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At least 1,513 records · Page 84

Structure of Cryptosporidium IMP dehydrogenase bound to an inhibitor with in vivo antiparasitic activity

Inosine 5'-monophosphate dehydrogenase (IMPDH) is a promising target for the treatment of Cryptosporidium infections. Here, the structure of C. parvum IMPDH ( Cp IMPDH) in complex with inosine 5'-monophosphate (IMP) and P131, an inhibitor with in vivo anticryptosporidial activity, is reported. P131 contains two aromatic groups, one of which interacts with the hypoxanthine ring of IMP, while the second interacts with the aromatic ring of a tyrosine in the adjacent subunit. In addition, the amine and NO 2 moieties bind in hydrated cavities, forming water-mediated hydrogen bonds to the protein. The design of compounds to replace these water molecules is a new strategy for the further optimization of C. parvum inhibitors for both antiparasitic and antibacterial applications.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure and chemistry of tricadmium digermanium tetraarsenide, Cd3Ge2As4

A cadmium germanium arsenide compound, i.e., Cd3Ge2As4, was synthesized using a double-containment fused quartz ampoule method within a rocking furnace and a melt-quench technique. The crystal structure was determined from single-crystal X-ray diffraction (XRD), scanning and transmission electron microscopies (i.e., SEM, STEM, TEM), and selected area diffraction (SAD) and confirmed with electron backscatter diffraction (EBSD). The chemistry was verified with electron energy loss spectroscopy (EELS).

Cd3Ge2As4, chalcopyrite↗

Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG) 2 duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinic P 2 1 lattice of hexagonal metric. The various twinning criteria give somewhat conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.

59 BASIC BIOLOGICAL SCIENCES↗

PRESAGE: Protecting Structured Address Generation against Soft Errors

Modern computer scaling trends in pursuit of larger component counts and power efficiency have, unfortunately, lead to less reliable hardware and consequently soft errors escaping into application data ("silent data corruptions"). Techniques to enhance system resilience hinge on the availability of efficient error detectors that have high detection rates, low false positive rates, and lower computational overhead. Unfortunately, efficient detectors to detect faults during address generation (to index large arrays) have not been widely researched. We present a novel lightweight compiler-driven technique called PRESAGE for detecting bit-flips affecting structured address computations. A key insight underlying PRESAGE is that any address computation scheme that flows an already incurred error is better than a scheme that corrupts one particular array access but otherwise (falsely) appears to compute perfectly. Enabling the flow of errors allows one to situate detectors at loop exit points, and helps turn silent corruptions into easily detectable error situations. Our experiments using PolyBench benchmark suite indicate that PRESAGE-based error detectors have a high error-detection rate while incurring low overheads.

Sharma, Vishal C.↗

Evolutionary significance of seed structure in Alpinioideae (Zingiberaceae): Seed Structure in Alpinioideae

Alpinioideae is the largest of the four subfamilies of Zingiberaceae and is widely distributed throughout the New and Old World tropics. Recent molecular studies have shown that, although Alpinioideae is a strongly supported monophyletic subfamily with two distinct tribes (Alpinieae and Riedelieae), large genera, such as Alpinia and Amomum, are polyphyletic and are in need of revision. Alpinia and Amomum have been shown to form seven and three distinct clades, respectively, but, for many of these clades, traditional vegetative and floral synapomorphies have not been found. A broad survey of seeds in Alpinioideae using light microscopy and synchrotron-based X-ray tomographic microscopy has shown that many clades have distinctive seed structures that serve as distinctive apomorphies. Tribes Riedelieae and Alpinieae can be distinguished on the basis of operculum structure, with the exception of three taxa analysed. The most significant seed characters were found to be various modifications of the micropylar and chalazal ends, the cell shape of the endotesta and exotesta, and the location of an endotestal gap. A chalazal chamber and hilar rim are reported for the first time in Zingiberaceae. In addition to characterizing clades of extant lineages, these data offer insights into the taxonomic placement of many fossil zingiberalean seeds that are critical to understanding the origin and evolution of Alpinioideae and Zingiberales as a whole.(c) 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178, 441-466..

59 BASIC BIOLOGICAL SCIENCES↗

Electronic structure of aqueous solutions: Bridging the gap between theory and experiments

Predicting the electronic properties of aqueous liquids has been a long-standing challenge for quantum mechanical methods. However, it is a crucial step in understanding and predicting the key role played by aqueous solutions and electrolytes in a wide variety of emerging energy and environmental technologies, including battery and photoelectrochemical cell design. Here, we propose an efficient and accurate approach to predict the electronic properties of aqueous solutions, on the basis of the combination of first-principles methods and experimental validation using state-of-the-art spectroscopic measurements. We present results of the photoelectron spectra of a broad range of solvated ions, showing that first-principles molecular dynamics simulations and electronic structure calculations using dielectric hybrid functionals provide a quantitative description of the electronic properties of the solvent and solutes, including excitation energies. The proposed computational framework is general and applicable to other liquids, thereby offering great promise in understanding and engineering solutions and liquid electrolytes for a variety of important energy technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

The aim of this paper is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. Finally, this study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Geology and in situ stress of the MH-2 borehole, Idaho, USA: Insights into western Snake River Plain structure from geothermal exploration drilling

Project HOTSPOT, the Snake River Scientific Drilling Project (International Continental Scientific Drilling Program), tested for deep geothermal resources and examined the petrology of volcanic rocks with three drillholes in the central and western Snake River Plain (western USA). The MH-2 drillhole targeted fractured crystalline and hydrothermally altered basalt in the area of the Mountain Home Air Force Base (Idaho) to a total depth of 1821 m. At 1745 m depth the drillhole encountered flowing artesian hydrothermal fluids of at least 150 °C. We integrate geological analyses of core, image log, and borehole geophysical data, and in situ stress analyses to describe the structural environment that produces permeability for artesian flow. The rocks in the lower 540 m of the drillhole consist of basalt flows as much as 30 m thick, altered basalt, and thin sedimentary horizons. The mechanical stratigraphy is defined by nine mechanical horizons that are in three ranges of rock strength on the basis of experimentally determined strength data, core logging, and geophysical log signatures. Hydrothermal alteration products and mineralization in the core are associated with three highly faulted sections; the lowermost section is associated with the zone of flowing thermal water. Shear slip indicators on faults observed in core indicate slip ranging from pure strike slip to normal failure mechanisms in the stronger horizons. The borehole breakouts indicate that the maximum horizontal stress, SH, is oriented 047° ± 7°, and drilling-induced tensile fractures indicate that SH is oriented at 67° ± 21°. The in situ stress orientations exhibit little variation over the depth of the measured interval, but the SH magnitude varies with depth, and is best explained by an oblique normal fault stress regime. The geomechanical model indicates that if pore pressures at depth are elevated above the normal hydrostatic gradient, as observed here, the system has the potential to deform by mixed normal and strike-slip failure. Our observations and interpretations suggest that the MH-2 borehole was drilled into oblique normal faults that intersect a buried 300°-trending fault block masked by the basaltic volcanic complex. These data indicate that the transition from the central to western Snake River Plain is characterized by complex structures developed in response to a transitional stress state related to Snake River Plain and western Basin and Range stress regimes. Furthermore, the western Basin and Range stress and tectonic regime may extend from northern Nevada into western Idaho and may enhance the potential for geothermal resources by creating interconnected fracture and fault-related permeability at depth.

15 GEOTHERMAL ENERGY↗

The Influence of Hydrogenation on the Structure, Magnetic and Magnetocaloric Properties of Tb–Dy–Co Alloys with a Laves Phase Structure

A complex study of structure, phase composition, surface topology, magnetic, and magnetocaloric properties was performed for TbCo{sub 2} and Tb{sub 0.3}Dy{sub 0.7}Co{sub 2} compounds and for a Tb{sub 0.3}Dy{sub 0.7}Co{sub 2}H{sub 0.5} hydride with a low hydrogen content. The hydrogenation was established to impact the structural features at the micro- and nanolevels, as well as the fundamental and functional properties. Introducing even a small amount of hydrogen in the crystal lattice of Tb{sub 0.3}Dy{sub 0.7}Co{sub 2} compound is found to cause an increase in both the Curie temperature and the magnetic moment at the cobalt atoms. The magnetic phase transition from the paramagnetic to the magnetically ordered state changes from the first (in Tb{sub 0.3}Dy{sub 0.7}Co{sub 2}) to the second (in TbCo{sub 2} and Tb{sub 0.3}Dy{sub 0.7}Co{sub 2}H{sub 0.5}) order, leading to a noticeable decrease in the magnetocaloric effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗