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Sample records for reveals unique surface

  1. Water-induced drag and air-induced creep of clasts - revealing two unique earth surface processes by physical experiments and numerical modelling

    NASA Astrophysics Data System (ADS)

    Dietze, Michael; Kleber, Arno

    2013-04-01

    Earth surface processes, especially in arid environments, have received attention for several hundreds of years and most relief-shaping mechanisms have been investigated thoroughly by now. However, the current state of process knowledge allows not to consistently explain many properties of a surface type, covering up to 15 % of terrestrial surfaces worldwide: stone pavements and the associated vesicular horizons, fine-grained aeolian veneers with a distinct foamy structure. Throughout hot to cold deserts, from semi-arid to hyper-arid conditions, stone pavements usually show slope aspect-controlled bimodal alignment patterns of their clast length axes and are able to recover from disturbance by lateral processes. Two yet disregarded earth surface processes play an essential role in both, recovery of disturbed sites and formation of the preferred clast alignment pattern. The vesicular horizon with its unique properties has fundamental control functions for the two processes. One process is unconcentrated overland flow, which supports rapid accumulation of clasts during the initial stages of recovery, given preconditions for sufficiently deep flows. The other process is clast creep due to air, escaping from the vesicular horizon upon rapid wetting. The latter process is unique in several aspects: it affects clasts but does not transport finer material and it is more effective the gentler the slope is. Both processes lead to clast rotation upon collision and thereby create the bimodal orientation pattern. Both processes are described conceptionally, explored by physical-based numerical modelling and consistently validated by laboratory experiments. Water-induced drag and air-induced creep of clasts may represent two key mechanisms to explain unresolved challenges of many desert surfaces and underlying soil-sediment complexes regarding i) stability versus fragility, ii) dust sink versus dust source, and iii) the palaeoenvironmental archive function.

  2. Piriform Spider Silk Sequences Reveal Unique Repetitive Elements

    PubMed Central

    Perry, David J.; Bittencourt, Daniela; Siltberg-Liberles, Jessica; Rech, Elibio L.; Lewis, Randolph V.

    2010-01-01

    Orb-weaving spider silk fibers are assembled from very large, highly repetitive proteins. The repeated segments contain, in turn, short, simple repetitive amino acid motifs that account for the physical and mechanical properties of the assembled fiber. Of the six orb-weaver silk fibroins, the piriform silk that makes the attachment discs, which lashes the joints of the web and attaches dragline silk to surfaces has not been previously characterized. Piriform silk protein cDNAs were isolated from phage libraries of three species, A. trifasciata, N. clavipes, and N. cruentata. The deduced amino acid sequences from these genes revealed two new repetitive motifs: an alternating proline motif where every other amino acid is proline, and a glutamine-rich motif of 6 to 8 amino acids. Similar to other spider silk proteins, the repeated segments are large (>200 amino acids) and highly homogenized within a species. There is also substantial sequence similarity across the genes from the three species with particular conservation of the repetitive motifs. Northern blot analysis revealed that the messenger RNA is larger than 11kb and is expressed exclusively in the piriform glands of the spider. Phylogenetic analysis of the C-terminal regions of the new proteins with published spidroins robustly shows that the pirifom sequences form an ortholog group. PMID:20954740

  3. Uranus' southern circulation revealed by Voyager 2: Unique characteristics

    NASA Astrophysics Data System (ADS)

    Karkoschka, Erich

    2015-04-01

    Revised calibration and processing of 1600 images of Uranus by Voyager 2 revealed dozens of discrete features south of -45° latitude, where only a single feature was known from Voyager images and none has been seen since. Tracking of these features over five weeks defined the southern rotational profile of Uranus with high accuracy and no significant gap. The profile has kinks unlike previous profiles and is strongly asymmetric with respect to the northern profile by Sromovsky et al. (Sromovsky, L.A., Fry, P.M., Hammel, H.B., de Pater, I., Rages, K.A. [2012]. Icarus 220, 694-712). The asymmetry is larger than that of all previous data on jovian planets. A spot that included the South Pole off-center rotated with a period of 12.24 h, 2 h outside the range of all previous observations of Uranus. The region between -68° and -59° latitude rotated almost like a solid body, with a shear that was about 30 times smaller than typical shears on Uranus. At lower latitudes, features were sheared into tightly wound spirals as Voyager watched. The zone at -84° latitude was exceptionally bland; reflectivity variations were only 18 ppm, consistent with a signal-to-noise ratio estimated at 55,000. The low noise was achieved by smoothing over dozens of pixels per image and averaging 1600 images. The presented data set in eight filters contains rich information about temporal evolution and spectral characteristics of features on Uranus that will be the basis for further analysis.

  4. Diatom Proteomics Reveals Unique Acclimation Strategies to Mitigate Fe Limitation

    PubMed Central

    Nunn, Brook L.; Faux, Jessica F.; Hippmann, Anna A.; Maldonado, Maria T.; Harvey, H. Rodger; Goodlett, David R.; Boyd, Philip W.; Strzepek, Robert F.

    2013-01-01

    Phytoplankton growth rates are limited by the supply of iron (Fe) in approximately one third of the open ocean, with major implications for carbon dioxide sequestration and carbon (C) biogeochemistry. To date, understanding how alteration of Fe supply changes phytoplankton physiology has focused on traditional metrics such as growth rate, elemental composition, and biophysical measurements such as photosynthetic competence (Fv/Fm). Researchers have subsequently employed transcriptomics to probe relationships between changes in Fe supply and phytoplankton physiology. Recently, studies have investigated longer-term (i.e. following acclimation) responses of phytoplankton to various Fe conditions. In the present study, the coastal diatom, Thalassiosira pseudonana, was acclimated (10 generations) to either low or high Fe conditions, i.e. Fe-limiting and Fe-replete. Quantitative proteomics and a newly developed proteomic profiling technique that identifies low abundance proteins were employed to examine the full complement of expressed proteins and consequently the metabolic pathways utilized by the diatom under the two Fe conditions. A total of 1850 proteins were confidently identified, nearly tripling previous identifications made from differential expression in diatoms. Given sufficient time to acclimate to Fe limitation, T. pseudonana up-regulates proteins involved in pathways associated with intracellular protein recycling, thereby decreasing dependence on extracellular nitrogen (N), C and Fe. The relative increase in the abundance of photorespiration and pentose phosphate pathway proteins reveal novel metabolic shifts, which create substrates that could support other well-established physiological responses, such as heavily silicified frustules observed for Fe-limited diatoms. Here, we discovered that proteins and hence pathways observed to be down-regulated in short-term Fe starvation studies are constitutively expressed when T. pseudonana is acclimated (i

  5. Plastic-casting intrinsic-surface unique identifier (tag)

    SciTech Connect

    Palm, R.G.; De Volpi, A.

    1995-04-01

    This report describes the development of an authenticated intrinsic-surf ace tagging method for unique- identification of controlled items. Although developed for control of items limited by an arms control treaty, this method has other potential applications to keep track of critical or high-value items. Each tag (unique-identifier) consists of the intrinsic, microscopic surface topography of a small designated area on a controlled item. It is implemented by making a baseline plastic casting of the designated tag area and usually placing a cover (for example, a bar-code label) over this area to protect the surface from environmental alteration. The plastic casting is returned to a laboratory and prepared for high-resolution scanning electron microscope imaging. Several images are digitized and stored for use as a standard for authentication of castings taken during future inspections. Authentication is determined by numerically comparing digital images. Commercially available hardware and software are used for this tag. Tag parameters are optimized, so unique casting images are obtained from original surfaces, and images obtained from attempted duplicate surfaces are detected. This optimization uses the modulation transfer function, a first principle of image analysis, to determine the parameters. Surface duplication experiments confirmed the optimization.

  6. The Laccaria and Tuber Genomes Reveal Unique Signatures of Mycorrhizal Symbiosis Evolution (2010 JGI User Meeting)

    SciTech Connect

    Knapp, Steve

    2010-03-24

    Francis Martin from the French agricultural research institute INRA talks on how "The Laccaria and Tuber genomes reveal unique signatures of mycorrhizal symbiosis evolution" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  7. Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes

    PubMed Central

    Rodriguez-Palacios, Alex; Kodani, Tomohiro; Kaydo, Lindsey; Pietropaoli, Davide; Corridoni, Daniele; Howell, Scott; Katz, Jeffry; Xin, Wei; Pizarro, Theresa T.; Cominelli, Fabio

    2015-01-01

    Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes (‘cobblestones' versus ‘villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals ‘liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD. PMID:26154811

  8. Unique carbon nanotube architectures via surface modification and capillary effects

    NASA Astrophysics Data System (ADS)

    Chakrapani, Nirupama

    The extraordinary material properties of carbon nanotubes make them an ideal candidate for a plethora of applications and many fundamental scientific studies. However, precise control over morphology of nanotube-based structures is required before their potential could be realized. A method for surface character alteration and controlled defect induction based on plasma chemistry is presented. This process induces defects in the nanotube structure by way of functionalization and the extent of disorder can be controlled by plasma time and power. This treatment has been characterized by time dependent Raman and X-ray photoelectron spectroscopy. A better understanding of the changes in the vibrational modes of nanotubes with changes in their structure could be gained from this study. Formation of visually arresting cellular structures from aligned nanotubes by the evaporation of water was discovered. Cellular patterns arise frequently in nature on length scales ranging from microscopic to macroscopic as a result of spatially periodic and random perturbations. However, a film of aligned carbon nanotubes present an unique, yet unstudied system where pattern formation arise from the collapse and reassembly of highly ordered, anisotropic, elastic, nanoscale rods with remarkable properties. The nanoscale dimensions of the nanotube arrays magnify the capillary forces exerted by the evaporating solvent from the interstitial spaces. Shrinkage induced crack formation in the films due to strong capillary forces of evaporating solvent and aided by strong van der Waals interactions between condensed nanotubes, result in the formation of stable cellular patterns and contiguous foams. These foams can be elastically deformed, transferred to other substrates, or floated out to produce free-standing macroscopic fabrics. The length-scale, orientation and shape of cell could be controlled by varying experimental conditions such as the length of nanotubes, rate of evaporation, and array

  9. Sequencing of Porcine Enterovirus Groups II and III Reveals Unique Features of Both Virus Groups

    PubMed Central

    Krumbholz, Andi; Dauber, Malte; Henke, Andreas; Birch-Hirschfeld, Eckhard; Knowles, Nick J.; Stelzner, Axel; Zell, Roland

    2002-01-01

    The molecular classification of the porcine enterovirus (PEV) groups II and III was investigated. The sequence of the almost complete PEV-8 (group II) genome reveals that this virus has unique L and 2A gene regions. A reclassification of this group into a new picornavirus genus is suggested. PEV group III viruses are typical enteroviruses. They differ from other enteroviruses by a prolonged stem-loop D of the 5′-cloverleaf structure. PMID:11992011

  10. Transcriptomic Sequencing Reveals a Set of Unique Genes Activated by Butyrate-Induced Histone Modification.

    PubMed

    Li, Cong-Jun; Li, Robert W; Baldwin, Ransom L; Blomberg, Le Ann; Wu, Sitao; Li, Weizhong

    2016-01-01

    Butyrate is a nutritional element with strong epigenetic regulatory activity as a histone deacetylase inhibitor. Based on the analysis of differentially expressed genes in the bovine epithelial cells using RNA sequencing technology, a set of unique genes that are activated only after butyrate treatment were revealed. A complementary bioinformatics analysis of the functional category, pathway, and integrated network, using Ingenuity Pathways Analysis, indicated that these genes activated by butyrate treatment are related to major cellular functions, including cell morphological changes, cell cycle arrest, and apoptosis. Our results offered insight into the butyrate-induced transcriptomic changes and will accelerate our discerning of the molecular fundamentals of epigenomic regulation. PMID:26819550

  11. Transcriptomic Sequencing Reveals a Set of Unique Genes Activated by Butyrate-Induced Histone Modification

    PubMed Central

    Li, Cong-Jun; Li, Robert W.; Baldwin, Ransom L.; Blomberg, Le Ann; Wu, Sitao; Li, Weizhong

    2016-01-01

    Butyrate is a nutritional element with strong epigenetic regulatory activity as a histone deacetylase inhibitor. Based on the analysis of differentially expressed genes in the bovine epithelial cells using RNA sequencing technology, a set of unique genes that are activated only after butyrate treatment were revealed. A complementary bioinformatics analysis of the functional category, pathway, and integrated network, using Ingenuity Pathways Analysis, indicated that these genes activated by butyrate treatment are related to major cellular functions, including cell morphological changes, cell cycle arrest, and apoptosis. Our results offered insight into the butyrate-induced transcriptomic changes and will accelerate our discerning of the molecular fundamentals of epigenomic regulation. PMID:26819550

  12. Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata.

    PubMed

    Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

    2013-01-01

    Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem-loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping-pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration. PMID:23166307

  13. Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata

    PubMed Central

    Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

    2013-01-01

    Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem–loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping–pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration. PMID:23166307

  14. Do surface effects explain the unique elasticity of polymer nanofibers?

    NASA Astrophysics Data System (ADS)

    Burman, M.; Arinstein, A.; Zussman, E.

    2011-10-01

    The elastic modulus of electrospun Polyamide (Nylon-6.6) nanofibers, which sharply increases in nanofibers with diameters below 500 nm, was measured by both bending and tensile deformation modes. Since the nanofiber surface energy contributes significantly to the elastic modulus measured by bending, but is negligible in the modulus obtained by stretching, the contribution of the surface energy to the modulus can be extrapolated from datasets collected after both types of deformation. The results unambiguously show that the abrupt increase in the elastic modulus of the nanofibers cannot be attributed either qualitatively or quantitatively, to a surface energy effect. The presented results contradict earlier claims with regards to the contribution of surface energy to the elastic modulus. In addition, these data suggest that the confinement of the supermolecular structures within nano-objects formed during nanofiber processing is responsible for the observed modification in elastic modulus.

  15. Unique developmental trajectories of cortical thickness and surface area.

    PubMed

    Wierenga, Lara M; Langen, Marieke; Oranje, Bob; Durston, Sarah

    2014-02-15

    There is evidence that the timing of developmental changes in cortical volume and thickness varies across the brain, although the processes behind these differences are not well understood. In contrast to volume and thickness, the regional developmental trajectories of cortical surface area have not yet been described. The present study used a combined cross-sectional and longitudinal design with 201 MRI-scans (acquired at 1.5-T) from 135 typically developing children and adolescents. Scans were processed using FreeSurfer software and the Desikan-Killiany atlas. Developmental trajectories were estimated using mixed model regression analysis. Within most regions, cortical thickness showed linear decreases with age, whereas both cortical volume and surface area showed curvilinear trajectories. On average, maximum surface area occurred later in development than maximum volume. Global gender differences were more pronounced in cortical volume and surface area than in average thickness. Our findings suggest that developmental trajectories of surface area and thickness differ across the brain, both in their pattern and their timing, and that they also differ from the developmental trajectory of global cortical volume. Taken together, these findings indicate that the development of surface area and thickness is driven by different processes, at least in part. PMID:24246495

  16. Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily.

    PubMed

    Yeung, Ho; Squire, Christopher J; Yosaatmadja, Yuliana; Panjikar, Santosh; López, Gemma; Molina, Antonio; Baker, Edward N; Harris, Paul W R; Brimble, Margaret A

    2016-07-01

    Proteins from the GASA/snakin superfamily are common in plant proteomes and have diverse functions, including hormonal crosstalk, development, and defense. One 63-residue member of this family, snakin-1, an antimicrobial protein from potatoes, has previously been chemically synthesized in a fully active form. Herein the 1.5 Å structure of snakin-1, determined by a novel combination of racemic protein crystallization and radiation-damage-induced phasing (RIP), is reported. Racemic crystals of snakin-1 and quasi-racemic crystals incorporating an unnatural 4-iodophenylalanine residue were prepared from chemically synthesized d- and l-proteins. Breakage of the C-I bonds in the quasi-racemic crystals facilitated structure determination by RIP. The crystal structure reveals a unique protein fold with six disulfide crosslinks, presenting a distinct electrostatic surface that may target the protein to microbial cell surfaces. PMID:27145301

  17. The Surface Contour Radar, a unique remote sensing instrument

    NASA Technical Reports Server (NTRS)

    Kenney, J. E.; Uliana, E. A.; Walsh, E. J.

    1979-01-01

    A 36 GHz computer controlled airborne Surface Contour Radar (SCR) is described, which was developed by the Naval Research Laboratory and NASA. The system uses pulse-compression techniques and dual frequency carriers spaced far enough apart to be decorrelated on the sea surface. The continuous wave transmitter is biphase modulated, the return signal is autocorrelated, and the code length and clock rate are variable, providing selectable range resolutions of 0.15, 0.30, 0.61 and 1.52 m. The SCR generates a false-color coded elevation map of the sea surface below the aircraft in real time, and can routinely produce ocean directional wave spectra with off-line data processing.

  18. Deucalionis Regio, Mars: Evidence for a unique mineralogic endmember and a crusted surface

    NASA Astrophysics Data System (ADS)

    Merenyi, E.; Edgett, K. S.; Singer, R. B.

    1993-03-01

    A small equatorial region south of Sinus Meridiani, Deucalionis Regio, has been found spectrally distinct from other regions as seen in a high spectral resolution telescopic image of the meridian hemisphere of Mars. Analysis of Viking IRTM and other related data suggest that Deucalionis Regio has a crusted surface. The crust-bonding minerals may contribute to the spectral uniqueness of this region. Two independent analyses of spectral images, linear spectral mixing and supervised classification based on the spectral shapes, showed that in addition to the well-known spectral endmember regions in this image (western Arabia, south Acidalia, and Sinus Meridiani), Deucalionis Regio has spectral properties that are unique enough to make it a principle endmember unit. In those earlier works, Deucalionis Regio was referred to as 'Meridiani Border.' Analysis of thermal inertia, rock abundance, and albedo information derived from Viking images and Infrared Thermal Mapper (IRTM) data obtained 1977-80 also indicate that Deucalionis Regio has a surface of distinctly different physical properties when compared to Arabia, Sinus Meridiani, and Acidalia. Deucalionis Regio has a thermal inertia equivalent to the Martian average, a low rock abundance (less than 5 percent), and an intermediate albedo and color. Considerable effort by previous investigators has revealed a consistent model for the surface (upper few cm) properties of the endmember reigons Arabia, Sinus Meridiani, and Acidalia. Compared with these regions, we consider that Deucalionis Regio is not a region of either (1) unconsolidated, fine bright dust like Arabia, (2) considerable windblown unconsolidated sand like Sinus Meridiani, or (3) a rocky-and-sandy surface like Acidalia. Thus, we are forced to consider that either the surface of Deucalionis Regio is made of unconsolidated fine to medium sand (about 250 microns) of an unusual and previously unreported color and albedo, or that the surface is crusted, fine

  19. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.

    PubMed

    Walker, C B; de la Torre, J R; Klotz, M G; Urakawa, H; Pinel, N; Arp, D J; Brochier-Armanet, C; Chain, P S G; Chan, P P; Gollabgir, A; Hemp, J; Hügler, M; Karr, E A; Könneke, M; Shin, M; Lawton, T J; Lowe, T; Martens-Habbena, W; Sayavedra-Soto, L A; Lang, D; Sievert, S M; Rosenzweig, A C; Manning, G; Stahl, D A

    2010-05-11

    Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus "Nitrosopumilus maritimus" strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen. PMID:20421470

  20. Sexuality and suicidality: matched-pairs analyses reveal unique characteristics in non-heterosexual suicidal behaviors.

    PubMed

    Harris, Keith M

    2013-07-01

    The present findings offer new perspectives on differences between suicide-risk heterosexuals and non-heterosexuals (lesbian, gay, bisexual, and questioning: LGBQ). Results from an anonymous online survey, employing standardized scales, showed that LGBQ participants reported significantly greater suicide-risk than heterosexuals. Seventy-nine matched pairs of suicide-risk LGBQ and heterosexuals were examined by individual suicide risk factors. Results showed no significant differences on separate measures of suicidal ideation; however, LGBQ participants were more likely to report suicide attempts, disclosure of suicidal intentions, and prediction of future suicide attempts. The LGBQ group also indicated greater likelihood of going online to develop new personal relationships. Multiple regression modeling was conducted to guide outreach and support efforts, revealing unique factors predicting help-seeking denial of suicide-risk LGBQ. Implications include the importance of online support and considering sexual minorities not just as a potential high-risk group, but also as a population with unique suicide risks and behaviors. PMID:23657812

  1. The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning.

    PubMed

    Hazen, Jennifer L; Faust, Gregory G; Rodriguez, Alberto R; Ferguson, William C; Shumilina, Svetlana; Clark, Royden A; Boland, Michael J; Martin, Greg; Chubukov, Pavel; Tsunemoto, Rachel K; Torkamani, Ali; Kupriyanov, Sergey; Hall, Ira M; Baldwin, Kristin K

    2016-03-16

    Somatic mutation in neurons is linked to neurologic disease and implicated in cell-type diversification. However, the origin, extent, and patterns of genomic mutation in neurons remain unknown. We established a nuclear transfer method to clonally amplify the genomes of neurons from adult mice for whole-genome sequencing. Comprehensive mutation detection and independent validation revealed that individual neurons harbor ∼100 unique mutations from all classes but lack recurrent rearrangements. Most neurons contain at least one gene-disrupting mutation and rare (0-2) mobile element insertions. The frequency and gene bias of neuronal mutations differ from other lineages, potentially due to novel mechanisms governing postmitotic mutation. Fertile mice were cloned from several neurons, establishing the compatibility of mutated adult neuronal genomes with reprogramming to pluripotency and development. PMID:26948891

  2. Revealing a steroid receptor ligand as a unique PPAR[gamma] agonist

    SciTech Connect

    Lin, Shengchen; Han, Ying; Shi, Yuzhe; Rong, Hui; Zheng, Songyang; Jin, Shikan; Lin, Shu-Yong; Lin, Sheng-Cai; Li, Yong

    2012-06-28

    Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) regulates metabolic homeostasis and is a molecular target for anti-diabetic drugs. We report here the identification of a steroid receptor ligand, RU-486, as an unexpected PPAR{gamma} agonist, thereby uncovering a novel signaling route for this steroid drug. Similar to rosiglitazone, RU-486 modulates the expression of key PPAR{gamma} target genes and promotes adipocyte differentiation, but with a lower adipogenic activity. Structural and functional studies of receptor-ligand interactions reveal the molecular basis for a unique binding mode for RU-486 in the PPAR{gamma} ligand-binding pocket with distinctive properties and epitopes, providing the molecular mechanisms for the discrimination of RU-486 from thiazolidinediones (TZDs) drugs. Our findings together indicate that steroid compounds may represent an alternative approach for designing non-TZD PPAR{gamma} ligands in the treatment of insulin resistance.

  3. Dynamic functional network connectivity reveals unique and overlapping profiles of insula subdivisions.

    PubMed

    Nomi, Jason S; Farrant, Kristafor; Damaraju, Eswar; Rachakonda, Srinivas; Calhoun, Vince D; Uddin, Lucina Q

    2016-05-01

    The human insular cortex consists of functionally diverse subdivisions that engage during tasks ranging from interoception to cognitive control. The multiplicity of functions subserved by insular subdivisions calls for a nuanced investigation of their functional connectivity profiles. Four insula subdivisions (dorsal anterior, dAI; ventral, VI; posterior, PI; middle, MI) derived using a data-driven approach were subjected to static- and dynamic functional network connectivity (s-FNC and d-FNC) analyses. Static-FNC analyses replicated previous work demonstrating a cognition-emotion-interoception division of the insula, where the dAI is functionally connected to frontal areas, the VI to limbic areas, and the PI and MI to sensorimotor areas. Dynamic-FNC analyses consisted of k-means clustering of sliding windows to identify variable insula connectivity states. The d-FNC analysis revealed that the most frequently occurring dynamic state mirrored the cognition-emotion-interoception division observed from the s-FNC analysis, with less frequently occurring states showing overlapping and unique subdivision connectivity profiles. In two of the states, all subdivisions exhibited largely overlapping profiles, consisting of subcortical, sensory, motor, and frontal connections. Two other states showed the dAI exhibited a unique connectivity profile compared with other insula subdivisions. Additionally, the dAI exhibited the most variable functional connections across the s-FNC and d-FNC analyses, and was the only subdivision to exhibit dynamic functional connections with regions of the default mode network. These results highlight how a d-FNC approach can capture functional dynamics masked by s-FNC approaches, and reveal dynamic functional connections enabling the functional flexibility of the insula across time. Hum Brain Mapp 37:1770-1787, 2016. © 2016 Wiley Periodicals, Inc. PMID:26880689

  4. An evolutionary analysis of flightin reveals a conserved motif unique and widespread in Pancrustacea.

    PubMed

    Soto-Adames, Felipe N; Alvarez-Ortiz, Pedro; Vigoreaux, Jim O

    2014-01-01

    Flightin is a thick filament protein that in Drosophila melanogaster is uniquely expressed in the asynchronous, indirect flight muscles (IFM). Flightin is required for the structure and function of the IFM and is indispensable for flight in Drosophila. Given the importance of flight acquisition in the evolutionary history of insects, here we study the phylogeny and distribution of flightin. Flightin was identified in 69 species of hexapods in classes Collembola (springtails), Protura, Diplura, and insect orders Thysanura (silverfish), Dictyoptera (roaches), Orthoptera (grasshoppers), Pthiraptera (lice), Hemiptera (true bugs), Coleoptera (beetles), Neuroptera (green lacewing), Hymenoptera (bees, ants, and wasps), Lepidoptera (moths), and Diptera (flies and mosquitoes). Flightin was also found in 14 species of crustaceans in orders Anostraca (water flea), Cladocera (brine shrimp), Isopoda (pill bugs), Amphipoda (scuds, sideswimmers), and Decapoda (lobsters, crabs, and shrimps). Flightin was not identified in representatives of chelicerates, myriapods, or any species outside Pancrustacea (Tetraconata, sensu Dohle). Alignment of amino acid sequences revealed a conserved region of 52 amino acids, referred herein as WYR, that is bound by strictly conserved tryptophan (W) and arginine (R) and an intervening sequence with a high content of tyrosines (Y). This motif has no homologs in GenBank or PROSITE and is unique to flightin and paraflightin, a putative flightin paralog identified in decapods. A third motif of unclear affinities to pancrustacean WYR was observed in chelicerates. Phylogenetic analysis of amino acid sequences of the conserved motif suggests that paraflightin originated before the divergence of amphipods, isopods, and decapods. We conclude that flightin originated de novo in the ancestor of Pancrustacea > 500 MYA, well before the divergence of insects (~400 MYA) and the origin of flight (~325 MYA), and that its IFM-specific function in Drosophila is a more

  5. Nanoscopy Reveals Surface-Metallic Black Phosphorus

    NASA Astrophysics Data System (ADS)

    Abate, Yohannes

    Nanolayer and two-dimensional (2D) materials............. 1 such as graphene... 2,3 , boron nitride... 1,4 , transition metal dichalcogenides... 1 , 5 - 8 (TMDCs), and black phosphorus (BP)... 1 , 9 - 13 have intriguing fundamental physical properties and bear promise of important applications in electronics and optics... 9 , 14 , 15 . Of them, BP... 11 , 12 , 16 is a novel layered material that has been theoretically predicted... 10 to acquire plasmonic behavior for frequencies below ~0.4 eV when highly doped. The electronic properties of BP are unique due to its anisotropic structure . Advantages of BP as a material for nanoelectronics and nanooptics are due to the fact that, in contrast to metals, the free carrier density in it can be dynamically controlled by chemical or electrostatic gating, which has been demonstrated by its use in field-effect transistors.... 9 , 14 , 15 Despite all the interest that BP attracts, near-field and plasmonic properties of BP have not yet been investigated experimentally. Here we report the first observation of nanoscopic near-field properties of BP. We have discovered near-field patterns of outside bright fringes and high surface polarizability of nanofilm BP consistent with its surface-metallic, plasmonic behavior at mid-infrared (mid-IR) frequencies below critical frequency ωm ~ 1176 cm -1 . This has allowed us to estimate plasma frequency ωp ~ 0 . 4 eV, carrier density n ~ 1 . 1 × 1011 nm-1 and the thickness of the surface metallic layer of ~ 1 nm . We have also observed similar behavior in other nanolayer semiconductors such as TMDC MoS 2 and topological insulator Bi 2 Te 3 but not in insulators such as boron nitride. This new phenomenon is attributed to surface band-bending and charging of the semiconductor nanofilms. The surface plasmonic behavior has been found for 10-40 nm BP thickness but absent for 4 nm BP thickness. This discovery opens up a new field of research and potential applications in nanoelectronics

  6. Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology.

    PubMed

    Oulas, Anastasis; Polymenakou, Paraskevi N; Seshadri, Rekha; Tripp, H James; Mandalakis, Manolis; Paez-Espino, A David; Pati, Amrita; Chain, Patrick; Nomikou, Paraskevi; Carey, Steven; Kilias, Stephanos; Christakis, Christos; Kotoulas, Georgios; Magoulas, Antonios; Ivanova, Natalia N; Kyrpides, Nikos C

    2016-04-01

    Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications. PMID:26487573

  7. The Affymetrix DMET Plus Platform Reveals Unique Distribution of ADME-Related Variants in Ethnic Arabs

    PubMed Central

    Wakil, Salma M.; Nguyen, Cao; Muiya, Nzioka P.; Andres, Editha; Lykowska-Tarnowska, Agnieszka; Baz, Batoul; Meyer, Brian F.; Morahan, Grant

    2015-01-01

    Background. The Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus Premier Pack has been designed to genotype 1936 gene variants thought to be essential for screening patients in personalized drug therapy. These variants include the cytochrome P450s (CYP450s), the key metabolizing enzymes, many other enzymes involved in phase I and phase II pharmacokinetic reactions, and signaling mediators associated with variability in clinical response to numerous drugs not only among individuals, but also between ethnic populations. Materials and Methods. We genotyped 600 Saudi individuals for 1936 variants on the DMET platform to evaluate their clinical potential in personalized medicine in ethnic Arabs. Results. Approximately 49% each of the 437 CYP450 variants, 56% of the 581 transporters, 56% of 419 transferases, 48% of the 104 dehydrogenases, and 58% of the remaining 390 variants were detected. Several variants, such as rs3740071, rs6193, rs258751, rs6199, rs11568421, and rs8187797, exhibited significantly either higher or lower minor allele frequencies (MAFs) than those in other ethnic groups. Discussion. The present study revealed some unique distribution trends for several variants in Arabs, which displayed partly inverse allelic prevalence compared to other ethnic populations. The results point therefore to the need to verify and ascertain the prevalence of a variant as a prerequisite for engaging it in clinical routine screening in personalized medicine in any given population. PMID:25802476

  8. A novel sigma factor reveals a unique regulon controlling cell-specific recombination in Mycoplasma genitalium.

    PubMed

    Torres-Puig, Sergi; Broto, Alicia; Querol, Enrique; Piñol, Jaume; Pich, Oscar Q

    2015-05-26

    The Mycoplasma genitalium MG428 protein shows homology to members of the sigma-70 family of sigma factors. Herein, we found that MG428 activates transcription of recA, ruvA and ruvB as well as several genes with unknown function. Deletion of MG_428 or some of the up-regulated unknown genes led to severe recombination defects. Single cell analyses revealed that activation of the MG428-regulon is a rare event under laboratory growth conditions. A conserved sequence with sigma-70 promoter architecture (TTGTCA-N(18/19)-ATTWAT) was identified in the upstream region of all of the MG428-regulated genes or operons. Primer extension analyses demonstrated that transcription initiates immediately downstream of this sigma70-type promoter in a MG428-dependent manner. Furthermore, mutagenesis of the conserved -10 and -35 elements corroborated the requirement of these regions for promoter function. Therefore, a new mycoplasma promoter directs transcription of a unique recombination regulon. Additionally, MG428 was found to interact with the RNAP core enzyme, reinforcing the predicted role of this protein as an alternative sigma factor. Finally, our results indicate that MG428 contributes to the generation of genetic diversity in this model organism. Since recombination is an important mechanism to generate antigenic variation, MG428 emerges as a novel factor contributing to M. genitalium virulence. PMID:25925568

  9. A novel sigma factor reveals a unique regulon controlling cell-specific recombination in Mycoplasma genitalium

    PubMed Central

    Torres-Puig, Sergi; Broto, Alicia; Querol, Enrique; Piñol, Jaume; Pich, Oscar Q.

    2015-01-01

    The Mycoplasma genitalium MG428 protein shows homology to members of the sigma-70 family of sigma factors. Herein, we found that MG428 activates transcription of recA, ruvA and ruvB as well as several genes with unknown function. Deletion of MG_428 or some of the up-regulated unknown genes led to severe recombination defects. Single cell analyses revealed that activation of the MG428-regulon is a rare event under laboratory growth conditions. A conserved sequence with sigma-70 promoter architecture (TTGTCA-N18/19-ATTWAT) was identified in the upstream region of all of the MG428-regulated genes or operons. Primer extension analyses demonstrated that transcription initiates immediately downstream of this sigma70-type promoter in a MG428-dependent manner. Furthermore, mutagenesis of the conserved −10 and −35 elements corroborated the requirement of these regions for promoter function. Therefore, a new mycoplasma promoter directs transcription of a unique recombination regulon. Additionally, MG428 was found to interact with the RNAP core enzyme, reinforcing the predicted role of this protein as an alternative sigma factor. Finally, our results indicate that MG428 contributes to the generation of genetic diversity in this model organism. Since recombination is an important mechanism to generate antigenic variation, MG428 emerges as a novel factor contributing to M. genitalium virulence. PMID:25925568

  10. Comparative Analysis of 35 Basidiomycete Genomes Reveals Diversity and Uniqueness of the Phylum

    SciTech Connect

    Riley, Robert; Salamov, Asaf; Otillar, Robert; Fagnan, Kirsten; Boussau, Bastien; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Held, Benjamin; Nagy, Laszlo; Floudas, Dimitris; Morin, Emmanuelle; Manning, Gerard; Baker, Scott; Martin, Francis; Blanchette, Robert; Hibbett, David; Grigoriev, Igor V.

    2013-03-11

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCA analysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth assays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.

  11. Silicon-wafer-surface damage revealed by surface photovoltage measurements

    NASA Astrophysics Data System (ADS)

    Goodman, Alvin M.

    1982-11-01

    Anomalous results of surface photovoltage (SPV) measurements on Si wafers are shown to be associated with a damaged region beneath the illuminated surface of the wafer being measured. The anomaly is a concave-upward curvature of the I0(α-1) plot with an r2 value, derived from linear regression analysis, less than the normally observed minimum value (˜0.98). Removal of the damaged region by an appropriate etching procedure allows subsequent SPV measurements whose results are substantially free of the previously observed anomaly. The qualitative character of the anomaly can be reproduced by a simple theoretical model in which only one effect of the damage is considered; this effect is a diminished quantum efficiency for hole-electron pair generation by photon absorption in the damaged region. The results suggest the use of SPV measurements as a test procedure for revealing the presence of surface damage in Si wafers.

  12. Uranus' Southern Circulation Revealed by Voyager-2 Images: Asymmetric, Unique, Unexpected

    NASA Astrophysics Data System (ADS)

    Karkoschka, Erich

    2014-11-01

    The southern half of Uranus' southern hemisphere of Uranus has been exceptionally bland. Only a single discrete feature was detected in Voyager-2 images, and none has been seen in thousands of HST and ground-based images since. All other observed regions on Uranus and jovian planets have many features that defined circulation patterns of the jovian planets, but the circulation of Uranus south of -45 deg latitude has been unknown.We performed a reanalysis of Voyager images of Uranus that revealed dozens of discrete features instead of the single feature known before. We improved flatfielding, pad-pixel treatment, and nonlinearity correction. We greatly decreased noise by averaging up to 1600 images. The result is a rotational profile without major gaps.Uranus' high southern latitudes are exceptional in several aspects: 1) The rotational profile has sharp kinks while it is smooth elsewhere on the ice giants. This puts current ideas of a simple Hadley cell on each hemisphere into question. 2) The rotational profile has a large north-south asymmetry, an order of magnitude larger than elsewhere on the jovian planets. 3) Between -68 and -59 deg latitude, the rotational shear is some 30 times lower than at other latitudes. Here, winds speeds around 200 m/s are regular to the 0.1 m/s level. 4) The South Pole had a spot off center rotating 5 h faster than the interior, which has not been observed elsewhere on jovian planets. 5) Uranus revealed spirals winding around the whole planet more than once that indicate very regular meridional motions, to the 2 cm/s level. 6) The latitude at -84 deg was featureless even at a signal-to-noise ratio of 55,000, one of the blandest zones in nature.Some features show significant evolution within the 5-week observing period providing constraints on dynamics. Features also show distinct spectral characteristics in the 8-filter data set providing constraints on the physical nature of features and their altitude. We have the data to

  13. Giraffe genome sequence reveals clues to its unique morphology and physiology.

    PubMed

    Agaba, Morris; Ishengoma, Edson; Miller, Webb C; McGrath, Barbara C; Hudson, Chelsea N; Bedoya Reina, Oscar C; Ratan, Aakrosh; Burhans, Rico; Chikhi, Rayan; Medvedev, Paul; Praul, Craig A; Wu-Cavener, Lan; Wood, Brendan; Robertson, Heather; Penfold, Linda; Cavener, Douglas R

    2016-01-01

    The origins of giraffe's imposing stature and associated cardiovascular adaptations are unknown. Okapi, which lacks these unique features, is giraffe's closest relative and provides a useful comparison, to identify genetic variation underlying giraffe's long neck and cardiovascular system. The genomes of giraffe and okapi were sequenced, and through comparative analyses genes and pathways were identified that exhibit unique genetic changes and likely contribute to giraffe's unique features. Some of these genes are in the HOX, NOTCH and FGF signalling pathways, which regulate both skeletal and cardiovascular development, suggesting that giraffe's stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes. Mitochondrial metabolism and volatile fatty acids transport genes are also evolutionarily diverged in giraffe and may be related to its unusual diet that includes toxic plants. Unexpectedly, substantial evolutionary changes have occurred in giraffe and okapi in double-strand break repair and centrosome functions. PMID:27187213

  14. Giraffe genome sequence reveals clues to its unique morphology and physiology

    PubMed Central

    Agaba, Morris; Ishengoma, Edson; Miller, Webb C.; McGrath, Barbara C.; Hudson, Chelsea N.; Bedoya Reina, Oscar C.; Ratan, Aakrosh; Burhans, Rico; Chikhi, Rayan; Medvedev, Paul; Praul, Craig A.; Wu-Cavener, Lan; Wood, Brendan; Robertson, Heather; Penfold, Linda; Cavener, Douglas R.

    2016-01-01

    The origins of giraffe's imposing stature and associated cardiovascular adaptations are unknown. Okapi, which lacks these unique features, is giraffe's closest relative and provides a useful comparison, to identify genetic variation underlying giraffe's long neck and cardiovascular system. The genomes of giraffe and okapi were sequenced, and through comparative analyses genes and pathways were identified that exhibit unique genetic changes and likely contribute to giraffe's unique features. Some of these genes are in the HOX, NOTCH and FGF signalling pathways, which regulate both skeletal and cardiovascular development, suggesting that giraffe's stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes. Mitochondrial metabolism and volatile fatty acids transport genes are also evolutionarily diverged in giraffe and may be related to its unusual diet that includes toxic plants. Unexpectedly, substantial evolutionary changes have occurred in giraffe and okapi in double-strand break repair and centrosome functions. PMID:27187213

  15. Transcriptomic sequencing reveals a set of unique genes activated by butyrate-induced histone modification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Butyrate is a nutritional element with strong epigenetic regulatory activity as an inhibitor of histone deacetylases (HDACs). Based on the analysis of differentially expressed genes induced by butyrate in the bovine epithelial cell using deep RNA-sequencing technology (RNA-seq), a set of unique gen...

  16. Unique gene program of rat small resistance mesenteric arteries as revealed by deep RNA sequencing

    PubMed Central

    Reho, John J; Shetty, Amol; Dippold, Rachael P; Mahurkar, Anup; Fisher, Steven A

    2015-01-01

    Deep sequencing of RNA samples from rat small mesenteric arteries (MA) and aorta (AO) identified common and unique features of their gene programs. ∼5% of mRNAs were quantitatively differentially expressed in MA versus AO. Unique transcriptional control in MA smooth muscle is suggested by the selective or enriched expression of transcription factors Nkx2-3, HAND2, and Tcf21 (Capsulin). Enrichment in AO of PPAR transcription factors and their target genes of mitochondrial function, lipid metabolism, and oxidative phosphorylation is consistent with slow (oxidative) tonic smooth muscle. In contrast MA was enriched in contractile and calcium channel mRNAs suggestive of components of fast (glycolytic) phasic smooth muscle. Myosin phosphatase regulatory subunit paralogs Mypt1 and p85 were expressed at similar levels, while smooth muscle MLCK was the only such kinase expressed, suggesting functional redundancy of the former but not the latter in accordance with mouse knockout studies. With regard to vaso-regulatory signals, purinergic receptors P2rx1 and P2rx5 were reciprocally expressed in MA versus AO, while the olfactory receptor Olr59 was enriched in MA. Alox15, which generates the EDHF HPETE, was enriched in MA while eNOS was equally expressed, consistent with the greater role of EDHF in the smaller arteries. mRNAs that were not expressed at a level consistent with impugned function include skeletal myogenic factors, IKK2, nonmuscle myosin, and Gnb3. This screening analysis of gene expression in the small mesenteric resistance arteries suggests testable hypotheses regarding unique aspects of small artery function in the regional control of blood flow. PMID:26156969

  17. Electron microscopy reveals unique microfossil preservation in 1 billion-year-old lakes

    NASA Astrophysics Data System (ADS)

    Saunders, M.; Kong, C.; Menon, S.; Wacey, D.

    2014-06-01

    Electron microscopy was applied to the study of 1 billion-year-old microfossils from northwest Scotland in order to investigate their 3D morphology and mode of fossilization. 3D-FIB-SEM revealed high quality preservation of organic cell walls with only minor amounts of post-mortem decomposition, followed by variable degrees of morphological alteration (folding and compression of cell walls) during sediment compaction. EFTEM mapping plus SAED revealed a diverse fossilizing mineral assemblage including K-rich clay, Fe-Mg-rich clay and calcium phosphate, with each mineral occupying specific microenvironments in proximity to carbonaceous microfossil cell walls.

  18. Unique lipid anchor attaches Vi antigen capsule to the surface of Salmonella enterica serovar Typhi.

    PubMed

    Liston, Sean D; Ovchinnikova, Olga G; Whitfield, Chris

    2016-06-14

    Polysaccharide capsules are surface structures that are critical for the virulence of many Gram-negative pathogenic bacteria. Salmonella enterica serovar Typhi is the etiological agent of typhoid fever. It produces a capsular polysaccharide known as "Vi antigen," which is composed of nonstoichiometrically O-acetylated α-1,4-linked N-acetylgalactosaminuronic acid residues. This glycan is a component of currently available vaccines. The genetic locus for Vi antigen production is also present in soil bacteria belonging to the genus Achromobacter Vi antigen assembly follows a widespread general strategy with a characteristic glycan export step involving an ATP-binding cassette transporter. However, Vi antigen producers lack the enzymes that build the conserved terminal glycolipid characterizing other capsules using this method. Achromobacter species possess a Vi antigen-specific depolymerase enzyme missing in S enterica Typhi, and we exploited this enzyme to isolate acylated Vi antigen termini. Mass spectrometry analysis revealed a reducing terminal N-acetylhexosamine residue modified with two β-hydroxyl acyl chains. This terminal structure resembles one half of lipid A, the hydrophobic portion of bacterial lipopolysaccharides. The VexE protein encoded in the Vi antigen biosynthesis locus shares similarity with LpxL, an acyltransferase from lipid A biosynthesis. In the absence of VexE, Vi antigen is produced, but its physical properties are altered, its export is impaired, and a Vi capsule structure is not assembled on the cell surface. The structure of the lipidated terminus dictates a unique assembly mechanism and has potential implications in pathogenesis and vaccine production. PMID:27226298

  19. Description of a unique machine tool permitting achievement of < 15-A rms diamond-turned surfaces

    SciTech Connect

    Miller, D.M.; Hauver, G.H.; Culverhouse, J.N.; Greenwell, E.N.

    1980-01-01

    A new machine tool now in the final stages of development at the Pacific Northwest Laboratory uses a unique tool motion to produce diamond-turned surfaces of exceptionally high quality. The cutting tool is programmed to move in 4-nm increments along two axes: an X axis and an Omega axis. Exceptionally stiff and accurate control of the tool is possible with this Omega-X system. Copper surfaces of revolution have been produced with a 12.3-A rms surface finish and a contour accuracy of 75 nm. In conjunction with a unique, thermally stabilized air bearing spindle and machine calibration equipment, the Omega-X system permits a significant advance in the fabrication of optical-quality surfaces for use with the visible spectrum.

  20. Nanoscopic characterization of the water vapor-salt interfacial layer reveals a unique biphasic adsorption process.

    PubMed

    Yang, Liu; He, Jianfeng; Shen, Yi; Li, Xiaowei; Sun, Jielin; Czajkowsky, Daniel M; Shao, Zhifeng

    2016-01-01

    Our quantitative understanding of water adsorption onto salt surfaces under ambient conditions is presently quite poor owing to the difficulties in directly characterizing this interfacial layer under these conditions. Here we determine the thickness of the interfacial layer on NaCl at different relative humidities (RH) based on a novel application of atomic force spectroscopy and capillary condensation theory. In particular, we take advantage of the microsecond-timescale of the capillary condensation process to directly resolve the magnitude of its contribution in the tip-sample interaction, from which the interfacial water thickness is determined. Further, to correlate this thickness with salt dissolution, we also measure surface conductance under similar conditions. We find that below 30% RH, there is essentially only the deposition of water molecules onto this surface, typical of conventional adsorption onto solid surfaces. However, above 30% RH, adsorption is simultaneous with the dissolution of ions, unlike conventional adsorption, leading to a rapid increase of surface conductance. Thus, water adsorption on NaCl is an unconventional biphasic process in which the interfacial layer not only exhibits quantitative differences in thickness but also qualitative differences in composition. PMID:27527905

  1. Nanoscopic characterization of the water vapor-salt interfacial layer reveals a unique biphasic adsorption process

    PubMed Central

    Yang, Liu; He, Jianfeng; Shen, Yi; Li, Xiaowei; Sun, Jielin; Czajkowsky, Daniel M.; Shao, Zhifeng

    2016-01-01

    Our quantitative understanding of water adsorption onto salt surfaces under ambient conditions is presently quite poor owing to the difficulties in directly characterizing this interfacial layer under these conditions. Here we determine the thickness of the interfacial layer on NaCl at different relative humidities (RH) based on a novel application of atomic force spectroscopy and capillary condensation theory. In particular, we take advantage of the microsecond-timescale of the capillary condensation process to directly resolve the magnitude of its contribution in the tip-sample interaction, from which the interfacial water thickness is determined. Further, to correlate this thickness with salt dissolution, we also measure surface conductance under similar conditions. We find that below 30% RH, there is essentially only the deposition of water molecules onto this surface, typical of conventional adsorption onto solid surfaces. However, above 30% RH, adsorption is simultaneous with the dissolution of ions, unlike conventional adsorption, leading to a rapid increase of surface conductance. Thus, water adsorption on NaCl is an unconventional biphasic process in which the interfacial layer not only exhibits quantitative differences in thickness but also qualitative differences in composition. PMID:27527905

  2. Existence and uniqueness of analytic solution for unsteady crystals with zero surface tension

    NASA Astrophysics Data System (ADS)

    Xie, Xuming

    2007-03-01

    We study the initial value problem for two-dimensional dendritic crystal growth with zero surface tension. If the initial data is analytic and close to Ivantsov steady solution, it is proved that unique analytic solution exists locally in time. The analysis is based on a Nirenberg Theorem on abstract Cauchy-Kovalevsky problem in properly chosen Banach spaces.

  3. Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures

    PubMed Central

    Dunn, Barbara; Levine, R Paul; Sherlock, Gavin

    2005-01-01

    Background Genetic differences between yeast strains used in wine-making may account for some of the variation seen in their fermentation properties and may also produce differing sensory characteristics in the final wine product itself. To investigate this, we have determined genomic differences among several Saccharomyces cerevisiae wine strains by using a "microarray karyotyping" (also known as "array-CGH" or "aCGH") technique. Results We have studied four commonly used commercial wine yeast strains, assaying three independent isolates from each strain. All four wine strains showed common differences with respect to the laboratory S. cerevisiae strain S288C, some of which may be specific to commercial wine yeasts. We observed very little intra-strain variation; i.e., the genomic karyotypes of different commercial isolates of the same strain looked very similar, although an exception to this was seen among the Montrachet isolates. A moderate amount of inter-strain genomic variation between the four wine strains was observed, mostly in the form of depletions or amplifications of single genes; these differences allowed unique identification of each strain. Many of the inter-strain differences appear to be in transporter genes, especially hexose transporters (HXT genes), metal ion sensors/transporters (CUP1, ZRT1, ENA genes), members of the major facilitator superfamily, and in genes involved in drug response (PDR3, SNQ1, QDR1, RDS1, AYT1, YAR068W). We therefore used halo assays to investigate the response of these strains to three different fungicidal drugs (cycloheximide, clotrimazole, sulfomethuron methyl). Strains with fewer copies of the CUP1 loci showed hypersensitivity to sulfomethuron methyl. Conclusion Microarray karyotyping is a useful tool for analyzing the genome structures of wine yeasts. Despite only small to moderate variations in gene copy numbers between different wine yeast strains and within different isolates of a given strain, there was enough

  4. Dawn at Ceres reveals an ammoniated surface

    NASA Astrophysics Data System (ADS)

    Pieters, Carle M.; De Sanctis, Maria Cristina; Ammannito, Eleonora; Raponi, Andrea; Combe, Jean-Philippe; McCord, Thomas B.; McSween, Harry; McFadden, Lucy A.; Marchi, Simone; Capaccioni, Fabrizio; Capria, Maria Teresa; Carrozzo, Giacomo; Ciarniello, Mauro; Longobardo, Andrea; Fonte, Sergio; Formisano, Michelangelo; Frigeri, Alessandro; Giardino, Marco; Magni, Gianfranco; Palomba, Enersto; Tosi, Federico; Turrini, Diego; Zambon, Francesca; Jaumann, Ralf; Feldman, William; Prettyman, Thomas; Toplis, Michael; Raymond, Carol A.; Russell, Christopher T.

    2015-11-01

    The Visible and Infrared Mapping Spectrometer (VIR) on board the Dawn spacecraft has observed Ceres’ surface and acquired spectra (0.5 to 5 µm) since January 2015. Here we report the average Ceres spectrum, including the important spectral range (2.6-2.9 µm) previously precluded from (telescopic) measurements due to telluric atmospheric absorptions. The VIR data confirm that the surface is very dark with an average albedo of 0.090 ±0.006 at 0.55 µm, consistent with Hubble Space Telescope data (Li et al., Icarus, 2006) and contains no prominent absorption features in the visible and near-Infrared at wavelengths less than 2.5 µm. Ceres’ average spectrum, however, is characterized by a prominent diagnostic absorption band at 2.7 µm along with weaker absorption bands observed between 3.05-3.1, 3.3-3.4 and 3.9-4 µm. We modeled the new VIR spectra of Ceres with various ices, meteorites, silicates, carbonates, and hydrates using Hapke theory. Results of the spectral modeling indicate that extensive water ice is not present in spectra representing the typical surface acquired to date at relatively low spatial resolution (<11 km/pixel). The best fit is obtained with a mixture of ammoniated phyllosilicates mixed with other clays, Mg-carbonates, serpentine, and a strongly absorbing material, such as magnetite (De Sanctis et al., Nature, 2015, in review). The presence of ammonia-bearing materials in the crust across much of the surface has implications for the origin of Ceres and its internal structure and evolution. At the time of this presentation the Dawn spacecraft will have also completed its high altitude mapping orbit to look for anticipated small-scale mineralogy variations across this remarkable dwarf planet.Acknowledgements: VIR is funded by the Italian Space Agency-ASI and was developed under the leadership of INAF, Rome-Italy. The instrument was built by Selex-Galileo, Florence-Italy. The analyses are supported by ASI, NASA, and the German Space Agency

  5. Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

    PubMed Central

    Wegrzyn, Jill L.; Liechty, John D.; Stevens, Kristian A.; Wu, Le-Shin; Loopstra, Carol A.; Vasquez-Gross, Hans A.; Dougherty, William M.; Lin, Brian Y.; Zieve, Jacob J.; Martínez-García, Pedro J.; Holt, Carson; Yandell, Mark; Zimin, Aleksey V.; Yorke, James A.; Crepeau, Marc W.; Puiu, Daniela; Salzberg, Steven L.; de Jong, Pieter J.; Mockaitis, Keithanne; Main, Doreen; Langley, Charles H.; Neale, David B.

    2014-01-01

    The largest genus in the conifer family Pinaceae is Pinus, with over 100 species. The size and complexity of their genomes (∼20–40 Gb, 2n = 24) have delayed the arrival of a well-annotated reference sequence. In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine (Pinus taeda L.), which comprises 20.1 Gb of sequence. The MAKER-P annotation pipeline combined evidence-based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 are classified as high confidence. Clustering these gene models with 13 other plant species resulted in 20,646 gene families, of which 1554 are predicted to be unique to conifers. Among the conifer gene families, 159 are composed exclusively of loblolly pine members. The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes. Conifer genomes are full of repetitive DNA, with the most significant contributions from long-terminal-repeat retrotransposons. In depth analysis of the tandem and interspersed repetitive content yielded a combined estimate of 82%. PMID:24653211

  6. Human Suv3 protein reveals unique features among SF2 helicases

    SciTech Connect

    Jedrzejczak, Robert; Wang, Jiawei; Dauter, Miroslawa; Szczesny, Roman J.; Stepien, Piotr P.; Dauter, Zbigniew

    2011-11-01

    Crystal structures of the human mitochondrial helicase hSuv3 in complex with AMPPNP and with a short strand of RNA are presented. Suv3 is a helicase that is involved in efficient turnover and surveillance of RNA in eukaryotes. In vitro studies show that human Suv3 (hSuv3) in complex with human polynucleotide phosphorylase has RNA degradosome activity. The enzyme is mainly localized in mitochondria, but small fractions are found in cell nuclei. Here, two X-ray crystallographic structures of human Suv3 in complex with AMPPNP, a nonhydrolysable analog of ATP, and with a short five-nucleotide strand of RNA are presented at resolutions of 2.08 and 2.9 Å, respectively. The structure of the enzyme is very similar in the two complexes and consists of four domains. Two RecA-like domains form the tandem typical of all helicases from the SF2 superfamily which together with the C-terminal all-helical domain makes a ring structure through which the nucleotide strand threads. The mostly helical N-terminal domain is positioned externally with respect to the core of the enzyme. Most of the typical helicase motifs are present in hSuv3, but the protein shows certain unique characteristics, suggesting that Suv3 enzymes may constitute a separate subfamily of helicases.

  7. Human Suv3 protein reveals unique features among SF2 helicases

    SciTech Connect

    Jedrzejczak, Robert; Wang, Jiawei; Dauter, Miroslawa; Szczesny, Roman J.; Stepien, Piotr P.; Dauter, Zbigniew

    2012-03-16

    Suv3 is a helicase that is involved in efficient turnover and surveillance of RNA in eukaryotes. In vitro studies show that human Suv3 (hSuv3) in complex with human polynucleotide phosphorylase has RNA degradosome activity. The enzyme is mainly localized in mitochondria, but small fractions are found in cell nuclei. Here, two X-ray crystallographic structures of human Suv3 in complex with AMPPNP, a nonhydrolysable analog of ATP, and with a short five-nucleotide strand of RNA are presented at resolutions of 2.08 and 2.9 {angstrom}, respectively. The structure of the enzyme is very similar in the two complexes and consists of four domains. Two RecA-like domains form the tandem typical of all helicases from the SF2 superfamily which together with the C-terminal all-helical domain makes a ring structure through which the nucleotide strand threads. The mostly helical N-terminal domain is positioned externally with respect to the core of the enzyme. Most of the typical helicase motifs are present in hSuv3, but the protein shows certain unique characteristics, suggesting that Suv3 enzymes may constitute a separate subfamily of helicases.

  8. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

    PubMed

    Wegrzyn, Jill L; Liechty, John D; Stevens, Kristian A; Wu, Le-Shin; Loopstra, Carol A; Vasquez-Gross, Hans A; Dougherty, William M; Lin, Brian Y; Zieve, Jacob J; Martínez-García, Pedro J; Holt, Carson; Yandell, Mark; Zimin, Aleksey V; Yorke, James A; Crepeau, Marc W; Puiu, Daniela; Salzberg, Steven L; Dejong, Pieter J; Mockaitis, Keithanne; Main, Doreen; Langley, Charles H; Neale, David B

    2014-03-01

    The largest genus in the conifer family Pinaceae is Pinus, with over 100 species. The size and complexity of their genomes (∼20-40 Gb, 2n = 24) have delayed the arrival of a well-annotated reference sequence. In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine (Pinus taeda L.), which comprises 20.1 Gb of sequence. The MAKER-P annotation pipeline combined evidence-based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 are classified as high confidence. Clustering these gene models with 13 other plant species resulted in 20,646 gene families, of which 1554 are predicted to be unique to conifers. Among the conifer gene families, 159 are composed exclusively of loblolly pine members. The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes. Conifer genomes are full of repetitive DNA, with the most significant contributions from long-terminal-repeat retrotransposons. In depth analysis of the tandem and interspersed repetitive content yielded a combined estimate of 82%. PMID:24653211

  9. Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA

    PubMed Central

    Školáková, Petra; Foldynová-Trantírková, Silvie; Bednářová, Klára; Fiala, Radovan; Vorlíčková, Michaela; Trantírek, Lukáš

    2015-01-01

    There are two basic mechanisms that are associated with the maintenance of the telomere length, which endows cancer cells with unlimited proliferative potential. One mechanism, referred to as alternative lengthening of telomeres (ALT), accounts for approximately 10–15% of all human cancers. Tumours engaged in the ALT pathway are characterised by the presence of the single stranded 5′-C-rich telomeric overhang (C-overhang). This recently identified hallmark of ALT cancers distinguishes them from healthy tissues and renders the C-overhang as a clear target for anticancer therapy. We analysed structures of the 5′-C-rich and 3′-G-rich telomeric overhangs from human and Caenorhabditis elegans, the recently established multicellular in vivo model of ALT tumours. We show that the telomeric DNA from C. elegans and humans forms fundamentally different secondary structures. The unique structural characteristics of C. elegans telomeric DNA that are distinct not only from those of humans but also from those of other multicellular eukaryotes allowed us to identify evolutionarily conserved properties of telomeric DNA. Differences in structural organisation of the telomeric DNA between the C. elegans and human impose limitations on the use of the C. elegans as an ALT tumour model. PMID:25855805

  10. Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA.

    PubMed

    Školáková, Petra; Foldynová-Trantírková, Silvie; Bednářová, Klára; Fiala, Radovan; Vorlíčková, Michaela; Trantírek, Lukáš

    2015-05-19

    There are two basic mechanisms that are associated with the maintenance of the telomere length, which endows cancer cells with unlimited proliferative potential. One mechanism, referred to as alternative lengthening of telomeres (ALT), accounts for approximately 10-15% of all human cancers. Tumours engaged in the ALT pathway are characterised by the presence of the single stranded 5'-C-rich telomeric overhang (C-overhang). This recently identified hallmark of ALT cancers distinguishes them from healthy tissues and renders the C-overhang as a clear target for anticancer therapy. We analysed structures of the 5'-C-rich and 3'-G-rich telomeric overhangs from human and Caenorhabditis elegans, the recently established multicellular in vivo model of ALT tumours. We show that the telomeric DNA from C. elegans and humans forms fundamentally different secondary structures. The unique structural characteristics of C. elegans telomeric DNA that are distinct not only from those of humans but also from those of other multicellular eukaryotes allowed us to identify evolutionarily conserved properties of telomeric DNA. Differences in structural organisation of the telomeric DNA between the C. elegans and human impose limitations on the use of the C. elegans as an ALT tumour model. PMID:25855805

  11. Multilocus sequence typing of hospital-associated Enterococcus faecium from Brazil reveals their unique evolutionary history.

    PubMed

    Titze-de-Almeida, Ricardo; Van Belkum, Alex; Felipe, Maria Sueli Soares; Zanella, Rosemeire C; Top, Janetta; Willems, Rob J L

    2006-01-01

    We studied the genetic relationships between vancomycin-susceptible (n = 11) and -resistant Enterococcus faecium (VRE, n = 20) recovered from Brazil using a multilocus sequence typing (MLST) scheme. Grouping of allelic profiles revealed six clusters of related sequence types (STs) that differ in no more than two of the seven alleles. Of these, one cluster harbored 16 of the 20 isolates recovered during the first VRE outbreak in Brazil. The ampicillin and gentamicin resistance profiles were stable in the isolates that clustered within the groups I-III. Comparison with the allelic profiles of 139 E. faecium from different geographical regions and origins found in the international database http://www.mlst.net revealed that the Brazilian outbreak clone did not cluster in the previously named complex-17. This genetic complex contains hospital epidemic and clinical isolates recovered from different countries and continents. Twenty two of the 31 Brazilian isolates, including the VRE outbreak clone, clustered apart from the E. faecium isolates from the database, suggesting that these Brazilian isolates have a distinct evolutionary history. PMID:16922628

  12. Genomic and Secretomic Analyses Reveal Unique Features of the Lignocellulolytic Enzyme System of Penicillium decumbens

    PubMed Central

    Qin, Yuqi; Ma, Liang; Li, Jie; Zheng, Huajun; Wang, Shengyue; Wang, Chengshu; Xun, Luying; Zhao, Guo-Ping; Zhou, Zhihua; Qu, Yinbo

    2013-01-01

    Many Penicillium species could produce extracellular enzyme systems with good lignocellulose hydrolysis performance. However, these species and their enzyme systems are still poorly understood and explored due to the lacking of genetic information. Here, we present the genomic and secretomic analyses of Penicillium decumbens that has been used in industrial production of lignocellulolytic enzymes in China for more than fifteen years. Comparative genomics analysis with the phylogenetically most similar species Penicillium chrysogenum revealed that P. decumbens has evolved with more genes involved in plant cell wall degradation, but fewer genes in cellular metabolism and regulation. Compared with the widely used cellulase producer Trichoderma reesei, P. decumbens has a lignocellulolytic enzyme system with more diverse components, particularly for cellulose binding domain-containing proteins and hemicellulases. Further, proteomic analysis of secretomes revealed that P. decumbens produced significantly more lignocellulolytic enzymes in the medium with cellulose-wheat bran as the carbon source than with glucose. The results expand our knowledge on the genetic information of lignocellulolytic enzyme systems in Penicillium species, and will facilitate rational strain improvement for the production of highly efficient enzyme systems used in lignocellulose utilization from Penicillium species. PMID:23383313

  13. Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens.

    PubMed

    Liu, Guodong; Zhang, Lei; Wei, Xiaomin; Zou, Gen; Qin, Yuqi; Ma, Liang; Li, Jie; Zheng, Huajun; Wang, Shengyue; Wang, Chengshu; Xun, Luying; Zhao, Guo-Ping; Zhou, Zhihua; Qu, Yinbo

    2013-01-01

    Many Penicillium species could produce extracellular enzyme systems with good lignocellulose hydrolysis performance. However, these species and their enzyme systems are still poorly understood and explored due to the lacking of genetic information. Here, we present the genomic and secretomic analyses of Penicillium decumbens that has been used in industrial production of lignocellulolytic enzymes in China for more than fifteen years. Comparative genomics analysis with the phylogenetically most similar species Penicillium chrysogenum revealed that P. decumbens has evolved with more genes involved in plant cell wall degradation, but fewer genes in cellular metabolism and regulation. Compared with the widely used cellulase producer Trichoderma reesei, P. decumbens has a lignocellulolytic enzyme system with more diverse components, particularly for cellulose binding domain-containing proteins and hemicellulases. Further, proteomic analysis of secretomes revealed that P. decumbens produced significantly more lignocellulolytic enzymes in the medium with cellulose-wheat bran as the carbon source than with glucose. The results expand our knowledge on the genetic information of lignocellulolytic enzyme systems in Penicillium species, and will facilitate rational strain improvement for the production of highly efficient enzyme systems used in lignocellulose utilization from Penicillium species. PMID:23383313

  14. Biochemical characterization of isocitrate dehydrogenase from Methylococcus capsulatus reveals a unique NAD+-dependent homotetrameric enzyme.

    PubMed

    Stokke, Runar; Madern, Dominique; Fedøy, Anita-Elin; Karlsen, Solveig; Birkeland, Nils-Kåre; Steen, Ida Helene

    2007-05-01

    The gene encoding isocitrate dehydrogenase (IDH) of Methylococcus capsulatus (McIDH) was cloned and overexpressed in Escherichia coli. The purified enzyme was NAD+-dependent with a thermal optimum for activity at 55-60 degrees C and an apparent midpoint melting temperature (Tm) of 70 degrees C. Analytical ultracentrifugation (AUC) revealed a homotetrameric state, and McIDH thus represents the first homotetrameric NAD+-dependent IDH that has been characterized. Based on a structural alignment of McIDH and homotetrameric homoisocitrate dehydrogenase (HDH) from Thermus thermophilus (TtHDH), we identified the clasp-like domain of McIDH as a likely site for tetramerization. McIDH showed moreover, higher sequence identity (48%) to TtHDH than to previously characterized IDHs. Putative NAD+-IDHs with high sequence identity (48-57%) to McIDH were however identified in a variety of bacteria showing that NAD+-dependent IDHs are indeed widespread within the domain, Bacteria. Phylogenetic analysis including these new sequences revealed a close relationship with eukaryal allosterically regulated NAD+-IDH and the subfamily III of IDH was redefined to include bacterial NAD+- and NADP+-dependent IDHs. This apparent relationship suggests that the mitochondrial genes encoding NAD+-IDH are derived from the McIDH-like IDHs. PMID:17160675

  15. Functional profiles reveal unique ecological roles of various biological soil crust organisms

    USGS Publications Warehouse

    Bowker, M.A.; Mau, R.L.; Maestre, F.T.; Escolar, C.; Castillo-Monroy, A. P.

    2011-01-01

    1. At the heart of the body of research on biodiversity effects on ecosystem function is the debate over whether different species tend to be functionally singular or redundant. When we consider ecosystem multi-function, the provision of multiple ecosystem functions simultaneously, we may find that seemingly redundant species may in fact play unique roles in ecosystems. 2. Over the last few decades, the significance of biological soil crusts (BSCs) as ecological boundaries and ecosystem engineers, and their multi-functional nature, has become increasingly well documented. We compiled 'functional profiles' of the organisms in this understudied community, to determine whether functional singularity emerges when multiple ecosystem functions are considered. 3. In two data sets, one representing multiple sites around the semi-arid regions of Spain (regional scale), and another from a single site in central Spain (local scale), we examined correlations between the abundance or frequency of BSC species in a community, and multiple surrogates of ecosystem functioning. There was a wide array of apparent effects of species on specific functions. 4. Notably, in gypsiferous soils and at regional scale, we found that indicators of carbon (C) and phosphorus cycling were apparently suppressed and promoted by the lichens Diploschistes diacapsis and Squamarina lentigera, respectively. The moss Pleurochaete squarrosa appears to promote C cycling in calcareous soils at this spatial scale. At the local scale in gypsiferous soils, D. diacapsis positively correlated with carbon cycling, but negatively with nitrogen cycling, whereas numerous lichens exhibited the opposite profile. 5. We found a high degree of functional singularity, i.e. that species were highly individualistic in their effects on multiple functions. Many functional attributes were not easily predictable from existing functional grouping systems based primarily on morphology. 6. Our results suggest that maintaining

  16. A dimeric peptide with erythropoiesis-stimulating activity uniquely affects erythropoietin receptor ligation and cell surface expression.

    PubMed

    Verma, Rakesh; Green, Jennifer M; Schatz, Peter J; Wojchowski, Don M

    2016-08-01

    Erythropoiesis-stimulating agents (ESAs) that exert long-acting antianemia effects have been developed recently, but their mechanisms are poorly understood. Analyses reveal unique erythropoietin receptor (EPOR)-binding properties for one such ESA, the synthetic EPOR agonist peginesatide. Compared with recombinant human EPO and darbepoietin, peginesatide exhibited a slow on rate, but sustained EPOR residency and resistant displacement. In EPO-dependent human erythroid progenitor UT7epo cells, culture in peginesatide unexpectedly upmodulated endogenous cell surface EPOR levels with parallel increases in full-length EPOR-68K levels. These unique properties are suggested to contribute to the durable activity of this (and perhaps additional) dimeric peptide hematopoietic growth factor receptor agonist. PMID:27174804

  17. Unique Features of a Japanese ‘Candidatus Liberibacter asiaticus’ Strain Revealed by Whole Genome Sequencing

    PubMed Central

    Katoh, Hiroshi; Miyata, Shin-ichi; Inoue, Hiromitsu; Iwanami, Toru

    2014-01-01

    Citrus greening (huanglongbing) is the most destructive disease of citrus worldwide. It is spread by citrus psyllids and is associated with phloem-limited bacteria of three species of α-Proteobacteria, namely, ‘Candidatus Liberibacter asiaticus’, ‘Ca. L. americanus’, and ‘Ca. L. africanus’. Recent findings suggested that some Japanese strains lack the bacteriophage-type DNA polymerase region (DNA pol), in contrast to the Floridian psy62 strain. The whole genome sequence of the pol-negative ‘Ca. L. asiaticus’ Japanese isolate Ishi-1 was determined by metagenomic analysis of DNA extracted from ‘Ca. L. asiaticus’-infected psyllids and leaf midribs. The 1.19-Mb genome has an average 36.32% GC content. Annotation revealed 13 operons encoding rRNA and 44 tRNA genes, but no typical bacterial pathogenesis-related genes were located within the genome, similar to the Floridian psy62 and Chinese gxpsy. In contrast to other ‘Ca. L. asiaticus’ strains, the genome of the Japanese Ishi-1 strain lacks a prophage-related region. PMID:25180586

  18. An in vitro assay for entry into cilia reveals unique properties of the soluble diffusion barrier.

    PubMed

    Breslow, David K; Koslover, Elena F; Seydel, Federica; Spakowitz, Andrew J; Nachury, Maxence V

    2013-10-14

    Specific proteins are concentrated within primary cilia, whereas others remain excluded. To understand the mechanistic basis of entry into cilia, we developed an in vitro assay using cells in which the plasma membrane was permeabilized, but the ciliary membrane was left intact. Using a diffusion-to-capture system and quantitative analysis, we find that proteins >9 nm in diameter (∼100 kD) are restricted from entering cilia, and we confirm these findings in vivo. Interference with the nuclear pore complex (NPC) or the actin cytoskeleton in permeabilized cells demonstrated that the ciliary diffusion barrier is mechanistically distinct from those of the NPC or the axon initial segment. Moreover, applying a mass transport model to this system revealed diffusion coefficients for soluble and membrane proteins within cilia that are compatible with rapid exploration of the ciliary space in the absence of active transport. Our results indicate that large proteins require active transport for entry into cilia but not necessarily for movement inside cilia. PMID:24100294

  19. An in vitro assay for entry into cilia reveals unique properties of the soluble diffusion barrier

    PubMed Central

    Breslow, David K.; Koslover, Elena F.; Seydel, Federica; Spakowitz, Andrew J.

    2013-01-01

    Specific proteins are concentrated within primary cilia, whereas others remain excluded. To understand the mechanistic basis of entry into cilia, we developed an in vitro assay using cells in which the plasma membrane was permeabilized, but the ciliary membrane was left intact. Using a diffusion-to-capture system and quantitative analysis, we find that proteins >9 nm in diameter (∼100 kD) are restricted from entering cilia, and we confirm these findings in vivo. Interference with the nuclear pore complex (NPC) or the actin cytoskeleton in permeabilized cells demonstrated that the ciliary diffusion barrier is mechanistically distinct from those of the NPC or the axon initial segment. Moreover, applying a mass transport model to this system revealed diffusion coefficients for soluble and membrane proteins within cilia that are compatible with rapid exploration of the ciliary space in the absence of active transport. Our results indicate that large proteins require active transport for entry into cilia but not necessarily for movement inside cilia. PMID:24100294

  20. Unique surface adsorption behaviors of serum proteins on chemically uniform and alternating surfaces

    NASA Astrophysics Data System (ADS)

    Song, Sheng

    With increasing interests of studying proteins adsorption on the surfaces with nanoscale features in biomedical field, it is crucial to have fundamental understandings on how the proteins are adsorbed on such a surface and what factors contribute to the driving forces of adsorption. Besides, exploring more available nanoscale templates would greatly offer more possibilities one could design surface bio-detection methods with favorable protein-surface interactions. Thus, to fulfill the purpose, the work in this dissertation has been made into three major sections. First, to probe the intermediate states which possibly exist between stable and unstable phases described in mean-field theory diagram, a solvent vapor annealing method is chosen to slowly induce the copolymer polystyrene-block-polyvinylpyridine (PS-b-PVP)'s both blocks undergoing micro-phase separations from initial spherical nanodomains into terminal cylindrical nanodomains. During this process, real time atomic force microscopy (AFM) has been conducted to capture other six intermediate states with different morphologies on the polymeric film surfaces. Secondly, upon recognizing each intermediate state, the solution of immunoglobulin gamma (IgG) proteins has been deposited on the surface and been rinsed off with buffer solution before the protein-bounded surface is imaged by AFM. It has been found IgG showing a strong adsorption preference on PS over P4VP block. Among all the six intermediate states, the proteins are almost exclusively adsorbed on PS nanodomains regardless the concentration and deposition time. Thirdly, a trinodular shape protein fibrinogen (Fg) is selected for investigating how geometry and surface charge of proteins would interplay with cylindrical nanodomains on a surface developed from Polystyrene -block-Poly-(methyl methacrylate) PS-b-PMMA. Also, Fg adsorptions on chemically homogeneous surfaces are included here to have a better contrast of showing how much difference it can make

  1. CDK1 structures reveal conserved and unique features of the essential cell cycle CDK

    NASA Astrophysics Data System (ADS)

    Brown, Nicholas R.; Korolchuk, Svitlana; Martin, Mathew P.; Stanley, Will A.; Moukhametzianov, Rouslan; Noble, Martin E. M.; Endicott, Jane A.

    2015-04-01

    CDK1 is the only essential cell cycle CDK in human cells and is required for successful completion of M-phase. It is the founding member of the CDK family and is conserved across all eukaryotes. Here we report the crystal structures of complexes of CDK1-Cks1 and CDK1-cyclin B-Cks2. These structures confirm the conserved nature of the inactive monomeric CDK fold and its ability to be remodelled by cyclin binding. Relative to CDK2-cyclin A, CDK1-cyclin B is less thermally stable, has a smaller interfacial surface, is more susceptible to activation segment dephosphorylation and shows differences in the substrate sequence features that determine activity. Both CDK1 and CDK2 are potential cancer targets for which selective compounds are required. We also describe the first structure of CDK1 bound to a potent ATP-competitive inhibitor and identify aspects of CDK1 structure and plasticity that might be exploited to develop CDK1-selective inhibitors.

  2. CDK1 structures reveal conserved and unique features of the essential cell cycle CDK

    PubMed Central

    Brown, Nicholas R.; Korolchuk, Svitlana; Martin, Mathew P.; Stanley, Will; Moukhametzianov, Rouslan; Noble, Martin E.M.; Endicott, Jane A.

    2015-01-01

    CDK1 is the only essential cell cycle CDK in human cells and is required for successful completion of M-phase. It is the founding member of the CDK family and is conserved across all eukaryotes. Here we report the crystal structures of complexes of CDK1–Cks1 and CDK1–cyclin B–Cks2. These structures confirm the conserved nature of the inactive monomeric CDK fold and its ability to be remodeled by cyclin binding. Relative to CDK2–cyclin A, CDK1–cyclin B is less thermally stable, has a smaller interfacial surface, is more susceptible to activation segment dephosphorylation, and shows differences in the substrate sequence features that determine activity. Both CDK1 and CDK2 are potential cancer targets for which selective compounds are required. We also describe the first structure of CDK1 bound to a potent ATP-competitive inhibitor and identify aspects of CDK1 structure and plasticity that might be exploited to develop CDK1-selective inhibitors. PMID:25864384

  3. On the Development of a Unique Arc Jet Test Apparatus for Control Surface Seal Evaluations

    NASA Technical Reports Server (NTRS)

    Finkbeiner, Joshua R.; Dunlap, Patrick H., Jr.; Steinetz, Bruce M.; Robbie, Malcolm; Baker, Gus; Erker, Arthur

    2004-01-01

    NASA Glenn has developed a unique test apparatus capable of evaluating control surface seal and flap designs under simulated reentry heating conditions in NASA Johnson's arc jet test facility. The test apparatus is capable of testing a variety of seal designs with a variety of control surface materials and designs using modular components. The flap angle can be varied during testing, allowing modification of the seal environment while testing is in progress. The flap angle is varied using an innovative transmission system which limits heat transfer from the hot flap structure to the motor, all while keeping the components properly aligned regardless of thermal expansion. A combination of active and passive cooling is employed to prevent thermal damage to the test fixture while still obtaining the target seal temperature.

  4. Many unique characteristics revealed by the complete mitochondrial genome of the scorpion Tityus serrulatus (Lutz e Mello 1922) (Chelicerata; Arachnida).

    PubMed

    Martins, Ana Paula Vimieiro; Carmo, Anderson Oliveira do; Mesquita, Flavia Oliveira; Pimenta, Ricardo José Gonzaga; Chagas, Aline Torres de Azevedo; Kalapothakis, Evanguedes

    2016-09-01

    This is the first complete mitochondrial genome of a Tityus species, although it is the most medically important genus in South America. Tityus serrulatus (Brazilian yellow scorpion) mtDNA revealed the same gene arrangement of three out of four other mitogenomes published by now for the same family (Centruroides limpidus, Mesobuthus gibbosus, M. martensii and Buthus occitanus). However, it presented many unique characteristics such as possession of Cox1 gene, different from all other protein-coding genes of scorpion mtDNA, starts with an atypical start codon (CTG). Moreover, no tRNA gene have complete typical secondary structure and the Tytius genome presented three non-coding regions longer than 100bp. Also, it contains the smallest scorpion 16S gene reported by now. Phylogenetic analysis using concatenated homologous genes confirmed Buthidae as a monophyletic clade and supports a monophyletic group including T. serrulatus and the other American species, C. limpidus. PMID:26370626

  5. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis*

    PubMed Central

    Truschel, Steven T.; Sengupta, Debrup; Foote, Adam; Heroux, Annie; Macbeth, Mark R.; Linstedt, Adam D.

    2011-01-01

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae. PMID:21515684

  6. The Crystal Structure of Escherichia coli Spermidine Synthase SpeE Reveals a Unique Substrate-binding Pocket

    SciTech Connect

    Zhou, X.; Chua, T; Tkaczuk, K; Bujnicki, J; Sivaraman, J

    2010-01-01

    Polyamines are essential in all branches of life. Biosynthesis of spermidine, one of the most ubiquitous polyamines, is catalyzed by spermidine synthase (SpeE). Although the function of this enzyme from Escherichia coli has been thoroughly characterized, its structural details remain unknown. Here, we report the crystal structure of E. coli SpeE and study its interaction with the ligands by isothermal titration calorimetry and computational modelling. SpeE consists of two domains - a small N-terminal {beta}-strand domain, and a C-terminal catalytic domain that adopts a canonical methyltransferase (MTase) Rossmann fold. The protein forms a dimer in the crystal and in solution. Structural comparison of E. coli SpeE to its homologs reveals that it has a large and unique substrate-binding cleft that may account for its lower amine substrate specificity.

  7. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

    SciTech Connect

    Truschel, S.T.; Heroux, A.; Sengupta, D.; Foote, A.; Macbeth, M. R.; Linstedt, A. D.

    2011-06-10

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  8. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

    SciTech Connect

    S Truschel; D Sengupta; A Foote; A Heroux; M Macbeth; A Linstedt

    2011-12-31

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  9. Structural and functional characterization of TesB from Yersinia pestis reveals a unique octameric arrangement of hotdog domains

    PubMed Central

    Swarbrick, C. M. D.; Perugini, M. A.; Cowieson, N.; Forwood, J. K.

    2015-01-01

    Acyl-CoA thioesterases catalyse the hydrolysis of the thioester bonds present within a wide range of acyl-CoA substrates, releasing free CoASH and the corresponding fatty-acyl conjugate. The TesB-type thioesterases are members of the TE4 thioesterase family, one of 25 thioesterase enzyme families characterized to date, and contain two fused hotdog domains in both prokaryote and eukaryote homologues. Only two structures have been elucidated within this enzyme family, and much of the current understanding of the TesB thioesterases has been based on the Escherichia coli structure. Yersinia pestis, a highly virulent bacterium, encodes only one TesB-type thioesterase in its genome; here, the structural and functional characterization of this enzyme are reported, revealing unique elements both within the protomer and quaternary arrangements of the hotdog domains which have not been reported previously in any thioesterase family. The quaternary structure, confirmed using a range of structural and biophysical techniques including crystallography, small-angle X-ray scattering, analytical ultracentrifugation and size-exclusion chromatography, exhibits a unique octameric arrangement of hotdog domains. Interestingly, the same biological unit appears to be present in both TesB structures solved to date, and is likely to be a conserved and distinguishing feature of TesB-type thioesterases. Analysis of the Y. pestis TesB thioesterase activity revealed a strong preference for octanoyl-CoA and this is supported by structural analysis of the active site. Overall, the results provide novel insights into the structure of TesB thioesterases which are likely to be conserved and distinguishing features of the TE4 thioesterase family. PMID:25849407

  10. Case-Only Survival Analysis Reveals Unique Effects of Genotype, Sex, and Coronary Disease Severity on Survivorship

    PubMed Central

    Qin, Xuejun; Horne, Benjamin D.; Carlquist, John F.; Singh, Abanish; Hurdle, Melissa; Grass, Elizabeth; Haynes, Carol; Gregory, Simon G.; Shah, Svati H.; Hauser, Elizabeth R.; Kraus, William E.

    2016-01-01

    Survival bias may unduly impact genetic association with complex diseases; gene-specific survival effects may further complicate such investigations. Coronary artery disease (CAD) is a complex phenotype for which little is understood about gene-specific survival effects; yet, such information can offer insight into refining genetic associations, improving replications, and can provide candidate genes for both mortality risk and improved survivorship in CAD. Building on our previous work, the purpose of this current study was to: evaluate LSAMP SNP-specific hazards for all-cause mortality post-catheterization in a larger cohort of our CAD cases; and, perform additional replication in an independent dataset. We examined two LSAMP SNPs—rs1462845 and rs6788787—using CAD case-only Cox proportional hazards regression for additive genetic effects, censored on time-to-all-cause mortality or last follow-up among Caucasian subjects from the Catheterization Genetics Study (CATHGEN; n = 2,224) and the Intermountain Heart Collaborative Study (IMHC; n = 3,008). Only after controlling for age, sex, body mass index, histories of smoking, type 2 diabetes, hyperlipidemia and hypertension (HR = 1.11, 95%CI = 1.01–1.22, p = 0.032), rs1462845 conferred significantly increased hazards of all-cause mortality among CAD cases. Even after controlling for multiple covariates, but in only the primary cohort, rs6788787 conferred significantly improved survival (HR = 0.80, 95% CI = 0.69–0.92, p = 0.002). Post-hoc analyses further stratifying by sex and disease severity revealed replicated effects for rs1462845: even after adjusting for aforementioned covariates and coronary interventional procedures, males with severe burden of CAD had significantly amplified hazards of death with the minor variant of rs1462845 in both cohorts (HR = 1.29, 95% CI = 1.08–1.55, p = 0.00456; replication HR = 1.25, 95% CI = 1.05–1.49, p = 0.013). Kaplan-Meier curves revealed unique cohort

  11. Case-Only Survival Analysis Reveals Unique Effects of Genotype, Sex, and Coronary Disease Severity on Survivorship.

    PubMed

    Dungan, Jennifer R; Qin, Xuejun; Horne, Benjamin D; Carlquist, John F; Singh, Abanish; Hurdle, Melissa; Grass, Elizabeth; Haynes, Carol; Gregory, Simon G; Shah, Svati H; Hauser, Elizabeth R; Kraus, William E

    2016-01-01

    Survival bias may unduly impact genetic association with complex diseases; gene-specific survival effects may further complicate such investigations. Coronary artery disease (CAD) is a complex phenotype for which little is understood about gene-specific survival effects; yet, such information can offer insight into refining genetic associations, improving replications, and can provide candidate genes for both mortality risk and improved survivorship in CAD. Building on our previous work, the purpose of this current study was to: evaluate LSAMP SNP-specific hazards for all-cause mortality post-catheterization in a larger cohort of our CAD cases; and, perform additional replication in an independent dataset. We examined two LSAMP SNPs-rs1462845 and rs6788787-using CAD case-only Cox proportional hazards regression for additive genetic effects, censored on time-to-all-cause mortality or last follow-up among Caucasian subjects from the Catheterization Genetics Study (CATHGEN; n = 2,224) and the Intermountain Heart Collaborative Study (IMHC; n = 3,008). Only after controlling for age, sex, body mass index, histories of smoking, type 2 diabetes, hyperlipidemia and hypertension (HR = 1.11, 95%CI = 1.01-1.22, p = 0.032), rs1462845 conferred significantly increased hazards of all-cause mortality among CAD cases. Even after controlling for multiple covariates, but in only the primary cohort, rs6788787 conferred significantly improved survival (HR = 0.80, 95% CI = 0.69-0.92, p = 0.002). Post-hoc analyses further stratifying by sex and disease severity revealed replicated effects for rs1462845: even after adjusting for aforementioned covariates and coronary interventional procedures, males with severe burden of CAD had significantly amplified hazards of death with the minor variant of rs1462845 in both cohorts (HR = 1.29, 95% CI = 1.08-1.55, p = 0.00456; replication HR = 1.25, 95% CI = 1.05-1.49, p = 0.013). Kaplan-Meier curves revealed unique cohort-specific genotype effects

  12. Co-culture of osteocytes and neurons on a unique patterned surface

    PubMed Central

    Boggs, Mary E.; Thompson, William R.; Farach-Carson, Mary C.; Duncan, Randall L.; Beebe, Thomas P.

    2011-01-01

    Neural and skeletal communication is essential for the maintenance of bone mass and transmission of pain, yet the mechanism(s) of signal transduction between these tissues is unknown. The authors established a novel system to co-culture murine long bone osteocyte-like cells (MLO-Y4) and primary murine dorsal root ganglia (DRG) neurons. Assessment of morphology and maturation marker expression on perlecan domain IV peptide (PlnDIV) and collagen type-1 (Col1) demonstrated that PlnDIV was an optimal matrix for MLO-Y4 culture. A novel matrix-specificity competition assay was developed to expose these cells to several extracellular matrix proteins such as PlnDIV, Col1, and laminin (Ln). The competition assay showed that approximately 70% of MLOY4 cells preferred either PlnDIV or Col1 to Ln. To co-culture MLO-Y4 and DRG, we developed patterned surfaces using micro-contact printing to create 40 μm × 1 cm alternating stripes of PlnDIV and Ln or PlnDIV and Col1. Co-culture on PlnDIV/Ln surfaces demonstrated that these matrix molecules provided unique cues for each cell type, with MLO-Y4 preferentially attaching to the PlnDIV lanes and DRG neurons to the Ln lanes. Approximately 80% of DRG were localized to Ln. Cellular processes from MLO-Y4 were closely associated with axonal extensions of DRG neurons. Approximately 57% of neuronal processes were in close proximity to nearby MLO-Y4 cells at the PlnDIV-Ln interface. The surfaces in this new assay provided a unique model system with which to study the communication between osteocyte-like cells and neurons in an in vitro environment. PMID:22239813

  13. A unique PDZ domain and arrestin-like fold interaction reveals mechanistic details of endocytic recycling by SNX27-retromer.

    PubMed

    Gallon, Matthew; Clairfeuille, Thomas; Steinberg, Florian; Mas, Caroline; Ghai, Rajesh; Sessions, Richard B; Teasdale, Rohan D; Collins, Brett M; Cullen, Peter J

    2014-09-01

    The sorting nexin 27 (SNX27)-retromer complex is a major regulator of endosome-to-plasma membrane recycling of transmembrane cargos that contain a PSD95, Dlg1, zo-1 (PDZ)-binding motif. Here we describe the core interaction in SNX27-retromer assembly and its functional relevance for cargo sorting. Crystal structures and NMR experiments reveal that an exposed β-hairpin in the SNX27 PDZ domain engages a groove in the arrestin-like structure of the vacuolar protein sorting 26A (VPS26A) retromer subunit. The structure establishes how the SNX27 PDZ domain simultaneously binds PDZ-binding motifs and retromer-associated VPS26. Importantly, VPS26A binding increases the affinity of the SNX27 PDZ domain for PDZ- binding motifs by an order of magnitude, revealing cooperativity in cargo selection. With disruption of SNX27 and retromer function linked to synaptic dysfunction and neurodegenerative disease, our work provides the first step, to our knowledge, in the molecular description of this important sorting complex, and more broadly describes a unique interaction between a PDZ domain and an arrestin-like fold. PMID:25136126

  14. Global Transcriptional Analysis Reveals Unique and Shared Responses in Arabidopsis thaliana Exposed to Combined Drought and Pathogen Stress.

    PubMed

    Gupta, Aarti; Sarkar, Ananda K; Senthil-Kumar, Muthappa

    2016-01-01

    With frequent fluctuations in global climate, plants are exposed to co-occurring drought and pathogen infection and this combination adversely affects plant survival. In the past, some studies indicated that morpho-physiological responses of plants to the combined stress are different from the individual stressed plants. However, interaction of drought stressed plants with pathogen has not been widely studied at molecular level. Such studies are important to understand the defense pathways that operate as part of combined stress tolerance mechanism. In this study, Arabidopsis thaliana was exposed to individual drought stress, Pseudomonas syringae pv tomato DC3000 (Pst DC3000) infection and their combination. Using Affymetrix WT gene 1.0 ST array, global transcriptome profiling of leaves under individual drought stress and pathogen infection was compared with their combination. The results obtained from pathway mapping (KAAS and MAPMAN) demonstrated the modulation in defense pathways in A. thaliana under drought and host pathogen Pst DC3000 infection. Further, our study revealed "tailored" responses under combined stress and the time of occurrence of each stress during their concurrence has shown differences in transcriptome profile. Our results from microarray and RT-qPCR revealed regulation of 20 novel genes uniquely during the stress interaction. This study indicates that plants exposed to concurrent drought and pathogen stress experience a new state of stress. Thus, under frequently changing climatic conditions, time of occurrence of each stress in the interaction defines the plant responses and should thus be studied explicitly. PMID:27252712

  15. Amygdala subnuclei connectivity in response to violence reveals unique influences of individual differences in psychopathic traits in a nonforensic sample.

    PubMed

    Yoder, Keith J; Porges, Eric C; Decety, Jean

    2015-04-01

    Atypical amygdala function and connectivity have reliably been associated with psychopathy. However, the amygdala is not a unitary structure. To examine how psychopathic traits in a nonforensic sample are linked to amygdala response to violence, this study used probabilistic tractography to classify amygdala subnuclei based on anatomical projections to and from amygdala subnuclei in a group of 43 male participants. The segmentation identified the basolateral complex (BLA; lateral, basal, and accessory basal subnuclei) and the central subnucleus (CE), which were used as seeds in a functional connectivity analysis to identify differences in neuronal coupling specific to observed violence. While a full amygdala seed showed significant connectivity only to right middle occipital gyrus, subnuclei seeds revealed unique connectivity patterns. BLA showed enhanced coupling with anterior cingulate and prefrontal regions, while CE showed increased connectivity with the brainstem, but reduced connectivity with superior parietal and precentral gyrus. Further, psychopathic personality factors were related to specific patterns of connectivity. Fearless Dominance scores on the psychopathic personality inventory predicted increased coupling between the BLA seed and sensory integration cortices, and increased connectivity between the CE seed and posterior insula. Conversely, Self-Centered Impulsivity scores were negatively correlated with coupling between BLA and ventrolateral prefrontal cortex, and Coldheartedness scores predicted increased functional connectivity between BLA and dorsal anterior cingulate cortex. Taken together, these findings demonstrate how subnuclei segmentations reveal important functional connectivity differences that are otherwise inaccessible. Such an approach yields a better understanding of amygdala dysfunction in psychopathy. PMID:25557777

  16. A unique PDZ domain and arrestin-like fold interaction reveals mechanistic details of endocytic recycling by SNX27-retromer

    PubMed Central

    Gallon, Matthew; Clairfeuille, Thomas; Steinberg, Florian; Mas, Caroline; Ghai, Rajesh; Sessions, Richard B.; Teasdale, Rohan D.; Collins, Brett M.; Cullen, Peter J.

    2014-01-01

    The sorting nexin 27 (SNX27)-retromer complex is a major regulator of endosome-to-plasma membrane recycling of transmembrane cargos that contain a PSD95, Dlg1, zo-1 (PDZ)-binding motif. Here we describe the core interaction in SNX27-retromer assembly and its functional relevance for cargo sorting. Crystal structures and NMR experiments reveal that an exposed β-hairpin in the SNX27 PDZ domain engages a groove in the arrestin-like structure of the vacuolar protein sorting 26A (VPS26A) retromer subunit. The structure establishes how the SNX27 PDZ domain simultaneously binds PDZ-binding motifs and retromer-associated VPS26. Importantly, VPS26A binding increases the affinity of the SNX27 PDZ domain for PDZ- binding motifs by an order of magnitude, revealing cooperativity in cargo selection. With disruption of SNX27 and retromer function linked to synaptic dysfunction and neurodegenerative disease, our work provides the first step, to our knowledge, in the molecular description of this important sorting complex, and more broadly describes a unique interaction between a PDZ domain and an arrestin-like fold. PMID:25136126

  17. Global Transcriptional Analysis Reveals Unique and Shared Responses in Arabidopsis thaliana Exposed to Combined Drought and Pathogen Stress

    PubMed Central

    Gupta, Aarti; Sarkar, Ananda K.; Senthil-Kumar, Muthappa

    2016-01-01

    With frequent fluctuations in global climate, plants are exposed to co-occurring drought and pathogen infection and this combination adversely affects plant survival. In the past, some studies indicated that morpho-physiological responses of plants to the combined stress are different from the individual stressed plants. However, interaction of drought stressed plants with pathogen has not been widely studied at molecular level. Such studies are important to understand the defense pathways that operate as part of combined stress tolerance mechanism. In this study, Arabidopsis thaliana was exposed to individual drought stress, Pseudomonas syringae pv tomato DC3000 (Pst DC3000) infection and their combination. Using Affymetrix WT gene 1.0 ST array, global transcriptome profiling of leaves under individual drought stress and pathogen infection was compared with their combination. The results obtained from pathway mapping (KAAS and MAPMAN) demonstrated the modulation in defense pathways in A. thaliana under drought and host pathogen Pst DC3000 infection. Further, our study revealed “tailored” responses under combined stress and the time of occurrence of each stress during their concurrence has shown differences in transcriptome profile. Our results from microarray and RT-qPCR revealed regulation of 20 novel genes uniquely during the stress interaction. This study indicates that plants exposed to concurrent drought and pathogen stress experience a new state of stress. Thus, under frequently changing climatic conditions, time of occurrence of each stress in the interaction defines the plant responses and should thus be studied explicitly. PMID:27252712

  18. Platinum electrode modification: Unique surface carbonization approach to improve performance and sensitivity.

    PubMed

    Lee, Hwi Yong; Barber, Cedrick; Minerick, Adrienne R

    2015-08-01

    Many microfluidic devices, also known as lab-on-a-chip devices, employ electrochemical detection methods using microelectrodes. Miniaturizing electrodes inevitably reduces electrode sensitivity and decreases the S/N, which limits applications within microfluidic devices. However, microelectrode surface modification can increase the surface area and sensitivity. In the present work, we report substantial improvement in platinum electrode performance and sensitivity by coating with carbon from red blood cells. The larger goal of this work was to measure DC electrical resistances of red blood cell suspensions in a microchannel for hematocrit determination. It was observed that as current responses of red blood cell suspensions were measured, the platinum electrode performance (reproducibility and S/N) improved with time. The platinum electrode electrocatalytic activity for red blood cell current measurements improved by 140%. Systematic experimentation revealed that red blood cells adsorb and carbonize the platinum electrode surfaces. The electrode surfaces before and after performance improvements were analyzed by field emission scanning electron microscopy, energy dispersive spectrometry, and Raman spectrometry. The formed carbon layers on the electrode surfaces were found to be proteomic and increased surface area with a porous three-dimensional structure, thus improving performance and stabilizing currents. PMID:26032065

  19. Unique secreted–surface protein complex of Lactobacillus rhamnosus, identified by phage display

    PubMed Central

    Gagic, Dragana; Wen, Wesley; Collett, Michael A; Rakonjac, Jasna

    2013-01-01

    Proteins are the most diverse structures on bacterial surfaces; hence, they are candidates for species- and strain-specific interactions of bacteria with the host, environment, and other microorganisms. Genomics has decoded thousands of bacterial surface and secreted proteins, yet the function of most cannot be predicted because of the enormous variability and a lack of experimental data that would allow deduction of function through homology. Here, we used phage display to identify a pair of interacting extracellular proteins in the probiotic bacterium Lactobacillus rhamnosus HN001. A secreted protein, SpcA, containing two bacterial immunoglobulin-like domains type 3 (Big-3) and a domain distantly related to plant pathogen response domain 1 (PR-1-like) was identified by screening of an L. rhamnosus HN001 library using HN001 cells as bait. The SpcA-“docking” protein, SpcB, was in turn detected by another phage display library screening, using purified SpcA as bait. SpcB is a 3275-residue cell-surface protein that contains general features of large glycosylated Serine-rich adhesins/fibrils from gram-positive bacteria, including the hallmark signal sequence motif KxYKxGKxW. Both proteins are encoded by genes within a L. rhamnosus-unique gene cluster that distinguishes this species from other lactobacilli. To our knowledge, this is the first example of a secreted-docking protein pair identified in lactobacilli. PMID:23233310

  20. Surface-adaptable all-metal micro-four-point probe with unique configuration

    NASA Astrophysics Data System (ADS)

    Kim, J. K.; Choi, Y. S.; Lee, D. W.

    2015-07-01

    In this paper, we propose a surface-adaptable all-metal micro-four-point probe (μ4PP) with a unique configuration. The μ4PP consists of four independent metallic sub-cantilevers with sharp Cu tips, and an SU-8 body structure to support the sub-cantilevers. The tip height is approximately 15 μm, and the tips are fabricated by anisotropic wet-etching of silicon followed by Cu electroplating. Each metallic cantilever connected to the SU-8 body structure acts as a flexible spring, so that the conducting tip can make gentle, non-destructive contact with fragile surfaces. To enhance the adhesion between the metallic sub-cantilevers and the SU-8 body, mushroom-shaped Cu structures were fabricated using an under-baked and under-exposed photolithography process. Various μ4PPs were designed and fabricated to verify their diverse range of applications, and preliminary experiments were performed using these fabricated μ4PPs. The resultant flexibility and reliability were experimentally confirmed on several samples, such as a polymer cantilever, a graphene flake, and curved metallic surfaces. We also expect that the proposed μ4PP will be suitable for measuring the anisotropic characteristics of crystal materials or the Hall effect in semiconductors.

  1. Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells

    PubMed Central

    Pashai, Nikta; Hao, Haiping; All, Angelo; Gupta, Siddharth; Chaerkady, Raghothama; De Los Angeles, Alejandro; Gearhart, John D.; Kerr, Candace L.

    2012-01-01

    Human embryonic germ cells (EGCs) provide a powerful model for identifying molecules involved in the pluripotent state when compared to their progenitors, primordial germ cells (PGCs), and other pluripotent stem cells. Microarray and Principal Component Analysis (PCA) reveals for the first time that human EGCs possess a transcription profile distinct from PGCs and other pluripotent stem cells. Validation with qRT-PCR confirms that human EGCs and PGCs express many pluripotency-associated genes but with quantifiable differences compared to pluripotent embryonic stem cells (ESCs), induced pluripotent stem cells (IPSCs), and embryonal carcinoma cells (ECCs). Analyses also identified a number of target genes that may be potentially associated with their unique pluripotent states. These include IPO7, MED7, RBM26, HSPD1, and KRAS which were upregulated in EGCs along with other pluripotent stem cells when compared to PGCs. Other potential target genes were also found which may contribute toward a primed ESC-like state. These genes were exclusively up-regulated in ESCs, IPSCs and ECCs including PARP1, CCNE1, CDK6, AURKA, MAD2L1, CCNG1, and CCNB1 which are involved in cell cycle regulation, cellular metabolism and DNA repair and replication. Gene classification analysis also confirmed that the distinguishing feature of EGCs compared to ESCs, ECCs, and IPSCs lies primarily in their genetic contribution to cellular metabolism, cell cycle, and cell adhesion. In contrast, several genes were found upregulated in PGCs which may help distinguish their unipotent state including HBA1, DMRT1, SPANXA1, and EHD2. Together, these findings provide the first glimpse into a unique genomic signature of human germ cells and pluripotent stem cells and provide genes potentially involved in defining different states of germ-line pluripotency. PMID:22737227

  2. A unique Critical State two-surface hyperplasticity model for fine-grained particulate media

    NASA Astrophysics Data System (ADS)

    Coombs, W. M.; Crouch, R. S.; Augarde, C. E.

    2013-01-01

    Even mild compression can cause re-arrangement of the internal structure of clay-like geomaterials, whereby clusters of particles rotate and collapse as face-to-face contacts between the constituent mineral platelets increase at the expense of edge-to-face (or edge-to-edge) contacts. The collective action of local particle re-orientation ultimately leads to path-independent isochoric macroscopic deformation under continuous shearing. This asymptotic condition is the governing feature of Critical State elasto-plasticity models. Unlike earlier formulations, the two-surface anisotropic model proposed herein is able to reproduce a unique isotropic Critical State stress envelope which agrees well with test data. Material point predictions are compared against triaxial experimental results and five other existing constitutive models. The hyperplastic formulation is seen to offer a significantly improved descriptor of the anisotropic behaviour of fine-grained particulate materials.

  3. Comparative proteomic analysis reveals unique tumor protein composition among the melanoma subtypes pure desmoplastic and superficial spreading.

    PubMed

    Schowalter, Michael K; Dulmage, Brittany O; Ho, Jonhan; Vu, John R; Falo, Louis D; Geskin, Larisa J

    2014-08-01

    The U.S. death rate for melanoma has not decreased, despite the use of depth at biopsy and sentinel lymph node status to determine the risk of metastasis. Additional prognostic indicators and therapeutic targets are required, and identification of candidate proteins was the goal of this study. We utilized comparative mass spectrometry to compare five samples of each of two forms of melanoma, pure desmoplastic, which by depth at diagnosis has a favorable prognosis, and superficial spreading. Ontological analysis was applied to identify proteins and networks that were increased in one of the two subtypes. Analysis revealed a protein signature increase in pure desmoplastic melanoma associated with cell-to-cell binding and a signature increase in superficial spreading melanoma responsible for the cellular stress response including a constellation of heat shock proteins. The two subtypes of melanoma compared in this study have two unique protein compositions that correlate with their phenotypes. Further validation studies are warranted to evaluate the utility of identified proteins as prognostic markers and therapeutic targets. PMID:24743055

  4. Light and Electron Microscopy of the European Beaver (Castor fiber) Stomach Reveal Unique Morphological Features with Possible General Biological Significance

    PubMed Central

    Petryński, Wojciech; Palkowska, Katarzyna; Prusik, Magdalena; Targońska, Krystyna; Giżejewski, Zygmunt; Przybylska-Gornowicz, Barbara

    2014-01-01

    Anatomical, histological, and ultrastructural studies of the European beaver stomach revealed several unique morphological features. The prominent attribute of its gross morphology was the cardiogastric gland (CGG), located near the oesophageal entrance. Light microscopy showed that the CGG was formed by invaginations of the mucosa into the submucosa, which contained densely packed proper gastric glands comprised primarily of parietal and chief cells. Mucous neck cells represented <0.1% of cells in the CGG gastric glands and 22–32% of cells in the proper gastric glands of the mucosa lining the stomach lumen. These data suggest that chief cells in the CGG develop from undifferentiated cells that migrate through the gastric gland neck rather than from mucous neck cells. Classical chief cell formation (i.e., arising from mucous neck cells) occurred in the mucosa lining the stomach lumen, however. The muscularis around the CGG consisted primarily of skeletal muscle tissue. The cardiac region was rudimentary while the fundus/corpus and pyloric regions were equally developed. Another unusual feature of the beaver stomach was the presence of specific mucus with a thickness up to 950 µm (in frozen, unfixed sections) that coated the mucosa. Our observations suggest that the formation of this mucus is complex and includes the secretory granule accumulation in the cytoplasm of pit cells, the granule aggregation inside cells, and the incorporation of degenerating cells into the mucus. PMID:24727802

  5. Dual RNA Sequencing Reveals the Expression of Unique Transcriptomic Signatures in Lipopolysaccharide-Induced BV-2 Microglial Cells

    PubMed Central

    Kim, Sun Hwa; Park, Kyoung Sun; Lee, Young Seek; Jung, Kyoung Hwa; Chai, Young Gyu

    2015-01-01

    transcriptomic analysis is the first to show a comparison of the family-wide differential expression of most known immune genes and also reveal transcription evidence of multiple gene families in BV-2 microglial cells. Collectively, these findings reveal unique transcriptomic signatures in BV-2 microglial cells required for homeostasis and effective immune responses. PMID:25811458

  6. RNA-Seq reveals common and unique PXR- and CAR-target gene signatures in the mouse liver transcriptome.

    PubMed

    Cui, Julia Yue; Klaassen, Curtis D

    2016-09-01

    entire hepatic transcriptome correlated with a marked change in the expression of many DNA and histone epigenetic modifiers. In conclusion, the present study has revealed known and novel, as well as common and unique targets of PXR and CAR in mouse liver following pharmacological activation using their prototypical ligands. Results from this study will further support the role of these receptors in regulating the homeostasis of xenobiotic and intermediary metabolism in the liver, and aid in distinguishing between PXR and CAR signaling at various physiological and pathophysiological conditions. This article is part of a Special Issue entitled: Xenobiotic nuclear receptors: New Tricks for An Old Dog, edited by Dr. Wen Xie. PMID:27113289

  7. Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host.

    PubMed

    Leontovyč, Roman; Young, Neil D; Korhonen, Pasi K; Hall, Ross S; Tan, Patrick; Mikeš, Libor; Kašný, Martin; Horák, Petr; Gasser, Robin B

    2016-02-01

    To date, most molecular investigations of schistosomatids have focused principally on blood flukes (schistosomes) of humans. Despite the clinical importance of cercarial dermatitis in humans caused by Trichobilharzia regenti and the serious neuropathologic disease that this parasite causes in its permissive avian hosts and accidental mammalian hosts, almost nothing is known about the molecular aspects of how this fluke invades its hosts, migrates in host tissues and how it interacts with its hosts' immune system. Here, we explored selected aspects using a transcriptomic-bioinformatic approach. To do this, we sequenced, assembled and annotated the transcriptome representing two consecutive life stages (cercariae and schistosomula) of T. regenti involved in the first phases of infection of the avian host. We identified key biological and metabolic pathways specific to each of these two developmental stages and also undertook comparative analyses using data available for taxonomically related blood flukes of the genus Schistosoma. Detailed comparative analyses revealed the unique involvement of carbohydrate metabolism, translation and amino acid metabolism, and calcium in T. regenti cercariae during their invasion and in growth and development, as well as the roles of cell adhesion molecules, microaerobic metabolism (citrate cycle and oxidative phosphorylation), peptidases (cathepsins) and other histolytic and lysozomal proteins in schistosomula during their particular migration in neural tissues of the avian host. In conclusion, the present transcriptomic exploration provides new and significant insights into the molecular biology of T. regenti, which should underpin future genomic and proteomic investigations of T. regenti and, importantly, provides a useful starting point for a range of comparative studies of schistosomatids and other trematodes. PMID:26863542

  8. Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host

    PubMed Central

    Leontovyč, Roman; Young, Neil D.; Korhonen, Pasi K.; Hall, Ross S.; Tan, Patrick; Mikeš, Libor; Kašný, Martin; Horák, Petr; Gasser, Robin B.

    2016-01-01

    To date, most molecular investigations of schistosomatids have focused principally on blood flukes (schistosomes) of humans. Despite the clinical importance of cercarial dermatitis in humans caused by Trichobilharzia regenti and the serious neuropathologic disease that this parasite causes in its permissive avian hosts and accidental mammalian hosts, almost nothing is known about the molecular aspects of how this fluke invades its hosts, migrates in host tissues and how it interacts with its hosts’ immune system. Here, we explored selected aspects using a transcriptomic-bioinformatic approach. To do this, we sequenced, assembled and annotated the transcriptome representing two consecutive life stages (cercariae and schistosomula) of T. regenti involved in the first phases of infection of the avian host. We identified key biological and metabolic pathways specific to each of these two developmental stages and also undertook comparative analyses using data available for taxonomically related blood flukes of the genus Schistosoma. Detailed comparative analyses revealed the unique involvement of carbohydrate metabolism, translation and amino acid metabolism, and calcium in T. regenti cercariae during their invasion and in growth and development, as well as the roles of cell adhesion molecules, microaerobic metabolism (citrate cycle and oxidative phosphorylation), peptidases (cathepsins) and other histolytic and lysozomal proteins in schistosomula during their particular migration in neural tissues of the avian host. In conclusion, the present transcriptomic exploration provides new and significant insights into the molecular biology of T. regenti, which should underpin future genomic and proteomic investigations of T. regenti and, importantly, provides a useful starting point for a range of comparative studies of schistosomatids and other trematodes. PMID:26863542

  9. The Crystal Structure of the Adenylation Enzyme VinN Reveals a Unique β-Amino Acid Recognition Mechanism*

    PubMed Central

    Miyanaga, Akimasa; Cieślak, Jolanta; Shinohara, Yuji; Kudo, Fumitaka; Eguchi, Tadashi

    2014-01-01

    Adenylation enzymes play important roles in the biosynthesis and degradation of primary and secondary metabolites. Mechanistic insights into the recognition of α-amino acid substrates have been obtained for α-amino acid adenylation enzymes. The Asp residue is invariant and is essential for the stabilization of the α-amino group of the substrate. In contrast, the β-amino acid recognition mechanism of adenylation enzymes is still unclear despite the importance of β-amino acid activation for the biosynthesis of various natural products. Herein, we report the crystal structure of the stand-alone adenylation enzyme VinN, which specifically activates (2S,3S)-3-methylaspartate (3-MeAsp) in vicenistatin biosynthesis. VinN has an overall structure similar to that of other adenylation enzymes. The structure of the complex with 3-MeAsp revealed that a conserved Asp230 residue is used in the recognition of the β-amino group of 3-MeAsp similar to α-amino acid adenylation enzymes. A mutational analysis and structural comparison with α-amino acid adenylation enzymes showed that the substrate-binding pocket of VinN has a unique architecture to accommodate 3-MeAsp as a β-amino acid substrate. Thus, the VinN structure allows the first visualization of the interaction of an adenylation enzyme with a β-amino acid and provides new mechanistic insights into the selective recognition of β-amino acids in this family of enzymes. PMID:25246523

  10. The crystal structure of the adenylation enzyme VinN reveals a unique β-amino acid recognition mechanism.

    PubMed

    Miyanaga, Akimasa; Cieślak, Jolanta; Shinohara, Yuji; Kudo, Fumitaka; Eguchi, Tadashi

    2014-11-01

    Adenylation enzymes play important roles in the biosynthesis and degradation of primary and secondary metabolites. Mechanistic insights into the recognition of α-amino acid substrates have been obtained for α-amino acid adenylation enzymes. The Asp residue is invariant and is essential for the stabilization of the α-amino group of the substrate. In contrast, the β-amino acid recognition mechanism of adenylation enzymes is still unclear despite the importance of β-amino acid activation for the biosynthesis of various natural products. Herein, we report the crystal structure of the stand-alone adenylation enzyme VinN, which specifically activates (2S,3S)-3-methylaspartate (3-MeAsp) in vicenistatin biosynthesis. VinN has an overall structure similar to that of other adenylation enzymes. The structure of the complex with 3-MeAsp revealed that a conserved Asp(230) residue is used in the recognition of the β-amino group of 3-MeAsp similar to α-amino acid adenylation enzymes. A mutational analysis and structural comparison with α-amino acid adenylation enzymes showed that the substrate-binding pocket of VinN has a unique architecture to accommodate 3-MeAsp as a β-amino acid substrate. Thus, the VinN structure allows the first visualization of the interaction of an adenylation enzyme with a β-amino acid and provides new mechanistic insights into the selective recognition of β-amino acids in this family of enzymes. PMID:25246523

  11. Unique diversity of the venom peptides from the scorpion Androctonus bicolor revealed by transcriptomic and proteomic analysis.

    PubMed

    Zhang, Lei; Shi, Wanxia; Zeng, Xian-Chun; Ge, Feng; Yang, Mingkun; Nie, Yao; Bao, Aorigele; Wu, Shifen; E, Guoji

    2015-10-14

    Androctonus bicolor is one of the most poisonous scorpion species in the world. However, little has been known about the venom composition of the scorpion. To better understand the molecular diversity and medical significance of the venom from the scorpion, we systematically analyzed the venom components by combining transcriptomic and proteomic surveys. Random sequencing of 1000 clones from a cDNA library prepared from the venom glands of the scorpion revealed that 70% of the total transcripts code for venom peptide precursors. Our efforts led to a discovery of 103 novel putative venom peptides. These peptides include NaTx-like, KTx-like and CaTx-like peptides, putative antimicrobial peptides, defensin-like peptides, BPP-like peptides, BmKa2-like peptides, Kunitz-type toxins and some new-type venom peptides without disulfide bridges, as well as many new-type venom peptides that are cross-linked with one, two, three, five or six disulfide bridges, respectively. We also identified three peptides that are identical to known toxins from scorpions. The venom was also analyzed using a proteomic technique. The presence of a total of 16 different venom peptides was confirmed by LC-MS/MS analysis. The discovery of a wide range of new and new-type venom peptides highlights the unique diversity of the venom peptides from A. bicolor. These data also provide a series of novel templates for the development of therapeutic drugs for treating ion channel-associated diseases and infections caused by antibiotic-resistant pathogens, and offer molecular probes for the exploration of structures and functions of various ion channels. PMID:26254009

  12. A soft solid surface on Titan as revealed by the Huygens Surface Science Package

    NASA Astrophysics Data System (ADS)

    Zarnecki, John C.; Leese, Mark R.; Hathi, Brijen; Ball, Andrew J.; Hagermann, Axel; Towner, Martin C.; Lorenz, Ralph D.; McDonnell, J. Anthony M.; Green, Simon F.; Patel, Manish R.; Ringrose, Timothy J.; Rosenberg, Philip D.; Atkinson, Karl R.; Paton, Mark D.; Banaszkiewicz, Marek; Clark, Benton C.; Ferri, Francesca; Fulchignoni, Marcello; Ghafoor, Nadeem A. L.; Kargl, Günter; Svedhem, Håkan; Delderfield, John; Grande, Manuel; Parker, David J.; Challenor, Peter G.; Geake, John E.

    2005-12-01

    The surface of Saturn's largest satellite-Titan-is largely obscured by an optically thick atmospheric haze, and so its nature has been the subject of considerable speculation and discussion. The Huygens probe entered Titan's atmosphere on 14 January 2005 and descended to the surface using a parachute system. Here we report measurements made just above and on the surface of Titan by the Huygens Surface Science Package. Acoustic sounding over the last 90m above the surface reveals a relatively smooth, but not completely flat, surface surrounding the landing site. Penetrometry and accelerometry measurements during the probe impact event reveal that the surface was neither hard (like solid ice) nor very compressible (like a blanket of fluffy aerosol); rather, the Huygens probe landed on a relatively soft solid surface whose properties are analogous to wet clay, lightly packed snow and wet or dry sand. The probe settled gradually by a few millimetres after landing.

  13. A soft solid surface on Titan as revealed by the Huygens Surface Science Package.

    PubMed

    Zarnecki, John C; Leese, Mark R; Hathi, Brijen; Ball, Andrew J; Hagermann, Axel; Towner, Martin C; Lorenz, Ralph D; McDonnell, J Anthony M; Green, Simon F; Patel, Manish R; Ringrose, Timothy J; Rosenberg, Philip D; Atkinson, Karl R; Paton, Mark D; Banaszkiewicz, Marek; Clark, Benton C; Ferri, Francesca; Fulchignoni, Marcello; Ghafoor, Nadeem A L; Kargl, Günter; Svedhem, Håkan; Delderfield, John; Grande, Manuel; Parker, David J; Challenor, Peter G; Geake, John E

    2005-12-01

    The surface of Saturn's largest satellite--Titan--is largely obscured by an optically thick atmospheric haze, and so its nature has been the subject of considerable speculation and discussion. The Huygens probe entered Titan's atmosphere on 14 January 2005 and descended to the surface using a parachute system. Here we report measurements made just above and on the surface of Titan by the Huygens Surface Science Package. Acoustic sounding over the last 90 m above the surface reveals a relatively smooth, but not completely flat, surface surrounding the landing site. Penetrometry and accelerometry measurements during the probe impact event reveal that the surface was neither hard (like solid ice) nor very compressible (like a blanket of fluffy aerosol); rather, the Huygens probe landed on a relatively soft solid surface whose properties are analogous to wet clay, lightly packed snow and wet or dry sand. The probe settled gradually by a few millimetres after landing. PMID:16319828

  14. The Structure of the Poxvirus A33 Protein Reveals a Dimer of Unique C-Type Lectin-Like Domains

    SciTech Connect

    Su, Hua-Poo; Singh, Kavita; Gittis, Apostolos G.; Garboczi, David N.

    2010-11-03

    The current vaccine against smallpox is an infectious form of vaccinia virus that has significant side effects. Alternative vaccine approaches using recombinant viral proteins are being developed. A target of subunit vaccine strategies is the poxvirus protein A33, a conserved protein in the Chordopoxvirinae subfamily of Poxviridae that is expressed on the outer viral envelope. Here we have determined the structure of the A33 ectodomain of vaccinia virus. The structure revealed C-type lectin-like domains (CTLDs) that occur as dimers in A33 crystals with five different crystal lattices. Comparison of the A33 dimer models shows that the A33 monomers have a degree of flexibility in position within the dimer. Structural comparisons show that the A33 monomer is a close match to the Link module class of CTLDs but that the A33 dimer is most similar to the natural killer (NK)-cell receptor class of CTLDs. Structural data on Link modules and NK-cell receptor-ligand complexes suggest a surface of A33 that could interact with viral or host ligands. The dimer interface is well conserved in all known A33 sequences, indicating an important role for the A33 dimer. The structure indicates how previously described A33 mutations disrupt protein folding and locates the positions of N-linked glycosylations and the epitope of a protective antibody.

  15. The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses

    PubMed Central

    2012-01-01

    Background Oomycetes are fungal-like microorganisms evolutionary distinct from true fungi, belonging to the Stramenopile lineage and comprising major plant pathogens. Both oomycetes and fungi express proteins able to interact with cellulose, a major component of plant and oomycete cell walls, through the presence of carbohydrate-binding module belonging to the family 1 (CBM1). Fungal CBM1-containing proteins were implicated in cellulose degradation whereas in oomycetes, the Cellulose Binding Elicitor Lectin (CBEL), a well-characterized CBM1-protein from Phytophthora parasitica, was implicated in cell wall integrity, adhesion to cellulosic substrates and induction of plant immunity. Results To extend our knowledge on CBM1-containing proteins in oomycetes, we have conducted a comprehensive analysis on 60 fungi and 7 oomycetes genomes leading to the identification of 518 CBM1-containing proteins. In plant-interacting microorganisms, the larger number of CBM1-protein coding genes is expressed by necrotroph and hemibiotrophic pathogens, whereas a strong reduction of these genes is observed in symbionts and biotrophs. In fungi, more than 70% of CBM1-containing proteins correspond to enzymatic proteins in which CBM1 is associated with a catalytic unit involved in cellulose degradation. In oomycetes more than 90% of proteins are similar to CBEL in which CBM1 is associated with a non-catalytic PAN/Apple domain, known to interact with specific carbohydrates or proteins. Distinct Stramenopile genomes like diatoms and brown algae are devoid of CBM1 coding genes. A CBM1-PAN/Apple association 3D structural modeling was built allowing the identification of amino acid residues interacting with cellulose and suggesting the putative interaction of the PAN/Apple domain with another type of glucan. By Surface Plasmon Resonance experiments, we showed that CBEL binds to glycoproteins through galactose or N-acetyl-galactosamine motifs. Conclusions This study provides insight into the

  16. Stellar Spectroscopy during Exoplanet Transits: Revealing structures across stellar surfaces

    NASA Astrophysics Data System (ADS)

    Dravins, Dainis; Ludwig, Hans-Günter; Dahlén, Erik

    2015-08-01

    Exoplanet transits permit to study stellar surface portions that successively become hidden behind the planet. Differential spectroscopy between various transit phases reveals spectra of those stellar surface segments that were hidden. The deduced center-to-limb behavior of stellar spectral line shapes, asymmetries and wavelength shifts enables detailed tests of 3-dimensional hydrodynamic models of stellar atmospheres, such that are required for any precise determination of abundances or seismic properties. Such models can now be computed for widely different classes of stars (including metal-poor ones and white dwarfs), but have been feasible to test and verify only for the Sun with its resolved surface structure. Exoplanet transits may also occur across features such as starspots, whose magnetic signatures will be retrieved from spectra of sufficient fidelity.Knowing the precise background stellar spectra, also properties of exoplanet atmospheres are better constrained: e.g., the Rossiter-McLaughlin effect becomes resolved as not only a simple change of stellar wavelength, but as a variation of the full line profiles and their asymmetries.Such studies are challenging since exoplanets cover only a tiny fraction of the stellar disk. Current work, analyzing sequences of high-fidelity ESO UVES spectra, demonstrate that such spatially resolved stellar spectra can already be (marginally) retrieved in a few cases with the brightest host stars. Already in a near future, ongoing exoplanet surveys are likely to find further bright hosts that will enable such studies for various stellar types. http://arxiv.org/abs/1408.1402

  17. Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer

    PubMed Central

    2011-01-01

    Background Brachyspira spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity. Brachyspira intermedia can cause production losses in chickens and strain PWS/AT now becomes the fourth genome to be completed in the genus Brachyspira. Results 15 classes of unique and shared genes were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B. pilosicoli. The largest number of unique genes was found in B. intermedia and B. murdochii. This indicates the presence of larger pan-genomes. In general, hypothetical protein annotations are overrepresented among the unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT. The plasmid was also present in the B. murdochii strain but not in nine other Brachyspira isolates. Within the Brachyspira genomes, genes had been translocated and also frequently switched between leading and lagging strands, a process that can be followed by different AT-skews in the third positions of synonymous codons. We also found evidence that bacteriophages were being remodeled and genes incorporated into them. Conclusions The accessory gene pool shapes species-specific traits. It is also influenced by reductive genome evolution and horizontal gene transfer. Gene-transfer events can cross both species and genus boundaries and bacteriophages appear to play an important role in this process. A mechanism for horizontal gene transfer appears to be gene translocations leading to remodeling of bacteriophages in combination with broad tropism. PMID:21816042

  18. Micro-nano hierarchically structured nylon 6,6 surfaces with unique wettability.

    PubMed

    Zhang, Liang; Zhang, Xiaoyan; Dai, Zhen; Wu, Junjie; Zhao, Ning; Xu, Jian

    2010-05-01

    A micro-nano hierarchically structured nylon 6,6 surface was easily fabricated by phase separation. Nylon 6,6 plate was swelled by formic acid and then immersed in a coagulate bath to precipitate. Micro particles with nano protrusions were generated and linked together covering over the surface. After dried up, the as-formed surface showed superhydrophilic ability. Inspired by lotus only employing 2-tier structure and ordinary plant wax to maintain superhydrophobicity, paraffin wax, a low surface energy material, was used to modify the hierarchically structured nylon 6,6 surface. The resultant surface had water contact angle (CA) of 155.2+/-1.3 degrees and a low sliding angle. The whole process was carried on under ambient condition and only need a few minutes. PMID:20144830

  19. Single neuron transcriptome analysis can reveal more than cell type classification: Does it matter if every neuron is unique?

    PubMed

    Harbom, Lise J; Chronister, William D; McConnell, Michael J

    2016-02-01

    A recent single cell mRNA sequencing study by Dueck et al. compares neuronal transcriptomes to the transcriptomes of adipocytes and cardiomyocytes. Single cell omic approaches such as those used by the authors are at the leading edge of molecular and biophysical measurement. Many groups are currently employing single cell sequencing approaches to understand cellular heterogeneity in cancer and during normal development. These single cell approaches also are beginning to address long-standing questions regarding nervous system diversity. Beyond an innate interest in cataloging cell type diversity in the brain, single cell neuronal diversity has important implications for neurotypic neural circuit function and for neurological disease. Herein, we review the authors' methods and findings, which most notably include evidence of unique expression profiles in some single neurons. PMID:26749010

  20. Metabolomic analysis of breath volatile organic compounds reveals unique breathprints in children with inflammatory bowel disease: A pilot study

    PubMed Central

    Patel, Nisha; Alkhouri, Naim; Eng, Katharine; Cikach, Frank; Mahajan, Lori; Yan, Chen; Grove, David; Rome, Ellen S.; Lopez, Rocio; Dweik, Raed A.

    2014-01-01

    Background Breath testing is becoming an important diagnostic method to evaluate many disease states. In light of rising healthcare costs, is important to develop a simple non-invasive tool to potentially identify pediatric patients who need endoscopy for suspected inflammatory bowel disease (IBD). Aim The primary aim of this study was to analyze exhaled volatile organic compounds (VOCs) to evaluate for the presence of a unique breath pattern to differentiate pediatric patients with (IBD) from healthy controls. Methods A cross-sectional, single-center study included pediatric IBD patients and healthy controls (age range, 5-21 years). The diagnosis of IBD was confirmed by endoscopic, histologic, and radiographic data. Exhaled breath was collected and analyzed using a selective ion flow tube mass spectroscopy (SIFT-MS) to identify new markers or patterns of IBD. Results 117 patients (62 with IBD and 55 healthy controls) were included in the study. Linear discriminant analysis and principle component analysis of mass scanning ion peak data demonstrated 21 pre-selected VOCs correctly classify patients with IBD or as healthy controls; p < 0.0001. Multivariable logistic regression analysis further showed 3 specific VOCs (1-octene, 1-decene, (E)-2-nonene) had excellent accuracy for predicting the presence of IBD with an area under the curve (AUC) of 0.96 (95% CI: 0.93, 0.99). No significant difference in VOCs was found between patients with Crohn's disease or ulcerative colitis and no significant correlation was seen with disease activity. Conclusion This pilot data supports the hypothesis that a unique breathprint potentially exists for pediatric IBD in the exhaled metabolome. PMID:25041596

  1. Complete sequencing of a gibbon hepatitis B virus genome reveals a unique genotype distantly related to the chimpanzee hepatitis B virus.

    PubMed

    Norder, H; Ebert, J W; Fields, H A; Mushahwar, I K; Magnius, L O

    1996-04-01

    We have sequenced the complete genome of a hepatitis B virus (HBV) strain that was transmitted from a gibbon with chronic hepatitis B to a chimpanzee that subsequently developed acute hepatitis B. The genome was 3,182 nucleotides long and had a genetic organization identical to and including the characteristics of other mammalian hepadnaviruses. Thus, the regulatory elements, the direct repeats, and the four open reading frames (ORFs) of this virus were all maintained, although there were amino acid substitutions affecting all the ORFs. Within the S gene encoding for the hepatitis B surface antigen (HBsAg), the subtype could be deduced as ayw3 in accordance with previous serological results. There were 25 amino acid substitutions affecting the P gene, 12 of which were within the spacer region. This region, which was the most divergent part of the genome compared to other HBV strains, also encodes for the pre-S proteins. A comparison with sequences of other hepadnaviruses revealed that the genome of gibbon HBV was unique as compared to previously described HBV genotypes. It was most similar to the chimpanzee HBV strain with which it shared 90.3% nucleic acid homology at the level of the complete genome and 96.3% homology at the level of the S-gene region corresponding to HBsAg, although being a distinct genotype as compared to the latter virus. Analyses performed using five different algorithms for phylogenetic tree construction showed more than 99% bootstrap support for the gibbon and the chimpanzee HBV to be grouped within the human HBV strains and that they represented later offshoots than the HBV strains of genotype F. However, in most of the dendrograms both the gibbon and the chimpanzee strains represented early lineages, indicating that these viruses are indigenous to their respective hosts and not recent acquisitions from man. PMID:8615024

  2. Whole-Genome Sequencing of Kaposi's Sarcoma-Associated Herpesvirus from Zambian Kaposi's Sarcoma Biopsy Specimens Reveals Unique Viral Diversity

    PubMed Central

    Olp, Landon N.; Jeanniard, Adrien; Marimo, Clemence; West, John T.

    2015-01-01

    ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent for Kaposi's sarcoma (KS). Both KSHV and KS are endemic in sub-Saharan Africa where approximately 84% of global KS cases occur. Nevertheless, whole-genome sequencing of KSHV has only been completed using isolates from Western countries—where KS is not endemic. The lack of whole-genome KSHV sequence data from the most clinically important geographical region, sub-Saharan Africa, represents an important gap since it remains unclear whether genomic diversity has a role on KSHV pathogenesis. We hypothesized that distinct KSHV genotypes might be present in sub-Saharan Africa compared to Western countries. Using a KSHV-targeted enrichment protocol followed by Illumina deep-sequencing, we generated and analyzed 16 unique Zambian, KS-derived, KSHV genomes. We enriched KSHV DNA over cellular DNA 1,851 to 18,235-fold. Enrichment provided coverage levels up to 24,740-fold; therefore, supporting highly confident polymorphism analysis. Multiple alignment of the 16 newly sequenced KSHV genomes showed low level variability across the entire central conserved region. This variability resulted in distinct phylogenetic clustering between Zambian KSHV genomic sequences and those derived from Western countries. Importantly, the phylogenetic segregation of Zambian from Western sequences occurred irrespective of inclusion of the highly variable genes K1 and K15. We also show that four genes within the more conserved region of the KSHV genome contained polymorphisms that partially, but not fully, contributed to the unique Zambian KSHV whole-genome phylogenetic structure. Taken together, our data suggest that the whole KSHV genome should be taken into consideration for accurate viral characterization. IMPORTANCE Our results represent the largest number of KSHV whole-genomic sequences published to date and the first time that multiple genomes have been sequenced from sub-Saharan Africa, a geographic area

  3. Oscillating gradient diffusion MRI reveals unique microstructural information in normal and hypoxia-ischemia injured mouse brains

    PubMed Central

    Wu, Dan; Martin, Lee J.; Northington, Frances J.; Zhang, Jiangyang

    2014-01-01

    Purpose We investigated whether oscillating gradient diffusion MRI (dMRI) can provide information on brain microstructural changes after formaldehyde fixation and after hypoxic-ischemic (HI) injury beyond that provided by conventional dMRI. Methods Pulsed gradient spin echo (PGSE) and oscillating gradient spin echo (OGSE) dMRI of the adult mouse brain was performed in vivo (50-200 Hz, b = 600 mm2/s), and a similar protocol was applied to neonatal mouse brains at 24 hours after unilateral hypoxia-ischemia. Animals were perfusion fixed with 4% paraformaldehyde for ex vivo dMRI and histology. Results Apparent diffusion coefficients (ADCs) measured in the live adult mouse brain presented tissue-dependent frequency-dependence. In vivo OGSE-ADC maps at high oscillating frequencies (>100Hz) showed clear contrast between the molecular layer and granule cell layer in the adult mouse cerebellum. Formaldehyde fixation significantly altered the temporal diffusion spectra in several brain regions. In neonatal mouse brains with HI injury, in vivo ADC measurements from edema regions showed diminished edema contrasts at 200 Hz compared to the PGSE results. Histology showed severe tissue swelling and necrosis in the edema regions. Conclusion The results demonstrate the unique ability of OGSE-dMRI in delineating tissue microstructures at different spatial scales. PMID:25168861

  4. Proteomic screening of variola virus reveals a unique NF-κB inhibitor that is highly conserved among pathogenic orthopoxviruses

    PubMed Central

    Mohamed, Mohamed R.; Rahman, Masmudur M.; Lanchbury, Jerry S.; Shattuck, Donna; Neff, Chris; Dufford, Max; van Buuren, Nick; Fagan, Katharine; Barry, Michele; Smith, Scott; Damon, Inger; McFadden, Grant

    2009-01-01

    Identification of the binary interactions between viral and host proteins has become a valuable tool for investigating viral tropism and pathogenesis. Here, we present the first systematic protein interaction screening of the unique variola virus proteome by using yeast 2-hybrid screening against a variety of human cDNA libraries. Several protein–protein interactions were identified, including an interaction between variola G1R, an ankryin/F-box containing protein, and human nuclear factor kappa-B1 (NF-κB1)/p105. This represents the first direct interaction between a pathogen-encoded protein and NF-κB1/p105. Orthologs of G1R are present in a variety of pathogenic orthopoxviruses, but not in vaccinia virus, and expression of any one of these viral proteins blocks NF-κB signaling in human cells. Thus, proteomic screening of variola virus has the potential to uncover modulators of the human innate antiviral responses. PMID:19451633

  5. Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain.

    PubMed

    Stroehlein, Andreas J; Young, Neil D; Korhonen, Pasi K; Chang, Bill C H; Sternberg, Paul W; La Rosa, Giuseppe; Pozio, Edoardo; Gasser, Robin B

    2016-01-01

    Parasitic worms of the genus Trichinella (phylum Nematoda; class Enoplea) represent a complex of at least twelve taxa that infect a range of different host animals, including humans, around the world. They are foodborne, intracellular nematodes, and their life cycles differ substantially from those of other nematodes. The recent characterization of the genomes and transcriptomes of all twelve recognized taxa of Trichinella now allows, for the first time, detailed studies of their molecular biology. In the present study, we defined, curated, and compared the protein kinase complements (kinomes) of Trichinella spiralis and T. pseudospiralis using an integrated bioinformatic workflow employing transcriptomic and genomic data sets. We examined how variation in the kinome might link to unique aspects of Trichinella morphology, biology, and evolution. Furthermore, we utilized in silico structural modeling to discover and characterize a novel, MOS-like kinase with an unusual, previously undescribed N-terminal domain. Taken together, the present findings provide a basis for comparative investigations of nematode kinomes, and might facilitate the identification of Enoplea-specific intervention and diagnostic targets. Importantly, the in silico modeling approach assessed here provides an exciting prospect of being able to identify and classify currently unknown (orphan) kinases, as a foundation for their subsequent structural and functional investigation. PMID:27412987

  6. First in situ observations of the deep-sea squid Grimalditeuthis bonplandi reveal unique use of tentacles

    PubMed Central

    Hoving, Hendrik J. T.; Zeidberg, Louis D.; Benfield, Mark C.; Bush, Stephanie L.; Robison, Bruce H.; Vecchione, Michael

    2013-01-01

    The deep-sea squid Grimalditeuthis bonplandi has tentacles unique among known squids. The elastic stalk is extremely thin and fragile, whereas the clubs bear no suckers, hooks or photophores. It is unknown whether and how these tentacles are used in prey capture and handling. We present, to our knowledge, the first in situ observations of this species obtained by remotely operated vehicles (ROVs) in the Atlantic and North Pacific. Unexpectedly, G. bonplandi is unable to rapidly extend and retract the tentacle stalk as do other squids, but instead manoeuvres the tentacles by undulation and flapping of the clubs’ trabecular protective membranes. These tentacle club movements superficially resemble the movements of small marine organisms and suggest the possibility that G. bonplandi uses aggressive mimicry by the tentacle clubs to lure prey, which we find to consist of crustaceans and cephalopods. In the darkness of the meso- and bathypelagic zones the flapping and undulatory movements of the tentacle may: (i) stimulate bioluminescence in the surrounding water, (ii) create low-frequency vibrations and/or (iii) produce a hydrodynamic wake. Potential prey of G. bonplandi may be attracted to one or more of these as signals. This singular use of the tentacle adds to the diverse foraging and feeding strategies known in deep-sea cephalopods. PMID:23986106

  7. Design and Conformational Analysis of Peptoids Containing N-Hydroxy Amides Reveals a Unique Sheet-Like Secondary Structure

    PubMed Central

    Crapster, J. Aaron; Stringer, Joseph R.; Guzei, Ilia A.; Blackwell, Helen E.

    2011-01-01

    N-hydroxy amides can be found in many naturally occurring and synthetic compounds and are known to act as both strong proton donors and chelators of metal cations. We have initiated studies of peptoids, or N-substituted glycines, that contain N-hydroxy amide side chains to investigate the potential effects of these functional groups on peptoid backbone amide rotamer equilibria and local conformations. We reasoned that the propensity of these functional groups to participate in hydrogen bonding could be exploited to enforce intramolecular or intermolecular interactions that yield new peptoid structures. Here, we report the design, synthesis, and detailed conformational analysis of a series of model N-hydroxy peptoids. These peptoids were readily synthesized, and their structures were analyzed in solution by 1D and 2D NMR and in the solid-state by X-ray crystallography. The N-hydroxy amides were found to strongly favor trans conformations with respect to the peptoid backbone in chloroform. More notably, unique sheet-like structures held together via intermolecular hydrogen bonds were observed in the X-ray crystal structures of an N-hydroxy amide peptoid dimer, which to our knowledge represent the first structure of this type reported for peptoids. These results suggest that the N-hydroxy amide can be utilized to control both local backbone geometries and longer-range intermolecular interactions in peptoids, and represents a new functional group in the peptoid design toolbox. PMID:22180908

  8. Structure of the Arabidopsis Glucan Phosphatase LIKE SEX FOUR2 Reveals a Unique Mechanism for Starch Dephosphorylation[W

    PubMed Central

    Meekins, David A.; Guo, Hou-Fu; Husodo, Satrio; Paasch, Bradley C.; Bridges, Travis M.; Santelia, Diana; Kötting, Oliver; Vander Kooi, Craig W.; Gentry, Matthew S.

    2013-01-01

    Starch is a water-insoluble, Glc-based biopolymer that is used for energy storage and is synthesized and degraded in a diurnal manner in plant leaves. Reversible phosphorylation is the only known natural starch modification and is required for starch degradation in planta. Critical to starch energy release is the activity of glucan phosphatases; however, the structural basis of dephosphorylation by glucan phosphatases is unknown. Here, we describe the structure of the Arabidopsis thaliana starch glucan phosphatase LIKE SEX FOUR2 (LSF2) both with and without phospho-glucan product bound at 2.3Å and 1.65Å, respectively. LSF2 binds maltohexaose-phosphate using an aromatic channel within an extended phosphatase active site and positions maltohexaose in a C3-specific orientation, which we show is critical for the specific glucan phosphatase activity of LSF2 toward native Arabidopsis starch. However, unlike other starch binding enzymes, LSF2 does not possess a carbohydrate binding module domain. Instead we identify two additional glucan binding sites located within the core LSF2 phosphatase domain. This structure is the first of a glucan-bound glucan phosphatase and provides new insights into the molecular basis of this agriculturally and industrially relevant enzyme family as well as the unique mechanism of LSF2 catalysis, substrate specificity, and interaction with starch granules. PMID:23832589

  9. Structure of the Arabidopsis glucan phosphatase like sex four2 reveals a unique mechanism for starch dephosphorylation.

    PubMed

    Meekins, David A; Guo, Hou-Fu; Husodo, Satrio; Paasch, Bradley C; Bridges, Travis M; Santelia, Diana; Kötting, Oliver; Vander Kooi, Craig W; Gentry, Matthew S

    2013-06-01

    Starch is a water-insoluble, Glc-based biopolymer that is used for energy storage and is synthesized and degraded in a diurnal manner in plant leaves. Reversible phosphorylation is the only known natural starch modification and is required for starch degradation in planta. Critical to starch energy release is the activity of glucan phosphatases; however, the structural basis of dephosphorylation by glucan phosphatases is unknown. Here, we describe the structure of the Arabidopsis thaliana starch glucan phosphatase like sex four2 (LSF2) both with and without phospho-glucan product bound at 2.3Å and 1.65Å, respectively. LSF2 binds maltohexaose-phosphate using an aromatic channel within an extended phosphatase active site and positions maltohexaose in a C3-specific orientation, which we show is critical for the specific glucan phosphatase activity of LSF2 toward native Arabidopsis starch. However, unlike other starch binding enzymes, LSF2 does not possess a carbohydrate binding module domain. Instead we identify two additional glucan binding sites located within the core LSF2 phosphatase domain. This structure is the first of a glucan-bound glucan phosphatase and provides new insights into the molecular basis of this agriculturally and industrially relevant enzyme family as well as the unique mechanism of LSF2 catalysis, substrate specificity, and interaction with starch granules. PMID:23832589

  10. Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain

    PubMed Central

    Stroehlein, Andreas J.; Young, Neil D.; Korhonen, Pasi K.; Chang, Bill C. H.; Sternberg, Paul W.; La Rosa, Giuseppe; Pozio, Edoardo; Gasser, Robin B.

    2016-01-01

    Parasitic worms of the genus Trichinella (phylum Nematoda; class Enoplea) represent a complex of at least twelve taxa that infect a range of different host animals, including humans, around the world. They are foodborne, intracellular nematodes, and their life cycles differ substantially from those of other nematodes. The recent characterization of the genomes and transcriptomes of all twelve recognized taxa of Trichinella now allows, for the first time, detailed studies of their molecular biology. In the present study, we defined, curated, and compared the protein kinase complements (kinomes) of Trichinella spiralis and T. pseudospiralis using an integrated bioinformatic workflow employing transcriptomic and genomic data sets. We examined how variation in the kinome might link to unique aspects of Trichinella morphology, biology, and evolution. Furthermore, we utilized in silico structural modeling to discover and characterize a novel, MOS-like kinase with an unusual, previously undescribed N-terminal domain. Taken together, the present findings provide a basis for comparative investigations of nematode kinomes, and might facilitate the identification of Enoplea-specific intervention and diagnostic targets. Importantly, the in silico modeling approach assessed here provides an exciting prospect of being able to identify and classify currently unknown (orphan) kinases, as a foundation for their subsequent structural and functional investigation. PMID:27412987

  11. The low density lipoprotein receptor-related protein 1: Unique tissue-specific functions revealed by selective gene knockout studies

    PubMed Central

    Lillis, Anna P.; Van Duyn, Lauren B.; Murphy-Ullrich, Joanne E.; Strickland, Dudley K.

    2008-01-01

    The low-density lipoprotein (LDL) receptor-related protein (originally called LRP, but now referred to as LRP1) is a large endocytic receptor that is widely expressed in several tissues. LRP1 is a member of the LDL receptor family that plays diverse roles in various biological processes including lipoprotein metabolism, degradation of proteases, activation of lysosomal enzymes and cellular entry of bacterial toxins and viruses. Deletion of the LRP1 gene leads to lethality in mice, revealing a critical, but as of yet, undefined role in development. Tissue-specific gene deletion studies reveal an important contribution of LRP1 in the vasculature, central nervous system, in macrophages and in adipocytes. Three important properties of LRP1 dictate its diverse role in physiology: first, its ability to recognize more than thirty distinct ligands; second, its ability to bind a large number of cytoplasmic adaptor proteins via determinants located on its cytoplasmic domain in a phosphorylation-specific manner; and third, its ability to associate with and modulate the activity of other transmembrane receptors such as integrins and receptor tyrosine kinases. PMID:18626063

  12. Comparative Transcriptional Profiling of 3 Murine Models of SLE Nephritis Reveals Both Unique and Shared Regulatory Networks

    PubMed Central

    Zhang, Weijia; Kretzler, Matthias; Davidson, Anne

    2013-01-01

    Objective To define shared and unique features of SLE nephritis in mouse models of proliferative and glomerulosclerotic renal disease. Methods Perfused kidneys from NZB/W F1, NZW/BXSB and NZM2410 mice were harvested before and after nephritis onset. Affymetrix based gene expression profiles of kidney RNA were analyzed using Genomatix Pathway Systems and Ingenuity Pathway Analysis software. Gene expression patterns were confirmed using real-time PCR. Results 955, 1168 and 755 genes were regulated in the kidneys of nephritic NZB/W F1, NZM2410 and NZW/BXSB mice respectively. 263 genes were regulated concordantly in all three strains reflecting immune cell infiltration, endothelial cell activation, complement activation, cytokine signaling, tissue remodeling and hypoxia. STAT3 was the top associated transcription factor, having a binding site in the gene promoter of 60/263 regulated genes. The two strains with proliferative nephritis shared a macrophage/DC infiltration and activation signature. NZB/W and NZM2410 mice shared a mitochondrial dysfunction signature. Dominant T cell and plasma cell signatures in NZB/W mice reflected lymphoid aggregates; this was the only strain with regulatory T cell infiltrates. NZW/BXSB mice manifested tubular regeneration and NZM2410 mice had the most metabolic stress and manifested loss of nephrin, indicating podocyte loss. Conclusions These findings identify shared inflammatory mechanisms of SLE nephritis that can be therapeutically targeted. Nevertheless, the heterogeneity of effector mechanisms suggests that individualized therapy might need to be based on biopsy findings. Some common mechanisms are shared with non-immune–mediated renal diseases, suggesting that strategies to prevent tissue hypoxia and remodeling may be useful in SLE nephritis. PMID:24167575

  13. In situ X-ray diffraction monitoring of a mechanochemical reaction reveals a unique topology metal-organic framework

    NASA Astrophysics Data System (ADS)

    Katsenis, Athanassios D.; Puškarić, Andreas; Štrukil, Vjekoslav; Mottillo, Cristina; Julien, Patrick A.; Užarević, Krunoslav; Pham, Minh-Hao; Do, Trong-On; Kimber, Simon A. J.; Lazić, Predrag; Magdysyuk, Oxana; Dinnebier, Robert E.; Halasz, Ivan; Friščić, Tomislav

    2015-03-01

    Chemical and physical transformations by milling are attracting enormous interest for their ability to access new materials and clean reactivity, and are central to a number of core industries, from mineral processing to pharmaceutical manufacturing. While continuous mechanical stress during milling is thought to create an environment supporting nonconventional reactivity and exotic intermediates, such speculations have remained without proof. Here we use in situ, real-time powder X-ray diffraction monitoring to discover and capture a metastable, novel-topology intermediate of a mechanochemical transformation. Monitoring the mechanochemical synthesis of an archetypal metal-organic framework ZIF-8 by in situ powder X-ray diffraction reveals unexpected amorphization, and on further milling recrystallization into a non-porous material via a metastable intermediate based on a previously unreported topology, herein named katsenite (kat). The discovery of this phase and topology provides direct evidence that milling transformations can involve short-lived, structurally unusual phases not yet accessed by conventional chemistry.

  14. Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic.

    PubMed

    Fischer, Cristine D B; Gräf, Tiago; Ikuta, Nilo; Lehmann, Fernanda K M; Passos, Daniel T; Makiejczuk, Aline; Silveira, Marcos A T; Fonseca, André S K; Canal, Cláudio W; Lunge, Vagner R

    2016-07-01

    Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study investigates the phylodynamics and amino-acid signatures of CDV epidemic in South America by analyzing a large dataset compiled from publicly available sequences and also by collecting new samples from Brazil. A population of 175 dogs with canine distemper (CD) signs was sampled, from which 89 were positive for CDV, generating 42 new CDV sequences. Phylogenetic analysis of the new and publicly available sequences revealed that Brazilian sequences mainly clustered in South America 1 (SA1) clade, which has its origin estimated to the late 1980's. The reconstruction of the demographic history in SA1 clade showed an epidemic expanding until the recent years, doubling in size every nine years. SA1 clade epidemic distinguished from the world CDV epidemic by the emergence of the R580Q strain, a very rare and potentially detrimental substitution in the viral genome. The R580Q substitution was estimated to have happened in one single evolutionary step in the epidemic history in SA1 clade, emerging shortly after introduction to the continent. Moreover, a high prevalence (11.9%) of the Y549H mutation was observed among the domestic dogs sampled here. This finding was associated (p<0.05) with outcome-death and higher frequency in mixed-breed dogs, the later being an indicator of a continuous exchange of CDV strains circulating among wild carnivores and domestic dogs. The results reported here highlight the diversity of the worldwide CDV epidemic and reveal local features that can be valuable for combating the disease. PMID:27060756

  15. Undulate Cu(111) Substrates: A Unique Surface for CVD Graphene Growth

    NASA Astrophysics Data System (ADS)

    Zhang, Yaqian; Zhang, Haoran; Zhang, Yanhui; Chen, Zhiying; Tang, Chunmiao; Sui, Yanping; Wang, Bin; Li, Xiaoliang; Xie, Xiaoming; Yu, Guanghui; Jin, Zhi; Liu, Xinyu

    2015-10-01

    Cu(111) is a suitable substrate for sixfold graphene domain synthesis, as confirmed theoretically and experimentally. However, an undulate striped structure, where stretched flower-like or approximate diamond-shaped graphene domains had formed, appeared on Cu(111) after annealing and growth in our study. Graphene domains were stretched along the undulate stripes. The Cu surface coated with graphene domains was flatter than the surrounding undulate striped structure. Oxygen plasma was used to remove the graphene coating, and the exposed Cu was also flat. We propose that slight steps formed on Cu(111) in the annealing process. The faster rate of graphene growth along these steps contributed to the stretching domain shape. Furthermore, the release of internal stress or the shrinking of Cu during cooling promotes the expansion step to form an undulate striped structure. However, the coated Cu step motion is limited by graphene. Consequently, the resulting surface is flat, thereby clearly indicating a graphene-Cu interaction.

  16. Anomalous correlation effects and unique phase diagram of electron-doped FeSe revealed by photoemission spectroscopy.

    PubMed

    Wen, C H P; Xu, H C; Chen, C; Huang, Z C; Lou, X; Pu, Y J; Song, Q; Xie, B P; Abdel-Hafiez, Mahmoud; Chareev, D A; Vasiliev, A N; Peng, R; Feng, D L

    2016-01-01

    FeSe layer-based superconductors exhibit exotic and distinctive properties. The undoped FeSe shows nematicity and superconductivity, while the heavily electron-doped KxFe2-ySe2 and single-layer FeSe/SrTiO3 possess high superconducting transition temperatures that pose theoretical challenges. However, a comprehensive study on the doping dependence of an FeSe layer-based superconductor is still lacking due to the lack of a clean means of doping control. Through angle-resolved photoemission spectroscopy studies on K-dosed thick FeSe films and FeSe0.93S0.07 bulk crystals, here we reveal the internal connections between these two types of FeSe-based superconductors, and obtain superconductivity below ∼46 K in an FeSe layer under electron doping without interfacial effects. Moreover, we discover an exotic phase diagram of FeSe with electron doping, including a nematic phase, a superconducting dome, a correlation-driven insulating phase and a metallic phase. Such an anomalous phase diagram unveils the remarkable complexity, and highlights the importance of correlations in FeSe layer-based superconductors. PMID:26952215

  17. Metagenomic Analysis of the Pygmy Loris Fecal Microbiome Reveals Unique Functional Capacity Related to Metabolism of Aromatic Compounds

    PubMed Central

    Xu, Bo; Xu, Weijiang; Yang, Fuya; Li, Junjun; Yang, Yunjuan; Tang, Xianghua; Mu, Yuelin; Zhou, Junpei; Huang, Zunxi

    2013-01-01

    The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host. An analysis of 78,619 pyrosequencing reads generated from pygmy loris fecal DNA extracts was performed to help better understand the microbial diversity and functional capacity of the pygmy loris gut microbiome. The taxonomic analysis of the metagenomic reads indicated that pygmy loris fecal microbiomes were dominated by Bacteroidetes and Proteobacteria phyla. The hierarchical clustering of several gastrointestinal metagenomes demonstrated the similarities of the microbial community structures of pygmy loris and mouse gut systems despite their differences in functional capacity. The comparative analysis of function classification revealed that the metagenome of the pygmy loris was characterized by an overrepresentation of those sequences involved in aromatic compound metabolism compared with humans and other animals. The key enzymes related to the benzoate degradation pathway were identified based on the Kyoto Encyclopedia of Genes and Genomes pathway assignment. These results would contribute to the limited body of primate metagenome studies and provide a framework for comparative metagenomic analysis between human and non-human primates, as well as a comparative understanding of the evolution of humans and their microbiome. However, future studies on the metagenome sequencing of pygmy loris and other prosimians regarding the effects of age, genetics, and environment on the composition and activity of the metagenomes are required. PMID:23457582

  18. Anomalous correlation effects and unique phase diagram of electron-doped FeSe revealed by photoemission spectroscopy

    PubMed Central

    Wen, C. H. P.; Xu, H. C.; Chen, C.; Huang, Z. C.; Lou, X.; Pu, Y. J.; Song, Q.; Xie, B. P.; Abdel-Hafiez, Mahmoud; Chareev, D. A.; Vasiliev, A. N.; Peng, R.; Feng, D. L.

    2016-01-01

    FeSe layer-based superconductors exhibit exotic and distinctive properties. The undoped FeSe shows nematicity and superconductivity, while the heavily electron-doped KxFe2−ySe2 and single-layer FeSe/SrTiO3 possess high superconducting transition temperatures that pose theoretical challenges. However, a comprehensive study on the doping dependence of an FeSe layer-based superconductor is still lacking due to the lack of a clean means of doping control. Through angle-resolved photoemission spectroscopy studies on K-dosed thick FeSe films and FeSe0.93S0.07 bulk crystals, here we reveal the internal connections between these two types of FeSe-based superconductors, and obtain superconductivity below ∼46 K in an FeSe layer under electron doping without interfacial effects. Moreover, we discover an exotic phase diagram of FeSe with electron doping, including a nematic phase, a superconducting dome, a correlation-driven insulating phase and a metallic phase. Such an anomalous phase diagram unveils the remarkable complexity, and highlights the importance of correlations in FeSe layer-based superconductors. PMID:26952215

  19. E. coli metabolic protein aldehyde-alcohol dehydrogenase-E binds to the ribosome: a unique moonlighting action revealed.

    PubMed

    Shasmal, Manidip; Dey, Sandip; Shaikh, Tanvir R; Bhakta, Sayan; Sengupta, Jayati

    2016-01-01

    It is becoming increasingly evident that a high degree of regulation is involved in the protein synthesis machinery entailing more interacting regulatory factors. A multitude of proteins have been identified recently which show regulatory function upon binding to the ribosome. Here, we identify tight association of a metabolic protein aldehyde-alcohol dehydrogenase E (AdhE) with the E. coli 70S ribosome isolated from cell extract under low salt wash conditions. Cryo-EM reconstruction of the ribosome sample allows us to localize its position on the head of the small subunit, near the mRNA entrance. Our study demonstrates substantial RNA unwinding activity of AdhE which can account for the ability of ribosome to translate through downstream of at least certain mRNA helices. Thus far, in E. coli, no ribosome-associated factor has been identified that shows downstream mRNA helicase activity. Additionally, the cryo-EM map reveals interaction of another extracellular protein, outer membrane protein C (OmpC), with the ribosome at the peripheral solvent side of the 50S subunit. Our result also provides important insight into plausible functional role of OmpC upon ribosome binding. Visualization of the ribosome purified directly from the cell lysate unveils for the first time interactions of additional regulatory proteins with the ribosome. PMID:26822933

  20. E. coli metabolic protein aldehyde-alcohol dehydrogenase-E binds to the ribosome: a unique moonlighting action revealed

    PubMed Central

    Shasmal, Manidip; Dey, Sandip; Shaikh, Tanvir R.; Bhakta, Sayan; Sengupta, Jayati

    2016-01-01

    It is becoming increasingly evident that a high degree of regulation is involved in the protein synthesis machinery entailing more interacting regulatory factors. A multitude of proteins have been identified recently which show regulatory function upon binding to the ribosome. Here, we identify tight association of a metabolic protein aldehyde-alcohol dehydrogenase E (AdhE) with the E. coli 70S ribosome isolated from cell extract under low salt wash conditions. Cryo-EM reconstruction of the ribosome sample allows us to localize its position on the head of the small subunit, near the mRNA entrance. Our study demonstrates substantial RNA unwinding activity of AdhE which can account for the ability of ribosome to translate through downstream of at least certain mRNA helices. Thus far, in E. coli, no ribosome-associated factor has been identified that shows downstream mRNA helicase activity. Additionally, the cryo-EM map reveals interaction of another extracellular protein, outer membrane protein C (OmpC), with the ribosome at the peripheral solvent side of the 50S subunit. Our result also provides important insight into plausible functional role of OmpC upon ribosome binding. Visualization of the ribosome purified directly from the cell lysate unveils for the first time interactions of additional regulatory proteins with the ribosome. PMID:26822933

  1. Anomalous correlation effects and unique phase diagram of electron-doped FeSe revealed by photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    Wen, C. H. P.; Xu, H. C.; Chen, C.; Huang, Z. C.; Lou, X.; Pu, Y. J.; Song, Q.; Xie, B. P.; Abdel-Hafiez, Mahmoud; Chareev, D. A.; Vasiliev, A. N.; Peng, R.; Feng, D. L.

    2016-03-01

    FeSe layer-based superconductors exhibit exotic and distinctive properties. The undoped FeSe shows nematicity and superconductivity, while the heavily electron-doped KxFe2-ySe2 and single-layer FeSe/SrTiO3 possess high superconducting transition temperatures that pose theoretical challenges. However, a comprehensive study on the doping dependence of an FeSe layer-based superconductor is still lacking due to the lack of a clean means of doping control. Through angle-resolved photoemission spectroscopy studies on K-dosed thick FeSe films and FeSe0.93S0.07 bulk crystals, here we reveal the internal connections between these two types of FeSe-based superconductors, and obtain superconductivity below ~46 K in an FeSe layer under electron doping without interfacial effects. Moreover, we discover an exotic phase diagram of FeSe with electron doping, including a nematic phase, a superconducting dome, a correlation-driven insulating phase and a metallic phase. Such an anomalous phase diagram unveils the remarkable complexity, and highlights the importance of correlations in FeSe layer-based superconductors.

  2. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.

    PubMed

    Mesquita, Rafael D; Vionette-Amaral, Raquel J; Lowenberger, Carl; Rivera-Pomar, Rolando; Monteiro, Fernando A; Minx, Patrick; Spieth, John; Carvalho, A Bernardo; Panzera, Francisco; Lawson, Daniel; Torres, André Q; Ribeiro, Jose M C; Sorgine, Marcos H F; Waterhouse, Robert M; Montague, Michael J; Abad-Franch, Fernando; Alves-Bezerra, Michele; Amaral, Laurence R; Araujo, Helena M; Araujo, Ricardo N; Aravind, L; Atella, Georgia C; Azambuja, Patricia; Berni, Mateus; Bittencourt-Cunha, Paula R; Braz, Gloria R C; Calderón-Fernández, Gustavo; Carareto, Claudia M A; Christensen, Mikkel B; Costa, Igor R; Costa, Samara G; Dansa, Marilvia; Daumas-Filho, Carlos R O; De-Paula, Iron F; Dias, Felipe A; Dimopoulos, George; Emrich, Scott J; Esponda-Behrens, Natalia; Fampa, Patricia; Fernandez-Medina, Rita D; da Fonseca, Rodrigo N; Fontenele, Marcio; Fronick, Catrina; Fulton, Lucinda A; Gandara, Ana Caroline; Garcia, Eloi S; Genta, Fernando A; Giraldo-Calderón, Gloria I; Gomes, Bruno; Gondim, Katia C; Granzotto, Adriana; Guarneri, Alessandra A; Guigó, Roderic; Harry, Myriam; Hughes, Daniel S T; Jablonka, Willy; Jacquin-Joly, Emmanuelle; Juárez, M Patricia; Koerich, Leonardo B; Lange, Angela B; Latorre-Estivalis, José Manuel; Lavore, Andrés; Lawrence, Gena G; Lazoski, Cristiano; Lazzari, Claudio R; Lopes, Raphael R; Lorenzo, Marcelo G; Lugon, Magda D; Majerowicz, David; Marcet, Paula L; Mariotti, Marco; Masuda, Hatisaburo; Megy, Karine; Melo, Ana C A; Missirlis, Fanis; Mota, Theo; Noriega, Fernando G; Nouzova, Marcela; Nunes, Rodrigo D; Oliveira, Raquel L L; Oliveira-Silveira, Gilbert; Ons, Sheila; Orchard, Ian; Pagola, Lucia; Paiva-Silva, Gabriela O; Pascual, Agustina; Pavan, Marcio G; Pedrini, Nicolás; Peixoto, Alexandre A; Pereira, Marcos H; Pike, Andrew; Polycarpo, Carla; Prosdocimi, Francisco; Ribeiro-Rodrigues, Rodrigo; Robertson, Hugh M; Salerno, Ana Paula; Salmon, Didier; Santesmasses, Didac; Schama, Renata; Seabra-Junior, Eloy S; Silva-Cardoso, Livia; Silva-Neto, Mario A C; Souza-Gomes, Matheus; Sterkel, Marcos; Taracena, Mabel L; Tojo, Marta; Tu, Zhijian Jake; Tubio, Jose M C; Ursic-Bedoya, Raul; Venancio, Thiago M; Walter-Nuno, Ana Beatriz; Wilson, Derek; Warren, Wesley C; Wilson, Richard K; Huebner, Erwin; Dotson, Ellen M; Oliveira, Pedro L

    2015-12-01

    Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼ 702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods. PMID:26627243

  3. Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

    PubMed Central

    Mesquita, Rafael D.; Vionette-Amaral, Raquel J.; Lowenberger, Carl; Rivera-Pomar, Rolando; Monteiro, Fernando A.; Minx, Patrick; Spieth, John; Carvalho, A. Bernardo; Panzera, Francisco; Lawson, Daniel; Torres, André Q.; Ribeiro, Jose M. C.; Sorgine, Marcos H. F.; Waterhouse, Robert M.; Abad-Franch, Fernando; Alves-Bezerra, Michele; Amaral, Laurence R.; Araujo, Helena M.; Aravind, L.; Atella, Georgia C.; Azambuja, Patricia; Berni, Mateus; Bittencourt-Cunha, Paula R.; Braz, Gloria R. C.; Calderón-Fernández, Gustavo; Carareto, Claudia M. A.; Christensen, Mikkel B.; Costa, Igor R.; Costa, Samara G.; Dansa, Marilvia; Daumas-Filho, Carlos R. O.; De-Paula, Iron F.; Dias, Felipe A.; Dimopoulos, George; Emrich, Scott J.; Esponda-Behrens, Natalia; Fampa, Patricia; Fernandez-Medina, Rita D.; da Fonseca, Rodrigo N.; Fontenele, Marcio; Fronick, Catrina; Fulton, Lucinda A.; Gandara, Ana Caroline; Garcia, Eloi S.; Genta, Fernando A.; Giraldo-Calderón, Gloria I.; Gomes, Bruno; Gondim, Katia C.; Granzotto, Adriana; Guarneri, Alessandra A.; Guigó, Roderic; Harry, Myriam; Hughes, Daniel S. T.; Jablonka, Willy; Jacquin-Joly, Emmanuelle; Juárez, M. Patricia; Koerich, Leonardo B.; Lange, Angela B.; Latorre-Estivalis, José Manuel; Lavore, Andrés; Lawrence, Gena G.; Lazoski, Cristiano; Lazzari, Claudio R.; Lopes, Raphael R.; Lorenzo, Marcelo G.; Lugon, Magda D.; Marcet, Paula L.; Mariotti, Marco; Masuda, Hatisaburo; Megy, Karine; Missirlis, Fanis; Mota, Theo; Noriega, Fernando G.; Nouzova, Marcela; Nunes, Rodrigo D.; Oliveira, Raquel L. L.; Oliveira-Silveira, Gilbert; Ons, Sheila; Orchard, Ian; Pagola, Lucia; Paiva-Silva, Gabriela O.; Pascual, Agustina; Pavan, Marcio G.; Pedrini, Nicolás; Peixoto, Alexandre A.; Pereira, Marcos H.; Pike, Andrew; Polycarpo, Carla; Prosdocimi, Francisco; Ribeiro-Rodrigues, Rodrigo; Robertson, Hugh M.; Salerno, Ana Paula; Salmon, Didier; Santesmasses, Didac; Schama, Renata; Seabra-Junior, Eloy S.; Silva-Cardoso, Livia; Silva-Neto, Mario A. C.; Souza-Gomes, Matheus; Sterkel, Marcos; Taracena, Mabel L.; Tojo, Marta; Tu, Zhijian Jake; Tubio, Jose M. C.; Ursic-Bedoya, Raul; Venancio, Thiago M.; Walter-Nuno, Ana Beatriz; Wilson, Derek; Warren, Wesley C.; Wilson, Richard K.; Huebner, Erwin; Dotson, Ellen M.; Oliveira, Pedro L.

    2015-01-01

    Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods. PMID:26627243

  4. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium

    PubMed Central

    Barbe, Valérie; Vallenet, David; Fonknechten, Nuria; Kreimeyer, Annett; Oztas, Sophie; Labarre, Laurent; Cruveiller, Stéphane; Robert, Catherine; Duprat, Simone; Wincker, Patrick; Ornston, L. Nicholas; Weissenbach, Jean; Marlière, Philippe; Cohen, Georges N.; Médigue, Claudine

    2004-01-01

    Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome <60% of the length of the Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1 revealed genes for metabolic pathways involved in utilization of a large variety of compounds. Almost all of these genes, with orthologs that are scattered in other species, are located in five major ‘islands of catabolic diversity’, now an apparent ‘archipelago of catabolic diversity’, within one-quarter of the overall genome. Acinetobacter ADP1 displays many features of other aerobic soil bacteria with metabolism oriented toward the degradation of organic compounds found in their natural habitat. A distinguishing feature of this genome is the absence of a gene corresponding to pyruvate kinase, the enzyme that generally catalyzes the terminal step in conversion of carbohydrates to pyruvate for respiration by the citric acid cycle. This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism. PMID:15514110

  5. Low dose irradiation of thyroid cells reveals a unique transcriptomic and epigenetic signature in RET/PTC-positive cells.

    PubMed

    Abou-El-Ardat, Khalil; Monsieurs, Pieter; Anastasov, Nataša; Atkinson, Mike; Derradji, Hanane; De Meyer, Tim; Bekaert, Sofie; Van Criekinge, Wim; Baatout, Sarah

    2012-03-01

    The high doses of radiation received in the wake of the Chernobyl incident and the atomic bombing of Hiroshima and Nagasaki have been linked to the increased appearance of thyroid cancer in the children living in the vicinity of the site. However, the data gathered on the effect of low doses of radiation on the thyroid remain limited. We have examined the genome wide transcriptional response of a culture of TPC-1 human cell line of papillary thyroid carcinoma origin with a RET/PTC1 translocation to various doses (0.0625, 0.5, and 4Gy) of X-rays and compared it to response of thyroids with a RET/PTC3 translocation and against wild-type mouse thyroids irradiated with the same doses using Affymetrix microarrays. We have found considerable overlap at a high dose of 4Gy in both RET/PTC-positive systems but no common genes at 62.5mGy. In addition, the response of RET/PTC-positive system at all doses was distinct from the response of wild-type thyroids with both systems signaling down different pathways. Analysis of the response of microRNAs in TPC-1 cells revealed a radiation-responsive signature of microRNAs in addition to dose-responsive microRNAs. Our results point to the fact that a low dose of X-rays seems to have a significant proliferative effect on normal thyroids. This observation should be studied further as opposed to its effect on RET/PTC-positive thyroids which was subtle, anti-proliferative and system-dependent. PMID:22027090

  6. Structural and Kinetic Analysis of Bacillus subtilis N-Acetylglucosaminidase Reveals a Unique Asp-His Dyad Mechanism*

    PubMed Central

    Litzinger, Silke; Fischer, Stefanie; Polzer, Patrick; Diederichs, Kay; Welte, Wolfram; Mayer, Christoph

    2010-01-01

    Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain β-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active site, at 1.84- and 1.40-Å resolution, respectively. The structures together with kinetic analyses of mutants revealed an Asp-His dyad involved in catalysis: His234 of BsNagZ acts as general acid/base catalyst and is hydrogen bonded by Asp232 for proper function. Replacement of both His234 and Asp232 with glycine reduced the rate of hydrolysis of the fluorogenic substrate 4′-methylumbelliferyl N-acetyl-β-d-glucosaminide 1900- and 4500-fold, respectively, and rendered activity pH-independent in the alkaline range consistent with a role of these residues in acid/base catalysis. N-Acetylglucosaminyl enzyme intermediate accumulated in the H234G mutant and β-azide product was formed in the presence of sodium azide in both mutants. The Asp-His dyad is conserved within β-N-acetylglucosaminidases but otherwise absent in β-glycosidases of family 3, which instead carry a “classical” glutamate acid/base catalyst. The acid/base glutamate of Hordeum vulgare exoglucanase (Exo1) superimposes with His234 of the dyad of BsNagZ and, in contrast to the latter, protrudes from a second domain of the enzyme into the active site. This is the first report of an Asp-His catalytic dyad involved in hydrolysis of glycosides resembling in function the Asp-His-Ser triad of serine proteases. Our findings will facilitate the development of mechanism-based inhibitors that selectively target family 3 β-N-acetylglucosaminidases, which are involved in bacterial cell wall turnover, spore germination, and induction of β-lactamase. PMID:20826810

  7. Uniquely Acquired Vintage Seismic Reflection Data Reveal the Stratigraphic and Tectonic History of the Montana Disturbed Belt, USA

    NASA Astrophysics Data System (ADS)

    Speece, M. A.; Link, C. A.; Stickney, M.

    2011-12-01

    techniques including linear noise suppression of the air wave and ground roll, refraction statics, and prestack migration. Reprocessing of these data using state-of-the-art seismic reflection processing techniques will provide a detailed picture of the stratigraphy and tectonic framework for this region. Moreover, extended correlations of the Vibroseis records to Moho depths might reveal new insights on crustal thickness and provide a framework for understanding crustal thickening during the Laramide Orogeny as well as later Cenozoic extension.

  8. Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold.

    PubMed

    Feliciano, Patricia R; Drennan, Catherine L; Nonato, M Cristina

    2016-08-30

    Fumarate hydratases (FHs) are essential metabolic enzymes grouped into two classes. Here, we present the crystal structure of a class I FH, the cytosolic FH from Leishmania major, which reveals a previously undiscovered protein fold that coordinates a catalytically essential [4Fe-4S] cluster. Our 2.05 Å resolution data further reveal a dimeric architecture for this FH that resembles a heart, with each lobe comprised of two domains that are arranged around the active site. Besides the active site, where the substrate S-malate is bound bidentate to the unique iron of the [4Fe-4S] cluster, other binding pockets are found near the dimeric enzyme interface, some of which are occupied by malonate, shown here to be a weak inhibitor of this enzyme. Taken together, these data provide a framework both for investigations of the class I FH catalytic mechanism and for drug design aimed at fighting neglected tropical diseases. PMID:27528683

  9. Synthesis, characterization, and evaluation of a superficially porous particle with unique, elongated pore channels normal to the surface.

    PubMed

    Wei, Ta-Chen; Mack, Anne; Chen, Wu; Liu, Jia; Dittmann, Monika; Wang, Xiaoli; Barber, William E

    2016-04-01

    In recent years, superficially porous particles (SPPs) have drawn great interest because of their special particle characteristics and improvement in separation efficiency. Superficially porous particles are currently manufactured by adding silica nanoparticles onto solid cores using either a multistep multilayer process or one-step coacervation process. The pore size is mainly controlled by the size of the silica nanoparticles and the tortuous pore channel geometry is determined by how those nanoparticles randomly aggregate. Such tortuous pore structure is also similar to that of all totally porous particles used in HPLC today. In this article, we report on the development of a next generation superficially porous particle with a unique pore structure that includes a thinner shell thickness and ordered pore channels oriented normal to the particle surface. The method of making the new superficially porous particles is a process called pseudomorphic transformation (PMT), which is a form of micelle templating. Porosity is no longer controlled by randomly aggregated nanoparticles but rather by micelles that have an ordered liquid crystal structure. The new particle possesses many advantages such as a narrower particle size distribution, thinner porous layer with high surface area and, most importantly, highly ordered, non-tortuous pore channels oriented normal to the particle surface. This PMT process has been applied to make 1.8-5.1μm SPPs with pore size controlled around 75Å and surface area around 100m(2)/g. All particles with different sizes show the same unique pore structure with tunable pore size and shell thickness. The impact of the novel pore structure on the performance of these particles is characterized by measuring van Deemter curves and constructing kinetic plots. Reduced plate heights as low as 1.0 have been achieved on conventional LC instruments. This indicates higher efficiency of such particles compared to conventional totally porous and

  10. Changes on Pluto's Surface Revealed with Long Timebase Photometry

    NASA Astrophysics Data System (ADS)

    George, Erin; Buie, M.

    2013-10-01

    We are continuing to monitor the long-term photometric behavior of Pluto in order to constrain volatile surface migration. As Pluto passes near the center of the galaxy, the fields are too crowded for normal aperture photometric techniques. We approached this problem with a combination of point-spread function (PSF) photometry and optimal image subtraction (OIS). Our data are from the 0.8-m robotic telescope at Lowell Observatory, the 1-m robotic telescope at New Mexico State Observatory, and the Faulkes 2-m robotic telescope at Siding Spring, part of Las Cumbres Observatory. Our latest results add photometric data up through 2012 to the data collected since discovery. Our new reduction scheme consists of background catalogs, image subtraction using deep templates, and Pluto photometry extraction. We also use the known photometric properties of Charon determined with HST to remove Charon's contribution from old and new data and compare these results with the HST data where Pluto is measured by itself. Data since 2002 show marked departures from the behavior prior to that time. These results provide clear evidence for time evolution of Pluto's surface albedo. We will present these results along with implications for present-day processes that are altering the surface of Pluto. This work also provides crucial insight into the effort required to provide ground-based support observations for the upcoming New Horizons flyby of Pluto in 2015. Support for this work was provided by NASA Planetary Astronomy Program, grant number NNX09AB43G.

  11. Unique signature of bivalent analyte surface plasmon resonance model: A model governed by non-linear differential equations

    NASA Astrophysics Data System (ADS)

    Tiwari, Purushottam; Wang, Xuewen; Darici, Yesim; He, Jin; Uren, Aykut

    Surface plasmon resonance (SPR) is a biophysical technique for the quantitative analysis of bimolecular interactions. Correct identification of the binding model is crucial for the interpretation of SPR data. Bivalent SPR model is governed by non-linear differential equations, which, in general, have no analytical solutions. Therefore, an analytical based approach cannot be employed in order to identify this particular model. There exists a unique signature in the bivalent analyte model, existence of an `optimal analyte concentration', which can distinguish this model from other biphasic models. The unambiguous identification and related analysis of the bivalent analyte model is demonstrated by using theoretical simulations and experimentally measured SPR sensorgrams. Experimental SPR sensorgrams were measured by using Biacore T200 instrument available in Biacore Molecular Interaction Shared Resource facility, supported by NIH Grant P30CA51008, at Georgetown University.

  12. Improving the uniqueness of shear wave velocity profiles derived from the inversion of multiple-mode surface wave dispersion data

    NASA Astrophysics Data System (ADS)

    Supranata, Yosep Erwin

    One of the factors, which contributes to errors in shear wave velocity profile obtained from the inversion of surface wave dispersion data is non-uniqueness due to the limited number of field dispersion data. In this research, a new procedure is developed to improve the uniqueness of the shear wave velocity profile resulting from the inversion. A new forward modeling algorithm using the smallest absolute eigenvalue as the screening parameter to generate Rayleigh wave modes from a theoretical model is developed. The theoretical model adopted in this research is the Dynamic Stiffness Matrix. The results indicate that the new technique is more reliable than the traditional method using the determinant as the screening parameter. The performance of the Broyden-Fletcher-Goldfarb-Shanno and Levenberg-Marquardt methods are evaluated in this research to determine the most suitable gradient method for surface wave inversion. Comparison of the performance of the two methods shows that the Levenberg-Marquardt method produces more accurate results than the Broyden-Fletcher-Goldfarb-Shanno method. An updated inversion technique which divides the inversion process into a number of stages, with each successive stage utilizing the shear wave velocities obtained from the previous stage as its initial model, is introduced. The number of stages is the same as the highest Rayleigh wave mode number, and the kth stage of the inversion utilizes the dispersion data from the 1st through kth modes. Shear wave velocities obtained from the updated inversion technique are more accurate than those obtained from the inversion procedure using an initial model constructed from fundamental mode dispersion data.

  13. An Integrated Drosophila Model System Reveals Unique Properties for F14512, a Novel Polyamine-Containing Anticancer Drug That Targets Topoisomerase II

    PubMed Central

    Chelouah, Sonia; Monod-Wissler, Caroline; Bailly, Christian; Barret, Jean-Marc; Guilbaud, Nicolas; Vispé, Stéphane; Käs, Emmanuel

    2011-01-01

    F14512 is a novel anti-tumor molecule based on an epipodophyllotoxin core coupled to a cancer-cell vectoring spermine moiety. This polyamine linkage is assumed to ensure the preferential uptake of F14512 by cancer cells, strong interaction with DNA and potent inhibition of topoisomerase II (Topo II). The antitumor activity of F14512 in human tumor models is significantly higher than that of other epipodophyllotoxins in spite of a lower induction of DNA breakage. Hence, the demonstrated superiority of F14512 over other Topo II poisons might not result solely from its preferential uptake by cancer cells, but could also be due to unique effects on Topo II interactions with DNA. To further dissect the mechanism of action of F14512, we used Drosophila melanogaster mutants whose genetic background leads to an easily scored phenotype that is sensitive to changes in Topo II activity and/or localization. F14512 has antiproliferative properties in Drosophila cells and stabilizes ternary Topo II/DNA cleavable complexes at unique sites located in moderately repeated sequences, suggesting that the drug specifically targets a select and limited subset of genomic sequences. Feeding F14512 to developing mutant Drosophila larvae led to the recovery of flies expressing a striking phenotype, "Eye wide shut," where one eye is replaced by a first thoracic segment. Other recovered F14512-induced gain- and loss-of-function phenotypes similarly correspond to precise genetic dysfunctions. These complex in vivo results obtained in a whole developing organism can be reconciled with known genetic anomalies and constitute a remarkable instance of specific alterations of gene expression by ingestion of a drug. "Drosophila-based anticancer pharmacology" hence reveals unique properties for F14512, demonstrating the usefulness of an assay system that provides a low-cost, rapid and effective complement to mammalian models and permits the elucidation of fundamental mechanisms of action of candidate

  14. The structure of Aquifex aeolicus ribosomal protein S8 reveals a unique subdomain that contributes to an extremely tight association with 16S rRNA.

    PubMed

    Menichelli, Elena; Edgcomb, Stephen P; Recht, Michael I; Williamson, James R

    2012-01-20

    The assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. The ribosomal protein S8 from Aquifex aeolicus (AS8) is unique in that there is a 41-residue insertion in the consensus S8 sequence. In addition, AS8 exhibits an unusually high affinity for the 16S ribosomal RNA, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than the equivalent interaction from Escherichia coli. Deletion analysis demonstrated that binding to the minimal site on helix 21 occurred at the same nanomolar affinity found for other bacterial species. The additional affinity required the presence of a three-helix junction between helices 20, 21, and 22. The crystal structure of AS8 was solved, revealing the helix-loop-helix geometry of the unique AS8 insertion region, while the core of the molecule is conserved with known S8 structures. The AS8 structure was modeled onto the structure of the 30S ribosomal subunit from E. coli, suggesting the possibility that the unique subdomain provides additional backbone and side-chain contacts between the protein and an unpaired base within the three-way junction of helices 20, 21, and 22. Point mutations in the protein insertion subdomain resulted in a significantly reduced RNA binding affinity with respect to wild-type AS8. These results indicate that the AS8-specific subdomain provides additional interactions with the three-way junction that contribute to the extremely tight binding to ribosomal RNA. PMID:22079365

  15. A Computer-Assisted 3D Model for Analyzing the Aggregation of Tumorigenic Cells Reveals Specialized Behaviors and Unique Cell Types that Facilitate Aggregate Coalescence

    PubMed Central

    Scherer, Amanda; Kuhl, Spencer; Wessels, Deborah; Lusche, Daniel F.; Hanson, Brett; Ambrose, Joseph; Voss, Edward; Fletcher, Emily; Goldman, Charles; Soll, David R.

    2015-01-01

    We have developed a 4D computer-assisted reconstruction and motion analysis system, J3D-DIAS 4.1, and applied it to the reconstruction and motion analysis of tumorigenic cells in a 3D matrix. The system is unique in that it is fast, high-resolution, acquires optical sections using DIC microscopy (hence there is no associated photoxicity), and is capable of long-term 4D reconstruction. Specifically, a z-series at 5 μm increments can be acquired in less than a minute on tissue samples embedded in a 1.5 mm thick 3D Matrigel matrix. Reconstruction can be repeated at intervals as short as every minute and continued for 30 days or longer. Images are converted to mathematical representations from which quantitative parameters can be derived. Application of this system to cancer cells from established lines and fresh tumor tissue has revealed unique behaviors and cell types not present in non-tumorigenic lines. We report here that cells from tumorigenic lines and tumors undergo rapid coalescence in 3D, mediated by specific cell types that we have named “facilitators” and “probes.” A third cell type, the “dervish”, is capable of rapid movement through the gel and does not adhere to it. These cell types have never before been described. Our data suggest that tumorigenesis in vitro is a developmental process involving coalescence facilitated by specialized cells that culminates in large hollow spheres with complex architecture. The unique effects of select monoclonal antibodies on these processes demonstrate the usefulness of the model for analyzing the mechanisms of anti-cancer drugs. PMID:25790299

  16. Structural Characterization of Proline-rich Tyrosine Kinase 2 (PYK2) Reveals a Unique (DFG-out) Conformation and Enables Inhibitor Design

    PubMed Central

    Han, Seungil; Mistry, Anil; Chang, Jeanne S.; Cunningham, David; Griffor, Matt; Bonnette, Peter C.; Wang, Hong; Chrunyk, Boris A.; Aspnes, Gary E.; Walker, Daniel P.; Brosius, Arthur D.; Buckbinder, Leonard

    2009-01-01

    Proline-rich tyrosine kinase 2 (PYK2) is a cytoplasmic, non-receptor tyrosine kinase implicated in multiple signaling pathways. It is a negative regulator of osteogenesis and considered a viable drug target for osteoporosis treatment. The high-resolution structures of the human PYK2 kinase domain with different inhibitor complexes establish the conventional bilobal kinase architecture and show the conformational variability of the DFG loop. The basis for the lack of selectivity for the classical kinase inhibitor, PF-431396, within the FAK family is explained by our structural analyses. Importantly, the novel DFG-out conformation with two diarylurea inhibitors (BIRB796, PF-4618433) reveals a distinct subclass of non-receptor tyrosine kinases identifiable by the gatekeeper Met-502 and the unique hinge loop conformation of Leu-504. This is the first example of a leucine residue in the hinge loop that blocks the ATP binding site in the DFG-out conformation. Our structural, biophysical, and pharmacological studies suggest that the unique features of the DFG motif, including Leu-504 hinge-loop variability, can be exploited for the development of selective protein kinase inhibitors. PMID:19244237

  17. Structural Characterization of Proline-rich Tyrosine Kinase 2 (PYK2) Reveals a Unique (DFG-out) Conformation and Enables Inhibitor Design

    SciTech Connect

    Han, Seungil; Mistry, Anil; Chang, Jeanne S.; Cunningham, David; Griffor, Matt; Bonnette, Peter C.; Wang, Hong; Chrunyk, Boris A.; Aspnes, Gary E.; Walker, Daniel P.; Brosius, Arthur D.; Buckbinder, Leonard; Pfizer

    2009-05-21

    Proline-rich tyrosine kinase 2 (PYK2) is a cytoplasmic, non-receptor tyrosine kinase implicated in multiple signaling pathways. It is a negative regulator of osteogenesis and considered a viable drug target for osteoporosis treatment. The high-resolution structures of the human PYK2 kinase domain with different inhibitor complexes establish the conventional bilobal kinase architecture and show the conformational variability of the DFG loop. The basis for the lack of selectivity for the classical kinase inhibitor, PF-431396, within the FAK family is explained by our structural analyses. Importantly, the novel DFG-out conformation with two diarylurea inhibitors (BIRB796, PF-4618433) reveals a distinct subclass of non-receptor tyrosine kinases identifiable by the gatekeeper Met-502 and the unique hinge loop conformation of Leu-504. This is the first example of a leucine residue in the hinge loop that blocks the ATP binding site in the DFG-out conformation. Our structural, biophysical, and pharmacological studies suggest that the unique features of the DFG motif, including Leu-504 hinge-loop variability, can be exploited for the development of selective protein kinase inhibitors.

  18. Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions

    SciTech Connect

    Ansong, Charles; Wu, Si; Meng, Da; Liu, Xiaowen; Brewer, Heather M.; Kaiser, Brooke LD; Nakayasu, Ernesto S.; Cort, John R.; Pevzner, Pavel A.; Smith, Richard D.; Heffron, Fred; Adkins, Joshua N.; Pasa-Tolic, Ljiljana

    2013-06-18

    Characterization of the mature protein complement in cells is crucial for a better understanding of cellular processes on a systems-wide scale. Bottom-up proteomic approaches often lead to loss of critical information about an endogenous protein’s actual state due to post translational modifications (PTMs) and other processes. Top-down approaches that involve analysis of the intact protein can address this concern but present significant analytical challenges related to the separation quality needed, measurement sensitivity, and speed that result in low throughput and limited coverage. Here we used single-dimension ultra high pressure liquid chromatography mass spectrometry to investigate the comprehensive ‘intact’ proteome of the Gram negative bacterial pathogen Salmonella Typhimurium. Top-down proteomics analysis revealed 563 unique proteins including 1665 proteoforms generated by PTMs, representing the largest microbial top-down dataset reported to date. Our analysis not only confirmed several previously recognized aspects of Salmonella biology and bacterial PTMs in general, but also revealed several novel biological insights. Of particular interest was differential utilization of the protein S-thiolation forms S-glutathionylation and S-cysteinylation in response to infection-like conditions versus basal conditions, which was corroborated by changes in corresponding biosynthetic pathways. This differential utilization highlights underlying metabolic mechanisms that modulate changes in cellular signaling, and represents to our knowledge the first report of S-cysteinylation in Gram negative bacteria. The demonstrated utility of our simple proteome-wide intact protein level measurement strategy for gaining biological insight should promote broader adoption and applications of top-down proteomics approaches.

  19. Structure of the Trichomonas vaginalis Myb3 DNA-binding domain bound to a promoter sequence reveals a unique C-terminal β-hairpin conformation.

    PubMed

    Wei, Shu-Yi; Lou, Yuan-Chao; Tsai, Jia-Yin; Ho, Meng-Ru; Chou, Chun-Chi; Rajasekaran, M; Hsu, Hong-Ming; Tai, Jung-Hsiang; Hsiao, Chwan-Deng; Chen, Chinpan

    2012-01-01

    Trichomonas vaginalis Myb3 transcription factor (tvMyb3) recognizes the MRE-1 promoter sequence and regulates ap65-1 gene, which encodes a hydrogenosomal malic enzyme that may play a role in the cytoadherence of the parasite. Here, we identified tvMyb3(53-180) as the essential fragment for DNA recognition and report the crystal structure of tvMyb3(53-180) bound to MRE-1 DNA. The N-terminal fragment adopts the classical conformation of an Myb DNA-binding domain, with the third helices of R2 and R3 motifs intercalating in the major groove of DNA. The C-terminal extension forms a β-hairpin followed by a flexible tail, which is stabilized by several interactions with the R3 motif and is not observed in other Myb proteins. Interestingly, this unique C-terminal fragment does not stably connect with DNA in the complex structure but is involved in DNA binding, as demonstrated by NMR chemical shift perturbation, (1)H-(15)N heteronuclear-nuclear Overhauser effect and intermolecular paramagnetic relaxation enhancement. Site-directed mutagenesis also revealed that this C-terminal fragment is crucial for DNA binding, especially the residue Arg(153) and the fragment K(170)KRK(173). We provide a structural basis for MRE-1 DNA recognition and suggest a possible post-translational regulation of tvMyb3 protein. PMID:21908401

  20. IlsA, A Unique Surface Protein of Bacillus cereus Required for Iron Acquisition from Heme, Hemoglobin and Ferritin

    PubMed Central

    Daou, Nadine; Buisson, Christophe; Gohar, Michel; Vidic, Jasmina; Bierne, Hélène; Kallassy, Mireille; Lereclus, Didier; Nielsen-LeRoux, Christina

    2009-01-01

    The human opportunistic pathogen Bacillus cereus belongs to the B. cereus group that includes bacteria with a broad host spectrum. The ability of these bacteria to colonize diverse hosts is reliant on the presence of adaptation factors. Previously, an IVET strategy led to the identification of a novel B. cereus protein (IlsA, Iron-regulated leucine rich surface protein), which is specifically expressed in the insect host or under iron restrictive conditions in vitro. Here, we show that IlsA is localized on the surface of B. cereus and hence has the potential to interact with host proteins. We report that B. cereus uses hemoglobin, heme and ferritin, but not transferrin and lactoferrin. In addition, affinity tests revealed that IlsA interacts with both hemoglobin and ferritin. Furthermore, IlsA directly binds heme probably through the NEAT domain. Inactivation of ilsA drastically decreases the ability of B. cereus to grow in the presence of hemoglobin, heme and ferritin, indicating that IlsA is essential for iron acquisition from these iron sources. In addition, the ilsA mutant displays a reduction in growth and virulence in an insect model. Hence, our results indicate that IlsA is a key factor within a new iron acquisition system, playing an important role in the general virulence strategy adapted by B. cereus to colonize susceptible hosts. PMID:19956654

  1. A unique surface membrane anchored purine-salvage enzyme is conserved among a group of primitive eukaryotic human pathogens.

    PubMed

    Debrabant, A; Bastien, P; Dwyer, D M

    2001-04-01

    Previously, we isolated and characterized the gene encoding the 3'-Nucleotidase/Nuclease (Ld3'NT/NU) from the human pathogen, Leishmania donovani. This unique cell surface enzyme has been shown to be involved in the salvage of host-derived purines, which are essential for the survival of this important protozoan parasite. In this report, we assessed whether the 3'-Nucleotidase/Nuclease was conserved amongst other pathogenic Leishmania and related trypanosomatid parasites. Results of pulsed field gel electrophoresis and Southern blotting showed that a Ld3'NT/NU gene homolog was present in each of the visceral and cutaneous Leishmania species tested (i.e. isolates of L. donovani, L. infantum, L. tropica, L. major and L. mexicana, respectively). Further, results of colorimetric assays using 3'-adenosine monophosphate as substrate demonstrated that each of these organisms also expressed significant levels of 3'-nucleotidase enzyme activity. In addition, we showed that a Ld3'NT/NU gene homolog was expressed in each of these Leishmania species as a > 40 kDa 3'-nucleotidase enzyme activity. A Ld3'NT/NU gene homolog was also identified in two Crithidia species (C. fasciculata and C. luciliae) and Leptomonas seymouri but was only marginally detectable in Trypanosoma brucei, Trypanosoma cruzi and Phytomonas serpens. Cumulatively, results of this study showed that an Ld3'NT/NU homolog was conserved amongst pathogenic Leishmania sp. which suggests that this enzyme must play an critical role in purine salvage for all members of this group of human pathogens. PMID:11451370

  2. Nanoscale periodic modulations on sodium chloride surface revealed by tuning fork atomic force microscopy.

    PubMed

    Clark, Kendal W; Qin, Shengyong; Zhang, X-G; Li, An-Ping

    2012-05-11

    The sodium chloride surface is one of the most common platforms for the study of catalysts, thin film growth, and atmospheric aerosols. Here we report a nanoscale periodic modulation pattern on the surface of a cleaved NaCl single crystal, revealed by non-contact atomic force microscopy with a tuning fork sensor. The surface pattern shows two orthogonal domains, extending over the entire cleavage surface. The spatial modulations exhibit a characteristic period of 5.4 nm, along <110> crystallographic directions of the NaCl. The modulations are robust in vacuum, not affected by the tip-induced electric field or gentle annealing (<300 °C); however, they are eliminated after exposure to water and an atomically flat surface can be recovered by subsequent thermal annealing after water exposure. A strong electrostatic charging is revealed on the cleavage surface which may facilitate the formation of the observed metastable surface reconstruction. PMID:22513484

  3. Nanoscale periodic modulations on sodium chloride surface revealed by tuning fork atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Clark, Kendal W.; Qin, Shengyong; Zhang, X.-G.; Li, An-Ping

    2012-05-01

    The sodium chloride surface is one of the most common platforms for the study of catalysts, thin film growth, and atmospheric aerosols. Here we report a nanoscale periodic modulation pattern on the surface of a cleaved NaCl single crystal, revealed by non-contact atomic force microscopy with a tuning fork sensor. The surface pattern shows two orthogonal domains, extending over the entire cleavage surface. The spatial modulations exhibit a characteristic period of 5.4 nm, along <110> crystallographic directions of the NaCl. The modulations are robust in vacuum, not affected by the tip-induced electric field or gentle annealing (<300 °C) however, they are eliminated after exposure to water and an atomically flat surface can be recovered by subsequent thermal annealing after water exposure. A strong electrostatic charging is revealed on the cleavage surface which may facilitate the formation of the observed metastable surface reconstruction.

  4. A Systems Biological Approach Reveals Multiple Crosstalk Mechanism between Gram-Positive and Negative Bacterial Infections: An Insight into Core Mechanism and Unique Molecular Signatures

    PubMed Central

    Thangam, Berla; Ahmed, Shiek S. S. J.

    2014-01-01

    Background Bacterial infections remain a major threat and a leading cause of death worldwide. Most of the bacterial infections are caused by gram-positive and negative bacteria, which are recognized by Toll-like receptor (TLR) 2 and 4, respectively. Activation of these TLRs initiates multiple pathways that subsequently lead to effective immune response. Although, both the TLRs share common signaling mechanism yet they may exhibit specificity as well, resulting in the release of diverse range of inflammatory mediators which could be used as candidate biomolecules for bacterial infections. Results We adopted systems biological approach to identify signaling pathways mediated by TLRs to determine candidate molecules associated with bacterial infections. We used bioinformatics concepts, including literature mining to construct protein-protein interaction network, prioritization of TLRs specific nodes using microarray data and pathway analysis. Our constructed PPI network for TLR 2 (nodes: 4091 and edges: 66068) and TLR 4 (node: 4076 and edges: 67898) showed 3207 common nodes, indicating that both the TLRs might share similar signaling events that are attributed to cell migration, MAPK pathway and several inflammatory cascades. Our results propose the potential collaboration between the shared signaling pathways of both the receptors may enhance the immune response against invading pathogens. Further, to identify candidate molecules, the TLRs specific nodes were prioritized using microarray differential expressed genes. Of the top prioritized TLR 2 molecules, 70% were co-expressed. A similar trend was also observed within TLR 4 nodes. Further, most of these molecules were preferentially found in blood plasma for feasible diagnosis. Conclusions The analysis reveals the common and unique mechanism regulated by both the TLRs that provide a broad perspective of signaling events in bacterial infections. Further, the identified candidate biomolecules could potentially aid

  5. Characterization of Dye-decolorizing Peroxidase (DyP) from Thermomonospora curvata Reveals Unique Catalytic Properties of A-type DyPs.

    PubMed

    Chen, Chao; Shrestha, Ruben; Jia, Kaimin; Gao, Philip F; Geisbrecht, Brian V; Bossmann, Stefan H; Shi, Jishu; Li, Ping

    2015-09-18

    Dye-decolorizing peroxidases (DyPs) comprise a new family of heme peroxidases, which has received much attention due to their potential applications in lignin degradation. A new DyP from Thermomonospora curvata (TcDyP) was identified and characterized. Unlike other A-type enzymes, TcDyP is highly active toward a wide range of substrates including model lignin compounds, in which the catalytic efficiency with ABTS (kcat(app)/Km(app) = (1.7 × 10(7)) m(-1) s(-1)) is close to that of fungal DyPs. Stopped-flow spectroscopy was employed to elucidate the transient intermediates as well as the catalytic cycle involving wild-type (wt) and mutant TcDyPs. Although residues Asp(220) and Arg(327) are found necessary for compound I formation, His(312) is proposed to play roles in compound II reduction. Transient kinetics of hydroquinone (HQ) oxidation by wt-TcDyP showed that conversion of the compound II to resting state is a rate-limiting step, which will explain the contradictory observation made with the aspartate mutants of A-type DyPs. Moreover, replacement of His(312) and Arg(327) has significant effects on the oligomerization and redox potential (E°') of the enzyme. Both mutants were found to promote the formation of dimeric state and to shift E°' to a more negative potential. Not only do these results reveal the unique catalytic property of the A-type DyPs, but they will also facilitate the development of these enzymes as lignin degraders. PMID:26205819

  6. The First Venomous Crustacean Revealed by Transcriptomics and Functional Morphology: Remipede Venom Glands Express a Unique Toxin Cocktail Dominated by Enzymes and a Neurotoxin

    PubMed Central

    von Reumont, Björn M.; Blanke, Alexander; Richter, Sandy; Alvarez, Fernando; Bleidorn, Christoph; Jenner, Ronald A.

    2014-01-01

    Animal venoms have evolved many times. Venomous species are especially common in three of the four main groups of arthropods (Chelicerata, Myriapoda, and Hexapoda), which together represent tens of thousands of species of venomous spiders, scorpions, centipedes, and hymenopterans. Surprisingly, despite their great diversity of body plans, there is no unambiguous evidence that any crustacean is venomous. We provide the first conclusive evidence that the aquatic, blind, and cave-dwelling remipede crustaceans are venomous and that venoms evolved in all four major arthropod groups. We produced a three-dimensional reconstruction of the venom delivery apparatus of the remipede Speleonectes tulumensis, showing that remipedes can inject venom in a controlled manner. A transcriptomic profile of its venom glands shows that they express a unique cocktail of transcripts coding for known venom toxins, including a diversity of enzymes and a probable paralytic neurotoxin very similar to one described from spider venom. We screened a transcriptomic library obtained from whole animals and identified a nontoxin paralog of the remipede neurotoxin that is not expressed in the venom glands. This allowed us to reconstruct its probable evolutionary origin and underlines the importance of incorporating data derived from nonvenom gland tissue to elucidate the evolution of candidate venom proteins. This first glimpse into the venom of a crustacean and primitively aquatic arthropod reveals conspicuous differences from the venoms of other predatory arthropods such as centipedes, scorpions, and spiders and contributes valuable information for ultimately disentangling the many factors shaping the biology and evolution of venoms and venomous species. PMID:24132120

  7. Gene expression analysis of early stage endometrial cancers reveals unique transcripts associated with grade and histology but not depth of invasion.

    PubMed

    Risinger, John I; Allard, Jay; Chandran, Uma; Day, Roger; Chandramouli, Gadisetti V R; Miller, Caela; Zahn, Christopher; Oliver, Julie; Litzi, Tracy; Marcus, Charlotte; Dubil, Elizabeth; Byrd, Kevin; Cassablanca, Yovanni; Becich, Michael; Berchuck, Andrew; Darcy, Kathleen M; Hamilton, Chad A; Conrads, Thomas P; Maxwell, G Larry

    2013-01-01

    Endometrial cancer is the most common gynecologic malignancy in the United States but it remains poorly understood at the molecular level. This investigation was conducted to specifically assess whether gene expression changes underlie the clinical and pathologic factors traditionally used for determining treatment regimens in women with stage I endometrial cancer. These include the effect of tumor grade, depth of myometrial invasion and histotype. We utilized oligonucleotide microarrays to assess the transcript expression profile in epithelial glandular cells laser microdissected from 79 endometrioid and 12 serous stage I endometrial cancers with a heterogeneous distribution of grade and depth of myometrial invasion, along with 12 normal post-menopausal endometrial samples. Unsupervised multidimensional scaling analyses revealed that serous and endometrioid stage I cancers have similar transcript expression patterns when compared to normal controls where 900 transcripts were identified to be differentially expressed by at least fourfold (univariate t-test, p < 0.001) between the cancers and normal endometrium. This analysis also identified transcript expression differences between serous and endometrioid cancers and tumor grade, but no apparent differences were identified as a function of depth of myometrial invasion. Four genes were validated by quantitative PCR on an independent set of cancer and normal endometrium samples. These findings indicate that unique gene expression profiles are associated with histologic type and grade, but not myometrial invasion among early stage endometrial cancers. These data provide a comprehensive perspective on the molecular alterations associated with stage I endometrial cancer, particularly those subtypes that have the worst prognosis. PMID:23785665

  8. Crystal structure of the halotolerant gamma-glutamyltranspeptidase from Bacillus subtilis in complex with glutamate reveals a unique architecture of the solvent-exposed catalytic pocket.

    PubMed

    Wada, Kei; Irie, Machiko; Suzuki, Hideyuki; Fukuyama, Keiichi

    2010-02-01

    gamma-Glutamyltranspeptidase (GGT; EC 2.3.2.2), an enzyme found in organisms from bacteria to mammals and plants, plays a central role in glutathione metabolism. Structural studies of GGTs from Escherichia coli and Helicobacter pylori have revealed detailed molecular mechanisms of catalysis and maturation. In these two GGTs, highly conserved residues form the catalytic pockets, conferring the ability of the loop segment to shield the bound gamma-glutamyl moiety from the solvent. Here, we have examined the Bacillus subtilis GGT, which apparently lacks the amino acids corresponding to the lid-loop that are present in mammalian and plant GGTs as well as in most bacterial GGTs. Another remarkable feature of B. subtilis GGT is its salt tolerance; it retains 86% of its activity even in 3 m NaCl. To better understand these characteristics of B. subtilis GGT, we determined its crystal structure in complex with glutamate, a product of the enzymatic reaction, at 1.95 A resolution. This structure revealed that, unlike the E. coli and H. pylori GGTs, the catalytic pocket of B. subtilis GGT has no segment that covers the bound glutamate; consequently, the glutamate is exposed to solvent. Furthermore, calculation of the electrostatic potential showed that strong acidic patches were distributed on the surface of the B. subtilis GGT, even under high-salt conditions, and this may allow the protein to remain in the hydrated state and avoid self-aggregation. The structural findings presented here have implications for the molecular mechanism of GGT. PMID:20088880

  9. Mechanism of Bacterial Cell-Surface Attachment Revealed by the Structure of Cellulosomal Type II Cohesin-dockerin Complex

    SciTech Connect

    Adams,J.; Pal, G.; Jia, Z.; Smith, S.

    2006-01-01

    Bacterial cell-surface attachment of macromolecular complexes maintains the microorganism in close proximity to extracellular substrates and allows for optimal uptake of hydrolytic byproducts. The cellulosome is a large multienzyme complex used by many anaerobic bacteria for the efficient degradation of plant cell-wall polysaccharides. The mechanism of cellulosome retention to the bacterial cell surface involves a calcium-mediated protein-protein interaction between the dockerin (Doc) module from the cellulosomal scaffold and a cohesin (Coh) module of cell-surface proteins located within the proteoglycan layer. Here, we report the structure of an ultra-high-affinity (K{sub a} = 1.44 x 10{sup 10} M{sup 1-}) complex between type II Doc, together with its neighboring X module from the cellulosome scaffold of Clostridium thermocellum, and a type II Coh module associated with the bacterial cell surface. Identification of X module-Doc and X module-Coh contacts reveal roles for the X module in Doc stability and enhanced Coh recognition. This extremely tight interaction involves one face of the Coh and both helices of the Doc and comprises significant hydrophobic character and a complementary extensive hydrogen-bond network. This structure represents a unique mechanism for cell-surface attachment in anaerobic bacteria and provides a rationale for discriminating between type I and type II Coh modules.

  10. Multivariable Regression Analysis in Schistosoma mansoni-Infected Individuals in the Sudan Reveals Unique Immunoepidemiological Profiles in Uninfected, egg+ and Non-egg+ Infected Individuals

    PubMed Central

    Wiszniewsky, Anna; Ritter, Manuel; Goreish, Ibtisam A.; Atti El Mekki, Misk El Yemen A.; Arriens, Sandra; Pfarr, Kenneth; Fimmers, Rolf; Doenhoff, Mike; Hoerauf, Achim; Layland, Laura E.

    2016-01-01

    Background In the Sudan, Schistosoma mansoni infections are a major cause of morbidity in school-aged children and infection rates are associated with available clean water sources. During infection, immune responses pass through a Th1 followed by Th2 and Treg phases and patterns can relate to different stages of infection or immunity. Methodology This retrospective study evaluated immunoepidemiological aspects in 234 individuals (range 4–85 years old) from Kassala and Khartoum states in 2011. Systemic immune profiles (cytokines and immunoglobulins) and epidemiological parameters were surveyed in n = 110 persons presenting patent S. mansoni infections (egg+), n = 63 individuals positive for S. mansoni via PCR in sera but egg negative (SmPCR+) and n = 61 people who were infection-free (Sm uninf). Immunoepidemiological findings were further investigated using two binary multivariable regression analysis. Principal Findings Nearly all egg+ individuals had no access to latrines and over 90% obtained water via the canal stemming from the Atbara River. With regards to age, infection and an egg+ status was linked to young and adolescent groups. In terms of immunology, S. mansoni infection per se was strongly associated with increased SEA-specific IgG4 but not IgE levels. IL-6, IL-13 and IL-10 were significantly elevated in patently-infected individuals and positively correlated with egg load. In contrast, IL-2 and IL-1β were significantly lower in SmPCR+ individuals when compared to Sm uninf and egg+ groups which was further confirmed during multivariate regression analysis. Conclusions/Significance Schistosomiasis remains an important public health problem in the Sudan with a high number of patent individuals. In addition, SmPCR diagnostics revealed another cohort of infected individuals with a unique immunological profile and provides an avenue for future studies on non-patent infection states. Future studies should investigate the downstream signalling pathways

  11. Population Structure and Comparative Genome Hybridization of European Flor Yeast Reveal a Unique Group of Saccharomyces cerevisiae Strains with Few Gene Duplications in Their Genome

    PubMed Central

    Legras, Jean-Luc; Erny, Claude; Charpentier, Claudine

    2014-01-01

    Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four countries, with that of three wine strains did not reveal any large segmental amplification. Nonetheless, some genes, including YKL221W/MCH2 and YKL222C, were amplified in the genome of four out of six flor strains. Finally, we correlated ICR1 ncRNA and FLO11 polymorphisms with flor yeast population structure, and associate the presence of wild type ICR1 and a long Flo11p with thin velum formation in a cluster of Jura strains. These results provide new insight into the diversity of flor yeast and show that combinations of different adaptive changes can lead to an increase of hydrophobicity and affect velum formation. PMID:25272156

  12. Structure of the N-terminal oligomerization domain of DnaD reveals a unique tetramerization motif and provides insights into scaffold formation.

    PubMed

    Schneider, S; Zhang, W; Soultanas, P; Paoli, M

    2008-03-01

    DnaD is a primosomal protein that remodels supercoiled plasmids. It binds to supercoiled forms and converts them to open forms without nicking. During this remodeling process, all the writhe is converted to twist and the plasmids are held around the periphery of large scaffolds made up of DnaD molecules. This DNA-remodeling function is the sum of a scaffold-forming activity on the N-terminal domain and a DNA-dependent oligomerization activity on the C-terminal domain. We have determined the crystal structure of the scaffold-forming N-terminal domain, which reveals a winged-helix architecture, with additional structural elements extending from both N- and C-termini. Four monomers form dimers that join into a tetramer. The N-terminal extension mediates dimerization and tetramerization, with extensive interactions and distinct interfaces. The wings and helices of the winged-helix domains remain exposed on the surface of the tetramer. Structure-guided mutagenesis and atomic force microscopy imaging indicate that these elements, together with the C-terminal extension, are involved in scaffold formation. Based upon our data, we propose a model for the DnaD-mediated scaffold formation. PMID:18206906

  13. Combined flow cytometric analysis of surface and intracellular antigens reveals surface molecule markers of human neuropoiesis.

    PubMed

    Turaç, Gizem; Hindley, Christopher J; Thomas, Ria; Davis, Jason A; Deleidi, Michela; Gasser, Thomas; Karaöz, Erdal; Pruszak, Jan

    2013-01-01

    Surface molecule profiles undergo dynamic changes in physiology and pathology, serve as markers of cellular state and phenotype and can be exploited for cell selection strategies and diagnostics. The isolation of well-defined cell subsets is needed for in vivo and in vitro applications in stem cell biology. In this technical report, we present an approach for defining a subset of interest in a mixed cell population by flow cytometric detection of intracellular antigens. We have developed a fully validated protocol that enables the co-detection of cluster of differentiation (CD) surface antigens on fixed, permeabilized neural cell populations defined by intracellular staining. Determining the degree of co-expression of surface marker candidates with intracellular target population markers (nestin, MAP2, doublecortin, TUJ1) on neuroblastoma cell lines (SH-SY5Y, BE(2)-M17) yielded a combinatorial CD49f(-)/CD200(high) surface marker panel. Its application in fluorescence-activated cell sorting (FACS) generated enriched neuronal cultures from differentiated cell suspensions derived from human induced pluripotent stem cells. Our data underlines the feasibility of using the described co-labeling protocol and co-expression analysis for quantitative assays in mammalian neurobiology and for screening approaches to identify much needed surface markers in stem cell biology. PMID:23826393

  14. Revealing the Restructured Surface of Li[Mn2]O4

    DOE PAGESBeta

    Amos, Charles D.; Roldan, Manuel A.; Varela, Maria; Goodenough, John B.; Ferreira, Paulo J.

    2016-03-29

    The spinel Revealing the Restructured Surface of Li[Mn2]O4 is a candidate cathode for a Li-ion battery, but its capacity fades over a charge/discharge cycle of Li1–x[Mn2]O4 (0 < x < 1) that is associated with a loss of Mn to the organic-liquid electrolyte. It is known that the disproportionation reaction 2Mn3+ = Mn2+ + Mn4+ occurs at the surface of a Mn spinel, and it is important to understand the atomic structure and composition of the surface of Revealing the Restructured Surface of Li[Mn2]O4 in order to understand how Mn loss occurs. We report a study of the surface reconstructionmore » of Revealing the Restructured Surface of Li[Mn2]O4 by aberration-corrected scanning transmission electron microscopy. The atomic structure coupled with Mn-valence and the distribution of the atomic ratio of oxygen obtained by electron energy loss spectroscopy reveals a thin, stable surface layer of Mn3O4, a subsurface region of Li1+x[Mn2]O4 with retention of bulk Li[Mn2]O4. We conclude that this observation is compatible with the disproportionation reaction coupled with oxygen deficiency and a displacement of surface Li+ from the Mn3O4 surface phase. These results provide a critical step toward understanding how Mn is lost from Li[Mn2]O4, once inside a battery.« less

  15. Surface-based morphometry reveals distinct cortical thickness and surface area profiles in Williams syndrome.

    PubMed

    Green, Tamar; Fierro, Kyle C; Raman, Mira M; Saggar, Manish; Sheau, Kristen E; Reiss, Allan L

    2016-04-01

    Morphometric investigations of brain volumes in Williams syndrome (WS) consistently show significant reductions in gray matter volume compared to controls. Cortical thickness (CT) and surface area (SA) are two constituent parts of cortical gray matter volume that are considered genetically distinguishable features of brain morphology. Yet, little is known about the independent contribution of cortical CT and SA to these volumetric differences in WS. Thus, our objectives were: (i) to evaluate whether the microdeletion in chromosome 7 associated with WS has a distinct effect on CT and SA, and (ii) to evaluate age-related variations in CT and SA within WS. We compared CT and SA values in 44 individuals with WS to 49 age- and sex-matched typically developing controls. Between-group differences in CT and SA were evaluated across two age groups: young (age range 6.6-18.9 years), and adults (age range 20.2-51.5 years). Overall, we found contrasting effects of WS on cortical thickness (increases) and surface area (decreases). With respect to brain topography, the between-group pattern of CT differences showed a scattered pattern while the between-group surface area pattern was widely distributed throughout the brain. In the adult subgroup, we observed a cluster of increases in cortical thickness in WS across the brain that was not observed in the young subgroup. Our findings suggest that extensive early reductions in surface area are the driving force for the overall reduction in brain volume in WS. The age-related cortical thickness findings might reflect delayed or even arrested development of specific brain regions in WS. PMID:26852730

  16. Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved α-helix for Act1 binding and IL-17 signaling

    SciTech Connect

    Zhang, Bing; Liu, Caini; Qian, Wen; Han, Yue; Li, Xiaoxia; Deng, Junpeng

    2014-05-01

    Crystal structure of the SEFIR domain from human IL-17 receptor A provides new insights into IL-17 signaling. Interleukin 17 (IL-17) cytokines play a crucial role in mediating inflammatory and autoimmune diseases. A unique intracellular signaling domain termed SEFIR is found within all IL-17 receptors (IL-17Rs) as well as the key adaptor protein Act1. SEFIR-mediated protein–protein interaction is a crucial step in IL-17 cytokine signaling. Here, the 2.3 Å resolution crystal structure of the SEFIR domain of IL-17RA, the most commonly shared receptor for IL-17 cytokine signaling, is reported. The structure includes the complete SEFIR domain and an additional α-helical C-terminal extension, which pack tightly together to form a compact unit. Structural comparison between the SEFIR domains of IL-17RA and IL-17RB reveals substantial differences in protein topology and folding. The uniquely long insertion between strand βC and helix αC in IL-17RA SEFIR is mostly well ordered, displaying a helix (αCC′{sub ins}) and a flexible loop (CC′). The DD′ loop in the IL-17RA SEFIR structure is much shorter; it rotates nearly 90° with respect to the counterpart in the IL-17RB SEFIR structure and shifts about 12 Å to accommodate the αCC′{sub ins} helix without forming any knots. Helix αC was identified as critical for its interaction with Act1 and IL-17-stimulated gene expression. The data suggest that the heterotypic SEFIR–SEFIR association via helix αC is a conserved and signature mechanism specific for IL-17 signaling. The structure also suggests that the downstream motif of IL-17RA SEFIR together with helix αC could provide a composite ligand-binding surface for recruiting Act1 during IL-17 signaling.

  17. Mass spectrometric analysis reveals remnants of host-pathogen molecular interactions at the starch granule surface in wheat endosperm.

    PubMed

    Wall, Michael L; Wheeler, Heather L; Smith, Jeffrey; Figeys, Daniel; Altosaar, Illimar

    2010-09-01

    The starch granules of wheat seed are solar energy-driven deposits of fixed carbon and, as such, present themselves as targets of pathogen attack. The seed's array of antimicrobial proteins, peptides, and small molecules comprises a molecular defense against penetrating pathogens. In turn, pathogens exhibit an arsenal of enzymes to facilitate the degradation of the host's endosperm. In this context, the starch granule surface is a relatively unexplored domain in which unique molecular barriers may be deployed to defend against and inhibit the late stages of infection. Therefore, it was compelling to explore the starch granule surface in mature wheat seed, which revealed evidence of host-pathogen molecular interactions that may have occurred during grain development. In this study, starch granules from the soft wheat Triticum aestivum cv. AC Andrew and hard wheat T. turgidum durum were isolated and water washed 20 times, and their surface proteins were digested in situ with trypsin. The peptides liberated into the supernatant and the peptides remaining at the starch granule surface were separately examined. In this way, we demonstrated that the identified proteins have a strong affinity for the starch granule surface. Proteins with known antimicrobial activity were identified, as well as several proteins from the plant pathogens Agrobacterium tumefaciens, Pectobacterium carotovorum, Fusarium graminearum, Magnaporthe grisea, Xanthomonas axonopodis, and X. oryzae. Although most of these peptides corresponded to uncharacterized hypothetical proteins of fungal pathogens, several peptide fragments were identical to cytosolic and membrane proteins of specific microbial pathogens. During development and maturation, wheat seed appeared to have resisted infection and lysed the pathogens where, upon desiccation, the molecular evidence remained fixed at the starch granule surface. PMID:20701481

  18. The functional integrity of the serpin domain of C1-inhibitor depends on the unique N-terminal domain, as revealed by a pathological mutant.

    PubMed

    Bos, Ineke G A; Lubbers, Yvonne T P; Roem, Dorina; Abrahams, Jan Pieter; Hack, C Erik; Eldering, Eric

    2003-08-01

    C1-inhibitor (C1-Inh) is a serine protease inhibitor (serpin) with a unique, non-conserved N-terminal domain of unknown function. Genetic deficiency of C1-Inh causes hereditary angioedema. A novel type of mutation (Delta 3) in exon 3 of the C1-Inh gene, resulting in deletion of Asp62-Thr116 in this unique domain, was encountered in a hereditary angioedema pedigree. Because the domain is supposedly not essential for inhibitory activity, the unexpected loss-of-function of this deletion mutant was further investigated. The Delta 3 mutant and three additional mutants starting at Pro76, Gly98, and Ser115, lacking increasing parts of the N-terminal domain, were produced recombinantly. C1-Inh76 and C1-Inh98 retained normal conformation and interaction kinetics with target proteases. In contrast, C1-Inh115 and Delta 3, which both lack the connection between the serpin and the non-serpin domain via two disulfide bridges, were completely non-functional because of a complex-like and multimeric conformation, as demonstrated by several criteria. The Delta 3 mutant also circulated in multimeric form in plasma from affected family members. The C1-Inh mutant reported here is unique in that deletion of an entire amino acid stretch from a domain not shared by other serpins leads to a loss-of-function. The deletion in the unique N-terminal domain results in a "multimerization phenotype" of C1-Inh, because of diminished stability of the central beta-sheet. This phenotype, as well as the location of the disulfide bridges between the serpin and the non-serpin domain of C1-Inh, suggests that the function of the N-terminal region may be similar to one of the effects of heparin in antithrombin III, maintenance of the metastable serpin conformation. PMID:12773530

  19. Bacterial populations on brewery filling hall surfaces as revealed by next-generation sequencing.

    PubMed

    Priha, Outi; Raulio, Mari; Maukonen, Johanna; Vehviläinen, Anna-Kaisa; Storgårds, Erna

    2016-01-01

    Due to the presence of moisture and nutrients, brewery filling line surfaces are susceptible to unwanted microbial attachment. Knowledge of the attaching microbes will aid in designing hygienic control of the process. In this study the bacterial diversity present on brewery filling line surfaces was revealed by next generation sequencing. The two filling lines studied maintained their characteristic bacterial community throughout three sampling times (13-163 days). On the glass bottle line, γ-proteobacteria dominated (35-82% of all OTUs), whereas on the canning line α-, β- and γ-proteobacteria and actinobacteria were most common. The most frequently detected genera were Acinetobacter, Propinobacterium and Pseudomonas. The halophilic genus Halomonas was commonly detected, which might be due to its tolerance to alkaline foam cleaners. This study has revealed a detailed overall picture of the bacterial groups present on filling line surfaces. Further effort should be given to determine the efficacy of washing procedures on different bacterial groups. PMID:27064426

  20. Problems at the Leading Edge of Space Weathering as Revealed by TEM Combined with Surface Science Techniques

    NASA Astrophysics Data System (ADS)

    Christoffersen, R.; Dukes, C. A.; Keller, L. P.; Rahman, Z.; Baragiola, R. A.

    2015-11-01

    Analytical field-emission TEM techniques cross-correlated with surface analyses by X-ray photoelectron spectroscopy (XPS) provides a unique two-prong approach for characterizing how solar wind ion processing contributes to space weathering.

  1. A Unique Procedure to Identify Cell Surface Markers Through a Spherical Self-Organizing Map Applied to DNA Microarray Analysis

    PubMed Central

    Sugii, Yuh; Kasai, Tomonari; Ikeda, Masashi; Vaidyanath, Arun; Kumon, Kazuki; Mizutani, Akifumi; Seno, Akimasa; Tokutaka, Heizo; Kudoh, Takayuki; Seno, Masaharu

    2016-01-01

    To identify cell-specific markers, we designed a DNA microarray platform with oligonucleotide probes for human membrane-anchored proteins. Human glioma cell lines were analyzed using microarray and compared with normal and fetal brain tissues. For the microarray analysis, we employed a spherical self-organizing map, which is a clustering method suitable for the conversion of multidimensional data into two-dimensional data and displays the relationship on a spherical surface. Based on the gene expression profile, the cell surface characteristics were successfully mirrored onto the spherical surface, thereby distinguishing normal brain tissue from the disease model based on the strength of gene expression. The clustered glioma-specific genes were further analyzed by polymerase chain reaction procedure and immunocytochemical staining of glioma cells. Our platform and the following procedure were successfully demonstrated to categorize the genes coding for cell surface proteins that are specific to glioma cells. Our assessment demonstrates that a spherical self-organizing map is a valuable tool for distinguishing cell surface markers and can be employed in marker discovery studies for the treatment of cancer. PMID:26966393

  2. Observation of unique blister-like surface features on amorphous metallic alloys following bombardment with deuterium ions

    NASA Astrophysics Data System (ADS)

    Bardamid, A. F.; Voitsenya, V. S.; Lytvyn, O. S.; Lytvyn, P. M.; Konovalov, V. G.; Shapoval, A. N.; Solodovchenko, S. I.; Yakimov, K. I.

    2008-05-01

    When investigating the impact of deuterium plasma ions (with energy 300 eV) on mirror specimen fabricated of bulk amorphous alloy Zr(41.2)Ti(13.8)Cu(12.5)Ni(10)Be(22.5) some unusual surface features were observed. Their shape differs from blisters observed on the surface of amorphous foils bombarded with high energy helium and hydrogen ions (Refs. [9-11]). In this Letter a short description of characteristics of these 'blister-like' features are presented.

  3. Properties of X-ray resonant scattering in the Bragg case revealed on the Riemann surface.

    PubMed

    Saka, Takashi

    2016-07-01

    Continuing the work described in the previous paper [Saka (2016). Acta Cryst. A72, 338-348], the dynamical theory for perfect crystals in the Bragg case is reformulated using the Riemann surface. In particular, diffraction under resonant scattering conditions is investigated. The characteristic features of the dispersion surface and the rocking curve are analytically revealed using four parameters, which are the real and imaginary parts of two quantities specifying the degree of departure from the exact Bragg conditions and the reflection strength. Characteristic properties that have been deduced through numerical analysis are derived analytically using these four parameters. Visualization of the geometric relationships between the four parameters on the Riemann surface is useful for understanding many properties such as symmetry and sharpness of the rocking curve under special conditions. Therefore, employing the Riemann surface is instructive for numerical analysis and useful for understanding dynamical diffraction in the Bragg case. PMID:27357849

  4. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.

    PubMed

    Sun, Tianjun; Gauthier, Sherry Y; Campbell, Robert L; Davies, Peter L

    2015-10-01

    Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters. PMID:26371748

  5. Cryovolcanic Features on Titan's Surface as Revealed by the Cassini RADAR

    NASA Technical Reports Server (NTRS)

    Lopes, R. M.; Elachi, C.; Stofan, E.; Paganelli, F.; Wood, C.; Kirk, R.; Lorenz, R.; Fortes, A. D.; Lunine, J.

    2005-01-01

    The Cassini Titan Radar Mapper obtained Synthetic Aperture radar images of about 1.1% of Titan's surface during the spacecraft s first targeted fly-by on October 26, 2004 (referred to as the Ta fly-by). These images revealed that Titan is very complex geologically. Features identified include a possible volcanic dome or shield, craters that appear to be of volcanic origin, and extensive flows. We will discuss these features and others that will likely be revealed during Cassini s T3 Titan fly-by of February 15, 2005, during which a swath covering comparable amount of the surface will be obtained. Additional information is included in the original extended abstract.

  6. Genetic characterization of the unique short segment of phocid herpesvirus type 1 reveals close relationships among alphaherpesviruses of hosts of the order Carnivora.

    PubMed

    Martina, B E E; Harder, T C; Osterhaus, A D M E

    2003-06-01

    To further characterize phocid herpesvirus type 1 (PhHV-1) at the molecular level, a cluster of genes comprising the complete unique short (Us) region of PhHV-1 has been cloned and sequenced. Within this region, ORFs were detected that code for the equivalent of the Us 2- protein of herpes simplex virus (HSV), a putative protein kinase, and for the glycoprotein equivalents gG, gD, gI and gE. In addition, two small ORFs downstream of gE, homologous to the Us 8.5 and Us 9 proteins of HSV were identified. Comparative analysis of the ORF encoding the gD equivalent of PhHV-1 identified the corresponding proteins of the alphaherpesviruses canine herpesvirus and, to lesser degree, feline herpesvirus as the closest relatives. PMID:12771410

  7. Alluvial Fans on Titan Reveal Atmosphere and Surface Interactions and Material Transport

    NASA Astrophysics Data System (ADS)

    Radebaugh, J.; Ventra, D.; Lorenz, R. D.; Farr, T. G.; Kirk, R. L.; Hayes, A.; Malaska, M. J.; Birch, S.; Liu, Z. Y. C.; Lunine, J. I.; Barnes, J. W.; Le Gall, A. A.; Lopes, R. M. C.; Stofan, E. R.; Wall, S. D.; Paillou, P.

    2015-12-01

    Alluvial fans, important depositional systems that record how sediment is stored and moved on planetary surfaces, are found on the surface of Titan, a body of significantly different materials and process rates than Earth. As seen by Cassini's Synthetic Aperture Radar (SAR) images at 350 m resolution, fans on Titan are found globally and are variable in size, shape and relationship to adjacent landforms. Their morphologies and SAR characteristics, which reveal roughness, textural patterns and other material properties, show similarities with fans in Death Valley seen by SAR and indicate there are regions of high relative relief locally, in the Ganesa, Xanadu and equatorial mountain belt regions. The Leilah Fluctus fans near Ganesa are ~30 km x 15 km, similar to the largest Death Valley fans, and revealing mountainous topography adjacent to plains. Others have gentle slopes over hundreds of kilometers, as in the high southern latitude lakes regions or the Mezzoramia southern midlatitudes, where a fan system is 200 km x 150 km, similar to the Qarn Alam fan emerging into the Rub al Khali in Oman. Additionally, there is evidence for a range of particle sizes, from relatively coarse (~2 cm or more) to fine, revealing long-term duration and variability in erosion by methane rainfall and transport. Some features have morphologies consistent with proximality to high-relief source areas and highly ephemeral runoff, while others appear to draw larger catchment areas and are perhaps characterized by more prolonged episodes of flow. The presence of many fans indicates the longevity of rainfall and erosion in Titan's surface processes and reveals that sediment transport and the precipitation that drives it are strongly episodic. Alluvial fans join rivers, lakes, eroded mountains, sand dunes and dissolution features in the list of surface morphologies derived from atmospheric and fluvial processes similar to those on Earth, strengthening comparisons between the two planetary

  8. Unique Surface Modification of Silica Nanoparticles with Polyethylenimine (PEI) for siRNA Delivery Using Cerium Cation Coordination Chemistry.

    PubMed

    Kapilov-Buchman, Yekaterina; Lellouche, Emmanuel; Michaeli, Shulamit; Lellouche, Jean-Paul

    2015-05-20

    The discovery of RNA interference (RNAi) as a naturally occurring mechanism for gene knockdown has attracted considerable attention toward the use of small interfering RNAs (siRNAs) for therapeutic purposes. The main obstacles of harnessing siRNAs as drugs are their inefficient delivery to cells and off-target effect making clinical applications very challenging. The positively charged, branched 25 kDa polyethylenimine (b-PEI) polymer is widely regarded as one of the most efficient nonviral commercially available transfection agents. However, it has also been shown that 25 kDa b-PEI is highly cytotoxic and can readily lead to cell death. In this specific context, this study presents the preparation and characterization of innovative 25 kDa b-PEI-decorated polycationic silica nanoparticles (SiO2 NPs) for cellular siRNA delivery and subsequent gene silencing. A new method of b-PEI attachment onto the SiO2 NP surface has been developed that makes use of cerium(III) cations (Ce(3+)), a lanthanide group element, as an effective noncovalent inorganic linker between both polyNH2-SiO2 nanoparticle (SPA NPs) surface and polycationic 25 kDa b-PEI polymer. Two resulting novel SPA-Ce-PEI NPs consist of similar amounts of b-PEI, while possessing different amounts of Ce(3+). Various analytical techniques (TEM, DLS, ζ potential, ICP-AES, and TGA) have been used to deeply characterize NPs physicochemical qualities. The observed results of Ce(3+)-dependent gene silencing and cytotoxic activities led us to conclusions about the role of Ce(3+)-N bonding during the chemical attachment of the 25 kDa b-PEI shell onto the NP surface. PMID:25830668

  9. Crystal structure analysis reveals Pseudomonas PilY1 as an essential calcium-dependent regulator of bacterial surface motility

    SciTech Connect

    Orans, Jillian; Johnson, Michael D.L.; Coggan, Kimberly A.; Sperlazza, Justin R.; Heiniger, Ryan W.; Wolfgang, Matthew C.; Redinbo, Matthew R.

    2010-09-21

    Several bacterial pathogens require the 'twitching' motility produced by filamentous type IV pili (T4P) to establish and maintain human infections. Two cytoplasmic ATPases function as an oscillatory motor that powers twitching motility via cycles of pilus extension and retraction. The regulation of this motor, however, has remained a mystery. We present the 2.1 {angstrom} resolution crystal structure of the Pseudomonas aeruginosa pilus-biogenesis factor PilY1, and identify a single site on this protein required for bacterial translocation. The structure reveals a modified {beta}-propeller fold and a distinct EF-hand-like calcium-binding site conserved in pathogens with retractile T4P. We show that preventing calcium binding by PilY1 using either an exogenous calcium chelator or mutation of a single residue disrupts Pseudomonas twitching motility by eliminating surface pili. In contrast, placing a lysine in this site to mimic the charge of a bound calcium interferes with motility in the opposite manner - by producing an abundance of nonfunctional surface pili. Our data indicate that calcium binding and release by the unique loop identified in the PilY1 crystal structure controls the opposing forces of pilus extension and retraction. Thus, PilY1 is an essential, calcium-dependent regulator of bacterial twitching motility.

  10. Crystal structure analysis reveals Pseudomonas PilY1 as an essential calcium-dependent regulator of bacterial surface motility.

    PubMed

    Orans, Jillian; Johnson, Michael D L; Coggan, Kimberly A; Sperlazza, Justin R; Heiniger, Ryan W; Wolfgang, Matthew C; Redinbo, Matthew R

    2010-01-19

    Several bacterial pathogens require the "twitching" motility produced by filamentous type IV pili (T4P) to establish and maintain human infections. Two cytoplasmic ATPases function as an oscillatory motor that powers twitching motility via cycles of pilus extension and retraction. The regulation of this motor, however, has remained a mystery. We present the 2.1 A resolution crystal structure of the Pseudomonas aeruginosa pilus-biogenesis factor PilY1, and identify a single site on this protein required for bacterial translocation. The structure reveals a modified beta-propeller fold and a distinct EF-hand-like calcium-binding site conserved in pathogens with retractile T4P. We show that preventing calcium binding by PilY1 using either an exogenous calcium chelator or mutation of a single residue disrupts Pseudomonas twitching motility by eliminating surface pili. In contrast, placing a lysine in this site to mimic the charge of a bound calcium interferes with motility in the opposite manner--by producing an abundance of nonfunctional surface pili. Our data indicate that calcium binding and release by the unique loop identified in the PilY1 crystal structure controls the opposing forces of pilus extension and retraction. Thus, PilY1 is an essential, calcium-dependent regulator of bacterial twitching motility. PMID:20080557

  11. Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces.

    PubMed

    Durso, Lisa M; Harhay, Gregory P; Smith, Timothy P L; Bono, James L; DeSantis, Todd Z; Clawson, Michael L

    2011-05-01

    The surface of beef cattle feedlot pens is commonly conceptualized as being packed uncomposted manure. Despite the important role that the feedlot pen may play in the transmission of veterinary and zoonotic pathogens, the bacterial ecology of feedlot surface material is not well understood. Our present study characterized the bacterial communities of the beef cattle feedlot pen surface material using 3647 full-length 16S rDNA sequences, and we compared the community composition of feedlot pens to the fecal source material. The feedlot surface composite was represented by members of the phylum Actinobacteria (42%), followed by Firmicutes (24%), Bacteroidetes (24%), and Proteobacteria (9%). The feedlot pen surface material bacterial communities were clearly distinct from those of the feces from animals in the same pen. Comparisons with previously published results of feces from the animals in the same pen reveal that, of 139 genera identified, only 25 were present in both habitats. These results indicate that, microbiologically, the feedlot pen surface material is separate and distinct from the fecal source material, suggesting that bacteria that originate in cattle feces face different selection pressures and survival challenges during their tenure in the feedlot pen, as compared to their residence in the gastrointestinal tract. PMID:21214381

  12. Revealing the Reconstructed Surface of Li[Mn2]O4.

    PubMed

    Amos, Charles D; Roldan, Manuel A; Varela, Maria; Goodenough, John B; Ferreira, Paulo J

    2016-05-11

    The spinel Li[Mn2]O4 is a candidate cathode for a Li-ion battery, but its capacity fades over a charge/discharge cycle of Li1-x[Mn2]O4 (0 < x < 1) that is associated with a loss of Mn to the organic-liquid electrolyte. It is known that the disproportionation reaction 2Mn(3+) = Mn(2+) + Mn(4+) occurs at the surface of a Mn spinel, and it is important to understand the atomic structure and composition of the surface of Li[Mn2]O4 in order to understand how Mn loss occurs. We report a study of the surface reconstruction of Li[Mn2]O4 by aberration-corrected scanning transmission electron microscopy. The atomic structure coupled with Mn-valence and the distribution of the atomic ratio of oxygen obtained by electron energy loss spectroscopy reveals a thin, stable surface layer of Mn3O4, a subsurface region of Li1+x[Mn2]O4 with retention of bulk Li[Mn2]O4. This observation is compatible with the disproportionation reaction coupled with oxygen deficiency and a displacement of surface Li(+) from the Mn3O4 surface phase. These results provide a critical step toward understanding how Mn is lost from Li[Mn2]O4, once inside a battery. PMID:27022834

  13. Complete genome and gene expression analyses of Asaia bogorensis reveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen

    PubMed Central

    Kawai, Mikihiko; Higashiura, Norie; Hayasaki, Kimie; Okamoto, Naruhei; Takami, Akiko; Hirakawa, Hideki; Matsushita, Kazunobu; Azuma, Yoshinao

    2015-01-01

    Asaia bogorensis, a member of acetic acid bacteria (AAB), is an aerobic bacterium isolated from flowers and fruits, as well as an opportunistic pathogen that causes human peritonitis and bacteraemia. Here, we determined the complete genomic sequence of the As. bogorensis type strain NBRC 16594, and conducted comparative analyses of gene expression under different conditions of co-culture with mammalian cells and standard AAB culture. The genome of As. bogorensis contained 2,758 protein-coding genes within a circular chromosome of 3,198,265 bp. There were two complete operons encoding cytochrome bo3-type ubiquinol terminal oxidases: cyoABCD-1 and cyoABCD-2. The cyoABCD-1 operon was phylogenetically common to AAB genomes, whereas the cyoABCD-2 operon belonged to a lineage distinctive from the cyoABCD-1 operon. Interestingly, cyoABCD-1 was less expressed under co-culture conditions than under the AAB culture conditions, whereas the converse was true for cyoABCD-2. Asaia bogorensis shared pathogenesis-related genes with another pathogenic AAB, Granulibacter bethesdensis, including a gene coding pathogen-specific large bacterial adhesin and additional genes for the inhibition of oxidation and antibiotic resistance. Expression alteration of the respiratory chain and unique hypothetical genes may be key traits that enable the bacterium to survive under the co-culture conditions. PMID:26358298

  14. Novel In Situ Collection of Tumor Interstitial Fluid from a Head and Neck Squamous Carcinoma Reveals a Unique Proteome with Diagnostic Potential

    PubMed Central

    Stone, Matthew D.; Odland, Rick M.; McGowan, Thomas; Onsongo, Getiria; Tang, Chaunning; Rhodus, Nelson L.; Jagtap, Pratik; Bandhakavi, Sricharan

    2010-01-01

    Introduction Tumors lack normal drainage of secreted fluids and consequently build up tumor interstitial fluid (TIF). Unlike other bodily fluids, TIF likely contains a high proportion of tumor-specific proteins with potential as biomarkers. Methods Here, we evaluated a novel technique using a unique ultrafiltration catheter for in situ collection of TIF and used it to generate the first catalog of TIF proteins from a head and neck squamous cell carcinoma (HNSCC). To maximize proteomic coverage, TIF was immunodepleted for high abundance proteins and digested with trypsin, and peptides were fractionated in three dimensions prior to mass spectrometry. Results We identified 525 proteins with high confidence. The HNSCC TIF proteome was distinct compared to proteomes of other bodily fluids. It contained a relatively high proportion of proteins annotated by Gene Ontology as “extracellular” compared to other secreted fluid and cellular proteomes, indicating minimal cell lysis from our in situ collection technique. Several proteins identified are putative biomarkers of HNSCC, supporting our catalog’s value as a source of potential biomarkers. Conclusions In all, we demonstrate a reliable new technique for in situ TIF collection and provide the first HNSCC TIF protein catalog with value as a guide for others seeking to develop tumor biomarkers. Electronic supplementary material The online version of this article (doi:10.1007/s12014-010-9050-3) contains supplementary material, which is available to authorized users. PMID:20930922

  15. Merozoite Surface Antigen 2 Proteins of Babesia bovis Vaccine Breakthrough Isolates Contain a Unique Hypervariable Region Composed of Degenerate Repeats

    PubMed Central

    Berens, Shawn J.; Brayton, Kelly A.; Molloy, John B.; Bock, Russell E.; Lew, Ala E.; McElwain, Terry F.

    2005-01-01

    The merozoite surface antigen 2 (MSA-2) proteins of Babesia bovis are members of the variable merozoite surface antigen (VMSA) family that have been implicated in erythrocyte invasion and are important targets for antibody-mediated blocking of invasion. Extensive sequence variation in another VMSA member, MSA-1, has been shown in all vaccine breakthrough isolates. To test the hypothesis that the msa-2 genes of vaccine breakthrough isolates would also encode a diverse set of proteins, the complete msa-2 locus was characterized from 12 Australian B. bovis strains and isolates, including two vaccine strains and eight vaccine breakthrough isolates, and compared to the loci in previously and newly characterized American strains. In contrast to American strains, the msa-2 loci of all Australian strains and isolates examined contain, in addition to msa-2c, only a solitary gene (designated msa-2a/b) closely related to American strain msa-2a and msa-2b. Nevertheless, the proteins encoded by these genes are quite diverse both between and within geographic regions and harbor evidence of genetic exchange among other VMSA family members, including msa-1. Moreover, all but one of the Australian breakthrough isolate MSA-2a/b proteins is markedly different from the vaccine strain from which immune escape occurred, consistent with their role in strain-specific protective immunity. The densest distribution of polymorphisms occurs in a hypervariable region (HVR) within the carboxy third of the molecule that is highly proline rich. Variation in length and content of the HVR is primarily attributable to differences in the order and number of degenerate nucleotide repeats encoding three motifs of unknown function. PMID:16239512

  16. In Situ X-Ray Probing Reveals Fingerprints of Surface Platinum Oxide

    SciTech Connect

    Friebel, Daniel

    2011-08-24

    In situ x-ray absorption spectroscopy (XAS) at the Pt L{sub 3} edge is a useful probe for Pt-O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard x-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF8 code and complementary extended x-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at high electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.

  17. A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR.

    PubMed

    Sgourakis, Nikolaos G; May, Nathan A; Boyd, Lisa F; Ying, Jinfa; Bax, Ad; Margulies, David H

    2015-11-27

    As part of its strategy to evade detection by the host immune system, murine cytomegalovirus (MCMV) encodes three proteins that modulate cell surface expression of major histocompatibility complex class I (MHC-I) molecules: the MHC-I homolog m152/gp40 as well as the m02-m16 family members m04/gp34 and m06/gp48. Previous studies of the m04 protein revealed a divergent Ig-like fold that is unique to immunoevasins of the m02-m16 family. Here, we engineer and characterize recombinant m06 and investigate its interactions with full-length and truncated forms of the MHC-I molecule H2-L(d) by several techniques. Furthermore, we employ solution NMR to map the interaction footprint of the m06 protein on MHC-I, taking advantage of a truncated H2-L(d), "mini-H2-L(d)," consisting of only the α1α2 platform domain. Mini-H2-L(d) refolded in vitro with a high affinity peptide yields a molecule that shows outstanding NMR spectral features, permitting complete backbone assignments. These NMR-based studies reveal that m06 binds tightly to a discrete site located under the peptide-binding platform that partially overlaps with the β2-microglobulin interface on the MHC-I heavy chain, consistent with in vitro binding experiments showing significantly reduced complex formation between m06 and β2-microglobulin-associated MHC-I. Moreover, we carry out NMR relaxation experiments to characterize the picosecond-nanosecond dynamics of the free mini-H2-L(d) MHC-I molecule, revealing that the site of interaction is highly ordered. This study provides insight into the mechanism of the interaction of m06 with MHC-I, suggesting a structural manipulation of the target MHC-I molecule at an early stage of the peptide-loading pathway. PMID:26463211

  18. Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori.

    PubMed

    Suetsugu, Yoshitaka; Futahashi, Ryo; Kanamori, Hiroyuki; Kadono-Okuda, Keiko; Sasanuma, Shun-ichi; Narukawa, Junko; Ajimura, Masahiro; Jouraku, Akiya; Namiki, Nobukazu; Shimomura, Michihiko; Sezutsu, Hideki; Osanai-Futahashi, Mizuko; Suzuki, Masataka G; Daimon, Takaaki; Shinoda, Tetsuro; Taniai, Kiyoko; Asaoka, Kiyoshi; Niwa, Ryusuke; Kawaoka, Shinpei; Katsuma, Susumu; Tamura, Toshiki; Noda, Hiroaki; Kasahara, Masahiro; Sugano, Sumio; Suzuki, Yutaka; Fujiwara, Haruhiko; Kataoka, Hiroshi; Arunkumar, Kallare P; Tomar, Archana; Nagaraju, Javaregowda; Goldsmith, Marian R; Feng, Qili; Xia, Qingyou; Yamamoto, Kimiko; Shimada, Toru; Mita, Kazuei

    2013-09-01

    The establishment of a complete genomic sequence of silkworm, the model species of Lepidoptera, laid a foundation for its functional genomics. A more complete annotation of the genome will benefit functional and comparative studies and accelerate extensive industrial applications for this insect. To realize these goals, we embarked upon a large-scale full-length cDNA collection from 21 full-length cDNA libraries derived from 14 tissues of the domesticated silkworm and performed full sequencing by primer walking for 11,104 full-length cDNAs. The large average intron size was 1904 bp, resulting from a high accumulation of transposons. Using gene models predicted by GLEAN and published mRNAs, we identified 16,823 gene loci on the silkworm genome assembly. Orthology analysis of 153 species, including 11 insects, revealed that among three Lepidoptera including Monarch and Heliconius butterflies, the 403 largest silkworm-specific genes were composed mainly of protective immunity, hormone-related, and characteristic structural proteins. Analysis of testis-/ovary-specific genes revealed distinctive features of sexual dimorphism, including depletion of ovary-specific genes on the Z chromosome in contrast to an enrichment of testis-specific genes. More than 40% of genes expressed in specific tissues mapped in tissue-specific chromosomal clusters. The newly obtained FL-cDNA sequences enabled us to annotate the genome of this lepidopteran model insect more accurately, enhancing genomic and functional studies of Lepidoptera and comparative analyses with other insect orders, and yielding new insights into the evolution and organization of lepidopteran-specific genes. PMID:23821615

  19. Large Scale Full-Length cDNA Sequencing Reveals a Unique Genomic Landscape in a Lepidopteran Model Insect, Bombyx mori

    PubMed Central

    Suetsugu, Yoshitaka; Futahashi, Ryo; Kanamori, Hiroyuki; Kadono-Okuda, Keiko; Sasanuma, Shun-ichi; Narukawa, Junko; Ajimura, Masahiro; Jouraku, Akiya; Namiki, Nobukazu; Shimomura, Michihiko; Sezutsu, Hideki; Osanai-Futahashi, Mizuko; Suzuki, Masataka G; Daimon, Takaaki; Shinoda, Tetsuro; Taniai, Kiyoko; Asaoka, Kiyoshi; Niwa, Ryusuke; Kawaoka, Shinpei; Katsuma, Susumu; Tamura, Toshiki; Noda, Hiroaki; Kasahara, Masahiro; Sugano, Sumio; Suzuki, Yutaka; Fujiwara, Haruhiko; Kataoka, Hiroshi; Arunkumar, Kallare P.; Tomar, Archana; Nagaraju, Javaregowda; Goldsmith, Marian R.; Feng, Qili; Xia, Qingyou; Yamamoto, Kimiko; Shimada, Toru; Mita, Kazuei

    2013-01-01

    The establishment of a complete genomic sequence of silkworm, the model species of Lepidoptera, laid a foundation for its functional genomics. A more complete annotation of the genome will benefit functional and comparative studies and accelerate extensive industrial applications for this insect. To realize these goals, we embarked upon a large-scale full-length cDNA collection from 21 full-length cDNA libraries derived from 14 tissues of the domesticated silkworm and performed full sequencing by primer walking for 11,104 full-length cDNAs. The large average intron size was 1904 bp, resulting from a high accumulation of transposons. Using gene models predicted by GLEAN and published mRNAs, we identified 16,823 gene loci on the silkworm genome assembly. Orthology analysis of 153 species, including 11 insects, revealed that among three Lepidoptera including Monarch and Heliconius butterflies, the 403 largest silkworm-specific genes were composed mainly of protective immunity, hormone-related, and characteristic structural proteins. Analysis of testis-/ovary-specific genes revealed distinctive features of sexual dimorphism, including depletion of ovary-specific genes on the Z chromosome in contrast to an enrichment of testis-specific genes. More than 40% of genes expressed in specific tissues mapped in tissue-specific chromosomal clusters. The newly obtained FL-cDNA sequences enabled us to annotate the genome of this lepidopteran model insect more accurately, enhancing genomic and functional studies of Lepidoptera and comparative analyses with other insect orders, and yielding new insights into the evolution and organization of lepidopteran-specific genes. PMID:23821615

  20. An optimized isolation of biotinylated cell surface proteins reveals novel players in cancer metastasis

    PubMed Central

    Karhemo, Piia-Riitta; Ravela, Suvi; Laakso, Marko; Ritamo, Ilja; Tatti, Olga; Mäkinen, Selina; Goodison, Steve; Stenman, Ulf-Håkan; Hölttä, Erkki; Hautaniemi, Sampsa; Valmu, Leena; Lehti, Kaisa; Laakkonen, Pirjo

    2012-01-01

    Details of metastasis, the deadliest aspect of cancer, are unclear. Cell surface proteins play central roles in adhesive contacts between the tumor cell and the stroma during metastasis. We optimized a fast, small-scale isolation of biotinylated cell surface proteins to reveal novel metastasis-associated players froman isogenic pair of human MDA-MB-435 cancer cells with opposite metastatic phenotypes. Isolated proteins were trypsin digested and analyzed using LC–MS/MS followed by quantitation with the Progenesis LC–MS software. Sixteen proteins displayed over twofold expression differences between the metastatic and non-metastatic cells. Interestingly, overexpression of most of them (14/16) in the metastatic cells indicates a gain of novel surface protein profile as compared to the non-metastatic one. All five validated, differentially expressed proteins showed higher expression in the metastatic cells in culture, and four of these were further validated in vivo. Moreover, we analyzed the expression of two of the identified proteins, CD109 and ITGA6 in 3-dimensional cultures of six melanoma cell lines. Both proteins marked the surface of cells derived from melanoma metastasis over cells derived from primary melanoma. These unbiased identification and validation of both known and novel metastasis-associated proteins indicate a reliable approach for the identification of differentially expressed surface proteins. PMID:22813880

  1. Nanoporous PdZr surface alloy as highly active non-platinum electrocatalyst toward oxygen reduction reaction with unique structure stability and methanol-tolerance

    NASA Astrophysics Data System (ADS)

    Duan, Huimei; Xu, Caixia

    2016-06-01

    Nanoporous (NP) PdZr alloy with controllable bimetallic ratio is successfully fabricated by a simple dealloying method. By leaching out the more reactive Al from PdZrAl precursor alloy, NP-PdZr alloy with smaller ligament size was generated, characterized by the nanoscaled interconnected network skeleton and hollow channels extending in all three dimensions. Upon voltammetric scan in acid solution, the dissolution of surface Zr atoms generates the highly active Pd-Zr surface alloy with a nearly pure Pd surface and Pd-Zr alloy core. The NP-Pd80Zr20 surface alloy exhibits markedly enhanced specific and mass activities as well as higher catalytic stability toward oxygen reduction reaction (ORR) compared with NP-Pd and the state-of-the-art Pt/C catalysts. In addition, the NP-Pd80Zr20 surface alloy shows a better selectivity for ORR than methanol in the 0.1 M HClO4 and 0.1 M methanol mixed solution. X-ray photoelectron spectroscopy and density functional theory calculations both demonstrate that the weakened Pd-O bond and improved ORR performances in turn depend on the downshifted d-band center of Pd due to the alloying Pd with Zr (20 at.%). The as-made NP-PdZr alloy holds prospective applications as a cathode electrocatalyst in fuel-cell-related technologies with the advantages of superior overall ORR performances, unique structure stability, and easy preparation.

  2. Nucleotide Sequence of the Envelope Gene of Gardner-Arnstein Feline Leukemia Virus B Reveals Unique Sequence Homologies with a Murine Mink Cell Focus-Forming Virus †

    PubMed Central

    Elder, John H.; Mullins, James I.

    1983-01-01

    The nucleotide sequence of the envelope gene and the adjacent 3′ long terminal repeat (LTR) of Gardner-Arnstein feline leukemia virus of subgroup B (GA-FeLV-B) has been determined. Comparison of the derived amino acid sequence of the gp70-p15E polyprotein to those of several previously reported murine retroviruses revealed striking homologies between GA-FeLV-B gp70 and the gp70 of a Moloney virus-derived mink cell focus-forming virus. These homologies were located within the substituted (presumably xenotropic) portion of the mink cell focus-forming virus envelope gene and comprised amino acid sequences not present in three ecotropic virus gp70s. In addition, areas of insertions and deletions, in general, were the same between GA-FeLV-B and Moloney mink cell focus-forming virus, although the sizes of the insertions and deletions differed. Homologies between GA-FeLV-B and mink cell focus-forming virus gp70s is functionally significant in that they both possess expanded host ranges, a property dictated by gp70. The amino acid sequence of FeLV-B contains 12 Asn-X-Ser/Thr sequences, indicating 12 possible sites of N-linked glycosylation as compared with 7 or 8 for its murine counterparts. Comparison of the 3′ LTR of GA-FeLV-B to AKR and Moloney virus LTRs revealed extensive conservation in several regions including the “CCAAT” and Goldberg-Hogness (TATA) boxes thought to be involved in promotion of transcription and in the repeat region of the LTR. The inverted repeats that flanked the LTR of GA-FeLV-B were identical to the murine inverted repeats, but were one base longer than the latter. The region of U3 corresponding to the approximately 75-nucleotide “enhancer sequence” is present in GA-FeLV-B, but contains deletions relative to AKR and Moloney virus and is not repeated. An interesting pallindrome in the repeat region immediately 3′ to the U3 region was noted in all the LTRs, but was particularly pronounced in GA-FeLV-B. Possible roles for this

  3. 187-gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution.

    PubMed

    Cavalier-Smith, Thomas; Chao, Ema E; Lewis, Rhodri

    2016-06-01

    Monophyly of protozoan phylum Amoebozoa, and subdivision into subphyla Conosa and Lobosa each with different cytoskeletons, are well established. However early diversification of non-ciliate lobose amoebae (Lobosa) is poorly understood. To clarify it we used recently available transcriptomes to construct a 187-gene amoebozoan tree for 30 species, the most comprehensive yet. This robustly places new genus Atrichosa (formerly lumped with Trichosphaerium) within lobosan class Tubulinea, not Discosea as previously supposed. We identified an earliest diverging lobosan clade comprising marine amoebae armoured by porose scaliform cell-envelopes, here made a novel class Cutosea with two pseudopodially distinct new families. Cutosea comprise Sapocribrum, ATCC PRA-29 misidentified as 'Pessonella', plus from other evidence Squamamoeba. We confirm that Acanthamoeba and ATCC 50982 misidentified as Stereomyxa ramosa are closely related. Discosea have a strongly supported major subclade comprising Thecamoebida plus Glycostylida (suborders Dactylopodina, Stygamoebina; Vannellina) phylogenetically distinct from Centramoebida. Stygamoeba is sister to Dactylopodina. Himatismenida are either sister to Centramoebida or deeper branching. Discosea usually appear holophyletic (rarely paraphyletic). Paramoeba transcriptomes include prokinetoplastid Perkinsela-like endosymbiont sequences. Cunea, misidentified as Mayorella, is closer to Paramoeba than Vexillifera within holophyletic Dactylopodina. Taxon-rich site-heterogeneous rDNA trees confirm cutosan distinctiveness, allow improved conosan taxonomy, and reveal previous dictyostelid tree misrooting. PMID:27001604

  4. FadA5 a thiolase from Mycobacterium tuberculosis - a unique steroid-binding pocket reveals the potential for drug development against tuberculosis

    PubMed Central

    Schaefer, Christin M.; Lu, Rui; Nesbitt, Natasha M.; Schiebel, Johannes; Sampson, Nicole S.; Kisker, Caroline

    2014-01-01

    Summary With the exception of HIV, tuberculosis (TB) is the leading cause of mortality among infectious diseases. The urgent need to develop new anti-tubercular drugs is apparent due to the increasing number of drug resistant Mycobacterium tuberculosis (Mtb) strains. Proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against TB. FadA5, a thiolase from Mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation under release of critical metabolites and was shown to be of importance during the chronic stage of TB infections. To gain structural and mechanistic insight on FadA5 we characterized the enzyme in different stages of the cleavage reaction and with a steroid bound to the binding pocket. Structural comparisons to human thiolases revealed that it should be possible to target FadA5 specifically and the steroid-bound structure provides a solid basis for the development of inhibitors against FadA5. PMID:25482540

  5. Complexity in Climatic Controls on Plant Species Distribution: Satellite Data Reveal Unique Climate for Giant Sequoia in the California Sierra Nevada

    NASA Astrophysics Data System (ADS)

    Waller, Eric Kindseth

    A better understanding of the environmental controls on current plant species distribution is essential if the impacts of such diverse challenges as invasive species, changing fire regimes, and global climate change are to be predicted and important diversity conserved. Climate, soil, hydrology, various biotic factors fire, history, and chance can all play a role, but disentangling these factors is a daunting task. Increasingly sophisticated statistical models relying on existing distributions and mapped climatic variables, among others, have been developed to try to answer these questions. Any failure to explain pattern with existing mapped climatic variables is often taken as a referendum on climate as a whole, rather than on the limitations of the particular maps or models. Every location has a unique and constantly changing climate so that any distribution could be explained by some aspect of climate. Chapter 1 of this dissertation reviews some of the major flaws in species distribution modeling and addresses concerns that climate may therefore not be predictive of, or even relevant to, species distributions. Despite problems with climate-based models, climate and climate-derived variables still have substantial merit for explaining species distribution patterns. Additional generation of relevant climate variables and improvements in other climate and climate-derived variables are still needed to demonstrate this more effectively. Satellite data have a long history of being used for vegetation mapping and even species distribution mapping. They have great potential for being used for additional climatic information, and for improved mapping of other climate and climate-derived variables. Improving the characterization of cloud cover frequency with satellite data is one way in which the mapping of important climate and climate-derived variables can be improved. An important input to water balance models, solar radiation maps could be vastly improved with a

  6. Genome Sequencing Reveals Unique Mutations in Characteristic Metabolic Pathways and the Transfer of Virulence Genes between V. mimicus and V. cholerae

    PubMed Central

    Zhou, Yanyan; Zhang, Qiuxiang; Zhang, Fanfei; Du, Pengcheng; Wang, Shujing; Chen, Chen; Kan, Biao

    2011-01-01

    Vibrio mimicus, the species most similar to V. cholerae, is a microbe present in the natural environmental and sometimes causes diarrhea and internal infections in humans. It shows similar phenotypes to V. cholerae but differs in some biochemical characteristics. The molecular mechanisms underlying the differences in biochemical metabolism between V. mimicus and V. cholerae are currently unclear. Several V. mimicus isolates have been found that carry cholera toxin genes (ctxAB) and cause cholera-like diarrhea in humans. Here, the genome of the V. mimicus isolate SX-4, which carries an intact CTX element, was sequenced and annotated. Analysis of its genome, together with those of other Vibrio species, revealed extensive differences within the Vibrionaceae. Common mutations in gene clusters involved in three biochemical metabolism pathways that are used for discrimination between V. mimicus and V. cholerae were found in V. mimicus strains. We also constructed detailed genomic structures and evolution maps for the general types of genomic drift associated with pathogenic characters in polysaccharides, CTX elements and toxin co-regulated pilus (TCP) gene clusters. Overall, the whole-genome sequencing of the V. mimicus strain carrying the cholera toxin gene provides detailed information for understanding genomic differences among Vibrio spp. V. mimicus has a large number of diverse gene and nucleotide differences from its nearest neighbor, V. cholerae. The observed mutations in the characteristic metabolism pathways may indicate different adaptations to different niches for these species and may be caused by ancient events in evolution before the divergence of V. cholerae and V. mimicus. Horizontal transfers of virulence-related genes from an uncommon clone of V. cholerae, rather than the seventh pandemic strains, have generated the pathogenic V. mimicus strain carrying cholera toxin genes. PMID:21731695

  7. The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader.

    PubMed

    Youssef, Noha H; Couger, M B; Struchtemeyer, Christopher G; Liggenstoffer, Audra S; Prade, Rolf A; Najar, Fares Z; Atiyeh, Hasan K; Wilkins, Mark R; Elshahed, Mostafa S

    2013-08-01

    Anaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production. PMID:23709508

  8. A selective screening platform reveals unique global expression patterns of microRNAs in a cohort of human soft-tissue sarcomas.

    PubMed

    Yu, Peter Y; Balkhi, Mumtaz Y; Ladner, Katherine J; Alder, Hansjuerg; Yu, Lianbo; Mo, Xiaokui; Kraybill, William G; Guttridge, Denis C; Hans Iwenofu, O

    2016-04-01

    Sarcomas are malignant heterogenous tumors of mesenchymal derivation. Emerging data suggest that miRNA might have a causal role in sarcomagenesis. Herein, we used a selective miRNA screening platform to study the comparative global miRNA expression signatures in a cohort of human sarcomas with the caveat that comparisons between tumor and non-tumor cells were performed from the same patients using formalin-fixed paraffin-embedded tissue. Five histologic types were examined that included: myxoid liposarcoma, well-differentiated liposarcoma, dedifferentiated liposarcoma, pleomorphic rhabdomyosarcoma, and synovial sarcoma. In addition, soft-tissue lipomas and normal fat were included as a separate set of controls for the lipogenic tumors. Clustering analysis showed a distinct global difference in expression patterns between the normal and sarcoma tissues. Expression signatures in an unsupervised hierarchical clustering analysis revealed tight clustering in synovial and myxoid liposarcomas, and the least clustering was observed in the pleomorphic rhabdomyosarcoma subtype. MiR-145 showed underexpression in pleomorphic rhabdomyosarcoma, well-differentiated liposarcoma, and synovial sarcoma. Unexpectedly, we found that a set of muscle-specific microRNAs (miRNAs; myomiRs): miR-133, miR-1, and miR-206 was significantly underexpressed in well-differentiated liposarcoma and synovial sarcoma, suggesting that they may function as tumor suppressors as described in muscle-relevant rhabdomyosarcomas. In addition, a tight linear progression of miRNA expression was identified from normal fat to dedifferentiated liposarcoma. These results suggest that miRNA expression profiles could elucidate classes of miRNAs that may elicit tumor-relevant activities in specific sarcoma subtypes. PMID:26878133

  9. Characterization of the Vaginal Microbiota of Ewes and Cows Reveals a Unique Microbiota with Low Levels of Lactobacilli and Near-Neutral pH

    PubMed Central

    Swartz, Jeffrey D.; Lachman, Medora; Westveer, Kelsey; O’Neill, Thomas; Geary, Thomas; Kott, Rodney W.; Berardinelli, James G.; Hatfield, Patrick G.; Thomson, Jennifer M.; Roberts, Andy; Yeoman, Carl J.

    2014-01-01

    Although a number of common reproductive disorders in livestock involve bacterial infection, very little is known about their normal vaginal microbiota. Therefore, we sought to determine the species composition of sheep and cattle vaginal microbiota. Twenty Rambouillet ewes and twenty crossbred cows varying in age and reproductive status were sampled by ectocervicovaginal lavage. We amplified and sequenced the V3–V4 region of the 16S ribosomal RNA (rRNA) contents yielding a total of 907,667 high-quality reads. Good’s Coverage estimates indicated that we obtained data on 98 ± 0.01% of the total microbial genera present in each sample. Cow and ewe vaginal microbiota displayed few differences. Cow microbiota exhibited greater (P ≤ 0.05) α-diversity compared to the ewe microbiota. Both livestock species differed (P ≤ 0.05) from all previously reported vaginal communities. While bacteria were numerically dominant, Archaea were detected in 95% of cow and ewe samples, mainly of the order Desulfurococcales. Both ewes and cows were predominately colonized by the bacterial phyla Bacteroidetes, Fusobacteria, and Proteobacteria. The most abundant genera were Aggregatibacter spp., and Streptobacillus spp. Lactobacillus spp. were detected in 80% of ewe and 90% of cow samples, but only at very low abundances. Bacteria previously described from culture-based studies as common to the cow and ewe vaginal tract, except for Escherichia, were variably present, and only in low abundance. Ewe and cow pH differed (P ≤ 0.05), with means (±SD) of 6.7 ± 0.38 and 7.3 ± 0.63, respectively. In conclusion, 16S rRNA sequencing of cow and ewe vaginal ectocervicovaginal lavages showed that cow and ewe vaginal microbiota differ from culture-led results, revealing a microbiota distinct from previously described vaginal ecosystems. PMID:26664918

  10. The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

    PubMed Central

    Youssef, Noha H.; Couger, M. B.; Struchtemeyer, Christopher G.; Liggenstoffer, Audra S.; Prade, Rolf A.; Najar, Fares Z.; Atiyeh, Hasan K.; Wilkins, Mark R.

    2013-01-01

    Anaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production. PMID:23709508

  11. Lectin staining and flow cytometry reveals female-induced sperm acrosome reaction and surface carbohydrate reorganization

    PubMed Central

    Kekäläinen, Jukka; Larma, Irma; Linden, Matthew; Evans, Jonathan P.

    2015-01-01

    All cells are covered by glycans, an individually unique layer of oligo- and polysaccharides that are critical moderators of self-recognition and other cellular-level interactions (e.g. fertilization). The functional similarity between these processes suggests that gamete surface glycans may also have an important, but currently overlooked, role in sexual selection. Here we develop a user-friendly methodological approach designed to facilitate future tests of this possibility. Our proposed method is based on flow cytometric quantification of female-induced sperm acrosome reaction and sperm surface glycan modifications in the Mediterranean mussel Mytilus galloprovincialis. In this species, as with many other taxa, eggs release water-soluble factors that attract conspecific sperm (chemoattraction) and promote potentially measurable changes in sperm behavior and physiology. We demonstrate that flow cytometry is able to identify sperm from other seawater particles as well as accurately measure both acrosome reaction and structural modifications in sperm glycans. This methodological approach can increase our understanding of chemically-moderated gamete-level interactions and individual-specific gamete recognition in Mytilus sp. and other taxa with similar, easily identifiable acrosome structure. Our approach is also likely to be applicable to several other species, since carbohydrate-mediated cellular-level interactions between gametes are universal among externally and internally fertilizing species. PMID:26470849

  12. Structure of the Legionella Virulence Factor, SidC Reveals a Unique PI(4)P-Specific Binding Domain Essential for Its Targeting to the Bacterial Phagosome

    PubMed Central

    Luo, Xi; Wasilko, David J.; Liu, Yao; Sun, Jiayi; Wu, Xiaochun; Luo, Zhao-Qing; Mao, Yuxin

    2015-01-01

    The opportunistic intracellular pathogen Legionella pneumophila is the causative agent of Legionnaires’ disease. L. pneumophila delivers nearly 300 effector proteins into host cells for the establishment of a replication-permissive compartment known as the Legionella-containing vacuole (LCV). SidC and its paralog SdcA are two effectors that have been shown to anchor on the LCV via binding to phosphatidylinositol-4-phosphate [PI(4)P] to facilitate the recruitment of ER proteins to the LCV. We recently reported that the N-terminal SNL (SidC N-terminal E3 Ligase) domain of SidC is a ubiquitin E3 ligase, and its activity is required for the recruitment of ER proteins to the LCV. Here we report the crystal structure of SidC (1-871). The structure reveals that SidC contains four domains that are packed into an arch-like shape. The P4C domain (PI(4)P binding of SidC) comprises a four α-helix bundle and covers the ubiquitin ligase catalytic site of the SNL domain. Strikingly, a pocket with characteristic positive electrostatic potentials is formed at one end of this bundle. Liposome binding assays of the P4C domain further identified the determinants of phosphoinositide recognition and membrane interaction. Interestingly, we also found that binding with PI(4)P stimulates the E3 ligase activity, presumably due to a conformational switch induced by PI(4)P from a closed form to an open active form. Mutations of key residues involved in PI(4)P binding significantly reduced the association of SidC with the LCV and abolished its activity in the recruitment of ER proteins and ubiquitin signals, highlighting that PI(4)P-mediated targeting of SidC is critical to its function in the remodeling of the bacterial phagosome membrane. Finally, a GFP-fusion with the P4C domain was demonstrated to be specifically localized to PI(4)P-enriched compartments in mammalian cells. This domain shows the potential to be developed into a sensitive and accurate PI(4)P probe in living cells. PMID

  13. Unique Mechanisms of Sheng Yu Decoction (聖愈湯 Shèng Yù Tang) on Ischemic Stroke Mice Revealed by an Integrated Neurofunctional and Transcriptome Analysis

    PubMed Central

    Hou, Yu-Chang; Lu, Chung-Kuang; Wang, Yea-Hwey; Chern, Chang-Ming; Liou, Kuo-Tong; Wang, Hsei-Wei; Shen, Yuh-Chiang

    2013-01-01

    Sheng Yu Decoction (聖愈湯 Shèng Yù Tang; SYD) is a popular traditional Chinese medicine (TCM) remedy used in treating cardiovascular and brain-related dysfunction clinically; yet, its neuroprotective mechanisms are still unclear. Here, mice were subjected to an acute ischemic stroke to examine the efficacy and mechanisms of action of SYD by an integrated neurofunctional and transcriptome analysis. More than 80% of the mice died within 2 days after ischemic stroke with vehicle treatment. Treatments with SYD (1.0 g/kg, twice daily, orally or p.o.) and recombinant thrombolytic tissue plasminogen activator (rt-PA; 10 mg/kg, once daily, intravenously or i.v.) both significantly extended the lifespan as compared to that of the vehicle-treated stroke group. SYD successfully restored brain function, ameliorated cerebral infarction and oxidative stress, and significantly improved neurological deficits in mice with stroke. Molecular impact of SYD by a genome-wide transcriptome analysis using brains from stroke mice showed a total of 162 out of 2081 ischemia-induced probe sets were significantly influenced by SYD. Mining the functional modules and genetic networks of these 162 genes revealed a significant upregulation of neuroprotective genes in Wnt receptor signaling pathway (3 genes) and regulation of cell communication (7 genes) and downregulation of destructive genes in response to stress (13 genes) and in the induction of inflammation (5 genes), cytokine production (4 genes), angiogenesis (3 genes), vasculature (6 genes) and blood vessel (5 genes) development, wound healing (7 genes), defense response (7 genes), chemotaxis (4 genes), immune response (7 genes), antigen processing and presenting (3 genes), and leukocyte-mediated cytotoxicity (2 genes) by SYD. Our results suggest that SYD could protect mice against ischemic stroke primarily through significantly downregulating the damaging genes involved in stress, inflammation, angiogenesis, blood vessel formation

  14. Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis

    PubMed Central

    2010-01-01

    Background Surface contamination of smear cheese by Listeria spp. is of major concern for the industry. Complex smear ecosystems have been shown to harbor antilisterial potential but the microorganisms and mechanisms involved in the inhibition mostly remain unclear, and are likely related to complex interactions than to production of single antimicrobial compounds. Bacterial biodiversity and population dynamics of complex smear ecosystems exhibiting antilisterial properties in situ were investigated by Temporal temperature gradient gel electrophoresis (TTGE), a culture independent technique, for two microbial consortia isolated from commercial Raclette type cheeses inoculated with defined commercial ripening cultures (F) or produced with an old-young smearing process (M). Results TTGE revealed nine bacterial species common to both F and M consortia, but consortium F exhibited a higher diversity than consortium M, with thirteen and ten species, respectively. Population dynamics were studied after application of the consortia on fresh-produced Raclette cheeses. TTGE analyses revealed a similar sequential development of the nine species common to both consortia. Beside common cheese surface bacteria (Staphylococcus equorum, Corynebacterium spp., Brevibacterium linens, Microbacterium gubbeenense, Agrococcus casei), the two consortia contained marine lactic acid bacteria (Alkalibacterium kapii, Marinilactibacillus psychrotolerans) that developed early in ripening (day 14 to 20), shortly after the growth of staphylococci (day 7). A decrease of Listeria counts was observed on cheese surface inoculated at day 7 with 0.1-1 × 102 CFU cm-2, when cheeses were smeared with consortium F or M. Listeria counts went below the detection limit of the method between day 14 and 28 and no subsequent regrowth was detected over 60 to 80 ripening days. In contrast, Listeria grew to high counts (105 CFU cm-2) on cheeses smeared with a defined surface culture. Conclusions This work reports

  15. Global transcriptional analysis reveals surface remodeling of Anaplasma marginale in the tick vector

    PubMed Central

    2014-01-01

    Background Pathogens dependent upon vectors for transmission to new hosts undergo environment specific changes in gene transcription dependent on whether they are replicating in the vector or the mammalian host. Differential gene transcription, especially of potential vaccine candidates, is of interest in Anaplasma marginale, the tick-borne causative agent of bovine anaplasmosis. Methods RNA-seq technology allowed a comprehensive analysis of the transcriptional status of A. marginale genes in two conditions: bovine host blood and tick derived cell culture, a model for the tick vector. Quantitative PCR was used to assess transcription of a set of genes in A. marginale infected tick midguts and salivary glands at two time points during the transmission cycle. Results Genes belonging to fourteen pathways or component groups were found to be differentially transcribed in A. marginale in the bovine host versus the tick vector. One of the most significantly altered groups was composed of surface proteins. Of the 56 genes included in the surface protein group, eight were up regulated and 26 were down regulated. The down regulated surface protein encoding genes include several that are well studied due to their immunogenicity and function. Quantitative PCR of a set of genes demonstrated that transcription in tick cell culture most closely approximates transcription in salivary glands of recently infected ticks. Conclusions The ISE6 tick cell culture line is an acceptable model for early infection in tick salivary glands, and reveals disproportionate down regulation of surface protein genes in the tick. Transcriptional profiling in other cell lines may help us simulate additional microenvironments. Understanding vector-specific alteration of gene transcription, especially of surface protein encoding genes, may aid in the development of vaccines or transmission blocking therapies. PMID:24751137

  16. Nanoporous PdZr surface alloy as highly active non-platinum electrocatalyst toward oxygen reduction reaction with unique structure stability and methanol-tolerance

    NASA Astrophysics Data System (ADS)

    Duan, Huimei; Xu, Caixia

    2016-06-01

    Nanoporous (NP) PdZr alloy with controllable bimetallic ratio is successfully fabricated by a simple dealloying method. By leaching out the more reactive Al from PdZrAl precursor alloy, NP-PdZr alloy with smaller ligament size was generated, characterized by the nanoscaled interconnected network skeleton and hollow channels extending in all three dimensions. Upon voltammetric scan in acid solution, the dissolution of surface Zr atoms generates the highly active Pd-Zr surface alloy with a nearly pure Pd surface and Pd-Zr alloy core. The NP-Pd80Zr20 surface alloy exhibits markedly enhanced specific and mass activities as well as higher catalytic stability toward oxygen reduction reaction (ORR) compared with NP-Pd and the state-of-the-art Pt/C catalysts. In addition, the NP-Pd80Zr20 surface alloy shows a better selectivity for ORR than methanol in the 0.1 M HClO4 and 0.1 M methanol mixed solution. X-ray photoelectron spectroscopy and density functional theory calculations both demonstrate that the weakened Pd-O bond and improved ORR performances in turn depend on the downshifted d-band center of Pd due to the alloying Pd with Zr (20 at.%). The as-made NP-PdZr alloy holds prospective applications as a cathode electrocatalyst in fuel-cell-related technologies with the advantages of superior overall ORR performances, unique structure stability, and easy preparation.

  17. Redox processes as revealed by voltammetry in the surface sediments of the Gotland Basin, Baltic Sea

    NASA Astrophysics Data System (ADS)

    Yücel, Mustafa; Dale, Andy; Sommer, Stefan; Pfannkuche, Olaf

    2014-05-01

    Sulfur cycling in marine sediments undergoes dramatic changes with changing redox conditions of the overlying waters. The upper sediments of the anoxic Gotland Basin, central Baltic Sea represent a dynamic redox environment with extensive mats of sulfide oxidizing bacteria covering the seafloor beneath the chemocline. In order to investigate sulfur redox cycling at the sediment-water interface, sediment cores were sampled over a transect covering 65 - 174 m water depth in August-September 2013. High resolution (0.25 mm minimum) vertical microprofiles of electroactive redox species including dissolved sulfide and iron were obtained with solid state Au-Hg voltammetric microelectrodes. This approach enabled a fine-scale comparison of porewater profiles across the basin. The steepest sulfide gradients (i.e. the highest sulfide consumption) occurred within the upper 10 mm in sediments covered by surficial mats (2.10 to 3.08 mmol m-2 day-1). In sediments under permanently anoxic waters (>140m), voltammetric signals for Fe(II) and aqueous FeS were detected below a subsurface maximum in dissolved sulfide, indicating a Fe flux originating from older, deeper sedimentary layers. Our results point to a unique sulfur cycling in the Gotland basin seafloor where sulfide accumulation is moderated by sulfide oxidation at the sediment surface and by FeS precipitation in deeper sediment layers. These processes may play an important role in minimizing benthic sulfide fluxes to bottom waters around the major basins of the Baltic Sea.

  18. T Cell Immunoglobulin Mucin-3 Crystal Structure Reveals a Galectin-9-Independent Ligand-Binding Surface

    SciTech Connect

    Cao,E.; Zang, X.; Ramagopal, U.; Mukhopadhaya, A.; Fedorov, A.; Fedorov, E.; Zencheck, W.; Lary, J.; Cole, J.; et al.

    2007-01-01

    The T cell immunoglobulin mucin (Tim) family of receptors regulates effector CD4+ T cell functions and is implicated in autoimmune and allergic diseases. Tim-3 induces immunological tolerance, and engagement of the Tim-3 immunoglobulin variable (IgV) domain by galectin-9 is important for appropriate termination of T helper 1-immune responses. The 2 {angstrom} crystal structure of the Tim-3 IgV domain demonstrated that four cysteines, which are invariant within the Tim family, form two noncanonical disulfide bonds, resulting in a surface not present in other immunoglobulin superfamily members. Biochemical and biophysical studies demonstrated that this unique structural feature mediates a previously unidentified galectin-9-independent binding process and suggested that this structural feature is conserved within the entire Tim family. The current work provided a graphic example of the relationship between sequence, structure, and function and suggested that the interplay between multiple Tim-3-binding activities contributes to the regulated assembly of signaling complexes required for effective Th1-mediated immunity.

  19. The Arthrobacter arilaitensis Re117 Genome Sequence Reveals Its Genetic Adaptation to the Surface of Cheese

    PubMed Central

    Monnet, Christophe; Loux, Valentin; Gibrat, Jean-François; Spinnler, Eric; Barbe, Valérie; Vacherie, Benoit; Gavory, Frederick; Gourbeyre, Edith; Siguier, Patricia; Chandler, Michaël; Elleuch, Rayda

    2010-01-01

    Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe3+/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids. PMID:21124797

  20. Revealing remodeler function: Varied and unique

    NASA Astrophysics Data System (ADS)

    Eastlund, Allen

    Chromatin remodelers perform a necessary and required function for the successful expression of our genetic code. By modifying, shifting, or ejecting nucleosomes from the chromatin structure they allow access to the underlying DNA to the rest of the cell's machinery. This research has focused on two major remodeler motors from major families of chromatin remodelers: the trimeric motor domain of RSC and the motor domain of the ISWI family, ISWI. Using primarily stopped-flow spectrofluorometry, I have categorized the time-dependent motions of these motor domains along their preferred substrate, double-stranded DNA. Combined with collected ATP utilization data, I present the subsequent analysis and associated conclusions that stem from the underlying assumptions and models. Interestingly, there is little in common between the investigated proteins aside from their favored medium. While RSC exhibits modest translocation characteristics and highly effective motion with the ability for large molecular forces, ISWI is not only structurally different but highly inefficient in its motion leading to difficulties in determining its specific translocation mechanics. While chromatin remodeling is a ubiquitous facet of eukaryotic life, there remains much to be understood about their general mechanisms.

  1. COCMP Surface Current Mapping Reveals Eddy and Upwelling Jet off Cape Mendocino

    NASA Astrophysics Data System (ADS)

    Crawford, G. B.; Halle, C.; Largier, J.; Stone, S.

    2008-12-01

    Ocean surface currents are now being measured continuously over a roughly 2000 km stretch of the western US continental shelf from south of Tijuana, Mexico to the Columbia River. A long-standing gap in this coverage was finally filled on August 12, 2008, with the installation of a long-range Seasonde radar system at Shelter Cove, California (as a part of California's COCMP project). During its first three weeks of operation, this radar has revealed a large (~170 km diameter), stable, anticyclonic eddy southwest of Cape Mendocino in this poorly studied region. Upwelling-favorable winds appear to create an upwelling jet along the eastern edge of the eddy, leading to maximum daily-averaged current speeds up to 80 cm/s, and MODIS-derived chlorophyll concentrations up to 30 mg/m3 in the jet (compared to ~1 mg/m3 in the eddy center). AVHRR data reveal SST differences between the jet and the eddy center of 1.5 to 2.5 °C during these 3 weeks. These complex circulation structures modify water pathways and may interrupt nutrient delivery to locations farther south. We discuss the spatial and temporal evolution of these features.

  2. Crystal Structure of West Nile Virus Envelope Glycoprotein Reveals Viral Surface Epitopes

    SciTech Connect

    Kanai,R.; Kar, K.; Anthony, K.; Gould, L.; Ledizet, M.; Fikrig, E.; Marasco, W.; Koski, R.; Modis, Y.

    2006-01-01

    West Nile virus, a member of the Flavivirus genus, causes fever that can progress to life-threatening encephalitis. The major envelope glycoprotein, E, of these viruses mediates viral attachment and entry by membrane fusion. We have determined the crystal structure of a soluble fragment of West Nile virus E. The structure adopts the same overall fold as that of the E proteins from dengue and tick-borne encephalitis viruses. The conformation of domain II is different from that in other prefusion E structures, however, and resembles the conformation of domain II in postfusion E structures. The epitopes of neutralizing West Nile virus-specific antibodies map to a region of domain III that is exposed on the viral surface and has been implicated in receptor binding. In contrast, we show that certain recombinant therapeutic antibodies, which cross-neutralize West Nile and dengue viruses, bind a peptide from domain I that is exposed only during the membrane fusion transition. By revealing the details of the molecular landscape of the West Nile virus surface, our structure will assist the design of antiviral vaccines and therapeutics.

  3. Surface plasmon delocalization in silver nanoparticle aggregates revealed by subdiffraction supercontinuum hot spots

    PubMed Central

    Borys, Nicholas J.; Shafran, Eyal; Lupton, John M.

    2013-01-01

    The plasmonic resonances of nanostructured silver films produce exceptional surface enhancement, enabling reproducible single-molecule Raman scattering measurements. Supporting a broad range of plasmonic resonances, these disordered systems are difficult to investigate with conventional far-field spectroscopy. Here, we use nonlinear excitation spectroscopy and polarization anisotropy of single optical hot spots of supercontinuum generation to track the transformation of these plasmon modes as the mesoscopic structure is tuned from a film of discrete nanoparticles to a semicontinuous layer of aggregated particles. We demonstrate how hot spot formation from diffractively-coupled nanoparticles with broad spectral resonances transitions to that from spatially delocalized surface plasmon excitations, exhibiting multiple excitation resonances as narrow as 13 meV. Photon-localization microscopy reveals that the delocalized plasmons are capable of focusing multiple narrow radiation bands over a broadband range to the same spatial region within 6 nm, underscoring the existence of novel plasmonic nanoresonators embedded in highly disordered systems. PMID:23807624

  4. fMRI Analysis-by-Synthesis Reveals a Dorsal Hierarchy That Extracts Surface Slant

    PubMed Central

    Ban, Hiroshi

    2015-01-01

    The brain's skill in estimating the 3-D orientation of viewed surfaces supports a range of behaviors, from placing an object on a nearby table, to planning the best route when hill walking. This ability relies on integrating depth signals across extensive regions of space that exceed the receptive fields of early sensory neurons. Although hierarchical selection and pooling is central to understanding of the ventral visual pathway, the successive operations in the dorsal stream are poorly understood. Here we use computational modeling of human fMRI signals to probe the computations that extract 3-D surface orientation from binocular disparity. To understand how representations evolve across the hierarchy, we developed an inference approach using a series of generative models to explain the empirical fMRI data in different cortical areas. Specifically, we simulated the responses of candidate visual processing algorithms and tested how well they explained fMRI responses. Thereby we demonstrate a hierarchical refinement of visual representations moving from the representation of edges and figure–ground segmentation (V1, V2) to spatially extensive disparity gradients in V3A. We show that responses in V3A are little affected by low-level image covariates, and have a partial tolerance to the overall depth position. Finally, we show that responses in V3A parallel perceptual judgments of slant. This reveals a relatively short computational hierarchy that captures key information about the 3-D structure of nearby surfaces, and more generally demonstrates an analysis approach that may be of merit in a diverse range of brain imaging domains. PMID:26156985

  5. Surface Polysaccharide Mutants Reveal that Absence of O Antigen Reduces Biofilm Formation of Actinobacillus pleuropneumoniae

    PubMed Central

    Hathroubi, S.; Hancock, M. A.; Langford, P. R.; Tremblay, Y. D. N.; Labrie, J.

    2015-01-01

    Actinobacillus pleuropneumoniae is a Gram-negative bacterium belonging to the Pasteurellaceae family and the causative agent of porcine pleuropneumonia, a highly contagious lung disease causing important economic losses. Surface polysaccharides, including lipopolysaccharides (LPS) and capsular polysaccharides (CPS), are implicated in the adhesion and virulence of A. pleuropneumoniae, but their role in biofilm formation is still unclear. In this study, we investigated the requirement for these surface polysaccharides in biofilm formation by A. pleuropneumoniae serotype 1. Well-characterized mutants were used: an O-antigen LPS mutant, a truncated core LPS mutant with an intact O antigen, a capsule mutant, and a poly-N-acetylglucosamine (PGA) mutant. We compared the amount of biofilm produced by the parental strain and the isogenic mutants using static and dynamic systems. Compared to the findings for the biofilm of the parental or other strains, the biofilm of the O antigen and the PGA mutants was dramatically reduced, and it had less cell-associated PGA. Real-time PCR analyses revealed a significant reduction in the level of pgaA, cpxR, and cpxA mRNA in the biofilm cells of the O-antigen mutant compared to that in the biofilm cells of the parental strain. Specific binding between PGA and LPS was consistently detected by surface plasmon resonance, but the lack of O antigen did not abolish these interactions. In conclusion, the absence of the O antigen reduces the ability of A. pleuropneumoniae to form a biofilm, and this is associated with the reduced expression and production of PGA. PMID:26483403

  6. fMRI Analysis-by-Synthesis Reveals a Dorsal Hierarchy That Extracts Surface Slant.

    PubMed

    Ban, Hiroshi; Welchman, Andrew E

    2015-07-01

    The brain's skill in estimating the 3-D orientation of viewed surfaces supports a range of behaviors, from placing an object on a nearby table, to planning the best route when hill walking. This ability relies on integrating depth signals across extensive regions of space that exceed the receptive fields of early sensory neurons. Although hierarchical selection and pooling is central to understanding of the ventral visual pathway, the successive operations in the dorsal stream are poorly understood. Here we use computational modeling of human fMRI signals to probe the computations that extract 3-D surface orientation from binocular disparity. To understand how representations evolve across the hierarchy, we developed an inference approach using a series of generative models to explain the empirical fMRI data in different cortical areas. Specifically, we simulated the responses of candidate visual processing algorithms and tested how well they explained fMRI responses. Thereby we demonstrate a hierarchical refinement of visual representations moving from the representation of edges and figure-ground segmentation (V1, V2) to spatially extensive disparity gradients in V3A. We show that responses in V3A are little affected by low-level image covariates, and have a partial tolerance to the overall depth position. Finally, we show that responses in V3A parallel perceptual judgments of slant. This reveals a relatively short computational hierarchy that captures key information about the 3-D structure of nearby surfaces, and more generally demonstrates an analysis approach that may be of merit in a diverse range of brain imaging domains. PMID:26156985

  7. Characterizing an Integrated Annual Global Measure of the Earth's Maximum Land Surface Temperatures from 2003 to 2012 Reveals Strong Biogeographic Influences

    NASA Astrophysics Data System (ADS)

    Mildrexler, D. J.; Zhao, M.; Running, S. W.

    2014-12-01

    Land Surface Temperature (LST) is a good indicator of the surface energy balance because it is determined by interactions and energy fluxes between the atmosphere and the ground. The variability of land surface properties and vegetation densities across the Earth's surface changes these interactions and gives LST a unique biogeographic influence. Natural and human-induced disturbances modify the surface characteristics and alter the expression of LST. This results in a heterogeneous and dynamic thermal environment. Measurements that merge these factors into a single global metric, while maintaining the important biophysical and biogeographical factors of the land surface's thermal environment are needed to better understand integrated temperature changes in the Earth system. Using satellite-based LST we have developed a new global metric that focuses on one critical component of LST that occurs when the relationship between vegetation density and surface temperature is strongly coupled: annual maximum LST (LSTmax). A 10 year evaluation of LSTmax histograms that include every 1-km pixel across the Earth's surface reveals that this integrative measurement is strongly influenced by the biogeographic patterns of the Earth's ecosystems, providing a unique comparative view of the planet every year that can be likened to the Earth's thermal maximum fingerprint. The biogeographical component is controlled by the frequency and distribution of vegetation types across the Earth's land surface and displays a trimodal distribution. The three modes are driven by ice covered polar regions, forests, and hot desert/shrubland environments. In ice covered areas the histograms show that the heat of fusion results in a convergence of surface temperatures around the melting point. The histograms also show low interannual variability reflecting two important global land surface dynamics; 1) only a small fraction of the Earth's surface is disturbed in any given year, and 2) when

  8. Seismic structure of the southern Apennines as revealed by waveform modelling of regional surface waves

    NASA Astrophysics Data System (ADS)

    Ökeler, Ahmet; Gu, Yu Jeffrey; Lerner-Lam, Arthur; Steckler, Michael S.

    2009-09-01

    We investigate the crust and upper-mantle structures beneath the southern Apennine mountain chain using three-component seismograms from the Calabria-Apennine-Tyrrhenian/Subduction-Collision-Accretion Network (CAT/SCAN) array. Surface wave waveforms from three moderate-sized (Mw > 5.0) regional earthquakes are modelled using multiple frequencies (0.03-0.06 and 0.05-0.2 Hz) and both forward and linearized-inversion algorithms. Our best-fitting shear velocity models clearly reflect the major tectonic units where, for example, the average seismic structure at depths above 50 km beneath Apulia is substantially faster than beneath the Apennine mountain chain. We identify a prominent low-velocity channel under the mountain belt at depths below ~25-30 km and a secondary low-velocity zone at 6-12 km depth near Mt Vulture (a once active volcano). Speed variations between Love and Rayleigh waves provide further constraints on the fabric and dynamic processes. Our analysis indicates that the crustal low-velocity zones are highly anisotropic (maximum 14 per cent) and allow transversely polarized shear waves to travel faster than vertically polarized shear waves. The upper crustal anomaly reveals a layer of highly deformed rocks caused by past collisions and by the active normal faults cutting across the thrust sheets, whereas hot mantle upwelling may be responsible for a high-temperature, partially molten lower crust beneath the southern Apennines.

  9. Complex Contact-Based Dynamics of Microsphere Monolayers Revealed by Resonant Attenuation of Surface Acoustic Waves.

    PubMed

    Hiraiwa, M; Abi Ghanem, M; Wallen, S P; Khanolkar, A; Maznev, A A; Boechler, N

    2016-05-13

    Contact-based vibrations play an essential role in the dynamics of granular materials. Significant insights into vibrational granular dynamics have previously been obtained with reduced-dimensional systems containing macroscale particles. We study contact-based vibrations of a two-dimensional monolayer of micron-sized spheres on a solid substrate that forms a microscale granular crystal. Measurements of the resonant attenuation of laser-generated surface acoustic waves reveal three collective vibrational modes that involve displacements and rotations of the microspheres, as well as interparticle and particle-substrate interactions. To identify the modes, we tune the interparticle stiffness, which shifts the frequency of the horizontal-rotational resonances while leaving the vertical resonance unaffected. From the measured contact resonance frequencies we determine both particle-substrate and interparticle contact stiffnesses and find that the former is an order of magnitude larger than the latter. This study paves the way for investigating complex contact-based dynamics of microscale granular crystals and yields a new approach to studying micro- to nanoscale contact mechanics in multiparticle networks. PMID:27232047

  10. Gross Morphological Features of the Organ Surface Primo-Vascular System Revealed by Hemacolor Staining

    PubMed Central

    Yoo, Jong-Hyun; Kim, Yongbaek; Lee, So Yeong

    2013-01-01

    The primo-vascular system (PVS), which consists of primo-vessels (PVs) and primo-nodes (PNs), is a novel thread-like structure identified in many animal species. Various observational methods have been used to clarify its anatomical properties. Here, we used Hemacolor staining to examine the gross morphology of organ-surface PVS in rats. We observed a sinus structure (20–50 μm) with a remarkably low cellularity within PNs and PVs and several lines of ductules (3–5 μm) filled with single cells or granules (~1 μm) in PV. Both sinuses and ductules were linearly aligned along the longitudinal axis of the PVS. Such morphology of the PVS was further confirmed by acridine orange staining. In PN slices, there was a honeycomb-like structure containing the granules with pentagonal lumens (~10 μm). Both PVs and PNs were densely filled with WBCs, RBCs, and putative mast cells (MCs), which were 90.3%, 5.9%, and 3.8% of the cell population, respectively. Granules in putative MCs showed spontaneous vibrating movements. In conclusion, the results show that Hemacolor, a simple and rapid staining system, can reveal the gross morphological features reported previously. Our findings may help to elucidate the structure and function of the PVS in normal and disease states in future studies. PMID:23986781

  11. Complex Contact-Based Dynamics of Microsphere Monolayers Revealed by Resonant Attenuation of Surface Acoustic Waves

    NASA Astrophysics Data System (ADS)

    Hiraiwa, M.; Abi Ghanem, M.; Wallen, S. P.; Khanolkar, A.; Maznev, A. A.; Boechler, N.

    2016-05-01

    Contact-based vibrations play an essential role in the dynamics of granular materials. Significant insights into vibrational granular dynamics have previously been obtained with reduced-dimensional systems containing macroscale particles. We study contact-based vibrations of a two-dimensional monolayer of micron-sized spheres on a solid substrate that forms a microscale granular crystal. Measurements of the resonant attenuation of laser-generated surface acoustic waves reveal three collective vibrational modes that involve displacements and rotations of the microspheres, as well as interparticle and particle-substrate interactions. To identify the modes, we tune the interparticle stiffness, which shifts the frequency of the horizontal-rotational resonances while leaving the vertical resonance unaffected. From the measured contact resonance frequencies we determine both particle-substrate and interparticle contact stiffnesses and find that the former is an order of magnitude larger than the latter. This study paves the way for investigating complex contact-based dynamics of microscale granular crystals and yields a new approach to studying micro- to nanoscale contact mechanics in multiparticle networks.

  12. Chromatogram Handler: A unique computer program that efficiently processes data generated in liquid chromatographic investigations of organic ligand adsorption on mineral surfaces

    NASA Astrophysics Data System (ADS)

    Kreller, David I.; Young, Stephen P.; Mendez, Eladio A.; McGunigale, Samantha L.

    2012-09-01

    We describe a unique C# computer program developed in our laboratory to efficiently manipulate data generated when a novel liquid chromatographic (LC) 'pulsed addition' technique is used to study organic ligand interactions with mineral surfaces. We are not aware of the existence of a program of this nature elsewhere. Geochemically-relevant ligands studied include dissolved organic matter (DOM) mixtures and single component low molecular weight organic acids. Although our LC system has three optical (absorbance and fluorescence) detection channels, the utility can process data from experiments in which data was collected in one, two or three detection channels. If not automated, data management and processing for the technique is prohibitively complex and time-consuming, due large data volumes and the number of operations involved. The input for the utility in a processing run is the set of detector output files generated during an LC experiment. During processing, the utility generates an MS Excel output file within which, for each detection channel: (i) chromatographic peak areas and peak retention times are determined, (ii) area-normalized per-injection and cumulative adsorption densities are calculated, and (iii) graphical representations of various quantities calculated from the raw data are automatically generated. When processing data from experiments with multiple detection channels, the utility additionally prepares graphs that compare recovery values calculated from data in different detection channels, and calculates (and plots) spectroscopic/chromatographic indices which are ratios of signals in various detection channels. The utility was programmed to perform these additional operations on data from multi-channel experiments because (i) 'Interchannel' comparisons of recovery provide insight into the differing surface behavior of distinct DOM sub-fractions, and (ii) the spectroscopic indices provide a useful new form of data that provides insight into

  13. An analysis of surface proteomics results reveals novel candidates for intracellular/surface moonlighting proteins in bacteria.

    PubMed

    Wang, Wangfei; Jeffery, Constance J

    2016-04-26

    Proteins expressed on the bacterial cell surface play important roles in infection and virulence and can be targets for vaccine development or used as biomarkers. Surprisingly, an increasing number of surface proteins are being found to be identical to intracellular enzymes and chaperones, and a few dozen intracellular/surface moonlighting proteins have been found that have different functions inside the cell and on the cell surface. The results of twenty-two published bacterial surface proteomics studies were analyzed using bioinformatics tools to consider how many additional intracellular proteins are also found on the cell surface. More than 1000 out of the 3619 proteins observed on the cell surface lack the transmembrane alpha-helices or transmembrane beta-barrels found in integral membrane proteins and also lack the signal peptides found in proteins secreted through the Sec pathway. Many of the proteins found on the cell surface are intracellular chaperones or enzymes involved in central metabolic pathways, including some that have previously been shown to have a moonlighting function on the cell surface in at least one species, such as Hsp60/GroEL, DnaK, glyceraldehyde 3-phosphate dehydrogenase, enolase, and fructose 1,6-bisphosphate aldolase. The results of the proteomics studies suggest they could also be moonlighting on the surface of many other species. Hundreds of other intracellular proteins are also found on the cell surface, although a second function on the surface has not yet been demonstrated, for example, glutamine synthetase, gamma-glutamyl phosphate reductase, and cysteine desulfurase. The presence of intracellular proteins on the cell surface is more common than previously expected and suggests that many additional proteins might be candidates for being intracellular/surface moonlighting proteins. PMID:26938107

  14. Ag@Au concave cuboctahedra: A unique probe for monitoring Au-catalyzed reduction and oxidation reactions by surface-enhanced Raman spectroscopy

    DOE PAGESBeta

    Zhang, Jiawei; Winget, Sarah A.; Wu, Yiren; Su, Dong; Sun, Xiaojun; Xie, Zhao -Xiong; Qin, Dong

    2016-01-26

    In this paper, we report a facile synthesis of Ag@Au concave cuboctahedra by titrating aqueous HAuCl4 into a suspension of Ag cuboctahedra in the presence of ascorbic acid (AA), NaOH, and poly(vinylpyrrolidone) (PVP) at room temperature. Initially, the Au atoms derived from the reduction of Au3+ by AA are conformally deposited on the entire surface of a Ag cuboctahedron. Upon the formation of a complete Au shell, however, the subsequently formed Au atoms are preferentially deposited onto the Au{100} facets, resulting in the formation of a Ag@Au cuboctahedron with concave structures at the sites of {111} facets. The concave cuboctahedramore » embrace excellent SERS activity that is more than 70-fold stronger than that of the original Ag cuboctahedra at an excitation wavelength of 785 nm. The concave cuboctahedra also exhibit remarkable stability in the presence of an oxidant such as H2O2 because of the protection by a complete Au shell. These two unique attributes enable in-situ SERS monitoring of the reduction of 4-nitrothiophenol (4-NTP) to 4-aminothiophenol (4-ATP) by NaBH4 through a 4,4'-dimercaptoazobenzene (trans-DMAB) intermediate and the subsequent oxidation of 4-ATP back to trans-DMAB upon the introduction of H2O2.« less

  15. Structural constraints for the binding of short peptides to claudin-4 revealed by surface plasmon resonance.

    PubMed

    Ling, Jun; Liao, Hailing; Clark, Robin; Wong, Mandy Sze Man; Lo, David D

    2008-11-01

    Claudin family transmembrane proteins play an important role in tight junction structure and function in epithelial cells. Among the 24 isoforms identified in mice and humans, claudin-4 and -3 serve as the receptor for Clostridium perfringens enterotoxin (Cpe). The second extracellular loop (Ecl2) of claudin-4 is responsible for the binding to the C-terminal 30 amino acids of Cpe (Cpe30). To define the structural constraints for the claudin-4/Cpe30 interaction, a surface plasmon resonance (SPR) method was developed. GST fusions with claudin-4 revealed that Ecl2 with the downstream transmembrane domain of claudin-4 reconstituted the basic structural requirement for optimal binding activity to Cpe30, with affinity in the nanomolar range. Two 12-mer peptides selected by phage display against claudin-4-transfected CHO cells and a 12-mer Cpe mutant peptide also showed significant affinity for claudin-4 with this SPR assay, suggesting that a short peptide can establish stable contact with Ecl2 with nanomolar affinity. Alignment of these short peptides unveiled a common Ecl2 binding motif: . Whereas the short peptides bound native claudin-4 on transfected CHO cells in pull-down assays, only the larger Cpe30 peptide affected trans-epithelial electrical resistance (TER) in peptide-treated Caco-2BBe monolayers. Importantly, Cpe30 retained its binding to claudin-4 when fused to the C terminus of influenza hemagglutinin, demonstrating that its binding activity can be maintained in a different biochemical context. These studies may help in the design of assays for membrane receptor interactions with soluble ligands, and in applying new targeting ligands to delivering attached "cargo" proteins. PMID:18782762

  16. Hepatitis B virus-associated diffuse large B-cell lymphoma: unique clinical features, poor outcome, and hepatitis B surface antigen-driven origin

    PubMed Central

    Deng, Lijuan; Song, Yuqin; Young, Ken H.; Hu, Shimin; Ding, Ning; Song, Weiwei; Li, Xianghong; Shi, Yunfei; Huang, Huiying; Liu, Weiping; Zheng, Wen; Wang, Xiaopei; Xie, Yan; Lin, Ningjing; Tu, Meifeng; Ping, Lingyan; Ying, Zhitao; Zhang, Chen; Sun, Yingli; Zhu, Jun

    2015-01-01

    While the epidemiologic association between hepatitis B virus (HBV) infection and diffuse large B-cell lymphoma (DLBCL) is established, little is known more than this epidemiologic evidence. We studied a cohort of 587 patients with DLBCL for HBV infection status, clinicopathologic features, and the immunoglobulin variable region in HBV surface antigen (HBsAg)-positive patients. Eighty-one (81/587, 13.8%) patients were HBsAg-positive. Compared with HBsAg-negative DLBCL, HBsAg-positive DLBCL displayed a younger median onset age (45 vs. 55 years), more frequent involvement of spleen or retroperitoneal lymph node (40.7% vs. 16.0% and 61.7% vs. 31.0% respectively, both p < 0.001), more advanced disease (stage III/IV: 76.5% vs 59.5%, p = 0.003), and significantly worse outcome (2-year overall survival: 47% versus 70%, p < 0.001). In HBsAg-positive DLBCL patients, almost all (45/47, 96%) amino acid sequences of heavy and light chain complementarity determining region 3 exhibited a high homology to antibodies specific for HBsAg, and the majority (45/50, 90%) of IgHV and IgLV genes were mutated. We conclude that 13.8% of DLBCL cases are HBV-associated in HBV-endemic China and show unique clinical features and poor outcomes. Furthermore, our study strongly suggests that HBV-associated DLBCL might arise from HBV antigen-selected B cells. PMID:26314957

  17. The surface-state of the topological insulator Bi2Se3 revealed by cyclotron resonance

    SciTech Connect

    Mcdonald, Ross D; Ayala - Valenzuela, Oscar E; Altarawneh, Moaz M; Analytis, James G

    2011-01-14

    Transport measurements of topological insulators are dominated by the conductivity of the bulk, leading to substantial difficulties in resolving the properties of the surface. To this end, we use high magnetic field, rf- and microwave-spectroscopy to selectively couple to the surface conductivity of Bi2Se3 at high frequency. In the frequency range of a few GHz we observe a crossover from quantum oscillations indicative of a small 3D Fermi surface, to cyclotron resonance indicative of a 2D surface state. By probing the conductivity at reduced skin depths, we have observed a 2D cyclotron resonance from a material whose bulk Fermi-surface is 3D. The frequency-magnetic field scaling of this resonance is inconsistent with the bulk effective mass, but more consistent with the dispersion and band filling of a Dirac-like surface state as observed by ARPES, with substantial manybody renormalization.

  18. Direct surface analysis coupled to high-resolution mass spectrometry reveals heterogeneous composition of the cuticle of Hibiscus trionum petals.

    PubMed

    Giorio, Chiara; Moyroud, Edwige; Glover, Beverley J; Skelton, Paul C; Kalberer, Markus

    2015-10-01

    Plant cuticle, which is the outermost layer covering the aerial parts of all plants including petals and leaves, can present a wide range of patterns that, combined with cell shape, can generate unique physical, mechanical, or optical properties. For example, arrays of regularly spaced nanoridges have been found on the dark (anthocyanin-rich) portion at the base of the petals of Hibiscus trionum. Those ridges act as a diffraction grating, producing an iridescent effect. Because the surface of the distal white region of the petals is smooth and noniridescent, a selective chemical characterization of the surface of the petals on different portions (i.e., ridged vs smooth) is needed to understand whether distinct cuticular patterns correlate with distinct chemical compositions of the cuticle. In the present study, a rapid screening method has been developed for the direct surface analysis of Hibiscus trionum petals using liquid extraction surface analysis (LESA) coupled with high-resolution mass spectrometry. The optimized method was used to characterize a wide range of plant metabolites and cuticle monomers on the upper (adaxial) surface of the petals on both the white/smooth and anthocyanic/ridged regions, and on the lower (abaxial) surface, which is entirely smooth. The main components detected on the surface of the petals are low-molecular-weight organic acids, sugars, and flavonoids. The ridged portion on the upper surface of the petal is enriched in long-chain fatty acids, which are constituents of the wax fraction of the cuticle. These compounds were not detected on the white/smooth region of the upper petal surface or on the smooth lower surface. PMID:26335385

  19. Coupled surface-subsurface hydrologic measurements reveal infiltration, recharge, and discharge dynamics across the swash zone of a sandy beach

    NASA Astrophysics Data System (ADS)

    Heiss, James W.; Puleo, Jack A.; Ullman, William J.; Michael, Holly A.

    2015-11-01

    Swash-groundwater interactions affect the biogeochemistry of beach aquifers and the transport of solutes and sediment across the beachface. Improved understanding of the complex, coupled dynamics of surface and subsurface flow processes in the swash zone is required to better estimate chemical fluxes to the sea and predict the morphological evolution of beaches. Simultaneous high-frequency measurements of saturation, water table elevation, and the cross-shore locations of runup and the boundary between the saturated and unsaturated beachface (surface saturation boundary) were collected on a sandy beach to link groundwater flow dynamics with swash zone forcing. Saturation and lysimeter measurements showed the dynamic response of subsurface saturation to swash events and permitted estimation of infiltration rates. Surface and subsurface observations revealed a decoupling of the surface saturation boundary and the intersection between the water table and the beachface. Surface measurements alone were insufficient to delineate the infiltration and discharge zones, which moved independently of the surface saturation boundary. Results show for the first time the motion and areal extent of infiltration and recharge zones, and constrain the maximum size of the subaerial discharge zone over swash and tidal time scales. The width of the infiltration zone was controlled by swash processes, and subaerial discharge was controlled primarily by tidal processes. These dynamics reveal the tightly coupled nature of surface and subsurface processes over multiple time scales, with implications for sediment transport and fluid and solute fluxes through the hydrologically and biogeochemically active intertidal zone of sandy beaches.

  20. Boundary condition in liquid thin films revealed through the thermal fluctuations of their free surfaces

    NASA Astrophysics Data System (ADS)

    Pottier, Basile; Talini, Laurence; Frétigny, Christian

    We investigate the properties of liquids confined at nanometric scales from a solid wall with a new noninvasive technique. The optical technique used consists of measuring the height of fluctuations of the free surface, using the reflection of a laser beam on that surface. We hence measure the spontaneous thermal fluctuations of the free surfaces of liquids to probe their hydrodynamic boundary condition at a solid wall. The surface fluctuations of a silicon oil film could be described with a no-slip boundary condition for film thicknesses down to 20 nm. Oppositely, a 4 nm negative slip length had to be introduced to describe the behavior of n-hexadecane, consistently with previous surface force apparatus data on the same system. Our results demonstrate that at vanishing flow, a nanometric solid-like layer close to the wall may exist according to the nature of the liquid. currently at Laboratoire de Physique ENS Lyon.

  1. Boundary Condition in Liquid Thin Films Revealed through the Thermal Fluctuations of Their Free Surfaces

    NASA Astrophysics Data System (ADS)

    Pottier, B.; Frétigny, C.; Talini, L.

    2015-06-01

    We investigate the properties of nanometric liquid films with a new noninvasive technique. We measure the spontaneous thermal fluctuations of the free surfaces of liquids to probe their hydrodynamic boundary condition at a solid wall. The surface fluctuations of a silicon oil film could be described with a no-slip boundary condition for film thicknesses down to 20 nm. Oppositely, a 4 nm negative slip length had to be introduced to describe the behavior of n -hexadecane, consistently with previous surface force apparatus data on the same system. Our results demonstrate that at vanishing flow a nanometric solidlike layer close to the wall may exist according to the nature of the liquid.

  2. Surface hardening induced by high flux plasma in tungsten revealed by nano-indentation

    NASA Astrophysics Data System (ADS)

    Terentyev, D.; Bakaeva, A.; Pardoen, T.; Favache, A.; Zhurkin, E. E.

    2016-08-01

    Surface hardness of tungsten after high flux deuterium plasma exposure has been characterized by nanoindentation. The effect of plasma exposure was rationalized on the basis of available theoretical models. Resistance to plastic penetration is enhanced within the 100 nm sub-surface region, attributed to the pinning of geometrically necessary dislocations on nanometric deuterium cavities - signature of plasma-induced defects and deuterium retention. Sub-surface extension of thereby registered plasma-induced damage is in excellent agreement with the results of alternative measurements. The study demonstrates suitability of nano-indentation to probe the impact of deposition of plasma-induced defects in tungsten on near surface plasticity under ITER-relevant plasma exposure conditions.

  3. Rapid cell-surface prion protein conversion revealed using a novel cell system

    PubMed Central

    Goold, R.; Rabbanian, S.; Sutton, L.; Andre, R.; Arora, P.; Moonga, J.; Clarke, A.R.; Schiavo, G.; Jat, P.; Collinge, J.; Tabrizi, S.J.

    2011-01-01

    Prion diseases are fatal neurodegenerative disorders with unique transmissible properties. The infectious and pathological agent is thought to be a misfolded conformer of the prion protein. Little is known about the initial events in prion infection because the infecting prion source has been immunologically indistinguishable from normal cellular prion protein (PrPC). Here we develop a unique cell system in which epitope-tagged PrPC is expressed in a PrP knockdown (KD) neuroblastoma cell line. The tagged PrPC, when expressed in our PrP-KD cells, supports prion replication with the production of bona fide epitope-tagged infectious misfolded PrP (PrPSc). Using this epitope-tagged PrPSc, we study the earliest events in cellular prion infection and PrP misfolding. We show that prion infection of cells is extremely rapid occurring within 1 min of prion exposure, and we demonstrate that the plasma membrane is the primary site of prion conversion. PMID:21505437

  4. Selective responses to specular surfaces in the macaque visual cortex revealed by fMRI.

    PubMed

    Okazawa, Gouki; Goda, Naokazu; Komatsu, Hidehiko

    2012-11-15

    The surface properties of objects, such as gloss, transparency and texture, provide important information about the material characteristics of objects in our visual environment. However, because there have been few reports on the neuronal responses to surface properties in primates, we still lack information about where and how surface properties are processed in the primate visual cortex. In this study, we used functional magnetic resonance imaging (fMRI) to examine the cortical responses to specular surfaces in the macaque visual cortex. Using computer graphics, we generated images of specular and matte objects and prepared scrambled images by locally randomizing the luminance phases of the images with specular and matte objects. In experiment 1, we contrasted the responses to specular images with those to matte and scrambled images. Activation was observed along the ventral visual pathway, including V1, V2, V3, V4 and the posterior inferior temporal (IT) cortex. In experiment 2, we manipulated the contrasts of images and found that the activation observed in these regions could not be explained solely by the global or local contrasts. These results suggest that image features related to specular surface are processed along the ventral visual pathway from V1 to specific regions in the IT cortex. This is consistent with previous human fMRI experiments that showed surface properties are processed in the ventral visual pathway. PMID:22885246

  5. Finding needles in haystacks: scanning tunneling microscopy reveals the complex reactivity of Si(100) surfaces.

    PubMed

    Skibinski, Erik S; Hines, Melissa A

    2015-07-21

    Many chemical reactions-etching, growth, and catalytic-produce highly faceted surfaces. Examples range from the atomically flat silicon surfaces produced by anisotropic etchants to the wide variety of faceted nanoparticles, including cubes, wires, plates, tetrapods, and more. This faceting is a macroscopic manifestation of highly site-specific surface reactions. In this Account, we show that these site-specific reactions literally write a record of their chemical reactivity in the morphology of the surface-a record that can be quantified with scanning tunneling microscopy. Paradoxically, the sites targeted by these highly site-specific reactions are extremely rare. This paradox can be understood from a simple kinetic argument. An etchant that produces atomically flat surfaces must rapidly etch every surface site except the terrace atoms on the perfectly flat surface. As a result, the etch morphology is dominated by the least reactive species (here, the terrace sites), not the most reactive species. In contrast, the most interesting chemical species-the site where the reaction occurs most rapidly and most selectively-is the hardest one to find. This highly reactive site, the key to the reaction, is the needle in the haystack, often occurring in densities far below 1% of a monolayer and thus invisible to surface spectroscopies. This kinetic argument is quite general and applies to a wide variety of reactions, not just etching reactions. Understanding these highly site-specific reactions requires a combination of experimental and computational techniques with both exquisite defect sensitivity and high chemical sensitivity. In this Account, we present examples of highly site-specific chemistry on the technologically important face of silicon, Si(100). In one example, we show that the high reactivity of one particular surface site, a silicon dihydride bound to a silicon monohydride, or an "α-dihydride", provides a fundamental explanation for anisotropic silicon etching

  6. Physicochemical state of the nanotopographic surface of commercially pure titanium following anodization-hydrothermal treatment reveals significantly improved hydrophilicity and surface energy profiles.

    PubMed

    Takebe, Jun; Ito, Shigeki; Miura, Shingo; Miyata, Kyohei; Ishibashi, Kanji

    2012-01-01

    A method of coating commercially pure titanium (cpTi) implants with a highly crystalline, thin hydroxyapatite (HA) layer using discharge anodic oxidation followed by hydrothermal treatment (Spark discharged Anodic oxidation treatment ; SA-treated cpTi) has been reported for use in clinical dentistry. We hypothesized that a thin HA layer with high crystallinity and nanostructured anodic titanium oxide film on such SA-treated cpTi implant surfaces might be a crucial function of their surface-specific potential energy. To test this, we analyzed anodic oxide (AO) cpTi and SA-treated cpTi disks by SEM and AFM. Contact angles and surface free energy of each disk surface was measured using FAMAS software. High-magnification SEM and AFM revealed the nanotopographic structure of the anodic titanium oxide film on SA-treated cpTi; however, this was not observed on the AO cpTi surface. The contact angle and surface free energy measurements were also significantly different between AO cpTi and SA-treated cpTi surfaces (Tukey's, P<0.05). These data indicated that the change of physicochemical properties of an anodic titanium oxide film with HA crystals on an SA-treated cpTi surface may play a key role in the phenomenon of osteoconduction during the process of osseointegration. PMID:23177772

  7. Surface force measurements between titanium dioxide surfaces prepared by atomic layer deposition in electrolyte solutions reveal non-DLVO interactions: influence of water and argon plasma cleaning.

    PubMed

    Walsh, Rick B; Evans, Drew; Craig, Vincent S J

    2014-03-01

    Surface force measurements between titania surfaces in electrolyte solutions have previously revealed an unexplained long-range repulsive force at high pH, not described by Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory. Here, the surface forces between titania surfaces produced by atomic layer deposition (ALD) and cleaned using a variety of methods have been measured to determine the influence of the cleaning protocol on the measured forces and test the hypothesis that water plasma cleaning of the surface results in non-DLVO forces at high pH. For argon plasma and water plasma cleaned surfaces, a diffuse double layer repulsion and van der Waals attraction is observed near the isoelectric point. At high pH, the force remained repulsive up until contact, and no van der Waals attraction or adhesion was observed. Differences in the measured forces are explained by modification of the surface chemistry during cleaning, which alters the density of charged groups on the surface, but this cannot explain the observed disagreement with DLVO theory at high pH. PMID:24548170

  8. Revealing the surface origin of green band emission from ZnO nanostructures by plasma immersion ion implantation induced quenching

    SciTech Connect

    Yang, Y.; Sun, X. W.; Tay, B. K.; Cao, Peter H. T.; Wang, J. X.; Zhang, X. H.

    2008-03-15

    Surface defect passivation for ZnO nanocombs (NCBs), random nanowires (RNWs), and aligned nanowires (ANWs) was performed through a metal plasma immersion ion implantation with low bias voltages ranging from 0 to 10 kV, where Ni was used as the modification ion. The depth of surface-originated green band (GB) emission is thus probed, revealing the surface origin of the GB. It is also found that the GB is closely related to oxygen gas content during growth of the nanostructures. The GB origin of NCBs and RNWs grown with higher oxygen content is shallower ({approx}0.5 nm), which can be completely quenched with no bias applied. However, the GB origin of ANWs grown at lower oxygen content is much deeper ({approx}7 nm) with a complete quenching bias of 10 kV. Quenching of the GB can be attributed to passivation of the surface hole or electron trapping sites (oxygen vacancies) by Ni ions.

  9. Chemical heterogeneity on Mercury's surface revealed by the MESSENGER X-Ray Spectrometer

    NASA Astrophysics Data System (ADS)

    Weider, Shoshana Z.; Nittler, Larry R.; Starr, Richard D.; McCoy, Timothy J.; Stockstill-Cahill, Karen R.; Byrne, Paul K.; Denevi, Brett W.; Head, James W.; Solomon, Sean C.

    2012-10-01

    We present the analysis of 205 spatially resolved measurements of the surface composition of Mercury from MESSENGER's X-Ray Spectrometer. The surface footprints of these measurements are categorized according to geological terrain. Northern smooth plains deposits and the plains interior to the Caloris basin differ compositionally from older terrain on Mercury. The older terrain generally has higher Mg/Si, S/Si, and Ca/Si ratios, and a lower Al/Si ratio than the smooth plains. Mercury's surface mineralogy is likely dominated by high-Mg mafic minerals (e.g., enstatite), plagioclase feldspar, and lesser amounts of Ca, Mg, and/or Fe sulfides (e.g., oldhamite). The compositional difference between the volcanic smooth plains and the older terrain reflects different abundances of these minerals and points to the crystallization of the smooth plains from a more chemically evolved magma source. High-degree partial melts of enstatite chondrite material provide a generally good compositional and mineralogical match for much of the surface of Mercury. An exception is Fe, for which the low surface abundance on Mercury is still higher than that of melts from enstatite chondrites and may indicate an exogenous contribution from meteoroid impacts.

  10. Zeeman effect of the topological surface states revealed by quantum oscillations up to 91 Tesla

    NASA Astrophysics Data System (ADS)

    Zhang, Zuocheng; Wei, Wei; Yang, Fangyuan; Zhu, Zengwei; Guo, Minghua; Feng, Yang; Yu, Dejing; Yao, Mengyu; Harrison, Neil; McDonald, Ross; Zhang, Yuanbo; Guan, Dandan; Qian, Dong; Jia, Jinfeng; Wang, Yayu

    2015-12-01

    We report quantum oscillation studies on the B i2T e3 -xSx topological insulator single crystals in pulsed magnetic fields up to 91 T. For the x =0.4 sample with the lowest bulk carrier density, the surface and bulk quantum oscillations can be disentangled by combined Shubnikov-de Haas and de Hass-van Alphen oscillations, as well as quantum oscillations in nanometer-thick peeled crystals. At high magnetic fields beyond the bulk quantum limit, our results suggest that the zeroth Landau level of topological surface states is shifted due to the Zeeman effect. The g factor of the topological surface states is estimated to be between 1.8 and 4.5. These observations shed new light on the quantum transport phenomena of topological insulators in ultrahigh magnetic fields.

  11. Boundary Condition in Liquid Thin Films Revealed through the Thermal Fluctuations of Their Free Surfaces.

    PubMed

    Pottier, B; Frétigny, C; Talini, L

    2015-06-01

    We investigate the properties of nanometric liquid films with a new noninvasive technique. We measure the spontaneous thermal fluctuations of the free surfaces of liquids to probe their hydrodynamic boundary condition at a solid wall. The surface fluctuations of a silicon oil film could be described with a no-slip boundary condition for film thicknesses down to 20 nm. Oppositely, a 4 nm negative slip length had to be introduced to describe the behavior of n-hexadecane, consistently with previous surface force apparatus data on the same system. Our results demonstrate that at vanishing flow a nanometric solidlike layer close to the wall may exist according to the nature of the liquid. PMID:26196646

  12. Near-surface Seismic Anisotropy of Taiwan Revealed by Coda Interferometry

    NASA Astrophysics Data System (ADS)

    Chen, Li-Wei; Chen, Ying-Nien; Gung, Yuancheng; Lee, Jian-Cheng; Liang, Wen-Tzong

    2016-04-01

    We report the near-surface (<400m) shear wave velocity (Vs) and Vs azimuthal anisotropy of Taiwan by applying seismic interferometry to 34 borehole-surface station pairs. We measure the Vs anisotropy by examining the azimuthal dependence of the empirical Green's functions of shear waves extracted from the coda waves of 398 local earthquakes with ML>4.0 during the time period from 2011 to 2014. We find the clear characteristic azimuthal dependence of Vs in all the measurements. Strengths of the obtained anisotropy are much stronger than those reported in seismic tomography and SWS measurements. Specifically, about half of the measured amplitudes of anisotropy are larger than 10%, and the strongest anisotropy is 34%. Patterns of the resulting anisotropy fall into two categories, and both are well correlated with the surface geology and ambient stress at the borehole sites. In general, the fast Vs polarization directions are parallel to sub-parallel to the mountain strikes in mountains belts, and to the directions of maximum compression stress in coastal plains and lowlands, suggesting that the anisotropy of shallow crust are dominated by orogeny-induced fabrics in mountain area and by stress-aligned cracks in places with sediments, respectively. From these new findings, together with results from our recent studies, we infer that the stress-aligned anisotropy are likely confined to the uppermost portion (< 3km) of the crust. These results represent direct robust measurements of the near-surface seismic structure. The characteristic patterns of observed azimuthal dependence of Vs and strong anisotropy suggest that anisotropy properties are fairly coherent in the near-surface structure. The strong near-surface anisotropy also implies that delay times contributed by the shallow crust might have been underestimated in studies of shear-wave splitting measurements using the direct arrivals of earthquake waves.

  13. Atmospheric Drivers of Greenland Surface Melt Revealed by Self-Organizing Maps

    NASA Technical Reports Server (NTRS)

    Mioduszewski, J. R.; Rennermalm, A. K.; Hammann, A.; Tedesco, M.; Noble, E. U.; Stroeve, J. C.; Mote, T. L.

    2016-01-01

    Recent acceleration in surface melt on the Greenland ice sheet (GrIS) has occurred concurrently with a rapidly warming Arctic and has been connected to persistent, anomalous atmospheric circulation patterns over Greenland. To identify synoptic setups favoring enhanced GrIS surface melt and their decadal changes, we develop a summer Arctic synoptic climatology by employing self-organizing maps. These are applied to daily 500 hPa geopotential height fields obtained from the Modern Era Retrospective Analysis for Research and Applications reanalysis, 1979-2014. Particular circulation regimes are related to meteorological conditions and GrIS surface melt estimated with outputs from the Modèle Atmosphérique Régional. Our results demonstrate that the largest positive melt anomalies occur in concert with positive height anomalies near Greenland associated with wind, temperature, and humidity patterns indicative of strong meridional transport of heat and moisture. We find an increased frequency in a 500 hPa ridge over Greenland coinciding with a 63% increase in GrIS melt between the 1979-1988 and 2005-2014 periods, with 75.0% of surface melt changes attributed to thermodynamics, 17% to dynamics, and 8.0% to a combination. We also confirm that the 2007-2012 time period has the largest dynamic forcing relative of any period but also demonstrate that increased surface energy fluxes, temperature, and moisture separate from dynamic changes contributed more to melt even during this period. This implies that GrIS surface melt is likely to continue to increase in response to an ever warmer future Arctic, regardless of future atmospheric circulation patterns.

  14. Surface oxidation of tin chalcogenide nanocrystals revealed by 119Sn-Mössbauer spectroscopy.

    PubMed

    de Kergommeaux, Antoine; Faure-Vincent, Jérôme; Pron, Adam; de Bettignies, Rémi; Malaman, Bernard; Reiss, Peter

    2012-07-18

    Narrow band gap tin(II) chalcogenide (SnS, SnSe, SnTe) nanocrystals are of high interest for optoelectronic applications such as thin film solar cells or photodetectors. However, charge transfer and charge transport processes strongly depend on nanocrystals' surface quality. Using (119)Sn-Mössbauer spectroscopy, which is the most sensitive tool for probing the Sn oxidation state, we show that SnS nanocrystals exhibit a Sn((IV))/Sn((II)) ratio of around 20:80 before and 40:60 after five minutes exposure to air. Regardless of the tin or sulfur precursors used, similar results are obtained using six different synthesis protocols. The Sn((IV)) content before air exposure arises from surface related SnS(2) and Sn(2)S(3) species as well as from surface Sn atoms bound to oleic acid ligands. The increase of the Sn((IV)) content upon air exposure results from surface oxidation. Full oxidation of the SnS nanocrystals without size change is achieved by annealing at 500 °C in air. With the goal to prevent surface oxidation, SnS nanocrystals are capped with a cadmium-phosphonate complex. A broad photoluminescence signal centered at 600 nm indicates successful capping, which however does not reduce the air sensitivity. Finally we demonstrate that SnSe nanocrystals exhibit a very similar behavior with a Sn((IV))/Sn((II)) ratio of 43:57 after air exposure. In the case of SnTe nanocrystals, the ratio of 55:45 is evidence of a more pronounced tendency for oxidation. These results demonstrate that prior to their use in optoelectronics further surface engineering of tin chalcogenide nanocrystals is required, which otherwise have to be stored and processed under inert atmosphere. PMID:22691030

  15. Revealing the role of catechol moieties in the interactions between peptides and inorganic surfaces.

    PubMed

    Das, Priyadip; Reches, Meital

    2016-08-18

    Catechol (1,2-dihydroxy benzene) moieties are being widely used today in new adhesive technologies. Understanding their mechanism of action is therefore of high importance for developing their applications in materials science. This paper describes a single-molecule study of the interactions between catechol-related amino acid residues and a well-defined titanium dioxide (TiO2) surface. It is the first quantified measurement of the adhesion of these residues with a well-defined TiO2 surface. Single-molecule force spectroscopy measurements with AFM determined the role of different substitutions of the catechol moiety on the aromatic ring in the adhesion to the surface. These results shed light on the nature of interactions between these residues and inorganic metal oxide surfaces. This information is important for the design and fabrication of catechol-based materials such as hydrogels, coatings, and composites. Specifically, the interaction with TiO2 is important for the development of solar cells. PMID:27503417

  16. Surface area and cortical thickness descriptors reveal different attributes of the structural human brain networks.

    PubMed

    Sanabria-Diaz, Gretel; Melie-García, Lester; Iturria-Medina, Yasser; Alemán-Gómez, Yasser; Hernández-González, Gertrudis; Valdés-Urrutia, Lourdes; Galán, Lídice; Valdés-Sosa, Pedro

    2010-05-01

    Recently, a related morphometry-based connection concept has been introduced using local mean cortical thickness and volume to study the underlying complex architecture of the brain networks. In this article, the surface area is employed as a morphometric descriptor to study the concurrent changes between brain structures and to build binarized connectivity graphs. The statistical similarity in surface area between pair of regions was measured by computing the partial correlation coefficient across 186 normal subjects of the Cuban Human Brain Mapping Project. We demonstrated that connectivity matrices obtained follow a small-world behavior for two different parcellations of the brain gray matter. The properties of the connectivity matrices were compared to the matrices obtained using the mean cortical thickness for the same cortical parcellations. The topology of the cortical thickness and surface area networks were statistically different, demonstrating that both capture distinct properties of the interaction or different aspects of the same interaction (mechanical, anatomical, chemical, etc.) between brain structures. This finding could be explained by the fact that each descriptor is driven by distinct cellular mechanisms as result of a distinct genetic origin. To our knowledge, this is the first time that surface area is used to study the morphological connectivity of brain networks. PMID:20083210

  17. Cell surface and secreted protein profiles of human thyroid cancer cell lines reveal distinct glycoprotein patterns.

    PubMed

    Arcinas, Arthur; Yen, Ten-Yang; Kebebew, Electron; Macher, Bruce A

    2009-08-01

    Cell surface proteins have been shown to be effective therapeutic targets. In addition, shed forms of these proteins and secreted proteins can serve as biomarkers for diseases, including cancer. Thus, identification of cell surface and secreted proteins has been a prime area of interest in the proteomics field. Most cell surface and secreted proteins are known to be glycosylated, and therefore, a proteomics strategy targeting these proteins was applied to obtain proteomic profiles from various thyroid cancer cell lines that represent the range of thyroid cancers of follicular cell origin. In this study, we oxidized the carbohydrates of secreted proteins and those on the cell surface with periodate and isolated them via covalent coupling to hydrazide resin. The glycoproteins obtained were identified from tryptic peptides and N-linked glycopeptides released from the hydrazide resin using two-dimensional liquid chromatography-tandem mass spectrometry in combination with the gas phase fractionation. Thyroid cancer cell lines derived from papillary thyroid cancer (TPC-1), follicular thyroid cancer (FTC-133), Hurthle cell carcinoma (XTC-1), and anaplastic thyroid cancer (ARO and DRO-1) were evaluated. An average of 150 glycoproteins were identified per cell line, of which more than 57% are known cell surface or secreted glycoproteins. The usefulness of the approach for identifying thyroid cancer associated biomarkers was validated by the identification of glycoproteins (e.g., CD44, galectin 3 and metalloproteinase inhibitor 1) that have been found to be useful markers for thyroid cancer. In addition to glycoproteins that are commonly expressed by all of the cell lines, we identified others that are only expressed in the more well-differentiated thyroid cancer cell lines (follicular, Hurthle cell and papillary), or by cell lines derived from undifferentiated tumors that are uniformly fatal forms of thyroid cancer (i.e., anaplastic). On the basis of the results obtained, a

  18. Typification of Natural Seasonal Dynamics of Vegetation to Reveal Impact of Land Surface Change on Environment (by Satellite Data)

    NASA Astrophysics Data System (ADS)

    Shevyrnogov, A.; Vysotskaya, G.; Sidko, A.; Dunaev, K.

    Deep insight into types of vegetation variability provided by AVHRR space scanner images of vegetation index spatial distribution helps reveal impact of land surface changes on environment.The Institute of Computational Modeling SB RAS has developed nonparametric algorithms of automatic to classify and recognize patterns of these images which helped to reveal: (1) major variability types (generally connected); (2) areas belonging to small classes, which can be used to reveal deviations from ``normal'' (e.g., forest fires, etc.); (3) deviation from a certain type of dynamics indicative of changes in condition of plants, which can be used to diagnose pathology at early stages; (4) impact of economical activities on vegetation in Norilsk area. The authors provide biological interpretation of the satellite data. Computer-animated dynamics and color maps are presented. Nonparametric algorithms of an automatic classification and pattern recognition were provided by the Institute of Computational Modeling SB RAS

  19. Rapid regional surface uplift of the northern Altiplano plateau revealed by multiproxy paleoclimate reconstruction

    NASA Astrophysics Data System (ADS)

    Kar, Nandini; Garzione, Carmala N.; Jaramillo, Carlos; Shanahan, Timothy; Carlotto, Victor; Pullen, Alex; Moreno, Federico; Anderson, Veronica; Moreno, Enrique; Eiler, John

    2016-08-01

    The central Altiplano is inferred to have experienced ∼ 2.5 ± 1km surface uplift between ∼10 and 6 Ma, while the southern Altiplano experienced a similar magnitude of surface uplift that began earlier, between ∼16 and 9 Ma. To properly constrain the along strike timing of the Altiplano plateau surface uplift, it is necessary to know how and when the northernmost part of the Altiplano plateau evolved. We reconstruct the paleoclimate and infer the corresponding paleoelevation from the Miocene-Pliocene deposits of the Descanso-Yauri basin (14-15°S) in the northernmost part of the Altiplano plateau using 4 different proxies, including carbonate clumped isotope composition (i.e., Δ47 values), carbonate δ18Oc, leaf wax δDwax and pollen assemblages from paleosol, lacustrine and palustrine carbonates and organic-rich sediments. The isotopic signatures reflect past climate conditions of mean annual air temperature (Δ47) and meteoric water isotope values (δ18Oc, δDwax). Our results show that the northernmost plateau remained at low elevation (0.9 ± 0.8 to 2.1 ± 0.9km) until late Miocene time (∼9 Ma) characterized by ∼15 °C warmer than modern temperature (mean annual air temperature of 23 ± 4 °C, 2σ), low elevation vegetation and precipitation signature with reconstructed □ δ18Omw (VSMOW) of - 8.3 ± 2.0 ‰ (2 σ) from carbonate (δ18Oc) and - 8.6 ± 1.8 ‰ (2 σ) from leaf wax (δDwax). Modern elevations of 4 km were not reached until 5.4 ± 1.0Ma, as indicated by a negative shift in δDwax (VSMOW) from - 143.4 ± 12.8 ‰ (2 σ) to - 209.2 ± 21.1 ‰ (2 σ) between 9.1 ± 0.7 and 5.4 ± 1.0Ma. The timing of surface uplift of the northernmost Altiplano is consistent with the evidence for late Miocene surface uplift of the central Altiplano (16-19°S) between 10 and 6 Ma, and indicates that regional scale uplift in the northern-central plateau significantly postdates the onset of surface uplift in the southern Altiplano (19-22°S) between ∼16

  20. Depth-variant azimuthal anisotropy in Tibet revealed by surface wave tomography

    NASA Astrophysics Data System (ADS)

    Pandey, Shantanu; Yuan, Xiaohui; Debayle, Eric; Tilmann, Frederik; Priestley, Keith; Li, Xueqing

    2015-06-01

    Azimuthal anisotropy derived from multimode Rayleigh wave tomography in China exhibits depth-dependent variations in Tibet, which can be explained as induced by the Cenozoic India-Eurasian collision. In west Tibet, the E-W fast polarization direction at depths <100 km is consistent with the accumulated shear strain in the Tibetan lithosphere, whereas the N-S fast direction at greater depths is aligned with Indian Plate motion. In northeast Tibet, depth-consistent NW-SE directions imply coupled deformation throughout the whole lithosphere, possibly also involving the underlying asthenosphere. Significant anisotropy at depths of 225 km in southeast Tibet reflects sublithospheric deformation induced by northward and eastward lithospheric subduction beneath the Himalaya and Burma, respectively. The multilayer anisotropic surface wave model can explain some features of SKS splitting measurements in Tibet, with differences probably attributable to the limited back azimuthal coverage of most SKS studies in Tibet and the limited horizontal resolution of the surface wave results.

  1. Chemical Heterogeneity on Mercury's Surface Revealed by the MESSENGER X-ray Spectrometer

    NASA Technical Reports Server (NTRS)

    Weider, Shoshana Z.; Nittler, Larry R.; Starr, Richard D.; McCoy, Timothy J.; Stockstill-Cahill, Karen R.; Byrne, Paul K.; Denevi, Brett W.; Head, James W.; Solomon, Sean C.

    2012-01-01

    We present the analysis of 205 spatially resolved measurements of the surfacecomposition of Mercury from MESSENGERs X-Ray Spectrometer. The surfacefootprints of these measurements are categorized according to geological terrain. Northernsmooth plains deposits and the plains interior to the Caloris basin differ compositionallyfrom older terrain on Mercury. The older terrain generally has higher MgSi, SSi, andCaSi ratios, and a lower AlSi ratio than the smooth plains. Mercurys surface mineralogyis likely dominated by high-Mg mafic minerals (e.g., enstatite), plagioclase feldspar, andlesser amounts of Ca, Mg, andor Fe sulfides (e.g., oldhamite). The compositionaldifference between the volcanic smooth plains and the older terrain reflects differentabundances of these minerals and points to the crystallization of the smooth plains from amore chemically evolved magma source. High-degree partial melts of enstatite chondritematerial provide a generally good compositional and mineralogical match for much ofthe surface of Mercury. An exception is Fe, for which the low surface abundance onMercury is still higher than that of melts from enstatite chondrites and may indicate anexogenous contribution from meteoroid impacts.

  2. Oxygen anomaly in near surface carbon dioxide reveals deep stratospheric intrusion

    PubMed Central

    Liang, Mao-Chang; Mahata, Sasadhar

    2015-01-01

    Stratosphere-troposphere exchange could be enhanced by tropopause folding, linked to variability in the subtropical jet stream. Relevant to tropospheric biogeochemistry is irreversible transport from the stratosphere, associated with deep intrusions. Here, oxygen anomalies in near surface air CO2 are used to study the irreversible transport from the stratosphere, where the triple oxygen isotopes of CO2 are distinct from those originating from the Earth’s surface. We show that the oxygen anomaly in CO2 is observable at sea level and the magnitude of the signal increases during the course of our sampling period (September 2013-February 2014), concordant with the strengthening of the subtropical jet system and the East Asia winter monsoon. The trend of the anomaly is found to be 0.1‰/month (R2 = 0.6) during the jet development period in October. Implications for utilizing the oxygen anomaly in CO2 for CO2 biogeochemical cycle study and stratospheric intrusion flux at the surface are discussed. PMID:26081178

  3. Cryovolcanic features on Titan's surface as revealed by the Cassini Titan Radar Mapper

    USGS Publications Warehouse

    Lopes, R.M.C.; Mitchell, K.L.; Stofan, E.R.; Lunine, J.I.; Lorenz, R.; Paganelli, F.; Kirk, R.L.; Wood, C.A.; Wall, S.D.; Robshaw, L.E.; Fortes, A.D.; Neish, C.D.; Radebaugh, J.; Reffet, E.; Ostro, S.J.; Elachi, C.; Allison, M.D.; Anderson, Y.; Boehmer, R.; Boubin, G.; Callahan, P.; Encrenaz, P.; Flamini, E.; Francescetti, G.; Gim, Y.; Hamilton, G.; Hensley, S.; Janssen, M.A.; Johnson, W.T.K.; Kelleher, K.; Muhleman, D.O.; Ori, G.; Orosei, R.; Picardi, G.; Posa, F.; Roth, L.E.; Seu, R.; Shaffer, S.; Soderblom, L.A.; Stiles, B.; Vetrella, S.; West, R.D.; Wye, L.; Zebker, H.A.

    2007-01-01

    The Cassini Titan Radar Mapper obtained Synthetic Aperture Radar images of Titan's surface during four fly-bys during the mission's first year. These images show that Titan's surface is very complex geologically, showing evidence of major planetary geologic processes, including cryovolcanism. This paper discusses the variety of cryovolcanic features identified from SAR images, their possible origin, and their geologic context. The features which we identify as cryovolcanic in origin include a large (180 km diameter) volcanic construct (dome or shield), several extensive flows, and three calderas which appear to be the source of flows. The composition of the cryomagma on Titan is still unknown, but constraints on rheological properties can be estimated using flow thickness. Rheological properties of one flow were estimated and appear inconsistent with ammonia-water slurries, and possibly more consistent with ammonia-water-methanol slurries. The extent of cryovolcanism on Titan is still not known, as only a small fraction of the surface has been imaged at sufficient resolution. Energetic considerations suggest that cryovolcanism may have been a dominant process in the resurfacing of Titan. ?? 2006 Elsevier Inc.

  4. Oxygen anomaly in near surface carbon dioxide reveals deep stratospheric intrusion.

    PubMed

    Liang, Mao-Chang; Mahata, Sasadhar

    2015-01-01

    Stratosphere-troposphere exchange could be enhanced by tropopause folding, linked to variability in the subtropical jet stream. Relevant to tropospheric biogeochemistry is irreversible transport from the stratosphere, associated with deep intrusions. Here, oxygen anomalies in near surface air CO2 are used to study the irreversible transport from the stratosphere, where the triple oxygen isotopes of CO2 are distinct from those originating from the Earth's surface. We show that the oxygen anomaly in CO2 is observable at sea level and the magnitude of the signal increases during the course of our sampling period (September 2013-February 2014), concordant with the strengthening of the subtropical jet system and the East Asia winter monsoon. The trend of the anomaly is found to be 0.1‰/month (R(2) = 0.6) during the jet development period in October. Implications for utilizing the oxygen anomaly in CO2 for CO2 biogeochemical cycle study and stratospheric intrusion flux at the surface are discussed. PMID:26081178

  5. Zika virus NS1 structure reveals diversity of electrostatic surfaces among flaviviruses.

    PubMed

    Song, Hao; Qi, Jianxun; Haywood, Joel; Shi, Yi; Gao, George F

    2016-05-01

    The association of Zika virus (ZIKV) infections with microcephaly has resulted in an ongoing public-health emergency. Here we report the crystal structure of a C-terminal fragment of ZIKV nonstructural protein 1 (NS1), a major host-interaction molecule that functions in flaviviral replication, pathogenesis and immune evasion. Comparison with West Nile and dengue virus NS1 structures reveals conserved features but diverse electrostatic characteristics at host-interaction interfaces, thus possibly implying different modes of flavivirus pathogenesis. PMID:27088990

  6. Aquarius sea surface salinity in the South Indian Ocean: Revealing annual-period planetary waves

    NASA Astrophysics Data System (ADS)

    Menezes, Viviane V.; Vianna, Marcio L.; Phillips, Helen E.

    2014-06-01

    A new milestone has been reached with the launch of two dedicated satellite missions to routinely measure the sea surface salinity (SSS) fields from space at global and regional scales. In the present work, a thorough analysis of the first 2 years of Aquarius SSS data in the South Indian Ocean is performed. This analysis is focused on three questions: How accurate is Aquarius SSS related to in situ data from the fresh Indonesian Throughflow and salty subtropical waters? Can Aquarius give a spatial context for the data measured by the RAMA mooring system? Are westward propagating annual-period signals described in recent model simulations reproduced by Aquarius-derived SSS? We find Aquarius observations to be highly correlated with those of Argo floats, with small disagreements occurring near oceanic fronts. Aquarius gives fresher SSS than in situ data in the tropical region due to rainfall effects, except in the eastern basin where the freshening seems to be related to sharp localized leakages of very fresh waters from the Indonesian seas that the Aquarius product is not able to properly resolve. Aquarius data are shown to reproduce quite well the annual cycle obtained from RAMA and Argo gridded data sets. The annual cycle in Aquarius is characterized by SSS propagating features with different characteristics west and east of the Ninety East Ridge. These features are strikingly different from sea surface height waves. Our results suggest that SSS annual propagation might be reflecting coupled ocean-atmosphere dynamics and surface-subsurface processes operating over the entire South Indian Ocean.

  7. Cells transplanted onto the surface of the glial scar reveal hidden potential for functional neural regeneration

    PubMed Central

    Sekiya, Tetsuji; Holley, Matthew C.; Hashido, Kento; Ono, Kazuya; Shimomura, Koichiro; Horie, Rie T.; Hamaguchi, Kiyomi; Yoshida, Atsuhiro; Sakamoto, Tatsunori; Ito, Juichi

    2015-01-01

    Cell transplantation therapy has long been investigated as a therapeutic intervention for neurodegenerative disorders, including spinal cord injury, Parkinson’s disease, and amyotrophic lateral sclerosis. Indeed, patients have high hopes for a cell-based therapy. However, there are numerous practical challenges for clinical translation. One major problem is that only very low numbers of donor cells survive and achieve functional integration into the host. Glial scar tissue in chronic neurodegenerative disorders strongly inhibits regeneration, and this inhibition must be overcome to accomplish successful cell transplantation. Intraneural cell transplantation is considered to be the best way to deliver cells to the host. We questioned this view with experiments in vivo on a rat glial scar model of the auditory system. Our results show that intraneural transplantation to the auditory nerve, preceded by chondroitinase ABC (ChABC)-treatment, is ineffective. There is no functional recovery, and almost all transplanted cells die within a few weeks. However, when donor cells are placed on the surface of a ChABC-treated gliotic auditory nerve, they autonomously migrate into it and recapitulate glia- and neuron-guided cell migration modes to repair the auditory pathway and recover auditory function. Surface transplantation may thus pave the way for improved functional integration of donor cells into host tissue, providing a less invasive approach to rescue clinically important neural tracts. PMID:26080415

  8. Eye movements reveal distinct encoding patterns for number and cumulative surface area in random dot arrays

    PubMed Central

    Odic, Darko; Halberda, Justin

    2015-01-01

    Humans can quickly and intuitively represent the number of objects in a scene using visual evidence through the Approximate Number System (ANS). But the computations that support the encoding of visual number—the transformation from the retinal input into ANS representations—remain controversial. Two types of number encoding theories have been proposed: those arguing that number is encoded through a dedicated, enumeration computation, and those arguing that visual number is inferred from nonnumber specific visual features, such as surface area, density, convex hull, etc. Here, we attempt to adjudicate between these two theories by testing participants on both a number and a cumulative area task while also tracking their eye-movements. We hypothesize that if approximate number and surface area depend on distinct encoding computations, saccadic signatures should be distinct for the two tasks, even if the visual stimuli are identical. Consistent with this hypothesis, we find that discriminating number versus cumulative area modulates both where participants look (i.e., participants spend more time looking at the more numerous set in the number task and the larger set in the cumulative area task), and how participants look (i.e., cumulative area encoding shows fewer, longer saccades, while number encoding shows many short saccades and many switches between targets). We further identify several saccadic signatures that are associated with task difficulty and correct versus incorrect trials for both dimensions. These results suggest distinct encoding algorithms for number and cumulative area extraction, and thereby distinct representations of these dimensions. PMID:26575191

  9. Cell-surface MHC density profiling reveals instability of autoimmunity-associated HLA

    PubMed Central

    Miyadera, Hiroko; Ohashi, Jun; Lernmark, Åke; Kitamura, Toshio; Tokunaga, Katsushi

    2014-01-01

    Polymorphisms within HLA gene loci are strongly associated with susceptibility to autoimmune disorders; however, it is not clear how genetic variations in these loci confer a disease risk. Here, we devised a cell-surface MHC expression assay to detect allelic differences in the intrinsic stability of HLA-DQ proteins. We found extreme variation in cell-surface MHC density among HLA-DQ alleles, indicating a dynamic allelic hierarchy in the intrinsic stability of HLA-DQ proteins. Using the case-control data for type 1 diabetes (T1D) for the Swedish and Japanese populations, we determined that T1D risk–associated HLA-DQ haplotypes, which also increase risk for autoimmune endocrinopathies and other autoimmune disorders, encode unstable proteins, whereas the T1D–protective haplotypes encode the most stable HLA-DQ proteins. Among the amino acid variants of HLA-DQ, alterations in 47α, the residue that is located on the outside of the peptide-binding groove and acts as a key stability regulator, showed strong association with T1D. Evolutionary analysis suggested that 47α variants have been the target of positive diversifying selection. Our study demonstrates a steep allelic hierarchy in the intrinsic stability of HLA-DQ that is associated with T1D risk and protection, suggesting that HLA instability mediates the development of autoimmune disorders. PMID:25485681

  10. Superresolution fluorescence mapping of single-nanoparticle catalysts reveals spatiotemporal variations in surface reactivity

    PubMed Central

    Zhang, Yuwei; Lucas, J. Matthew; Song, Ping; Beberwyck, Brandon; Fu, Qiang; Xu, Weilin; Alivisatos, A. Paul

    2015-01-01

    For the practical application of nanocatalysts, it is desirable to understand the spatiotemporal fluctuations of nanocatalytic activity at the single-nanoparticle level. Here we use time-lapsed superresolution mapping of single-molecule catalysis events on individual nanoparticles to observe time-varying changes in the spatial distribution of catalysis events on Sb-doped TiO2 nanorods and Au triangle nanoplates. Compared with the active sites on well-defined surface facets, the defects of the nanoparticle catalysts possess higher intrinsic reactivity but lower stability. Corners and ends are more reactive but also less stable than flat surfaces. Averaged over time, the most stable sites dominate the total apparent activity of single nanocatalysts. However, the active sites with higher intrinsic activity but lower stability show activity at earlier time points before deactivating. Unexpectedly, some active sites are found to recover their activity (“self-healing”) after deactivation, which is probably due to desorption of the adsorbate. Our superresolution measurement of different types of active catalytic sites, over both space and time, leads to a more comprehensive understanding of reactivity patterns and may enable the design of new and more productive heterogeneous catalysts. PMID:26150516