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At least 487 records · Page 27

JBrowse: a dynamic web platform for genome visualization and analysis

JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. JBrowse is a mature web application suitable for genome visualization and analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Local lattice distortions and electronic orders in strongly correlated systems by resonant total x-ray scattering: A case study of A Pt 2 X 2 intermetallics ( A = U , Ce, or La and X = Si or Ge)

Revealing local lattice distortions in physical systems is nontrivial, largely because such structural features often are not necessarily amenable to traditional crystallographic investigations. This poses limits to our understanding of the underlying physic, particularly in the case of strongly correlated systems where structural, electronic and magnetic degrees of freedom are intertwined. Using resonant total x-ray scattering coupled to differential pair distribution function analysis, we reveal the presence of pronounced local lattice distortions in the square net Pt planes in the prototypical strongly correlated APt 2 X 2 intermetallics (A = U, Ce or La and X = Si or Ge). The distortions are present before charge density wave, magnetic, Kondo lattice coherence and/or superconducting orders emerge in these materials and, as density functional calculations suggest, are likely to affect them. Finally, our study sheds light on the poorly known interactions between electronic orders and structural disorder in strongly correlated systems and also demonstrates an advanced experimental approach to determine it that is relevant to any physical system showing deviations from perfect crystallinity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Identification and molecular characterization of the switchgrass AP2/ERF transcription factor superfamily, and overexpression of PvERF001 for improvement of biomass characteristics for biofuel

The APETALA2/ethylene response factor (AP2/ERF) superfamily of transcription factors (TFs) plays essential roles in the regulation of various growth and developmental programs including stress responses. Members of these TFs in other plant species have been implicated to play a role in the regulation of cell wall biosynthesis. Here, we identified a total of 207 AP2/ERF TF genes in the switchgrass genome and grouped into four gene families comprised of 25 AP2-, 121 ERF-, 55 DREB (dehydration responsive element binding)-, and 5 RAV (related to API3/VP) genes, as well as a singleton gene not fitting any of the above families. The ERF and DREB subfamilies comprised seven and four distinct groups, respectively. Analysis of exon/intron structures of switchgrass AP2/ERF genes showed high diversity in the distribution of introns in AP2 genes versus a single or no intron in most genes in the ERF and RAV families. The majority of the subfamilies or groups within it were characterized by the presence of one or more specific conserved protein motifs. In silico functional analysis revealed that many genes in these families might be associated with the regulation of responses to environmental stimuli via transcriptional regulation of the response genes. Moreover, these genes had diverse endogenous expression patterns in switchgrass during seed germination, vegetative growth, flower development, and seed formation. Interestingly, several members of the ERF and DREB families were found to be highly expressed in plant tissues where active lignification occurs. These results provide vital resources to select candidate genes to potentially impart tolerance to environmental stress as well as reduced recalcitrance. Furthermore, overexpression of one of the ERF genes ( PvERF001 ) in switchgrass was associated with increased biomass yield and sugar release efficiency in transgenic lines, exemplifying the potential of these TFs in the development of lignocellulosic feedstocks with improved biomass characteristics for biofuels.

09 BIOMASS FUELS↗

Visualization of texture components using MTEX

Knowledge of the appearance of texture components and fibres in pole figures, in inverse pole figures and in Euler space is fundamental for texture analysis. For cubic crystal systems, such as steels, an extensive literature exists and, for example, the book by Matthies, Vinel & Helming [Standard Distributions in Texture Analysis: Maps for the Case of Cubic Orthorhomic Symmetry, (1987), Akademie-Verlag Berlin] provides an atlas to identify texture components. For lower crystal symmetries, however, equivalent comprehensive overviews that can serve as guidance for the interpretation of experimental textures do not exist. Here, this paper closes this gap by providing a set of scripts for the MTEX package [Bachmann, Hielscher & Schaeben (2010). Solid State Phenom.160, 63–68] that allow the texture practitioner to compile such an atlas for a given material system, thus aiding orientation distribution function analysis also for non-cubic systems.

36 MATERIALS SCIENCE↗

Surface enhanced performance of La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3-δ cathodes by infiltration Pr-Ni-Mn-O progress

Herein the present study reports the enhancement of electrochemical oxygen reduction activity of porous La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3–δ (LSCF) cathodes by coating a thin film of Pr-Ni-Mn oxide (PNM5) using a multi-step infiltration process. XRD examination reveals that PNM5 mainly contains a multiphase mixture of Pr 6 O 11 , PrNiO 3 , MnO and NiO. SEM morphology shows a thin PNM5 film and small particles are formed on the surface of LSCF backbone particles. Impedance spectrum analysis indicates that PNM5 infiltrated LSCF exhibits dramatically reduced polarization resistance (R p ), reaching R p of 0.244 Ω cm 2 at 973 K, which is one-half of the baseline LSCF cathode. The activation energy of LSCF cathodes infiltrated with PNM5 is 1.45 eV, slightly lower than the baseline LSCF cathode (1.77 eV). Distribution of relaxation time (DRT) function analysis shows PNM5 infiltration layer significantly promotes the oxygen reduction reaction (ORR) of cathode surface. With the increase in firing temperature, the total resistance increases and R p changes from ion transport to oxygen reduction reaction. Degradation rate of the PNM5-infiltrated LSCF is also lower, 0.02168% vs 0.07093% for the baseline LSCF over a 200-h period. A single cell testing indicated that the peak power density of the PNM5-infiltrated cell was increased by 140.66%. Overall, PNM5 could be a potential catalyst for boosting the performance of a commercial LSCF cathode for solid oxide fuel cells (SOFC).

36 MATERIALS SCIENCE↗

Functional dichotomy in the 16S rRNA (m 1 A1408) methyltransferase family and control of catalytic activity via a novel tryptophan mediated loop reorganization

Methylation of the bacterial small ribosomal subunit (16S) rRNA on the N1 position of A1408 confers exceptionally high-level resistance to a broad spectrum of aminoglycoside antibiotics. Here, we present a detailed structural and functional analysis of the Catenulisporales acidiphilia 16S rRNA (m 1 A1408) methyltransferase (‘CacKam’). The apo CacKam structure closely resembles other m1A1408 methyltransferases within its conserved SAM-binding fold but the region linking core β strands 6 and 7 (the ‘β6/7 linker’) has a unique, extended structure that partially occludes the putative 16S rRNA binding surface, and sequesters the conserved and functionally critical W203 outside of the CacKam active site. Substitution of conserved residues in the SAM binding pocket reveals a functional dichotomy in the 16S rRNA (m 1 A1408) methyltransferase family, with two apparently distinct molecular mechanisms coupling cosubstrate/ substrate binding to catalytic activity. Our results additionally suggest that CacKam exploits the W203-mediated remodeling of the β6/7 linker as a novel mechanism to control 30S substrate recognition and enzymatic turnover.

59 BASIC BIOLOGICAL SCIENCES↗

Comparison of gamma-ray spectral analysis methods for thick-walled UF 6 cylinders

Three data analysis methods were compared for gamma ray spectra collected by planar and coaxial high-purity germanium detectors (HPGe) on thick-walled uranium hexafluoride cylinders. The cylinder contents range from natural to low-enriched uranium (4.95% 235 U). Each spectrum was analyzed with the traditional 185.7 keV enrichment meter method, a 185.7/1001 keV ratio method, and the Fixed Energy Response Function Analysis with Multiple Efficiency (FRAM) software that utilizes low- and high-energy gamma rays and X-rays. When results for all cylinders were compared, the enrichment meter method and the 185.7/1001 keV peak ratio method consistently provided the most accurate data for all detector types. The error on the enrichment calculations analyzed with FRAM did not meet the international target value whereas those calculated with the enrichment meter and ratio method did. Enrichments calculated by FRAM were found to skew to higher values on natural uranium and to lower values on low-enriched uranium. FRAM calculated the least-precise enrichments; replicate analyses of single cylinders resulted in 235 U values that varied by as much as 19%. FRAM does have the significant advantages in that it does not require the use of calibration cylinders, infinite thickness criteria are not necessary, and it can be applied to any HPGe detector. Finally, if calibration cylinders are available, the enrichment meter and 185.7/1001 peak ratio are the recommended methods as they are the most accurate and precise.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Local Structural Investigations, Defect Formation, and Ionic Conductivity of the Lithium Ionic Conductor Li 4 P 2 S 6

Glassy, glass–ceramic, and crystalline lithium thiophosphates have attracted interest in their use as solid electrolytes in all-solid-state batteries. Despite similar structural motifs, including PS 4 3– , P 2 S 6 4– , and P 2 S 7 4– polyhedra, these materials exhibit a wide range of possible compositions, crystal structures, and ionic conductivities. Here, we present a combined approach of Bragg diffraction, pair distribution function analysis, Raman spectroscopy, and 31 P magic angle spinning nuclear magnetic resonance spectroscopy to study the underlying crystal structure of Li 4 P 2 S 6 . In this work, we show that the material crystallizes in a planar structural arrangement as a glass ceramic composite, explaining the observed relatively low ionic conductivity, depending on the fraction of glass content. Calculations based on density functional theory provide an understanding of occurring diffusion pathways and ionic conductivity of this Li + ionic conductor.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Towards the synthetic design of camelina oil enriched in tailored acetyl-triacylglycerols with medium-chain fatty acids

Here, the ability to manipulate expression of key biosynthetic enzymes has allowed the development of genetically modified plants that synthesise unusual lipids that are useful for biofuel and industrial applications. By taking advantage of the unique activities of enzymes from different species, tailored lipids with a targeted structure can be conceived. In this study we demonstrate the successful implementation of such an approach by metabolically engineering the oilseed crop Camelina sativa to produce 3-acetyl-1,2-diacyl-sn-glycerols (acetyl-TAGs) with medium-chain fatty acids (MCFAs). Different transgenic camelina lines that had been genetically modified to produce MCFAs through the expression of MCFA-specific thioesterases and acyltransferases were retransformed with the Euonymus alatus gene for diacylglycerol acetyltransferase (EaDAcT) that synthesises acetyl-TAGs. Concomitant RNAi suppression of acyl-CoA:diacylglycerol acyltransferase increased the levels of acetyl-TAG, with up to 77 mole percent in the best lines. However, the total oil content was reduced. Analysis of the composition of the acetyl-TAG molecular species using electrospray ionisation mass spectrometry demonstrated the successful synthesis of acetyl-TAG containing MCFAs. Field growth of high-yielding plants generated enough oil for quantification of viscosity. As part of an ongoing design–test–learn cycle, these results, which include not only the synthesis of ‘designer’ lipids but also their functional analysis, will lead to the future production of such molecules tailored for specific applications.

59 BASIC BIOLOGICAL SCIENCES↗

GSAS-II (GENERAL STRUCTURE AND ALAYSIS SYSTEM-II)

GSAS-II is a comprehensive data analysis and simulation software package for determining atomistic structures from single-crystal and powder diffraction data. X-ray, neutron and electron data may be used. Constant-wavelength, time-of-flight and pink-beam sources may be employed and analyses may combine different types of data. The package is oriented towards materials characterization problems, but protein crystallography, pair-distribution function analysis, small-angle scattering and reflectometry analysis are all included. GSAS-II provides tools for indexing and solving structures from powder diffraction data, in addition to structure, data and results visualization tools

TOBY, BRIANH↗

First comprehensive structural and biophysical analysis of MAPK13 inhibitors targeting DFG-in and DFG-out binding modes

Background: P38 MAP kinases are centrally involved in mediating extracellular signaling in various diseases. While much attention has previously been focused on the ubiquitously expressed family member MAPK14 (p38α), recent studies indicate that family members such as MAPK13 (p38δ) display a more selective cellular and tissue expression and might therefore represent a specific kinase to target in certain diseases. Methods: To facilitate the design of potent and specific inhibitors, we present in this paper the structural, biophysical, and functional characterization of two new MAPK13-inhibitor complexes, as well as the first comprehensive structural, biophysical, and functional analysis of MAPK13 complexes with four different inhibitor compounds of greatly varying potency. Results: These inhibitors display IC 50 values either in the nanomolar range or micromolar range (> 800-fold range). The nanomolar inhibitors exhibit much longer ligand-enzyme complex half-lives compared to the micromolar inhibitors as measured by biolayer interferometry. Crystal structures of the MAPK13 inhibitor complexes reveal that the nanomolar inhibitors engage MAPK13 in the DFG-out binding mode, while the micromolar inhibitors are in the DFG-in mode. Detailed structural and computational docking analyses suggest that this difference in binding mode engagement is driven by conformational restraints imposed by the chemical structure of the inhibitors, and may be fortified by an additional hydrogen bond to MAPK13 in the nanomolar inhibitors. Conclusions: These studies provide a structural basis for understanding the differences in potency exhibited by these inhibitors. General significance: They also provide the groundwork for future studies to improve specificity, potency, pharmacodynamics, and pharmacokinetic properties.

59 BASIC BIOLOGICAL SCIENCES↗

High-resolution analysis of clay minerals and amorphous materials in martian analog environments

Mudrocks and mud-sized sediments (i.e., silt to clay) dominate the surface of Earth and Mars. These fine-grained sediments preserve a rich history of sedimentary processes from source to sink and shed light on ancient climates. However, both the physical and chemical nature of these materials make them difficult to fully characterize with traditional laboratory techniques. Here, we explore a cross-disciplinary and high-resolution approach using synchrotron radiation for X-ray diffraction, pair distribution function analysis, and submicrometer-scale X-ray fluorescence, combined with transmission electron microscopy, to better understand the nanostructure and composition of mud-sized sediments from a glacio-fluvial watershed in southwest Iceland. Our results demonstrate that sediments in the cold and wet climate of Iceland are more altered than previously thought, as evidenced by the identification of kaolinite and mixed-layer kaolinite-smectite. Additionally, sediments are enriched in amorphous materials and nanocrystalline phases, as determined from grain morphologies and compositions consistent with allophane, hisingerite, ferrihydrite, and halloysite. These alteration products are present as intimate mixtures that vary across depositional sites, demonstrating the dynamic nature of the secondary assemblage from source to sink. This work has implications for Mars, where, for example, basalt-sourced sedimentary rocks from Gale crater are abundant in clay minerals and amorphous materials. Finally, this work underpins the importance of using high-resolution techniques, a coordinated methodology, and developing innovative approaches for future planetary sample return missions (e.g., Mars sample return).

36 MATERIALS SCIENCE↗

Phosphorylation of a NAC Transcription Factor by a Calcium/Calmodulin-Dependent Protein Kinase Regulates Abscisic Acid-Induced Antioxidant Defense in Maize [Phosphorylation of a NAC Transcription Factor by ZmCCaMK Regulates Abscisic Acid-Induced Antioxidant Defense in Maize]

Calcium/calmodulin-dependent protein kinase (CCaMK) has been shown to play an important role in abscisic acid (ABA)-induced antioxidant defense and enhance the tolerance of plants to drought stress. However, its downstream molecular events are poorly understood. Here, we identify a NAC transcription factor, ZmNAC84, in maize, which physically interacts with ZmCCaMK in vitro and in vivo. ZmNAC84 display a partially overlapping expression pattern with ZmCCaMK after ABA treatment and H 2 O 2 is required for ABA-induced ZmNAC84 expression. Functional analysis reveals that ZmNAC84 is essential for ABA-induced antioxidant defense in a ZmCCaMK-dependent manner. Furthermore, ZmCCaMK directly phosphorylates S113 of ZmNAC84 in vitro, and S113 is essential for the ABA-induced stimulation of antioxidant defense by ZmCCaMK. Moreover, overexpression of ZmNAC84 in tobacco can improve drought tolerance, and alleviate drought-induced oxidative damage of transgenic plants. These results define a mechanism for ZmCCaMK function in ABA-induced antioxidant defense, where ABA-produced H 2 O 2 first induces expression of ZmCCaMK and ZmNAC84 and activates ZmCCaMK, and subsequently the activated ZmCCaMK phosphorylates ZmNAC84 at S113, thereby inducing antioxidant defense by activating downstream genes.

59 BASIC BIOLOGICAL SCIENCES↗

Galaxy and Mass Assembly (GAMA): Exploring the WISE Web in G12

We present an analysis of the mid-infrared Wide-field Infrared Survey Explorer (WISE) sources seen within the equatorial GAMA G12 field, located in the North Galactic Cap. Our motivation is to study and characterize the behavior of WISE source populations in anticipation of the deep multiwavelength surveys that will define the next decade, with the principal science goal of mapping the 3D large-scale structures and determining the global physical attributes of the host galaxies. In combination with cosmological redshifts, we identify galaxies from their WISE W1 (3.4 μm) resolved emission, and we also perform a star-galaxy separation using apparent magnitude, colors, and statistical modeling of star counts. The resulting galaxy catalog has ≃590,000 sources in 60 deg{sup 2}, reaching a W1 5σ depth of 31 μJy. At the faint end, where redshifts are not available, we employ a luminosity function analysis to show that approximately 27% of all WISE extragalactic sources to a limit of 17.5 mag (31 μJy) are at high redshift, z>1. The spatial distribution is investigated using two-point correlation functions and a 3D source density characterization at 5 Mpc and 20 Mpc scales. For angular distributions, we find that brighter and more massive sources are strongly clustered relative to fainter sources with lower mass; likewise, based on WISE colors, spheroidal galaxies have the strongest clustering, while late-type disk galaxies have the lowest clustering amplitudes. In three dimensions, we find a number of distinct groupings, often bridged by filaments and superstructures. Using special visualization tools, we map these structures, exploring how clustering may play a role with stellar mass and galaxy type.

79 ASTRONOMY AND ASTROPHYSICS↗

A DEEP 1.2 mm MAP OF THE LOCKMAN HOLE NORTH FIELD

We present deep 1.2 mm continuum mapping of a 566 arcmin{sup 2} area within the Lockman Hole North (LHN) field, previously a target of the Spitzer Wide-Area Infrared Extragalactic survey and extremely deep 20 cm mapping with the Very Large Array, which we have obtained using the Max-Planck millimeter bolometer (MAMBO) array on the IRAM 30 m telescope. After filtering, our full map has an rms sensitivity ranging from 0.45 to 1.5 mJy beam{sup -1}, with an average of 0.75 mJy beam{sup -1}. Using the pixel flux distribution (PFD) in a map made from our best data, we determine the shape, normalization, and approximate flux density cutoff for 1.2 mm number counts well below our nominal sensitivity and confusion limits. After validating our full data set through comparison with this map, we successfully detect 41 1.2 mm sources with signal-to-noise ratio (S/N) > 4.0 and S{sub 1.2{sub mm}} {approx_equal} 2-5 mJy. We use the most significant of these detections to directly determine the integral number counts down to 1.8 mJy, which are consistent with the results of the PFD analysis. Ninety-three percent of our 41 individual detections have 20 cm counterparts, 49% have Spitzer/MIPS 24 {mu}m counterparts, and one may have a significant Chandra X-ray counterpart. We resolve {approx_equal} 3% of the cosmic infrared background (CIB) at 1.2 mm into significant detections and directly estimate a 0.05 mJy faint-end cutoff for the counts that is consistent with the full intensity of the 1.2 mm CIB. The median redshift of our 17 detections with spectroscopic or robust photometric redshifts is z{sub median} = 2.3, and rises to z{sub median} = 2.9 when we include redshifts estimated from the radio/far-infrared spectral index. By using a nearest neighbor and angular correlation function analysis, we find evidence that our S/N > 4.0 detections are clustered at the 95% confidence level.

79 ASTRONOMY AND ASTROPHYSICS↗

Real-space visualization of short-range antiferromagnetic correlations in a magnetically enhanced thermoelectric

Short-range magnetic correlations can significantly increase the thermopower of magnetic semiconductors, representing a noteworthy development in the decades-long effort to develop high-performance thermoelectric materials. Here, we reveal the nature of the thermopower-enhancing magnetic correlations in the antiferromagnetic semiconductor MnTe. Using magnetic pair distribution function analysis of neutron scattering data, we obtain a detailed, real-space view of robust, nanometer-scale, antiferromagnetic correlations that persist into the paramagnetic phase above the Neel temperature $T_N$ = 307 K. In this work, the magnetic correlation length in the paramagnetic state is significantly longer along the crystallographic c axis than within the ab plane, pointing to anisotropic magnetic interactions. Ab initio calculations of the spin-spin correlations using density functional theory in the disordered local moment approach reproduce this result with quantitative accuracy. These findings constitute the first real-space picture of short-range spin correlations in a magnetically enhanced thermoelectric and inform future efforts to optimize thermoelectric performance by magnetic means.

36 MATERIALS SCIENCE↗

Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms

ABSTRACT Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well as for bioremediation. However, cultivating soil microorganisms while maintaining a broad microorganism diversity to enable phenotyping and functional analysis of as diverse individual isolates as possible remains challenging. In this study, we developed and tested the ability of several culture media formulations that contain defined soil metabolites or soil extracts to maintain microorganism diversity during culture. We also assessed their performance in microfluidic droplet cultivation where single-soil microorganism isolates were encapsulated and cultivated in picoliter-volume water-in-oil emulsion droplets to enable clonal growth needed for downstream functional analyses. Our results show that droplet cultivation with media supplemented by soil extract or soil metabolites enables the recovery of soil microorganisms with higher diversity (up to 1.5-fold higher richness) compared to bulk cultivation methods. Importantly, 1.7-fold more of less abundant (<1%) phyla and 11-fold more of unique genera were recovered, demonstrating the utility of this method for interrogating highly diverse soil microorganisms for broad ranges of applications. IMPORTANCE Although soil microorganisms hold a significant value in bioproduction and bioremediation, only a small fraction—less than 1%—can be cultured under specific media and cultivation conditions. This indicates that there are ample opportunities in harvesting the diverse environmental microorganisms if isolating and recovering these uncultured microorganisms are possible. This paper presents a new cultivation technique composed of isolating single-soil microorganism cell from anin situsoil microorganism community in microfluidic droplets and conducting in-droplet cultivation in media supplemented by soil extract or soil metabolites. This method enables the recovery of a broader diversity of the original microorganism community, laying the groundwork for a high-throughput phenotyping of these diverse microorganisms from their natural habitats.

Biotechnology & Applied Microbiology↗

Microsegregation effects on the thermal conductivity of silicon-germanium alloys

A silicon-germanium (SiGe) alloy is a promising candidate for thermoelectric materials; while it shows a significantly reduced thermal conductivity (κ) as compared to pure Si and Ge, the κ values obtained from previous experiments and computations tend to be widely scattered. We present here a computational analysis of thermal transport in SiGe, particularly the effects of the local segregation (microsegregation) of alloying elements. Our nonequilibrium molecular dynamics simulations confirm the strong dependence of κ on the Si:Ge ratio and the occurrence of the minimum κ around Si{sub 0.8}Ge{sub 0.2}, consistent with existing experimental observations. Moreover, our study clearly demonstrates that the κ of Si{sub 0.8}Ge{sub 0.2} increases substantially and monotonically as Ge atoms undergo segregation; that is, the magnitude of alloy scattering is found to be sensitive to homogeneity in the distribution of alloying elements. Nonequilibrium Green's function analysis also shows that such microsegregation enhances phonon transmission due to the reduced number of scattering centers. The findings highlight that distribution homogeneity, along with composition, can be a critical factor in determining the κ of SiGe alloys.

36 MATERIALS SCIENCE↗