Did the earth move for you? British Geological Survey has asked if Cumbrians felt an earth tremor last week  News & Star

Solution structure of β-amylase 2 from Arabidopsis thaliana shows the role of the conserved N-terminus in enzyme tetramer formation.

Structures of the immunodominant protein P46 from M. hyopneumoniae has been determined by X-ray crystallography and it is shown that P46 can bind a diversity of oligosaccharides, particularly xylose, which exhibits a very high affinity for this protein. Structures of a monoclonal antibody, both alone and in complex with P46, that was raised against M. hyopnemoniae cells and specifically recognizes P46 are also reported.

The crystal structures of dirubidium potassium dysprosium bis­(vanadate), Rb2KDy(VO4)2, and caesium potassium gadolinium bis­(vanadate), Cs1.52K1.48Gd(VO4)2, were solved from single-crystal X-ray diffraction data. Both compounds, synthesized by the reactive flux method, crystallize in the space group Poverline{3}m1 with the glaserite structure type. VO4 tetra­hedra are linked to DyO6 or GdO6 octa­hedra by common vertices to form sheets stacking along the c axis. The large twelve-coordinate Cs+ or Rb+ cations are sandwiched between these layers in tunnels along the a and b axes, while the K+ cations, surrounded by ten oxygen atoms, are localized in cavities.

Copper-containing nitrite reductases (CuNiRs) that convert NO2− to NO via a CuCAT–His–Cys–CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD−, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2− a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.

Meta-magnetic shape-memory alloys combine ferroelastic order with ferromagnetic order and exhibit attractive multifunctional properties, but they are extremely brittle, showing hardly any tensile deformability, which impedes their practical application. Here, for the first time, an Ni–Cu–Co–Mn–In microwire has been developed that simultaneously exhibits a magnetic field-induced first-order meta-magnetic phase transition and huge tensile superelasticity. A temperature-dependent in situ synchrotron high-energy X-ray diffraction investigation reveals that the martensite of this Ni43.7Cu1.5Co5.1Mn36.7In13 microwire shows a monoclinic six-layered modulated structure and the austenite shows a cubic structure. This microwire exhibits an oligocrystalline structure with bamboo grains, which remarkably reduces the strain incompatibility during deformation and martensitic transformation. As a result, huge tensile superelasticity with a recoverable strain of 13% is achieved in the microwire. This huge tensile superelasticity is in agreement with our theoretical calculations based on the crystal structure and lattice correspondence of austenite and martensite and the crystallographic orientation of the grains. Owing to the large magnetization difference between austenite and martensite, a pronounced magnetic field-induced magnetostructural transition is achieved in the microwire, which could give rise to a variety of magnetically driven functional properties. For example, a large magnetocaloric effect with an isothermal entropy change of 12.7 J kg−1 K−1 (under 5 T) is obtained. The realization of magnetic-field- and tensile-stress-induced structural transformations in the microwire may pave the way for exploiting the multifunctional properties under the coupling of magnetic field and stress for applications in miniature multifunctional devices.

Indanomycin is biosynthesized by a hybrid nonribosomal peptide synthase/polyketide synthase (NRPS/PKS) followed by a number of `tailoring' steps to form the two ring systems that are present in the mature product. It had previously been hypothesized that the indane ring of indanomycin was formed by the action of IdmH using a Diels–Alder reaction. Here, the crystal structure of a selenomethionine-labelled truncated form of IdmH (IdmH-Δ99–107) was solved using single-wavelength anomalous dispersion (SAD) phasing. This truncated variant allows consistent and easy crystallization, but importantly the structure was used as a search model in molecular replacement, allowing the full-length IdmH structure to be determined to 2.7 Å resolution. IdmH is a homodimer, with the individual protomers consisting of an α+β barrel. Each protomer contains a deep hydrophobic pocket which is proposed to constitute the active site of the enzyme. To investigate the reaction catalysed by IdmH, 88% of the backbone NMR resonances were assigned, and using chemical shift perturbation of [15N]-labelled IdmH it was demonstrated that indanomycin binds in the active-site pocket. Finally, combined quantum mechanical/molecular mechanical (QM/MM) modelling of the IdmH reaction shows that the active site of the enzyme provides an appropriate environment to promote indane-ring formation, supporting the assignment of IdmH as the key Diels–Alderase catalysing the final step in the biosynthesis of indanomycin through a similar mechanism to other recently characterized Diels–Alderases involved in polyketide-tailoring reactions. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at https://proteopedia.org/w/Journal:IUCrJ:S2052252519012399.

In the past three years, Dirac half-metals (DHMs) have attracted considerable attention and become a high-profile topic in spintronics becuase of their excellent physical properties such as 100% spin polarization and massless Dirac fermions. Two-dimensional DHMs proposed recently have not yet been experimentally synthesized and thus remain theoretical. As a result, their characteristics cannot be experimentally confirmed. In addition, many theoretically predicted Dirac materials have only a single cone, resulting in a nonlinear electromagnetic response with insufficient intensity and inadequate transport carrier efficiency near the Fermi level. Therefore, after several attempts, we have focused on a novel class of DHMs with multiple Dirac crossings to address the above limitations. In particular, we direct our attention to three-dimensional bulk materials. In this study, the discovery via first principles of an experimentally synthesized DHM LaNiO3 with many Dirac cones and complete spin polarization near the Fermi level is reported. It is also shown that the crystal structures of these materials are strongly correlated with their physical properties. The results indicate that many rhombohedral materials with the general formula LnNiO3 (Ln = La, Ce, Nd, Pm, Gd, Tb, Dy, Ho, Er, Lu) in the space group R3c are potential DHMs with multiple Dirac cones.

Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.

Using the typical WC–Co cemented carbide as an example, the interactions of dislocations within the ceramic matrix and the binder metal, as well as the possible cooperation and competition between the matrix and binder during deformation of the nanocrystalline cermets, were studied by molecular dynamics simulations. It was found that at the same level of strain, the dislocations in Co have more complex configurations in the cermet with higher Co content. With loading, the ratio between mobile and sessile dislocations in Co becomes stable earlier in the high-Co cermet. The strain threshold for the nucleation of dislocations in WC increases with Co content. At the later stage of deformation, the growth rate of WC dislocation density increases more rapidly in the cermet with lower Co content, which exhibits an opposite tendency compared with Co dislocation density. The relative contribution of Co and WC to the plasticity of the cermet varies in the deformation process. With a low Co content, the density of WC dislocations becomes higher than that of Co dislocations at larger strains, indicating that WC may contribute more than Co to the plasticity of the nanocrystalline cermet at the final deformation stage. The findings in the present work will be applicable to a large variety of ceramic–metal composite materials.

Malaria is a devastating disease caused by a protozoan parasite. It affects over 300 million individuals and results in over 400 000 deaths annually, most of whom are young children under the age of five. Hexokinase, the first enzyme in glucose metabolism, plays an important role in the infection process and represents a promising target for therapeutic intervention. Here, cryo-EM structures of two conformational states of Plasmodium vivax hexokinase (PvHK) are reported at resolutions of ∼3 Å. It is shown that unlike other known hexokinase structures, PvHK displays a unique tetrameric organization (∼220 kDa) that can exist in either open or closed quaternary conformational states. Despite the resemblance of the active site of PvHK to its mammalian counterparts, this tetrameric organization is distinct from that of human hexokinases, providing a foundation for the structure-guided design of parasite-selective antimalarial drugs.

Human septins 3, 9 and 12 are the only members of a specific subgroup of septins that display several unusual features, including the absence of a C-terminal coiled coil. This particular subgroup (the SEPT3 septins) are present in rod-like octameric protofilaments but are lacking in similar hexameric assemblies, which only contain representatives of the three remaining subgroups. Both hexamers and octamers can self-assemble into mixed filaments by end-to-end association, implying that the SEPT3 septins may facilitate polymerization but not necessarily function. These filaments frequently associate into higher order complexes which associate with biological membranes, triggering a wide range of cellular events. In the present work, a complete compendium of crystal structures for the GTP-binding domains of all of the SEPT3 subgroup members when bound to either GDP or to a GTP analogue is provided. The structures reveal a unique degree of plasticity at one of the filamentous interfaces (dubbed NC). Specifically, structures of the GDP and GTPγS complexes of SEPT9 reveal a squeezing mechanism at the NC interface which would expel a polybasic region from its binding site and render it free to interact with negatively charged membranes. On the other hand, a polyacidic region associated with helix α5', the orientation of which is particular to this subgroup, provides a safe haven for the polybasic region when retracted within the interface. Together, these results suggest a mechanism which couples GTP binding and hydrolysis to membrane association and implies a unique role for the SEPT3 subgroup in this process. These observations can be accounted for by constellations of specific amino-acid residues that are found only in this subgroup and by the absence of the C-terminal coiled coil. Such conclusions can only be reached owing to the completeness of the structural studies presented here.

Current software tools for the automated building of models for macro­molecular X-ray crystal structures are capable of assembling high-quality models for ordered macromolecule and small-molecule scattering components with minimal or no user supervision. Many of these tools also incorporate robust functionality for modelling the ordered water molecules that are found in nearly all macromolecular crystal structures. However, no current tools focus on differentiating these ubiquitous water molecules from other frequently occurring multi-atom solvent species, such as sulfate, or the automated building of models for such species. PeakProbe has been developed specifically to address the need for such a tool. PeakProbe predicts likely solvent models for a given point (termed a `peak') in a structure based on analysis (`probing') of its local electron density and chemical environment. PeakProbe maps a total of 19 resolution-dependent features associated with electron density and two associated with the local chemical environment to a two-dimensional score space that is independent of resolution. Peaks are classified based on the relative frequencies with which four different classes of solvent (including water) are observed within a given region of this score space as determined by large-scale sampling of solvent models in the Protein Data Bank. Designed to classify peaks generated from difference density maxima, PeakProbe also incorporates functionality for identifying peaks associated with model errors or clusters of peaks likely to correspond to multi-atom solvent, and for the validation of existing solvent models using solvent-omit electron-density maps. When tasked with classifying peaks into one of four distinct solvent classes, PeakProbe achieves greater than 99% accuracy for both peaks derived directly from the atomic coordinates of existing solvent models and those based on difference density maxima. While the program is still under development, a fully functional version is publicly available. PeakProbe makes extensive use of cctbx libraries, and requires a PHENIX licence and an up-to-date phenix.python environment for execution.

Afamin, which is a human blood plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome, poses multiple challenges for crystallographic structure determination, both practically and in analysis of the models. Several hundred crystals were analysed, and an unusual variability in cell volume and difficulty in solving the structure despite an ∼34% sequence identity with nonglycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite the simplified glycosylation in insect cell-expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilize the orthorhombic crystal form, reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational state of the protein. An iterative strategy using fully automatic experiments available on MASSIF-1 was used to quickly determine the optimal protocol to achieve the phase transition, which should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computational modelling purposes given that the conformational state of the binding sites and the electron density in the binding site, which is likely to result from PEGs, greatly varies between models. This also holds for the analysis of nonspecific low-affinity ligands, where often a variety of fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin also seems to bind gadoteridol, a magnetic resonance imaging contrast compound, in at least two sites. One pair of gadoteridol molecules is located near the human albumin Sudlow site, and a second gadoteridol molecule is located at an intermolecular site in proximity to domain IA. The data from the co-crystals support modern metrics of data quality in the context of the information that can be gleaned from data sets that would be abandoned on classical measures.

Atrazine is an s-triazine-based herbicide that is used in many countries around the world in many millions of tons per year. A small number of organisms, such as Pseudomonas sp. strain ADP, have evolved to use this modified s-triazine as a food source, and the various genes required to metabolize atrazine can be found on a single plasmid. The atomic structures of seven of the eight proteins involved in the breakdown of atrazine by Pseudomonas sp. strain ADP have been determined by X-ray crystallography, but the structures of the proteins required by the cell to import atrazine for use as an energy source are still lacking. The structure of AtzT, a periplasmic binding protein that may be involved in the transport of a derivative of atrazine, 2-hydroxyatrazine, into the cell for mineralization, has now been determined. The structure was determined by SAD phasing using an ethylmercury phosphate derivative that diffracted X-rays to beyond 1.9 Å resolution. `Native' (guanine-bound) and 2-hydroxyatrazine-bound structures were also determined to high resolution (1.67 and 1.65 Å, respectively), showing that 2-hydroxyatrazine binds in a similar way to the purportedly native ligand. Structural similarities led to the belief that it may be possible to evolve AtzT from a purine-binding protein to a protein that can bind and detect atrazine in the environment.

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.

Inelastic X-ray scattering is a powerful and versatile technique for studying lattice dynamics in materials of scientific and technological importance. In this article, the design and capabilities of the momentum-resolved high-energy-resolution inelastic X-ray spectrometer (HERIX) at beamline 30-ID of the Advanced Photon Source are reported. The instrument operates at 23.724 keV and has an energy resolution of 1.3–1.7 meV. It can accommodate momentum transfers of up to 72  nm−1, at a typical X-ray flux of 4.5 × 109 photons s−1 meV−1 at the sample. A suite of in situ sample environments are provided, including high pressure, static magnetic fields and uniaxial strains, all at high or cryogenic temperatures.

The electron linear accelerators driving modern X-ray free-electron lasers can emit intense, tunable, quasi-monochromatic terahertz (THz) transients with peak electric fields of V Å−1 and peak magnetic fields in excess of 10 T when a purpose-built, compact, superconducting THz undulator is implemented. New research avenues such as X-ray movies of THz-driven mode-selective chemistry come into reach by making dual use of the ultra-short GeV electron bunches, possible by a rather minor extension of the infrastructure.

The laser annealing process for AuNi nanoparticles has been visualized using coherent X-ray diffraction imaging (CXDI). AuNi bimetallic alloy nanoparticles, originally phase separated due to the miscibility gap, transform to metastable mixed alloy particles with rounded surface as they are irradiated by laser pulses. A three-dimensional CXDI shows that the internal part of the AuNi particles is in the mixed phase with preferred compositions at ∼29 at% of Au and ∼90 at% of Au.

The optical design of a Hettrick–Underwood-style soft X-ray spectrometer with Wolter type 1 mirrors is presented. The spectrometer with a nominal length of 3.1 m can achieve a high resolving power (resolving power higher than 10000) in the soft X-ray regime when a small source beam (<3 µm in the grating dispersion direction) and small pixel detector (5 µm effective pixel size) are used. Adding Wolter mirrors to the spectrometer before its dispersive elements can realize the spatial imaging capability, which finds applications in the spectroscopic studies of spatially dependent electronic structures in tandem catalysts, heterostructures, etc. In the pump–probe experiments where the pump beam perturbs the materials followed by the time-delayed probe beam to reveal the transient evolution of electronic structures, the imaging capability of the Wolter mirrors can offer the pixel-equivalent femtosecond time delay between the pump and probe beams when their wavefronts are not collinear. In combination with some special sample handing systems, such as liquid jets and droplets, the imaging capability can also be used to study the time-dependent electronic structure of chemical transformation spanning multiple time domains from microseconds to nanoseconds. The proposed Wolter mirrors can also be adopted to the existing soft X-ray spectrometers that use the Hettrick–Underwood optical scheme, expanding their capabilities in materials research.

It is shown that the 2p3d resonant inelastic X-ray scattering intensity is distorted by saturation and self-absorption effects, i.e. by incident-energy-dependent saturation and by emission-energy-dependent self-absorption.

Convolutional neural networks are useful for classifying grazing-incidence small-angle X-ray scattering patterns. They are also useful for classifying real experimental data.

Single-crystal elastic constants have been derived by lattice strain measurements using neutron diffraction on polycrystalline Ti-6Al-4V, Ti-6Al-2Sn-4Zr-6Mo and Ti-3Al-8V-6Cr-4Zr-4Mo alloy samples. A variety of model approximations for the grain-to-grain interactions, namely approaches by Voigt, Reuss, Hill, Kroener, de Wit and Matthies, including texture weightings, have been applied and compared. A load-transfer approach for multiphase alloys was also implemented and the results are compared with single-phase data. For the materials under investigation, the results for multiphase alloys agree well with the results for single-phase materials in the corresponding phases. In this respect, all eight elastic constants in the dual-phase Ti-6Al-2Sn-4Zr-6Mo alloy have been derived for the first time.

Errors in the article by Opara, Martiel, Arnold, Braun, Stahlberg, Makita, David & Padeste [J. Appl. Cryst. (2017), 50, 909–918] are corrected.

The residual strain distribution has been measured as a function of depth in both top coat and bond coat in as-received and heat-treated air plasma sprayed thermal barrier coating samples. High-energy synchrotron X-ray beams were used in transmission to produce full Debye–Scherrer rings whose non-circular aspect ratio gave the in-plane and out-of-plane strains far more efficiently than the sin2ψ method. The residual strain in the bond coat is found to be tensile and the strain in the β phase of the as-received sample was measured. The residual strains observed in the top coat were generally compressive (increasing towards the interface), with two kinds of nonlinear trend. These was a `jump' feature near the interface, and in some cases there was another `jump' feature near the surface. It is shown how these trend differences can be correlated to cracks in the coating.

An energy resolution of <10 µeV for the measurement of phonon energy change is achieved with the inelastic neutron spin echo technique on a conventional neutron triple-axis spectrometer.

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.

Five billion years from now, our Milky Way galaxy will collide with the Andromeda galaxy. This will mark a moment of both destruction and creation. The galaxies will lose their separate identities as they merge into one. At the same time, cosmic clouds of gas and dust will smash together, triggering the birth of new stars.

The post The Spitzer Photo Atlas of Galactic “Train Wrecks” appeared first on Smithsonian Insider.

Smithsonian scientists have confirmed that chytridiomycosis, a rapidly spreading amphibian disease, has reached a site near Panama’s Darien region. This was the last area in the entire mountainous neotropics to be free of the disease. This is troubling news for the Panama Amphibian Rescue and Conservation Project, a consortium of nine U.S. and Panamanian institutions that aims to rescue 20 species of frogs in imminent danger of extinction.

The post Deadly amphibian disease detected in the last disease-free region of Central America appeared first on Smithsonian Insider.

To prevent the loss of Inupiaq words for ice and the knowledge that it embodies, Igor Krupnik, ethnologist at the Arctic Studies Center of the National Museum of Natural History, and Wales native Winton Weyapuk Jr., recently compiled an illustrated dictionary of some 120 Kingikmiut words used in Wales to describe different types of ice.

The post Dictionary captures traditional ice knowledge of the Inupiaq people of Wales, Alaska appeared first on Smithsonian Insider.

Alaska’s pristine coastline is ripe for an influx of invasive marine species such as the European green crab and the rough periwinkle (an Atlantic sea snail) warns a new study by a team of scientists from the Smithsonian Environmental Research Center.

The post Alaska’s cold waters no barrier to invasive marine species, scientists say appeared first on Smithsonian Insider.

Observations by the NASA/ESA Hubble Space Telescope have come up with a new class of planet, a waterworld enshrouded by a thick, steamy atmosphere. It’s smaller than Uranus but larger than Earth.

The post Waterworld enshrouded by a thick, steamy atmosphere is new class of planet appeared first on Smithsonian Insider.

The Sun’s Active Region 1429 has been shooting off flares and coronal mass ejections since it rotated into Earth’s view on March 2, 2012. Two X-class flares have been released overnight, an X1.3 and an X5.4.

The post X-Class flares released by the Sun, March 6, captured by Atmospheric Imaging Assembly appeared first on Smithsonian Insider.

The same device used to detect early warning signs of heart disease in humans will now benefit two male sub-adult gorillas at the Smithsonian’s National Zoo.

The post Heart disease study to benefit lowland gorillas at the National Zoo appeared first on Smithsonian Insider.

The newfound jets may be related to mysterious gamma-ray bubbles that Fermi detected in 2010. Those bubbles also stretch 27,000 light-years from the center of the Milky Way.

The post Ghostly gamma-ray beams blast from Milky Way’s center appeared first on Smithsonian Insider.

“The Age of Plastic: Ingenuity + Responsibility” a public Smithsonian Symposium that will take an uncommon look at the most common of materials. On Thursday, June […]

The post The Age of Plastic: Symposium June 7 & 8, 2012 appeared first on Smithsonian Insider.

On June 7, 2011, our Sun erupted, blasting tons of hot plasma into space. Some of that plasma splashed back down onto the Sun’s surface, […]

The post Solar splashdown appeared first on Smithsonian Insider.

In June, Odile Madden, materials scientist at the Smithsonian’s Museum Conservation Institute, was a participant on a 6-day interdisciplinary expedition to a number of beaches […]

The post Q&A: Plastics expert Odile Madden on plastic debris in Alaskan waters appeared first on Smithsonian Insider.

In 2009, during an expedition by a Russian research ship, a small length of yellow flesh about 5 centimeters long was dredged up from the […]

The post Last seen 140 years ago, deep sea worm resurfaces, delighting scientists appeared first on Smithsonian Insider.

Grow fast, die young is not a lifestyle normally associated with trees. But in the forests of the Northeastern United States the red maple follows […]

The post Effects of human impact are long lasting for forests in Northeast U.S. appeared first on Smithsonian Insider.

A newly released study focusing on an extinct species, the Caribbean monk seal (Monachus tropicalis), has revealed just how evolutionarily unique its only two living […]

The post Too valuable to lose: Extinct relative reveals rarity of last two remaining monk seal species appeared first on Smithsonian Insider.

For life as we know it to develop on other planets, those planets would need liquid water, or oceans. Geologic evidence suggests that Earth’s oceans […]

The post Super-Earths Have Long-Lasting Oceans appeared first on Smithsonian Insider.

For more than 60 years, researchers have tried to successfully cryopreserve (or freeze) the embryo of zebrafish, a species that is an important medical model […]

The post Gold nanotechnology and lasers used to successfully freeze fish embryos appeared first on Smithsonian Insider.

The world’s most indestructible species, the tardigrade, an eight-legged micro-animal, also known as the water bear, will survive until the Sun dies, according to a […]

The post Study determines microscopic water bears will be Earth’s last survivors appeared first on Smithsonian Insider.

In a new study in which one of humankind’s most high-tech tools was used to analyze one of its most primitive, scientists have uncovered evidence […]

The post Laser beams unveil secrets locked inside primitive stone spear points appeared first on Smithsonian Insider.

Plastic debris floating in the ocean has become a powerful new passport to far-away destinations for a wide variety of invasive species, according to new […]

The post Tsunami reveals drifting ocean plastic opens globe to invasive castaways appeared first on Smithsonian Insider.

A team of astrophysicists and planetary scientists has predicted that Neptune-like planets located near the center of the Milky Way galaxy have been transformed into […]

The post Black hole blasts may transform “Mini-Neptunes” into rocky worlds appeared first on Smithsonian Insider.

Mycoplasma hyopneumoniae is a prokaryotic pathogen that colonizes the respiratory ciliated epithelial cells in swine. Infected animals suffer respiratory lesions, causing major economic losses in the porcine industry. Characterization of the immunodominant membrane-associated proteins from M. hyopneumoniae may be instrumental in the development of new therapeutic approaches. Here, the crystal structure of P46, one of the main surface-antigen proteins, from M. hyopneumoniae is presented and shows N- and C-terminal α/β domains connected by a hinge. The structures solved in this work include a ligand-free open form of P46 (3.1 Å resolution) and two ligand-bound structures of P46 with maltose (2.5 Å resolution) and xylose (3.5 Å resolution) in open and closed conformations, respectively. The ligand-binding site is buried in the cleft between the domains at the hinge region. The two domains of P46 can rotate with respect to each other, giving open or closed alternative conformations. In agreement with this structural information, sequence analyses show similarities to substrate-binding members of the ABC transporter superfamily, with P46 facing the extracellular side as a functional subunit. In the structure with xylose, P46 was also bound to a high-affinity (Kd = 29 nM) Fab fragment from a monoclonal antibody, allowing the characterization of a structural epitope in P46 that exclusively involves residues from the C-terminal domain. The Fab structure in the complex with P46 shows only small conformational rearrangements in the six complementarity-determining regions (CDRs) with respect to the unbound Fab (the structure of which is also determined in this work at 1.95 Å resolution). The structural information that is now available should contribute to a better understanding of sugar nutrient intake by M. hyopneumoniae. This information will also allow the design of protocols and strategies for the generation of new vaccines against this important swine pathogen.