Methods for Quantitative Local Structure Analysis of Crystalline Materials Employing High Performance Computing

A fundamental computational methodology was investigated to extract quantitative local structure information from single crystal diffuse scattering data. The principles of a highly efficient, parallelizable local structure analysis using massively parallel computing resources at Oak Ridge National Laboratory (ORNL) are demonstrated on an organic hydrocarbon compound containing stacking faults, Tris(bicyclo[2.1.1]hexeno)benzene. A probabilistic model of the stacking variations with a five layer interaction depth was developed. The final model structure motif statistics are verified using the steady state distribution of Markov matrix representing the four to five layer transitions. The computations revealed that highly parallelizable “structure-clones” could replace less computationally efficient “structure lots”. Further testing of the method is under way, using a new comprehensive modeling software suite ZODS (Zürich Oak Ridge Disorder Simulations) developed in Zürich, on synchrotron and lab X-Ray data of a highly efficient light-upconversion member of the NaLnF44 [Sodium Lanthanide tetra fluoride] family. Initially, a synchrotron data set was collected at the high resolution Swiss-Norwegian Beam Line at the European Synchrotron Radiation Facility and is being analyzed. High resolution neutron diffraction data were recently collected at the time-of-flight Laue single crystal diffractometer TOPAZ at the Spallation Neutron Source at ORNL using the newly available event-mode processing. Currently, exploration of the event-mode data treatment and event based corrections for data preparation are under way. Simultaneous massively parallel local structure simulations of NaLaF4 [Sodium Lanthanum tetra fluoride] using ZODS on the National Energy Research Scientific Computing Center are in progress. A step-wise modeling approach was adopted. The largest contributors to the X-Ray diffuse scattering, La2 [Lanthanum 2] and Na2 [Sodium 2] column neighbor interactions were modeled first, followed by F1 [Fluorine 1] shift from its average position toward La [Lanthanum] and away from Na [Sodium]. This work provides a basis for streamlining diffuse scattering analysis and yields a quantitative interpretation of the local atomic arrangement of crystalline materials, which may provide valuable information for interpreting their structure property relationships

Response to novel objects and foraging tasks by common marmoset (Callithrix Jacchus) female Pairs

Many studies have shown that environmental enrichment can significantly improve the psychological well-being of captive primates, increasing the occurrence of explorative behavior and thus reducing boredom. The response of primates to enrichment devices may be affected by many factors such as species, sex, age, personality and social context. Environmental enrichment is particularly important for social primates living in unnatural social groupings (i.e. same-sex pairs or singly housed animals), who have very few, or no, benefits from the presence of social companions in addition to all the problems related to captivity (e.g. increased inactivity). This study analyses the effects of enrichment devices (i.e. novel objects and foraging tasks) on the behavior of common marmoset (Callithrix jacchus) female pairs, a species that usually lives in family groups. It aims to determine which aspects of an enrichment device are more likely to elicit explorative behaviors, and how aggressive and stress-related behaviors are affected by its presence. Overall, the marmosets explored foraging tasks significantly longer than novel objects. The type of object, which varied in size, shape and aural responsiveness (i.e. they made a noise when the monkey touched them), did not affect the response of the monkeys, but they explored objects that were placed higher in the enclosure more than those placed lower down.Younger monkeys were more attracted to the enrichment devices than the older ones. Finally, stress-related behavior (i.e. scratching) significantly decreased when the monkeys were presented with the objects; aggressive behavior as unaffected. This study supports the importance of environmental enrichment for captive primates and shows that in marmosets its effectiveness strongly depends upon the height of the device in the enclosure and the presence of hidden food. The findings can be explained ifone considers the foraging behavior of wild common marmosets. Broader applications for the research findings are suggested in relation to enrichment

StraboSpot data system for structural geology

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.StraboSpot is a geologic data system that allows researchers to digitally collect, store, and share both field and laboratory data. StraboSpot is based on how geologists actually work to collect field data; although initially developed for the structural geology research community, the approach is easily extensible to other disciplines. The data system uses two main concepts to organize data: spots and tags. A spot is any observation that characterizes a specific area, a concept applicable at any spatial scale from regional to microscopic. Spots are related in a purely spatial manner, and consequently, one spot can enclose multiple other spots that themselves contain other spots. In contrast, tags provide conceptual grouping of spots, allowing linkages between spots that are independent of their spatial position. The StraboSpot data system uses a graph database, rather than a relational database approach, to increase flexibility and to track geologically complex relationships. StraboSpot operates on two different platform types: (1) a fieldbased application that runs on iOS and Android mobile devices, which can function in either Internet-connected or disconnected environments; and (2) a web application that runs only in Internet-connected settings. We are presently engaged in incorporating microstructural data into StraboSpot, as well as expanding to include additional field-based (sedimentology, petrology) and lab-based (experimental rock deformation) data. The StraboSpot database will be linked to other existing and future databases in order to provide integration with other digital efforts in the geological sciences and allow researchers to do types of science that were not possible without easy access to digital data

Tools for crushing diatoms – opal teeth in copepods feature a rubber-like bearing composed of resilin

Diatoms are generally known for superior mechanical properties of their mineralised shells. Nevertheless, many copepod crustaceans are able to crush such shells using their mandibles. This ability very likely requires feeding tools with specific material compositions and properties. For mandibles of several copepod species silica-containing parts called opal teeth have been described. The present study reveals the existence of complex composite structures, which contain, in addition to silica, the soft and elastic protein resilin and form opal teeth with a rubber-like bearing in the mandibles of the copepod Centropages hamatus. These composite structures likely increase the efficiency of the opal teeth while simultaneously reducing the risk of mechanical damage. They are supposed to have coevolved with the diatom shells in the evolutionary arms race, and their development might have been the basis for the dominance of the copepods within today's marine zooplankton

High-speed fixed-target serial virus crystallography

We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities

Molecular chaperone-mediated rescue of mitophagy by a Parkin RING1 domain mutant

Mitochondrial dysfunction is characteristic of many neurodegenerative diseases. The Parkinson's disease-associated ubiquitin–protein ligase, Parkin, is important in the elimination of damaged mitochondria by autophagy (mitophagy) in a multistep process. Here, we show that a Parkin RING domain mutant (C289G) fails to redistribute to damaged mitochondria and cannot induce mitophagy after treatment with the mitochondrial uncoupler carbonyl cyanide m-methylhydrazone, because of protein misfolding and aggregation. Parkin(C289G) aggregation and inclusion formation were suppressed by the neuronal DnaJ/Hsp40 chaperone HSJ1a(DNAJB2a). Importantly, HSJ1a and DNAJB6 also restored mitophagy by promoting the relocation of Parkin(C289G) and the autophagy marker LC3 to depolarized mitochondria. The rescue of Parkin activity and suppression of aggregation were J domain dependent for HSJ1a, suggesting the involvement of Hsp70 in these processes, but were not dependent on the HSJ1a ubiquitin interaction motif. HSJ1a expression did not enhance mitophagy mediated by wild-type Parkin. These data show the potential of molecular chaperones to mediate the functional recovery of Parkin misfolding mutants and to combat deficits associated with Parkin aggregation in Parkinson's disease

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012

Global Transcriptome Profiling of the Pine Shoot Beetle, Tomicus yunnanensis (Coleoptera: Scolytinae)

Background: The pine shoot beetle Tomicus yunnanensis (Coleoptera: Scolytinae) is an economically important pest of Pinus yunnanensis in southwestern China. Developed resistance to insecticides due to chemical pesticides being used for a long time is a factor involved in its serious damage, which poses a challenge for management. In addition, highly efficient adaptation to divergent environmental ecologies results in this pest posing great potential threat to pine forests. However, the molecular mechanisms remain unknown as only limited nucleotide sequence data for this species is available. Methodology/Principal Findings: In this study, we applied next generation sequencing (Illumina sequencing) to sequence the adult transcriptome of T. yunnanensis. A total of 51,822,230 reads were obtained. They were assembled into 140,702 scaffolds, and 60,031 unigenes. The unigenes were further functionally annotated with gene descriptions, Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genome (KEGG). In total, 80,932 unigenes were classified into GO, 13,599 unigenes were assigned to COG, and 33,875 unigenes were found in KO categories. A biochemical pathway database containing 219 predicted pathways was also created based on the annotations. In depth analysis of the data revealed a large number of genes related to insecticides resistance and heat shock protein genes associated with environmental stress. Conclusions/Significance: The results facilitate the investigations of molecular resistance mechanisms to insecticides an