmon farm, the authors found concentrations of an anti-sea-lice drug that were high enough to kill some crabs, shrimps and lobsters. However, they suggest the drug is not likely to pose a risk to humans.

Municipal wastewater is a major source of pharmaceuticals in the aquatic environment. Results from a recent study suggest that collecting and treating urine separately from other forms of sewage could be a cost-effective way to reduce the harmful effects of pharmaceuticals on the environment, while also providing a source of nutrients for fertilising agricultural crops.

In a previous post, I introduced a model simulating the exponential spread of a phenomenon like COVID-19. With more and more talks in the news about deconfinement plans, I thought it would be interesting to run multiple simulations with different deconfinement scenarios and observe the potential outcomes.... read more >>

Pedestrians are exposed to different levels of pollution on the pavements depending on how parked cars at the roadside are arranged, according to the first in a series of new studies in this area. The researchers modelled different parking regimes and found that less pollution reached the pavement when cars were parked sideways on, rather than at an angle to the street. Their results may help urban planners design more pedestrian-friendly streets.

Grey took a secret photo, Myke took a chance, and they both cannot agree on how long you should stick it out.

SUFFOLK – The Virginia Department of Transportation Hampton Roads District (VDOT) is suspending lane closures on Interstate 64 and Interstate 664...

SUFFOLK– As Hurricane Florence approaches the coast, the Virginia Department of Transportation (VDOT) Hampton Roads District continues to monitor...

Poh Ling Yeow, a MasterChef Australia winner and now also a contestant, hasn’t been able to see her husband Jono Bennett for a month because of coronavirus travel restrictions.

Get on board! Connect with fellow green-minded Twitterers as you find new people to follow and pick up new followers of your own.

When a California Whole Foods store put three stalks of asparagus in a bottle of water and sold it for $5.99, the Internet called them on it.