Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) applied through DiSCaMB software library in the structure refinement against X-ray diffraction data largely improves the X—H bond lengths and make them comparable to the averaged neutron bond lengths.

Insights were obtained into the structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway for the biosynthesis of lysine.

The crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum is reported. It has high structural similarity to other gluconate 5-dehydrogenase proteins, demonstrating that this enzyme is highly conserved.

A putative open reading frame encoding GTP cyclohydrolase I from Listeria monocytogenes was expressed in a recombinant Escherichia coli strain. The recombinant protein was purified and was confirmed to convert GTP to dihydroneopterin triphosphate (Km = 53 µM; vmax = 180 nmol mg−1 min−1). The protein was crystallized from 1.3 M sodium citrate pH 7.3 and the crystal structure was solved at a resolution of 2.4 Å (Rfree = 0.226) by molecular replacement using human GTP cyclohydrolase I as a template. The protein is a D5-symmetric decamer with ten topologically equivalent active sites. Screening a small library of about 9000 compounds afforded several inhibitors with IC50 values in the low-micromolar range. Several inhibitors had significant selectivity with regard to human GTP cyclohydrolase I. Hence, GTP cyclohydrolase I may be a potential target for novel drugs directed at microbial infections, including listeriosis, a rare disease with high mortality.

Santa Claus and his sleigh full of gifts has been upstaged early this holiday season by news of autonomous drones possibly delivering packages to your […]

The post Package-delivering drones? Q&A with Roger Connor of the National Air and Space Museum appeared first on Smithsonian Insider.

Many animals change sex at some point in their lives, often after reaching a certain size. Snails called slipper limpets begin life as males, and […]

The post The Power of Touch: Sex-changing snails switch sooner when together appeared first on Smithsonian Insider.

Laura O'Regan, Giancarlo Barone, Rozita Adib, Chang Gok Woo, Hui Jeong Jeong, Emily L. Richardson, Mark W. Richards, Patricia A.J. Muller, Spencer J. Collis, Dean A. Fennell, Jene Choi, Richard Bayliss, and Andrew M. Fry

EML4-ALK is an oncogenic fusion present in ~5% non-small cell lung cancers. However, alternative breakpoints in the EML4 gene lead to distinct variants with different patient outcomes. Here, we show in cell models that EML4-ALK variant 3 (V3), which is linked to accelerated metastatic spread, causes microtubule stabilization, formation of extended cytoplasmic protrusions and increased cell migration. It also recruits the NEK9 and NEK7 kinase to microtubules via the N-terminal EML4 microtubule-binding region. Overexpression of wild-type EML4 as well as constitutive activation of NEK9 also perturb cell morphology and accelerate migration in a microtubule-dependent manner that requires the downstream kinase NEK7 but not ALK activity. Strikingly, elevated NEK9 expression is associated with reduced progression-free survival in EML4-ALK patients. Hence, we propose that EML4-ALK V3 promotes microtubule stabilization through NEK9 and NEK7 leading to increased cell migration. This represents a novel actionable pathway that could drive metastatic disease progression in EML4-ALK lung cancer.

Kasun Buddika, Ishara S. Ariyapala, Mary A. Hazuga, Derek Riffert, and Nicholas S. Sokol

Stressed cells downregulate translation initiation and assemble membrane-less foci termed stress granules (SGs). Extensively characterized in cultured cells, the existence of such structures in stressed adult stem cell pools remain poorly characterized. Here we report that Drosophila orthologs of mammalian SG components AGO1, ATX2, CAPRIN, eIF4E, FMRP, G3BP, LIN-28, PABP, and TIAR are enriched in adult intestinal progenitor cells where they accumulate in small cytoplasmic messenger ribonucleoprotein complexes (mRNPs). Treatment with sodium arsenite or rapamycin reorganized these mRNPs into large cytoplasmic granules. Formation of these intestinal progenitor stress granules (IPSGs) depended on polysome disassembly, led to translational downregulation, and was reversible. While canonical SG nucleators ATX2 and G3BP were sufficient for IPSG formation in the absence of stress, neither of them, nor TIAR, either individually or collectively, were required for stress-induced IPSG formation. This work therefore finds that IPSGs do not assemble via a canonical mechanism, raising the possibility that other stem cell populations employ a similar stress-response mechanism.

Two grass species that had been relatively rare in the plots, Spartina patens and Distichlis spicata, began to respond vigorously to the excess nitrogen. Eventually the grasses became much more abundant. Nitrogen ultimately changed the composition of the ecosystem as well as its capacity to store carbon.

The post Scientists find excess nitrogen favors plants that respond poorly to rising CO2 appeared first on Smithsonian Insider.

On crime scene investigation shows, forensic scientists use remnants of genetic material to solve mysteries in a matter of hours. Researchers at the Smithsonian Environmental […]

The post Environmental “Forensics” Pieces Together Mysterious Plant Invasion appeared first on Smithsonian Insider.

Compared with X-rays, electron diffraction faces a crucial challenge: dynamical electron scattering compromises structure solution and its effects can only be modelled in specific cases. Dynamical scattering can be reduced experimentally by decreasing crystal size but not without a penalty, as it also reduces the overall diffracted intensity. In this article it is shown that nanometre-sized crystals from organic pharmaceuticals allow positional refinement of the hydrogen atoms, even whilst ignoring the effects of dynamical scattering during refinement. To boost the very weak diffraction data, a highly sensitive hybrid pixel detector was employed. A general likelihood-based computational approach was also introduced for further reducing the adverse effects of dynamic scattering, which significantly improved model accuracy, even for protein crystal data at substantially lower resolution.

The crystal structure of tri­phenyl­methanol, C19H16O, has been redetermined using data collected at 295 and 153 K, and is compared to the model published by Ferguson et al. over 25 years ago [Ferguson et al. (1992). Acta Cryst. C48, 1272–1275] and that published by Serrano-González et al., using neutron and X-ray diffraction data [Serrano-González et al. (1999). J. Phys. Chem. B, 103, 6215–6223]. As predicted by these authors, the hy­droxy groups are involved in weak inter­molecular hydrogen bonds in the crystal, forming tetra­hedral tetra­­mers based on the two independent mol­ecules in the asymmetric unit, one of which is placed on the threefold symmetry axis of the Roverline{3} space group. However, the reliable determination of the hy­droxy H-atom positions is difficult to achieve, for two reasons. Firstly, a positional disorder affects the full asymmetric unit, which is split over two sets of positions, with occupancy factors of ca 0.74 and 0.26. Secondly, all hy­droxy H atoms are further disordered, either by symmetry, or through a positional disorder in the case of parts placed in general positions. We show that the correct description of the hydrogen-bonding scheme is possible only if diffraction data are collected at low temperature. The pro­chiral character of the hydrogen-bonded tetra­meric supra­molecular clusters leads to enanti­omorphic three-dimensional graphs in each tetra­mer. The crystal is thus a racemic mixture of supS and supR motifs, consistent with the centro­symmetric nature of the Roverline{3} space group.

Experimental electron-density studies based on high-resolution diffraction experiments allow halogen bonds between heavy halogens to be classified. The topological properties of the electron density in Cl⋯Cl contacts vary smoothly as a function of the inter­action distance. The situation is less straightforward for halogen bonds between iodine and small electronegative nucleophiles, such as nitro­gen or oxygen, where the electron density in the bond critical point does not simply increase for shorter distances. The number of successful charge–density studies involving iodine is small, but at least individual examples for three cases have been observed. (a) Very short halogen bonds between electron-rich nucleophiles and heavy halogen atoms resemble three-centre–four-electron bonds, with a rather symmetric heavy halogen and without an appreciable σ hole. (b) For a narrow inter­mediate range of halogen bonds, the asymmetric electronic situation for the heavy halogen with a pronounced σ hole leads to rather low electron density in the (3,−1) critical point of the halogen bond; the properties of this bond critical point cannot fully describe the nature of the associated inter­action. (c) For longer and presumably weaker contacts, the electron density in the halogen bond critical point is only to a minor extent reduced by the presence of the σ hole and hence may be higher than in the aforementioned case. In addition to the electron density and its derived properties, the halogen–carbon bond distance opposite to the σ hole and the Raman frequency for the associated vibration emerge as alternative criteria to gauge the halogen-bond strength. We find exceptionally long C—I distances for tetra­fluoro­diiodo­benzene molecules in cocrystals with short halogen bonds and a significant red shift for their Raman vibrations.

Crystals of the rare earth metal polytelluride LaTe1.82(1), namely, lanthanum telluride (1/1.8), have been grown by molten alkali halide flux reactions and vapour-assisted crystallization with iodine. The two-dimensionally incommensurately modulated crystal structure has been investigated by X-ray diffraction experiments. In contrast to the tetra­gonal average structure with unit-cell dimensions of a = 4.4996 (5) and c = 9.179 (1) Å at 296 (1) K, which was solved and refined in the space group P4/nmm (No. 129), the satellite reflections are not compatible with a tetra­gonal symmetry but enforce a symmetry reduction. Possible space groups have been derived by group–subgroup relationships and by consideration of previous reports on similar rare earth metal polychalcogenide structures. Two structural models in the ortho­rhom­bic superspace group, i.e. Pmmn(α,β,1 over 2)000(−α,β,1 over 2)000 (No. 59.2.51.39) and Pm21n(α,β,1 over 2)000(−α,β,1 over 2)000 (No. 31.2.51.35), with modulation wave vectors q1 = αa* + βb* + 1 over 2c* and q2 = −αa* + βb* + 1 over 2c* [α = 0.272 (1) and β = 0.314 (1)], have been established and evaluated against each other. The modulation describes the distribution of defects in the planar [Te] layer, coupled to a displacive modulation due to the formation of different Te anions. The bonding situation in the planar [Te] layer and the different Te anion species have been investigated by density functional theory (DFT) methods and an electron localizability indicator (ELI-D)-based bonding analysis on three different approximants. The temperature-dependent electrical resistance revealed a semiconducting behaviour with an estimated band gap of 0.17 eV.

Norbert Volkmar
Apr 24, 2020; 133:jcs243519-jcs243519
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Jordi Lambert
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Cancer-causing chemicals that occur naturally in foods are far more numerous in the human diet than synthetic carcinogens, yet both types are consumed at levels so low that they currently appear to pose little threat to human health, a committee of the National Research Council said in a report released today.

A new report from the National Research Council has upheld the listing of styrene as “reasonably anticipated to be a human carcinogen” in the National Toxicology Program’s 12th Report on Carcinogens (RoC).

A new report from the National Research Council has upheld the listing of formaldehyde as “known to be a human carcinogen” in the National Toxicology Program 12th Report on Carcinogens (RoC).

A new report from the National Academies of Sciences, Engineering, and Medicine offers guidance to the Consumer Product Safety Commission (CPSC) on how to conduct a hazard assessment of nonpolymeric, additive organohalogen flame retardants (OFRs), which are used in some consumer products.

NFL Commissioner Roger Goodell talks during a press conference at the Hilton Hotel on Sept. 19, 2014 in New York City. Goodell spoke about the NFL's failure to address domestic violence, sexual assault and drug abuse in the league.; Credit: Elsa/Getty Images

Update 1:04 p.m. Goodell: 'Same mistakes can never be repeated'

Commissioner Roger Goodell says the NFL wants to implement new personal conduct policies by the Super Bowl. At a news conference Friday, Goodell made his first public statements in more than a week about the rash of NFL players involved in domestic violence. He did not announce any specific changes, but said he has not considered resigning.

"Unfortunately, over the past several weeks, we have seen all too much of the NFL doing wrong," he said. "That starts with me."

The league has faced increasing criticism that it has not acted quickly or emphatically enough concerning the domestic abuse cases.

The commissioner reiterated that he botched the handling of the Ray Rice case.

"The same mistakes can never be repeated," he said.

Goodell now oversees all personal conduct cases, deciding guilt and penalties.

He said he believes he has the support of the NFL's owners, his bosses.

"That has been clear to me," he said.

The Indianapolis Colts' Darius Butler was among those who tweeted criticism of the press conference:

Colts tweet 1

Colts tweet 2

The commissioner and some NFL teams have been heavily criticized for lenient or delayed punishment of Rice, Adrian Peterson and other players involved in recent domestic violence cases. Less than three weeks into the season, five such cases have made headlines, the others involving Greg Hardy, Ray McDonald and Jonathan Dwyer.

Vikings star running back Peterson, Carolina defensive end Hardy and Arizona running back Dwyer are on a special commissioner's exemption list and are being paid while they go through the legal process. McDonald, a defensive end for San Francisco, continues to practice and play while being investigated on suspicion of domestic violence.

As these cases have come to light, such groups as the National Organization of Women and league partners and sponsors have come down hard on the NFL to be more responsive in dealing with them. Congress also is watching to see how the NFL reacts.

In response to the criticism, the NFL announced it is partnering with a domestic violence hotline and a sexual violence resource center.

Goodell also said in a memo to the clubs late Thursday that within the next 30 days, all NFL and team personnel will participate in education sessions on domestic violence and sexual assault. The memo said the league will work with the union in providing the "information and tools to understand and recognize domestic violence and sexual assault."

The league will provide financial, operational and promotional support to the National Domestic Violence Hotline and the National Sexual Violence Resource Center.

12:07 p.m. Roger Goodell to break silence on domestic abuse and the NFL

Roger Goodell will make his first public statements in more than a week about the rash of NFL players involved in domestic violence when he holds a news conference Friday.

The NFL commissioner will address the league's personal conduct policy. The league has faced increasing criticism it has not acted quickly or emphatically enough concerning the domestic abuse cases.

His last public appearance was at a high school in North Carolina on Sept. 10.

The commissioner and some NFL teams have been heavily criticized for lenient or delayed punishment of Ray Rice, Adrian Peterson and other players involved in recent domestic violence cases. Less than three weeks into the season, five such cases have made headlines, the others involving Greg Hardy, Ray McDonald and Jonathan Dwyer.

Vikings star running back Peterson, Carolina defensive end Hardy and Arizona running back Dwyer are on a special commissioner's exemption list and are being paid while they go through the legal process. McDonald, a defensive end for San Francisco, continues to practice and play while being investigated on suspicion of domestic violence.

As these cases have come to light, such groups as the National Organization of Women and league partners and sponsors have come down hard on the NFL to be more responsive in dealing with them. Congress also is watching to see how the NFL reacts.

In response to the criticism, the NFL announced it is partnering with a domestic violence hotline and a sexual violence resource center.

Goodell also said in a memo to the clubs late Thursday that within the next 30 days, all NFL and team personnel will participate in education sessions on domestic violence and sexual assault. The memo said the league will work with the union in providing the "information and tools to understand and recognize domestic violence and sexual assault."

The league will provide financial, operational and promotional support to the National Domestic Violence Hotline and the National Sexual Violence Resource Center.

"These commitments will enable both the hotline and NSVRC to help more people affected by domestic violence and sexual assault," Goodell said in the memo.

The National Domestic Violence Hotline provides domestic violence victims and survivors access to a national network of resources and shelters. It is available 24 hours a day, seven days a week in 170 languages. Goodell noted that the hotline received 84 percent more calls from Sept. 8-15, and the organization said more than 50 percent of those calls went unanswered because of lack of staff.

"The hotline will add 25 full-time advocates over the next few weeks that will result in an additional 750 calls a day being answered," he said.

NSVRC supports sexual violence coalitions across the United States. The NFL's initial support will be directed toward state coalitions to provide additional resources to sexual assault hotlines.

This story has been updated.

Individuals can assess how their behaviour is affecting nitrogen pollution with a newly developed nitrogen footprint calculator, which was developed by a team from the University of Virginia (U.S.) and the Energy Research Centre (ECN, the Netherlands). For many people in wealthy countries, reducing protein consumption to the recommended levels and reducing the amount of red meat and energy they consume would significantly lower their nitrogen footprint.

The presence of wild bees alongside honeybees was found to increase almond orchard production in a recent study. The findings demonstrate how increased biodiversity enhances ecosystem services, such as pollination, and provide an opportunity to increase agricultural yields whilst also benefitting wildlife.

Emissions of sulphur dioxide (SO2) and nitrogen oxides (NOx) have fallen significantly across Europe since 1960. According to recent research, this is caused by a combination of factors including improved energy efficiency, a changing fuel mix and specific emission control measures. At the same time CO₂ emissions have only increased moderately, mainly due to improvements in energy efficiency.

A new approach to modelling land use change developed at UBC could help cities and towns better coordinate their land-use planning efforts.

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Khudoleĭ, K. M

Fire frequency is changing globally, yet it is unclear how such changes affect soil carbon and nitrogen storage, and, in turn, impact on ecosystem productivity. A study was conducted to evaluate how increased fire frequency drives changes in soil carbon and nitrogen over multiple decades. Data from 48 sites that have experienced altered fire frequency were analysed, spanning up to 65 years. The meta-analysis found that frequently burned sites experienced a significant decline in surface soil carbon and nitrogen over time — on average having 36% less carbon and 38% less nitrogen, after 64 years, than sites that were protected from fire. The researchers also observed comparable changes in an independent field dataset and in dynamic model simulations of global vegetation. The results indicate that future changes in fire frequency may lead to long-term changes in the amount of carbon and nitrogen stored in soils, especially in savanna grasslands and broadleaf forests. This has implications for the global carbon cycle and for ecosystem productivity and should, therefore, be considered in the design and implementation of relevant policy instruments.

New research has shown that policy measures in Denmark have successfully reduced total nitrogen loading to 10 estuaries by 39% in recent decades. However, to fully meet the targets of the EU Nitrates Directive and comply with the EU Water Framework Directive in a cost-effective manner, further mitigation measures must be tailored and focused to particular areas.

Ireland's national agri-environment scheme can reduce nitrate leaching from beef farming, shows a recent study. Nitrate leached at an average rate of 17.3 kilograms per hectare (kg/ha) on studied plots which complied with the scheme. This compares with 63.1 kg/ha on intensively farmed plots. The programme can therefore help Ireland meet requirements of the EU’s Water Framework Directive (WFD) and Nitrates Directive, the researchers suggest.

Constructed wetlands can remove disease-causing bacteria from wastewater, but their performance is highly dependent on the systems they use, a new study shows. Researchers reviewed results from a wide range of studies on constructed wetlands and found that combining different approaches increased removal of bacteria. However, further research and improvement of wetland systems is required to produce water that is safe for reuse.

Areas of mariculture — where marine organisms are cultivated for food — have been identified as important source areas for the dispersal of invasive alien species (IAS) via artificial floating litter. In order to identify IAS at high risk of dispersal via this method, researchers have analysed fouled anthropogenic litter sampled on beaches in two important European mariculture areas. Overall, the team detected eight aquaculture-related IAS attached to anthropogenic litter. All of these species are well adapted to rafting on artificial surfaces and have high potential to disperse in this way, suggesting that they are suitable candidates for closer monitoring and policy action in the future.

The presence of wild bees alongside honeybees was found to increase almond orchard production in a recent study. The findings demonstrate how increased biodiversity enhances ecosystem services, such as pollination, and provide an opportunity to increase agricultural yields whilst also benefitting wildlife.

Increased plant biodiversity improves grassland soil quality by boosting its nitrogen levels, even in the absence of nitrogen-fixing plants, recent research has found. Previous research has shown that grasslands with higher biodiversity had higher levels of carbon and nitrogen. However, in the case of nitrogen it has been suggested that this was purely a result of increased numbers of nitrogen-fixing legumes, such as clover. This study was the first to show that, even without legumes, increased numbers of grassland species increased both carbon and nitrogen soil stocks.

Milder winters under climate change could increase the extent of alder tree (Alnus glutinosa) decline in Europe due to the increased spread of the pathogen Phytophthora alni, a recent study has found. However, this may be offset by hotter summers, which reduce the severity of the disease.

Increased soil biodiversity can reduce nitrogen pollution, improve nutrient uptake by plants and even increase crop yields, new research suggests. The two-year study found that levels of nitrogen leaching from soil with an abundant soil life were nearly 25% lower than for soil with a reduced level of soil life. Practices which enhance soil biodiversity such as reduced tilling, crop rotation and organic farming may therefore help reduce the environmental impacts of fertilisers and improve agricultural sustainability, the researchers say.

Pollination and pest control are essential to global food production. This study shows that — as well as their individual benefits — they have synergistic effects on yield. Their joint effect increased the yield of oilseed rape by 23%, and the economic benefit from their combined effects was almost twice that of their individual contributions. These findings have implications for sustainable agricultural policy.

Computer models can be powerful tools when developing policies to address nitrogen pollution from agriculture. In a new study, researchers have made recommendations regarding the best design and use of these models to aid the effective implementation of European legislation on nitrogen.

Brown trout (Salmo trutta) embryos exposed to oestrogen during development hatched earlier, grew more slowly and had a lower heart rate than unexposed individuals, according to a recent Swiss study. These findings may indicate that oestrogen pollution in some European rivers is contributing to the decline of wild populations of such species.

The risk of eutrophication as a result of nitrogen and phosphorus pollution in Europe’s freshwaters fell by 22% in lakes and by 38% in rivers between 1985 and 2011, new research has shown. The researchers analysed data across 88 European river basins using a new statistical approach which could be used to help identify factors which increase eutrophication risks.

Nitrogen and phosphorus pollution change the relationship between the tropical coral Stylophora pistillata and the algae living inside its tissues, a recent study has found. The researchers say the pollutants, mainly from urban and agricultural discharges, affect algae photosynthesis and the essential transfer of carbon from algae to the coral.

Farming fish together with seaweed and other species could help improve the sustainability of aquaculture and reduce pollution. A new study provides a tool for designing sustainable fish farming systems and calculates their potential to recycle waste. An example of a salmon farming system incorporating seaweed and sea urchins could reduce nitrogen releases to the environment by 45%.

Oestrogens are ‘female’ hormones that can enter the aquatic environment after excretion by humans and animals, causing ‘feminisation’ of male fish. This study carried out a risk assessment for oestrogen-like endocrine disruption in the UK in the 2050s, based on likely changes to the human population, river flows and temperature. The authors found that risk is likely to increase under future conditions and recommend further research to assess whether improving sewage treatment could reduce oestrogen pollution.

Soil biodiversity, soil quality, and soil health are integral to protecting the natural environment. Soils are crucial to food production and human well-being, as highlighted by the UN Sustainable Development Goals (SDGs). The abundance of soil biota is of great importance for the provision of associated ecosystem services (ES) and fundamental driver of self-regulation in soil. This study explores how the presence, or absence, of earthworms affects aspects of crop health and productivity, focusing on their shielding of winter wheat from the toxic plant fungi Fusarium.

A new study suggests that widespread adoption of hydrogen fuel could have major benefits for tackling climate change and air pollution. The researchers modelled the impacts of replacing petrol with hydrogen as a fuel for cars and claim their methods, which employ a new modelling tool, could be useful in planning and policymaking.

Using hydrogen as an energy carrier can help reduce air pollution and greenhouse gas (GHG) emissions associated with fossil fuels, according to recent research. However, if used on a large-scale, it is important that hydrogen does not leak significantly into the atmosphere as it might have some negative environmental effects, such as increasing the lifetime of methane, increasing climate effects and causing some depletion of the ozone layer.

The EU's Nitrates Directive has led to significant decreases in nitrogen pollution in Europe, a new study suggests. Modelled scenarios with and without implementation of the Directive showed that it had resulted in a 16% reduction of nitrate leaching by 2008. These improvements could be further increased as implementation becomes stricter, the researchers conclude.