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Sample records for reveals unique surface

  1. Two Unique Glioma Subtypes Revealed.

    PubMed

    Poh, Alissa

    2016-04-01

    A comprehensive analysis of 1,122 diffuse glioma samples from The Cancer Genome Atlas has revealed two new subtypes of this common brain cancer, with molecular and clinical features that diverge from the norm. The study findings also support the use of DNA methylation profiles to improve glioma classification and treatment.

  2. The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation.

    PubMed

    Winter, Jody A; Christofi, Panayiotis; Morroll, Shaun; Bunting, Karen A

    2009-08-22

    The high intracellular salt concentration required to maintain a halophilic lifestyle poses challenges to haloarchaeal proteins that must stay soluble, stable and functional in this extreme environment. Proliferating cell nuclear antigen (PCNA) is a fundamental protein involved in maintaining genome integrity, with roles in both DNA replication and repair. To investigate the halophilic adaptation of such a key protein we have crystallised and solved the structure of Haloferax volcanii PCNA (HvPCNA) to a resolution of 2.0 A. The overall architecture of HvPCNA is very similar to other known PCNAs, which are highly structurally conserved. Three commonly observed adaptations in halophilic proteins are higher surface acidity, bound ions and increased numbers of intermolecular ion pairs (in oligomeric proteins). HvPCNA possesses the former two adaptations but not the latter, despite functioning as a homotrimer. Strikingly, the positive surface charge considered key to PCNA's role as a sliding clamp is dramatically reduced in the halophilic protein. Instead, bound cations within the solvation shell of HvPCNA may permit sliding along negatively charged DNA by reducing electrostatic repulsion effects. The extent to which individual proteins adapt to halophilic conditions varies, presumably due to their diverse characteristics and roles within the cell. The number of ion pairs observed in the HvPCNA monomer-monomer interface was unexpectedly low. This may reflect the fact that the trimer is intrinsically stable over a wide range of salt concentrations and therefore additional modifications for trimer maintenance in high salt conditions are not required. Halophilic proteins frequently bind anions and cations and in HvPCNA cation binding may compensate for the remarkable reduction in positive charge in the pore region, to facilitate functional interactions with DNA. In this way, HvPCNA may harness its environment as opposed to simply surviving in extreme halophilic conditions.

  3. 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.

  4. Uniqueness of static photon surfaces: Perturbative approach

    NASA Astrophysics Data System (ADS)

    Yoshino, Hirotaka

    2017-02-01

    A photon surface S is defined as a three-dimensional timelike hypersurface such that any null geodesic initially tangent to S continues to be included in S , like r =3 M of the Schwarzschild spacetime. Using analytic solutions to static perturbations of a Schwarzschild spacetime, we examine whether a nonspherical spacetime can possess a distorted static photon surface. It is shown that if the region outside of r =3 M is vacuum, no distorted photon surface can be present. Therefore, we establish the perturbative uniqueness for an asymptotically flat vacuum spacetime with a static photon surface. It is also pointed out that if matter is present in the outside region, there is a possibility that a distorted photon surface could form.

  5. On the uniqueness of the surface sources of evoked potentials.

    PubMed

    Cabo, A; Handy, C; Bessis, D

    2001-10-01

    The uniqueness of a surface density of sources localized inside a spatial region R and producing a given electric potential distribution in its boundary B0 is revisited. The situation in which R is filled with various subregions, each one having a definite constant value for the electric conductivity is considered. It is argued that the knowledge of the potential in all B0 fully determines the surface-located sources for a general class of surfaces supporting them and also a wide type of those sources. The class of surfaces can be defined as a union of an arbitrary but finite number of open or closed surfaces. The only restriction upon them is that no one of the closed surfaces contains inside it another (nesting) of the closed or open ones. The types of sources are surface charge densities and double layer (dipolar) densities for the open surfaces and more restrictively, only surface charge densities for the closed ones. A two-dimensional analytically solvable example illustrating the drastic appearance of uniqueness after arbitrarily small holes are opened in nested surfaces is discussed.

  6. 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

  7. 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.

  8. 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.

  9. Unique topological surface states of full-Heusler topological crystalline insulators

    NASA Astrophysics Data System (ADS)

    Pham, Anh; Li, Sean

    2017-03-01

    Our theoretical analysis reveals that a family of full-Heusler materials exhibit unique topological surface states with type-I and type-II Dirac quasiparticles. The type-I Dirac surface state is characterized by an enclosed Fermi surface, while the type-II Dirac surfaces occur at the touching of the electron and hole pockets. In addition, due to the layered nature of the full-Heusler crystals structured with a wide range of various elements, such structures induce multiple Dirac surface states with different Lifshitz transitions protected by more than one mirror plane.

  10. 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

  11. 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

  12. Unique lift-off of droplet impact on high temperature nanotube surfaces

    NASA Astrophysics Data System (ADS)

    Tong, Wei; Qiu, Lu; Jin, Jian; Sun, Lidong; Duan, Fei

    2017-08-01

    A unique liquid film lift-off during a falling water droplet impacting on a heated titanium oxide nanotube surface has been experimentally revealed through a high speed visualization system. It is suggested that the Leidenfrost point on the nanotube surface has been significantly delayed, as compared to that on the bare titanium surface. Such delay is inferred to be a result of the increase in the surface wettability and the capillary effect by the nanoscale tube structure. By measuring the liquid lift-off distance from the substrate surface, a droplet lift-off is typically divided into four stages, namely, first contact, first lift-off, second contact, and second lift-off. The residence time at each stage is quantitatively evaluated. As the surface temperature increases, the duration time is significantly reduced for both the first contact and the first lift-off stages.

  13. SR2067 reveals a unique kinetic and structural signature for PPARγ partial agonism

    SciTech Connect

    van Marrewijk, Laura M.; Polyak, Steven W.; Hijnen, Marcel; Kuruvilla, Dana; Chang, Mi Ra; Shin, Youseung; Kamenecka, Theodore M.; Griffin, Patrick R.; Bruning, John B.

    2015-11-18

    Here, synthetic full agonists of PPARγ have been prescribed for the treatment of diabetes due to their ability to regulate glucose homeostasis and insulin sensitization. While the use of full agonists of PPARγ has been hampered due to severe side effects, partial agonists have shown promise due to their decreased incidence of such side effects in preclinical models. No kinetic information has been forthcoming in regard to the mechanism of full versus partial agonism of PPARγ to date. In this paper, we describe the discovery of a partial agonist, SR2067. A co-crystal structure obtained at 2.2 Å resolution demonstrates that interactions with the β-sheet are driven exclusively via hydrophobic interactions mediated through a naphthalene group, an observation that is unique from other partial agonists. Finally, surface plasmon resonance revealed that SR2067 binds to the receptor with higher affinity (KD = 513 nM) as compared to that of full agonist rosiglitazone, yet it has a much slower off rate compared to that of rosiglitazone.

  14. SR2067 reveals a unique kinetic and structural signature for PPARγ partial agonism

    DOE PAGES

    van Marrewijk, Laura M.; Polyak, Steven W.; Hijnen, Marcel; ...

    2015-11-18

    Here, synthetic full agonists of PPARγ have been prescribed for the treatment of diabetes due to their ability to regulate glucose homeostasis and insulin sensitization. While the use of full agonists of PPARγ has been hampered due to severe side effects, partial agonists have shown promise due to their decreased incidence of such side effects in preclinical models. No kinetic information has been forthcoming in regard to the mechanism of full versus partial agonism of PPARγ to date. In this paper, we describe the discovery of a partial agonist, SR2067. A co-crystal structure obtained at 2.2 Å resolution demonstrates thatmore » interactions with the β-sheet are driven exclusively via hydrophobic interactions mediated through a naphthalene group, an observation that is unique from other partial agonists. Finally, surface plasmon resonance revealed that SR2067 binds to the receptor with higher affinity (KD = 513 nM) as compared to that of full agonist rosiglitazone, yet it has a much slower off rate compared to that of rosiglitazone.« less

  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.

  16. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

    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

  18. Pattern Recognition Analysis Reveals Unique Contrast Sensitivity Isocontours Using Static Perimetry Thresholds Across the Visual Field

    PubMed Central

    Phu, Jack; Khuu, Sieu K.; Nivison-Smith, Lisa; Zangerl, Barbara; Choi, Agnes Yiu Jeung; Jones, Bryan W.; Pfeiffer, Rebecca L.; Marc, Robert E.; Kalloniatis, Michael

    2017-01-01

    Purpose To determine the locus of test locations that exhibit statistically similar age-related decline in sensitivity to light increments and age-corrected contrast sensitivity isocontours (CSIs) across the central visual field (VF). We compared these CSIs with test point clusters used by the Glaucoma Hemifield Test (GHT). Methods Sixty healthy observers underwent testing on the Humphrey Field Analyzer 30-2 test grid using Goldmann (G) stimulus sizes I-V. Age-correction factors for GI-V were determined using linear regression analysis. Pattern recognition analysis was used to cluster test locations across the VF exhibiting equal age-related sensitivity decline (age-related CSIs), and points of equal age-corrected sensitivity (age-corrected CSIs) for GI-V. Results There was a small but significant test size–dependent sensitivity decline with age, with smaller stimuli declining more rapidly. Age-related decline in sensitivity was more rapid in the periphery. A greater number of unique age-related CSIs was revealed when using smaller stimuli, particularly in the mid-periphery. Cluster analysis of age-corrected sensitivity thresholds revealed unique CSIs for GI-V, with smaller stimuli having a greater number of unique clusters. Zones examined by the GHT consisted of test locations that did not necessarily belong to the same CSI, particularly in the periphery. Conclusions Cluster analysis reveals statistically significant groups of test locations within the 30-2 test grid exhibiting the same age-related decline. CSIs facilitate pooling of sensitivities to reduce the variability of individual test locations. These CSIs could guide future structure-function and alternate hemifield asymmetry analyses by comparing matched areas of similar sensitivity signatures. PMID:28973333

  19. 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

  20. 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

    2013-01-07

    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.

  1. Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors

    PubMed Central

    Hughes, Andrew E. O.; Enright, Jennifer M.; Myers, Connie A.; Shen, Susan Q.; Corbo, Joseph C.

    2017-01-01

    Rod photoreceptors are specialized neurons that mediate vision in dim light and are the predominant photoreceptor type in nocturnal mammals. The rods of nocturnal mammals are unique among vertebrate cell types in having an ‘inverted’ nuclear architecture, with a dense mass of heterochromatin in the center of the nucleus rather than dispersed clumps at the periphery. To test if this unique nuclear architecture is correlated with a unique epigenomic landscape, we performed ATAC-seq on mouse rods and their most closely related cell type, cone photoreceptors. We find that thousands of loci are selectively closed in rods relative to cones as well as >60 additional cell types. Furthermore, we find that the open chromatin profile of photoreceptors lacking the rod master regulator Nrl is nearly indistinguishable from that of native cones, indicating that Nrl is required for selective chromatin closure in rods. Finally, we identified distinct enrichments of transcription factor binding sites in rods and cones, revealing key differences in the cis-regulatory grammar of these cell types. Taken together, these data provide insight into the development and maintenance of photoreceptor identity, and highlight rods as an attractive system for studying the relationship between nuclear organization and local changes in gene regulation. PMID:28256534

  2. 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

  3. 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.

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

    PubMed Central

    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.; 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.

    2010-01-01

    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

  5. Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis

    PubMed Central

    Liu, Wenjun; Zhang, Jiachao; Wu, Chunyan; Cai, Shunfeng; Huang, Weiqiang; Chen, Jing; XI, Xiaoxia; Liang, Zebin; Hou, Qiangchuan; Zhou, Bing; Qin, Nan; Zhang, Heping

    2016-01-01

    The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults gut microbiota by shotgun metagenomic sequencing and compared the intestinal microbiome among Mongolians, the Hans and European cohorts. The results showed that the taxonomic profile of intestinal microbiome among cohorts revealed the Actinobaceria and Bifidobacterium were the key microbes contributing to the differences among Mongolians, the Hans and Europeans at the phylum level and genus level, respectively. Metagenomic species analysis indicated that Faecalibacterium prausnitzii and Coprococcus comeswere enrich in Mongolian people which might contribute to gut health through anti-inflammatory properties and butyrate production, respectively. On the other hand, the enriched genus Collinsella, biomarker in symptomatic atherosclerosis patients, might be associated with the high morbidity of cardiovascular and cerebrovascular diseases in Mongolian adults. At the functional level, a unique microbial metabolic pathway profile was present in Mongolian’s gut which mainly distributed in amino acid metabolism, carbohydrate metabolism, energy metabolism, lipid metabolism, glycan biosynthesis and metabolism. We can attribute the specific signatures of Mongolian gut microbiome to their unique genotype, dietary habits and living environment. PMID:27708392

  6. Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis.

    PubMed

    Liu, Wenjun; Zhang, Jiachao; Wu, Chunyan; Cai, Shunfeng; Huang, Weiqiang; Chen, Jing; Xi, Xiaoxia; Liang, Zebin; Hou, Qiangchuan; Zhou, Bing; Qin, Nan; Zhang, Heping

    2016-10-06

    The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults gut microbiota by shotgun metagenomic sequencing and compared the intestinal microbiome among Mongolians, the Hans and European cohorts. The results showed that the taxonomic profile of intestinal microbiome among cohorts revealed the Actinobaceria and Bifidobacterium were the key microbes contributing to the differences among Mongolians, the Hans and Europeans at the phylum level and genus level, respectively. Metagenomic species analysis indicated that Faecalibacterium prausnitzii and Coprococcus comeswere enrich in Mongolian people which might contribute to gut health through anti-inflammatory properties and butyrate production, respectively. On the other hand, the enriched genus Collinsella, biomarker in symptomatic atherosclerosis patients, might be associated with the high morbidity of cardiovascular and cerebrovascular diseases in Mongolian adults. At the functional level, a unique microbial metabolic pathway profile was present in Mongolian's gut which mainly distributed in amino acid metabolism, carbohydrate metabolism, energy metabolism, lipid metabolism, glycan biosynthesis and metabolism. We can attribute the specific signatures of Mongolian gut microbiome to their unique genotype, dietary habits and living environment.

  7. 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.

  8. The complete genome sequences, unique mutational spectra and developmental potency of adult neurons revealed by cloning

    PubMed Central

    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.

    2016-01-01

    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 differs from other lineages, potentially due to novel mechanisms governing post-mitotic mutation. Fertile mice were cloned from several neurons, establishing the compatibility of mutated adult neuronal genomes with reprogramming to pluripotency and development. PMID:26948891

  9. Research Resource: RNA-Seq Reveals Unique Features of the Pancreatic β-Cell Transcriptome

    PubMed Central

    Ku, Gregory M.; Kim, Hail; Vaughn, Ian W.; Hangauer, Matthew J.; Myung Oh, Chang

    2012-01-01

    The pancreatic β-cell is critical for the maintenance of glycemic control. Knowing the compendium of genes expressed in β-cells will further our understanding of this critical cell type and may allow the identification of future antidiabetes drug targets. Here, we report the use of next-generation sequencing to obtain nearly 1 billion reads from the polyadenylated RNA of islets and purified β-cells from mice. These data reveal novel examples of β-cell-specific splicing events, promoter usage, and over 1000 long intergenic noncoding RNA expressed in mouse β-cells. Many of these long intergenic noncoding RNA are β-cell specific, and we hypothesize that this large set of novel RNA may play important roles in β-cell function. Our data demonstrate unique features of the β-cell transcriptome. PMID:22915829

  10. Genetic and molecular characterization reveals a unique nucleobase cation symporter 1 in Arabidopsis.

    PubMed

    Mourad, George S; Tippmann-Crosby, Julie; Hunt, Kevin A; Gicheru, Yvonne; Bade, Kaely; Mansfield, Tyler A; Schultes, Neil P

    2012-05-07

    Locus At5g03555 encodes a nucleobase cation symporter 1 (AtNCS1) in the Arabidopsis genome. Arabidopsis insertion mutants, AtNcs1-1 and AtNcs1-3, were used for in planta toxic nucleobase analog growth studies and radio-labeled nucleobase uptake assays to characterize solute transport specificities. These results correlate with similar growth and uptake studies of AtNCS1 expressed in Saccharomyces cerevisiae. Both in planta and heterologous expression studies in yeast revealed a unique solute transport profile for AtNCS1 in moving adenine, guanine and uracil. This is in stark contrast to the canonical transport profiles determined for the well-characterized S. cerevisiae NCS1 proteins FUR4 (uracil transport) or FCY2 (adenine, guanine, and cytosine transport).

  11. 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.

  12. 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.

  13. The surface layer protein of Bacillus thuringiensis CTC forms unique intracellular parasporal inclusion body.

    PubMed

    Zhu, Chenguang; Yu, Ziniu

    2008-08-01

    Bacillus thuringiensis subsp. finitimus strain CTC forms round parasporal inclusion body. The inclusion body protein gene ctc has been cloned and characterized. Sequence homology analysis reveals that the amino acid sequence of CTC protein shows 87% identity with the surface layer (S-layer) protein Sap (GenBank Z36946) in B. anthracis. In this report, transmission electron microscope observation showed that CTC formed intracellular parasporal inclusion body and sheet structure of S-layer-like protein at the spore phase. Furthermore, the ctc gene was transformed into an acrystalliferous B. thuringiensis strain BMB171. The resulting transformant could form parasporal body which had the same shape and molecular weight of protein with that of B. thuringiensis CTC. These results, together with the sequence homology analysis of ctc gene, confirmed that the unique intracellular parasporal inclusion body of B. thuringiensis was comprised of S-layer protein.

  14. Myelin-phagocytosing macrophages in isolated sciatic and optic nerves reveal a unique reactive phenotype.

    PubMed

    van Rossum, Denise; Hilbert, Sören; Strassenburg, Silke; Hanisch, Uwe-Karsten; Brück, Wolfgang

    2008-02-01

    Macrophages are key effectors in demyelinating diseases of the central and peripheral nervous system by phagocytosing myelin and releasing immunoregulatory mediators. Here, we report on a distinct, a priori anti-inflammatory reaction of macrophages phagocytosing myelin upon contact with damaged nerve tissue. Macrophages rapidly invaded peripheral (sciatic) and central (optic) nerve tissues in vitro, readily incorporated myelin and expressed high levels of phagocytosis-associated molecules (e.g., Fc and scavenger receptors). In contrast, factors involved in antigen presentation (MHC class-II, CD80, CD86) revealed only a restricted expression. In parallel, a highly ordered appearance of cytokines and chemokines was detected. IL-10, IL-6, CCL22, and CXCL1 were immediately but transiently induced, whereas CCL2, CCL11, and TGFbeta revealed more persisting levels. Such a profile would attract neutrophils, monocytes/macrophages, and Th2 cells as well as bias for a Th2-supporting environment. Importantly, proinflammatory/Th1-supporting factors, such as TNFalpha, IL-12p70, CCL3, and CCL5, were not induced. Still the simultaneous presence of TGFbeta and IL-6 could assist Th17 development, further depending on yet not present IL-23. The release pattern was clearly distinct from reactive phenotypes induced in isolated macrophages and microglia upon treatment with IL-4, IL-13, bacterial lipopolysaccharide, IFNgamma, or purified myelin. Nerve-exposed macrophages thus commit to a unique functional orientation.

  15. Comparative study of the human ficolins reveals unique features of Ficolin-3 (Hakata antigen).

    PubMed

    Hummelshoj, Tina; Fog, Lea Munthe; Madsen, Hans O; Sim, Robert B; Garred, Peter

    2008-03-01

    The ficolins and mannose-binding lectin (MBL) are collagen-like defence proteins that serve as recognition molecules in lectin complement pathway. Differential features that may indicate diverse functions of these proteins are poorly understood. In this study we compared important biological features of the ficolins and MBL. We investigated the tissue distribution of the FCN1-3 and the MBL2 genes encoding the ficolins and MBL by quantitative PCR. Recombinant proteins were produced and structural and biological characteristics were investigated and compared. Our main findings were that FCN3 mRNA was highly expressed in the liver and lung compared with the other genes revealing the lung as the tissue with the highest FCN3 expression pattern. Ficolin-3 revealed higher complement activating capacity compared with Ficolin-2, MBL and Ficolin-1 and was highly resistant to bacterial collagenase treatment, which is different from the other ficolins and MBL. We discovered several unique properties of Ficolin-3 showing that FCN3 is the most highly expressed gene in liver and lung among the lectin complement pathway initiators. Moreover, Ficolin-3 has a high complement activating potential and is the only collagenase proteolytic resistant molecule among the lectin complement pathway initiators.

  16. 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

  17. Chætognath transcriptome reveals ancestral and unique features among bilaterians

    PubMed Central

    Marlétaz, Ferdinand; Gilles, André; Caubit, Xavier; Perez, Yvan; Dossat, Carole; Samain, Sylvie; Gyapay, Gabor; Wincker, Patrick; Le Parco, Yannick

    2008-01-01

    Background The chætognaths (arrow worms) have puzzled zoologists for years because of their astonishing morphological and developmental characteristics. Despite their deuterostome-like development, phylogenomic studies recently positioned the chætognath phylum in protostomes, most likely in an early branching. This key phylogenetic position and the peculiar characteristics of chætognaths prompted further investigation of their genomic features. Results Transcriptomic and genomic data were collected from the chætognath Spadella cephaloptera through the sequencing of expressed sequence tags and genomic bacterial artificial chromosome clones. Transcript comparisons at various taxonomic scales emphasized the conservation of a core gene set and phylogenomic analysis confirmed the basal position of chætognaths among protostomes. A detailed survey of transcript diversity and individual genotyping revealed a past genome duplication event in the chætognath lineage, which was, surprisingly, followed by a high retention rate of duplicated genes. Moreover, striking genetic heterogeneity was detected within the sampled population at the nuclear and mitochondrial levels but cannot be explained by cryptic speciation. Finally, we found evidence for trans-splicing maturation of transcripts through splice-leader addition in the chætognath phylum and we further report that this processing is associated with operonic transcription. Conclusion These findings reveal both shared ancestral and unique derived characteristics of the chætognath genome, which suggests that this genome is likely the product of a very original evolutionary history. These features promote chætognaths as a pivotal model for comparative genomics, which could provide new clues for the investigation of the evolution of animal genomes. PMID:18533022

  18. 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.

  19. In situ structure of trypanosomal ATP synthase dimer reveals a unique arrangement of catalytic subunits

    PubMed Central

    Mühleip, Alexander W.; Dewar, Caroline E.; Schnaufer, Achim; Kühlbrandt, Werner; Davies, Karen M.

    2017-01-01

    We used electron cryotomography and subtomogram averaging to determine the in situ structures of mitochondrial ATP synthase dimers from two organisms belonging to the phylum euglenozoa: Trypanosoma brucei, a lethal human parasite, and Euglena gracilis, a photosynthetic protist. At a resolution of 32.5 Å and 27.5 Å, respectively, the two structures clearly exhibit a noncanonical F1 head, in which the catalytic (αβ)3 assembly forms a triangular pyramid rather than the pseudo-sixfold ring arrangement typical of all other ATP synthases investigated so far. Fitting of known X-ray structures reveals that this unusual geometry results from a phylum-specific cleavage of the α subunit, in which the C-terminal αC fragments are displaced by ∼20 Å and rotated by ∼30° from their expected positions. In this location, the αC fragment is unable to form the conserved catalytic interface that was thought to be essential for ATP synthesis, and cannot convert γ-subunit rotation into the conformational changes implicit in rotary catalysis. The new arrangement of catalytic subunits suggests that the mechanism of ATP generation by rotary ATPases is less strictly conserved than has been generally assumed. The ATP synthases of these organisms present a unique model system for discerning the individual contributions of the α and β subunits to the fundamental process of ATP synthesis. PMID:28096380

  20. 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

  1. Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen.

    PubMed

    Adissu, Hibret A; Estabel, Jeanne; Sunter, David; Tuck, Elizabeth; Hooks, Yvette; Carragher, Damian M; Clarke, Kay; Karp, Natasha A; Newbigging, Susan; Jones, Nora; Morikawa, Lily; White, Jacqueline K; McKerlie, Colin

    2014-05-01

    The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.

  2. 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.

  3. 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.

  4. The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods

    PubMed Central

    Cao, Zhijian; Yu, Yao; Wu, Yingliang; Hao, Pei; Di, Zhiyong; He, Yawen; Chen, Zongyun; Yang, Weishan; Shen, Zhiyong; He, Xiaohua; Sheng, Jia; Xu, Xiaobo; Pan, Bohu; Feng, Jing; Yang, Xiaojuan; Hong, Wei; Zhao, Wenjuan; Li, Zhongjie; Huang, Kai; Li, Tian; Kong, Yimeng; Liu, Hui; Jiang, Dahe; Zhang, Binyan; Hu, Jun; Hu, Youtian; Wang, Bin; Dai, Jianliang; Yuan, Bifeng; Feng, Yuqi; Huang, Wei; Xing, Xiaojing; Zhao, Guoping; Li, Xuan; Li, Yixue; Li, Wenxin

    2013-01-01

    Representing a basal branch of arachnids, scorpions are known as ‘living fossils’ that maintain an ancient anatomy and are adapted to have survived extreme climate changes. Here we report the genome sequence of Mesobuthus martensii, containing 32,016 protein-coding genes, the most among sequenced arthropods. Although M. martensii appears to evolve conservatively, it has a greater gene family turnover than the insects that have undergone diverse morphological and physiological changes, suggesting the decoupling of the molecular and morphological evolution in scorpions. Underlying the long-term adaptation of scorpions is the expansion of the gene families enriched in basic metabolic pathways, signalling pathways, neurotoxins and cytochrome P450, and the different dynamics of expansion between the shared and the scorpion lineage-specific gene families. Genomic and transcriptomic analyses further illustrate the important genetic features associated with prey, nocturnal behaviour, feeding and detoxification. The M. martensii genome reveals a unique adaptation model of arthropods, offering new insights into the genetic bases of the living fossils. PMID:24129506

  5. In situ structure of trypanosomal ATP synthase dimer reveals a unique arrangement of catalytic subunits.

    PubMed

    Mühleip, Alexander W; Dewar, Caroline E; Schnaufer, Achim; Kühlbrandt, Werner; Davies, Karen M

    2017-01-31

    We used electron cryotomography and subtomogram averaging to determine the in situ structures of mitochondrial ATP synthase dimers from two organisms belonging to the phylum euglenozoa: Trypanosoma brucei, a lethal human parasite, and Euglena gracilis, a photosynthetic protist. At a resolution of 32.5 Å and 27.5 Å, respectively, the two structures clearly exhibit a noncanonical F1 head, in which the catalytic (αβ)3 assembly forms a triangular pyramid rather than the pseudo-sixfold ring arrangement typical of all other ATP synthases investigated so far. Fitting of known X-ray structures reveals that this unusual geometry results from a phylum-specific cleavage of the α subunit, in which the C-terminal αC fragments are displaced by ∼20 Å and rotated by ∼30° from their expected positions. In this location, the αC fragment is unable to form the conserved catalytic interface that was thought to be essential for ATP synthesis, and cannot convert γ-subunit rotation into the conformational changes implicit in rotary catalysis. The new arrangement of catalytic subunits suggests that the mechanism of ATP generation by rotary ATPases is less strictly conserved than has been generally assumed. The ATP synthases of these organisms present a unique model system for discerning the individual contributions of the α and β subunits to the fundamental process of ATP synthesis.

  6. Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen

    PubMed Central

    Adissu, Hibret A.; Estabel, Jeanne; Sunter, David; Tuck, Elizabeth; Hooks, Yvette; Carragher, Damian M.; Clarke, Kay; Karp, Natasha A.; Project, Sanger Mouse Genetics; Newbigging, Susan; Jones, Nora; Morikawa, Lily; White, Jacqueline K.; McKerlie, Colin

    2014-01-01

    The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice. PMID:24652767

  7. Real-time imaging reveals unique heterogeneous population features in insect cell cultures.

    PubMed

    Hidalgo, David; Paz, Enrique; Palomares, Laura A; Ramírez, Octavio T

    2017-10-10

    Heterogeneity of cellular populations has been frequently observed. We used live cell imaging to follow Sf9 insect cells before and after infection with baculovirus, to understand population dynamics. It was possible to identify in real time cells with distinctive phenotypes. Mobile cells with an elongated bipolar shape were observed. They extended pseudopods and actively moved about the culture surface. The presence of actively moving elongated cells increased when cultures were subjected to oxygen limiting or excessive conditions, suggesting that stress triggered differentiation of cells to the mobile phenotype. A dual reporter baculovirus (DRBac), coding for two fluorescent proteins under promoters with different temporality, was designed to follow sequential phenomena through infection. Oxygen limitation reduced the number of cells that expressed the reporter proteins, possibly because it reduced the efficiency of baculovirus infection. Elongated cells did not show signs of infection. To our knowledge, this is the first time that actively moving cells are observed in real time in Sf9 cultures, which had distinctive responses towards infection. Anoxia was identified as a factor that modulates baculovirus infection. Results open a new approach for understanding the insect-cell baculovirus system. Particular cellular phenotypes with unique traits can be isolated for specific applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Systematic analyses reveal uniqueness and origin of the CFEM domain in fungi

    PubMed Central

    Zhang, Zhen-Na; Wu, Qin-Yi; Zhang, Gui-Zhi; Zhu, Yue-Yan; Murphy, Robert W.; Liu, Zhen; Zou, Cheng-Gang

    2015-01-01

    CFEM domain commonly occurs in fungal extracellular membrane proteins. To provide insights for understanding putative functions of CFEM, we investigate the evolutionary dynamics of CFEM domains by systematic comparative genomic analyses among diverse animals, plants, and more than 100 fungal species, which are representative across the entire group of fungi. We here show that CFEM domain is unique to fungi. Experiments using tissue culture demonstrate that the CFEM-containing ESTs in some plants originate from endophytic fungi. We also find that CFEM domain does not occur in all fungi. Its single origin dates to the most recent common ancestors of Ascomycota and Basidiomycota, instead of multiple origins. Although the length and architecture of CFEM domains are relatively conserved, the domain-number varies significantly among different fungal species. In general, pathogenic fungi have a larger number of domains compared to other species. Domain-expansion across fungal genomes appears to be driven by domain duplication and gene duplication via recombination. These findings generate a clear evolutionary trajectory of CFEM domains and provide novel insights into the functional exchange of CFEM-containing proteins from cell-surface components to mediators in host-pathogen interactions. PMID:26255557

  9. Bone marrow chimeric rats reveal the unique distribution of resident and recruited macrophages in the contused rat spinal cord.

    PubMed

    Popovich, P G; Hickey, W F

    2001-07-01

    Brain and spinal cord inflammation that develops after traumatic injury is believed to differentially influence the structural and/or physiological integrity of surviving neurons and glia. It is possible that the functional dichotomy of CNS inflammation results from the activity of a heterogeneous macrophage population elicited by trauma. Indeed, unique functions have been attributed to macrophages derived from resident microglia versus those originating from infiltrating monocytes. Thus, whether progressive tissue injury or repair is favored could be explained by the disproportionate contributions of one macrophage subset relative to the other. Descriptive neuroanatomical studies are a reasonable first approach to revealing a relationship between microglia, recruited blood monocytes/macrophages, and regions of tissue degeneration and/or repair. Unfortunately, it is not possible to differentiate between CNS macrophage subsets using conventional immunohistochemical approaches. In the present study, we have used radiation bone marrow chimeric rats to definitively characterize the macrophage reaction elicited by experimental spinal contusion injury. In chimeric animals, antibodies raised against unique cell surface molecules expressed on bone marrow-derived cells (BMCs) were used to distinguish infiltrating BMCs from resident microglial-derived macrophages. Our findings indicate that the onset and plateau of macrophage activation (previously shown to be 3 and 7 days postinjury, respectively) is dominated initially by microglial-derived macrophages and then is supplanted by hematogenous cells. While resident macrophages are ubiquitously distributed throughout the injury site, leukocyte-derived monocytes exclusively infiltrate the gray matter and to a lesser extent subpial white matter. Generally, monocyte foci in white matter remain associated with the lumen or abluminal surface of blood vessels, i.e. few cells actually infiltrate the parenchyma. If functional

  10. Uniqueness of the Gossypium mustelinum Genome Revealed by GISH and 45S rDNA FISH

    PubMed Central

    Wu, Qiong; Liu, Fang; Li, Shaohui; Song, Guoli; Wang, Chunying; Zhang, Xiangdi; Wang, Yuhong; Stelly, David; Wang, Kunbo

    2013-01-01

    Gossypium mustelinum ((AD)4) is one of five disomic species in Gossypium. Three 45S ribosomal DNA (rDNA) loci were detected in (AD)4 with 45S rDNA as probe, and three pairs of brighter signals were detected with genomic DNA (gDNA) of Gossypium D genome species as probes. The size and the location of these brighter signals were the same as those detected with 45S rDNA as probe, and were named GISH-NOR. One of them was super-major, which accounted for the fact that about one-half of its chromosome at metaphase was located at chromosome 3, and other two were minor and located at chromosomes 5 and 9, respectively. All GISH-NORs were located in A sub-genome chromosomes, separate from the other four allopolyploid cotton species. GISH-NOR were detected with D genome species as probe, but not A. The greatly abnormal sizes and sites of (AD)4 NORs or GISH-NORs indicate a possible mechanism for 45S rDNA diversification following (AD)4 speciation. Comparisons of GISH intensities and GISH-NOR production with gDNA probes between A and D genomes show that the better relationship of (AD)4 is with A genome. The shortest two chromosomes of A sub-genome of G. mustelinum were shorter than the longest chromosome of D sub-genome chromosomes. Therefore, the longest 13 chromosomes of tetraploid cotton being classified as A sub-genome, while the shorter 13 chromosomes being classified as D sub-genome in traditional cytogenetic and karyotype analyses may not be entirely correct. Wu Q, Liu F, Li S, Song G, Wang C, Zhang X, Wang Y, Stelly D, Wang K (2013) Uniqueness of the Gossypium mustelinum genome revealed by GISH and 45S rDNA FISH. J. Integr. Plant Biol. 55(7), 654–662. PMID:23758934

  11. Dissection of Ire1 Functions Reveals Stress Response Mechanisms Uniquely Evolved in Candida glabrata

    PubMed Central

    Miyazaki, Taiga; Nakayama, Hironobu; Nagayoshi, Yohsuke; Kakeya, Hiroshi; Kohno, Shigeru

    2013-01-01

    Proper protein folding in the endoplasmic reticulum (ER) is vital in all eukaryotes. When misfolded proteins accumulate in the ER lumen, the transmembrane kinase/endoribonuclease Ire1 initiates splicing of HAC1 mRNA to generate the bZIP transcription factor Hac1, which subsequently activates its target genes to increase the protein-folding capacity of the ER. This cellular machinery, called the unfolded protein response (UPR), is believed to be an evolutionarily conserved mechanism in eukaryotes. In this study, we comprehensively characterized mutant phenotypes of IRE1 and other related genes in the human fungal pathogen Candida glabrata. Unexpectedly, Ire1 was required for the ER stress response independently of Hac1 in this fungus. C. glabrata Ire1 did not cleave mRNAs encoding Hac1 and other bZIP transcription factors identified in the C. glabrata genome. Microarray analysis revealed that the transcriptional response to ER stress is not mediated by Ire1, but instead is dependent largely on calcineurin signaling and partially on the Slt2 MAPK pathway. The loss of Ire1 alone did not confer increased antifungal susceptibility in C. glabrata contrary to UPR-defective mutants in other fungi. Taken together, our results suggest that the canonical Ire1-Hac1 UPR is not conserved in C. glabrata. It is known in metazoans that active Ire1 nonspecifically cleaves and degrades a subset of ER-localized mRNAs to reduce the ER load. Intriguingly, this cellular response could occur in an Ire1 nuclease-dependent fashion in C. glabrata. We also uncovered the attenuated virulence of the C. glabrata Δire1 mutant in a mouse model of disseminated candidiasis. This study has unveiled the unique evolution of ER stress response mechanisms in C. glabrata. PMID:23382685

  12. Uniqueness of the equilibrium of an electron plasma on magnetic surfaces

    SciTech Connect

    Durand de Gevigney, Benoit

    2011-01-15

    The equilibrium of an electron plasma on magnetic surfaces is governed by a Poisson-Boltzmann equation. The electrons follow a Boltzmann distribution on each surface and the charge density depends exponentially on the electric potential. It is a well-known property that the classical Poisson's equation, for which the charge density is an independent parameter, possesses a unique solution provided suitable boundary conditions are given. Here we show that the Poisson-Boltzmann equation describing electron plasmas on magnetic surfaces also has a unique solution.

  13. Salmonella enteritidis fimbriae displaying a heterologous epitope reveal a uniquely flexible structure and assembly mechanism.

    PubMed

    White, A P; Collinson, S K; Banser, P A; Dolhaine, D J; Kay, W W

    2000-02-18

    Two distinct Salmonella fimbrins, AgfA and SefA, comprising thin aggregative fimbriae SEF17 and SEF14, respectively, were each genetically engineered to carry PT3, an alpha-helical 16-amino acid Leishmania T-cell epitope derived from the metalloprotease gp63. To identify regions within AgfA and SefA fimbrins amenable to replacement with this epitope, PCR-generated chimeric fimbrin genes were constructed and used to replace the native chromosomal agfA and sefA genes in Salmonella enteritidis. Immunoblot analysis using anti-SEF17 and anti-PT3 sera demonstrated that all ten AgfA chimeric fimbrin proteins were expressed by S. enteritidis under normal growth conditions. Immunoelectron microscopy confirmed that eight of the AgfA::PT3 proteins were effectively assembled into cell surface-exposed fimbriae. The PT3 replacements in AgfA altered Congo red (CR) binding, cell-cell adhesion and cell surface properties of S. enteritidis to varying degrees. However, these chimeric fimbriae were still highly stable, being resistant to proteinase K digestion and requiring harsh formic acid treatment for depolymerization. In marked contrast to AgfA, none of the chimeric SefA proteins were expressed or assembled into fimbriae. Since each PT3 replacement constituted over 10% of the AgfA amino acid sequence and all ten replacements collectively represented greater than 75% of the entire AgfA primary sequence, the ability of AgfA to accept large sequence substitutions and still assemble into fibers is unique among fimbriae and other structural proteins. This structural flexibility may be related to the novel fivefold repeating sequence of AgfA and its recently proposed structure Proper formation of chimeric fimbrial fibers suggests an unusual assembly mechanism for thin aggregative fimbriae which tolerates aberrant structures. This study opens a range of possibilities for Salmonella thin aggregative fimbriae as a carrier of heterologous epitopes and as an experimental model for studies

  14. 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

    2016-05-17

    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.

  15. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed Central

    Liston, Sean D.; Ovchinnikova, Olga G.

    2016-01-01

    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

  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.

  19. Tomographic reconstruction reveals the morphology of a unique cellular organelle, the aggregated macrotubules (Macrotubuli aggregati) of human retinal horizontal cells.

    PubMed

    Jastrow, Holger; Yarwood, Andrew; Majorovits, Endre; Harris, J Robin

    2015-04-01

    Horizontal cells of the human retina contain unique tubular organelles that have a diameter which is about 10 times larger than that of microtubules (~230 nm). These macrotubuli in most cases form regular aggregates. Therefore we propose to introduce them as Macrotubuli aggregati in the Terminologia histologica. Tomographic investigation of the structures revealed that the walls of the tubules most probably consist of intermediate filaments running nearly parallel to each other and show somewhat regularly attached ribosomes on their inner and also outer surface. About 2% of the organelles exhibit double- to multiple layered walls and less than 1% resemble large scrolls. The tubules may extend 10 to over 20 μm in the cytoplasm and are also encountered in soma-near processes extending into the outer plexiform layer. It remains unclear why these structures are only present in humans and few other species and why almost only in horizontal cells. Speculations on possible functions are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Nanomechanics of Yeast Surfaces Revealed by AFM

    NASA Astrophysics Data System (ADS)

    Dague, Etienne; Beaussart, Audrey; Alsteens, David

    Despite the large and well-documented characterization of the microbial cell wall in terms of chemical composition, the determination of the mechanical properties of surface molecules in relation to their function remains a key challenge in cell biology.The emergence of powerful tools allowing molecular manipulations has already revolutionized our understanding of the surface properties of fungal cells. At the frontier between nanophysics and molecular biology, atomic force microscopy (AFM), and more specifically single-molecule force spectroscopy (SMFS), has strongly contributed to our current knowledge of the cell wall organization and nanomechanical properties. However, due to the complexity of the technique, measurements on live cells are still at their infancy.In this chapter, we describe the cell wall composition and recapitulate the principles of AFM as well as the main current methodologies used to perform AFM measurements on live cells, including sample immobilization and tip functionalization.The current status of the progress in probing nanomechanics of the yeast surface is illustrated through three recent breakthrough studies. Determination of the cell wall nanostructure and elasticity is presented through two examples: the mechanical response of mannoproteins from brewing yeasts and elasticity measurements on lacking polysaccharide mutant strains. Additionally, an elegant study on force-induced unfolding and clustering of adhesion proteins located at the cell surface is also presented.

  1. 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

  2. Parapoxvirus (PPV) of red deer reveals subclinical infection and confirms a unique species.

    PubMed

    Friederichs, Schirin; Krebs, Stefan; Blum, Helmut; Lang, Heike; Büttner, Mathias

    2015-06-01

    Parapoxvirus (PPV) infections are of worldwide importance, particularly in sheep and goat herds. Owing to the zoonotic potential of all PPV species, they are a permanent threat to human health as well. The virus is also known to affect wildlife, as reported for pinnipeds, red deer and several other wild ruminants. PPVs found in red deer have been claimed as a unique species according to certain genomic features. So far infection of wildlife has been recognized because of clinical manifestation such as inflammation, stomatitis or typical pox-like lesions in the skin or mucous membranes. Here we report the use of targeted molecular diagnostics for the presence of PPV genomes in tonsil swabs of apparently healthy red deer in the Bavarian Alps. Out of 1764 swabs, 0.79 % tested positive for PPV genome presence. From one sample, PPV was successfully isolated in cell culture. This virus became the subject of complete genome characterization using next generation sequencing and various subsidiary PCR protocols. Strikingly, about a quarter of all ORFs were found to be larger than the corresponding ORFs in the reference PPV genome sequences used for comparison. To our knowledge this is the first genome-wide analysis that confirms red deer PPV as a unique species within the genus Parapoxvirus in Europe. Persistence of PPV in Alpine red deer indicates a source for virus transmission to susceptible livestock and hunters. The findings provide a further example of wildlife animals playing an important role as an inconspicuous reservoir of zoonotic diseases.

  3. Identification and characterization of the genes encoding a unique surface (S-) layer of Tannerella forsythia.

    PubMed

    Lee, Seok-Woo; Sabet, Mojgan; Um, Heung-Sik; Yang, Jun; Kim, Hyeong C; Zhu, Weidong

    2006-04-12

    A newly emerged periodontopathic pathogen Tannerella forsythia (formerly Bacteroides forsythus), a Gram-negative, filament-shaped, strict anaerobic, non-pigmented oral bacterium, possesses a surface (S-) layer. In our previous studies, the S-layer has been isolated, and shown to mediate hemagglutination, adhesion/invasion of epithelial cell, and murine subcutaneous abscess formation. In the present study, biochemical and molecular genetic characterization of the S-layer are reported. Amino acid sequencing and mass spectrometry indicated that the S-layer is composed of two different proteins, termed 200 and 210 kDa proteins. It was also shown that these proteins are glycosylated. The genes encoding the core proteins of these glycoproteins, designated as tfsA and tfsB, have been identified in silico, cloned, and their sequences have been determined. The tfsA (3.5 kb) and tfsB (4.1 kb) genes are located in tandem, and encode for 135 and 152 kDa proteins, respectively. An apparent discrepancy in molecular weights, 135 vs. 200 kDa and 152 vs. 210 kDa, is accounted for carbohydrate residues attached to the core proteins. Amino acid sequence comparison exhibited a 24% similarity between the 200 and 210 kDa proteins. Further sequence analyses showed that TfsA and TfsB possess putative signal peptide sequences with cleavage sites at alanine residues, and transmembrane domains on the C-terminal region. Northern blot and RT-PCR analyses confirmed an operon structure of tfsAB, suggesting co-regulation of these genes in producing the S-layer. Putative promoter sequences and transcription termination sequences for this operon have also been identified. Comparison with database indicates that the S-layer of T. forsythia has a unique structure exhibiting no homology to other known S-layers of prokaryotic organisms. The present study shows that the T. forsythia S-layer is very unique, since it appears to be composed of two large glycoproteins, and it does not reveal any homology to

  4. 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

  5. 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

    2016-08-16

    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.

  6. 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

  7. What determines the relationship between color naming, unique hues, and sensory singularities: Illuminations, surfaces, or photoreceptors?

    PubMed

    Witzel, Christoph; Cinotti, François; O'Regan, J Kevin

    2015-01-01

    The relationship between the sensory signal of the photoreceptors on one hand and color appearance and language on the other hand is completely unclear. A recent finding established a surprisingly accurate correlation between focal colors, unique hues, and so-called singularities in the laws governing how sensory signals for different surfaces change across illuminations. This article examines how this correlation with singularities depends on reflectances, illuminants, and cone sensitivities. Results show that this correlation holds for a large range of illuminants and for a large range of sensors, including sensors that are fundamentally different from human photoreceptors. In contrast, the spectral characteristics of the reflectance spectra turned out to be the key factor that determines the correlation between focal colors, unique hues, and sensory singularities. These findings suggest that the origins of color appearance and color language may be found in particular characteristics of the reflectance spectra that correspond to focal colors and unique hues.

  8. The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components

    PubMed Central

    Gao, Haixiao; Ayub, Maximiliano Juri; Levin, Mariano J.; Frank, Joachim

    2005-01-01

    We present analysis, by cryo-electron microscopy and single-particle reconstruction, of the structure of the 80S ribosome from Trypanosoma cruzi, the kinetoplastid protozoan pathogen that causes Chagas disease. The density map of the T. cruzi 80S ribosome shows the phylogenetically conserved eukaryotic rRNA core structure, together with distinctive structural features in both the small and large subunits. Remarkably, a previously undescribed helical structure appears in the small subunit in the vicinity of the mRNA exit channel. We propose that this rRNA structure likely participates in the recruitment of ribosome onto the 5′ end of mRNA, in facilitating and modulating the initiation of translation that is unique to the trypanosomes. PMID:16014419

  9. Unique Lipid Chemistry of Synaptic Vesicle and Synaptosome Membrane Revealed Using Mass Spectrometry.

    PubMed

    Lewis, Kenneth T; Maddipati, Krishna R; Naik, Akshata R; Jena, Bhanu P

    2017-03-02

    Synaptic vesicles measuring 30-50 nm in diameter containing neurotransmitters either completely collapse at the presynaptic membrane or dock and transiently fuse at the base of specialized 15 nm cup-shaped lipoprotein structures called porosomes at the presynaptic membrane of synaptosomes to release neurotransmitters. Recent study reports the unique composition of major lipids associated with neuronal porosomes. Given that lipids greatly influence the association and functions of membrane proteins, differences in lipid composition of synaptic vesicle and the synaptosome membrane was hypothesized. To test this hypothesis, the lipidome of isolated synaptosome, synaptosome membrane, and synaptic vesicle preparation were determined by using mass spectrometry in the current study. Results from the study demonstrate the enriched presence of triacyl glycerols and sphingomyelins in synaptic vesicles, as opposed to the enriched presence of phospholipids in the synaptosome membrane fraction, reflecting on the tight regulation of nerve cells in compartmentalization of membrane lipids at the nerve terminal.

  10. Genomic Dissection of Hurthle Cell Carcinoma Reveals a Unique Class of Thyroid Malignancy

    PubMed Central

    Ganly, Ian; Ricarte Filho, Julio; Eng, Stephanie; Ghossein, Ronald; Morris, Luc G. T.; Liang, Yupu; Socci, Nicholas; Kannan, Kasthuri; Mo, Qianxing; Fagin, James A.

    2013-01-01

    Context: Hurthle cell cancer (HCC) is an understudied cancer with poor prognosis. Objective: Our objective was to elucidate the genomic foundations of HCC. Design and Setting: We conducted a large-scale integrated analysis of mutations, gene expression profiles, and copy number alterations in HCC at a single tertiary-care cancer institution. Methods: Mass spectrometry-based genotyping was used to interrogate hot spot point mutations in the most common thyroid oncogenes: BRAF, RET, NRAS, HRAS, KRAS, PIK3CA, MAP2K1, and AKT1. In addition, common oncogenic fusions of RET and NTRK1 as well as PAX8/PPARγ and AKAP9-BRAF were also assessed by RT-PCR. Global copy number changes and gene expression profiles were determined in the same tumor set as the mutational analyses. Results: We report that the mutational, transcriptional, and copy number profiles of HCC were distinct from those of papillary thyroid cancer and follicular thyroid cancer, indicating HCC to be a unique type of thyroid malignancy. Unsupervised hierarchical clustering of gene expression showed the 3 groups of Hurthle tumors (Hurthle cell adenoma [HA], minimally invasive Hurthle cell carcinoma [HMIN], and widely invasive Hurthle cell carcinoma [HWIDE] clustered separately with a marked difference between HWIDE and HA. Global copy number analysis also indicated distinct subgroups of tumors that may arise as HWIDE and HMIN. Molecular pathways that differentiate HA from HWIDE included the PIK3CA-Akt-mTOR and Wnt/β-catenin pathways, potentially providing a rationale for new targets for this type of malignancy. Conclusions: Our data provide evidence that HCC may be a unique thyroid cancer distinct from papillary and follicular thyroid cancer. PMID:23543667

  11. 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

  12. Characterization of Karyopherin Cargoes Reveals Unique Mechanisms of Kap121p-Mediated Nuclear Import

    PubMed Central

    Leslie, Deena M.; Zhang, Wenzhu; Timney, Benjamin L.; Chait, Brian T.; Rout, Michael P.; Wozniak, Richard W.; Aitchison, John D.

    2004-01-01

    In yeast there are at least 14 members of the β-karyopherin protein family that govern the movement of a diverse set of cargoes between the nucleus and cytoplasm. Knowledge of the cargoes carried by each karyopherin and insight into the mechanisms of transport are fundamental to understanding constitutive and regulated transport and elucidating how they impact normal cellular functions. Here, we have focused on the identification of nuclear import cargoes for the essential yeast β-karyopherin, Kap121p. Using an overlay blot assay and coimmunopurification studies, we have identified 30 putative Kap121p cargoes. Among these were Nop1p and Sof1p, two essential trans-acting protein factors required at the early stages of ribosome biogenesis. Characterization of the Kap121p-Nop1p and Kap121p-Sof1p interactions demonstrated that, in addition to lysine-rich nuclear localization signals (NLSs), Kap121p recognizes a unique class of signals distinguished by the abundance of arginine and glycine residues and consequently termed rg-NLSs. Kap104p is also known to recognize rg-NLSs, and here we show that it compensates for the loss of Kap121p function. Sof1p is also transported by Kap121p; however, its import can be mediated by a piggyback mechanism with Nop1p bridging the interaction between Sof1p and Kap121p. Together, our data elucidate additional levels of complexity in these nuclear transport pathways. PMID:15367670

  13. A vertebrate myosin-I structure reveals unique insights into myosin mechanochemical tuning.

    PubMed

    Shuman, Henry; Greenberg, Michael J; Zwolak, Adam; Lin, Tianming; Sindelar, Charles V; Dominguez, Roberto; Ostap, E Michael

    2014-02-11

    Myosins are molecular motors that power diverse cellular processes, such as rapid organelle transport, muscle contraction, and tension-sensitive anchoring. The structural adaptations in the motor that allow for this functional diversity are not known, due, in part, to the lack of high-resolution structures of highly tension-sensitive myosins. We determined a 2.3-Å resolution structure of apo-myosin-Ib (Myo1b), which is the most tension-sensitive myosin characterized. We identified a striking unique orientation of structural elements that position the motor's lever arm. This orientation results in a cavity between the motor and lever arm that holds a 10-residue stretch of N-terminal amino acids, a region that is divergent among myosins. Single-molecule and biochemical analyses show that the N terminus plays an important role in stabilizing the post power-stroke conformation of Myo1b and in tuning the rate of the force-sensitive transition. We propose that this region plays a general role in tuning the mechanochemical properties of myosins.

  14. Transcript profiling of CD16-positive monocytes reveals a unique molecular fingerprint.

    PubMed

    Frankenberger, Marion; Hofer, Thomas P J; Marei, Ayman; Dayyani, Farshid; Schewe, Stefan; Strasser, Christine; Aldraihim, Asaad; Stanzel, Franz; Lang, Roland; Hoffmann, Reinhard; Prazeres da Costa, Olivia; Buch, Thorsten; Ziegler-Heitbrock, Loems

    2012-04-01

    CD16-positive (CD14(++) CD16(+) and CD14(+) CD16(++) ) monocytes have unique features with respect to phenotype and function. We have used transcriptional profiling for comparison of CD16-positive monocytes and classical monocytes. We show herein that 187 genes are greater than fivefold differentially expressed, including 90 genes relevant to immune response and inflammation. Hierarchical clustering of data for monocyte subsets and CD1c(+) myeloid blood dendritic cells (DCs) demonstrate that CD16-positive cells are more closely related to classical monocytes than to DCs. Reverse transcriptase polymerase chain reaction for ten genes with the strongest differential expression confirmed the pattern including a lower messenger RNA level for CD14, CD163, and versican in CD16-positive monocytes. The pattern was similar for CD16-positive monocytes at rest and after exercise mobilization from the marginal pool. By contrast, alveolar macrophages, small sputum macrophages, breast milk macrophages, and synovial macrophages all showed a different pattern. When monocyte-derived macrophages (MDMs) were generated from CD16-positive monocytes by culture with macrophage colony-stimulating factor in vitro, then the MDMs maintained properties of their progeny with lower expression of CD14, CD163, and versican compared with CD14(++) CD16(-) MDMs. Furthermore, CD16-positive MDMs showed a higher phagocytosis for opsonized Escherichia coli. The data demonstrate that CD16-positive monocytes form a distinct type of cell, which gives rise to a distinct macrophage phenotype.

  15. Human Suv3 protein reveals unique features among SF2 helicases

    PubMed Central

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

    2011-01-01

    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. PMID:22101826

  16. Reciprocal gene replacements reveal unique functions for Phox2 genes during neural differentiation

    PubMed Central

    Coppola, Eva; Pattyn, Alexandre; Guthrie, Sarah C; Goridis, Christo; Studer, Michèle

    2005-01-01

    The paralogous paired-like homeobox genes Phox2a and Phox2b are involved in the development of specific neural subtypes in the central and peripheral nervous systems. The different phenotypes of Phox2 knockout mutants, together with their asynchronous onset of expression, prompted us to generate two knock-in mutant mice, in which Phox2a is replaced by the Phox2b coding sequence, and vice versa. Our results indicate that Phox2a and Phox2b are not functionally equivalent, as only Phox2b can fulfill the role of Phox2a in the structures that depend on both genes. Furthermore, we demonstrate unique roles of Phox2 genes in the differentiation of specific motor neurons. Whereas the oculomotor and the trochlear neurons require Phox2a for their proper development, the migration of the facial branchiomotor neurons depends on Phox2b. Therefore, our analysis strongly indicates that biochemical differences between the proteins rather than temporal regulation of their expression account for the specific function of each paralogue. PMID:16319924

  17. Pyrosequencing reveals unique microbial signatures associated with healthy and failing dental implants.

    PubMed

    Kumar, Purnima S; Mason, Matthew R; Brooker, Michael R; O'Brien, Kelly

    2012-05-01

    Although it is established that peri-implantitis is a bacterially induced disease, little is known about the bacterial profile of peri-implant communities in health and disease. The purpose of the present investigation was to examine the microbial signatures of the peri-implant microbiome in health and disease. Subgingival and submucosal plaque samples were collected from forty subjects with periodontitis, peri-implantitis, periodontal and peri-implant health and analysed using 16S pyrosequencing. Peri-implant biofilms demonstrated significantly lower diversity than subgingival biofilms in both health and disease, however, several species, including previously unsuspected and unknown organisms, were unique to this niche. The predominant species in peri-implant communities belonged to the genera Butyrivibrio, Campylobacter, Eubacterium, Prevotella, Selenomonas, Streptococcus, Actinomyces, Leptotrichia, Propionibacterium, Peptococcus, Lactococcus and Treponema. Peri-implant disease was associated with lower levels of Prevotella and Leptotrichia and higher levels of Actinomyces, Peptococcus, Campylobacter, non-mutans Streptococcus, Butyrivibrio and Streptococcus mutans than healthy implants. These communities also demonstrated lower levels of Prevotella, non-mutans Streptococcus, Lactobacillus, Selenomonas, Leptotrichia, Actinomyces and higher levels of Peptococcus, Mycoplasma, Eubacterium, Campylobacter, Butyrivibrio, S. mutans and Treponema when compared to periodontitis-associated biofilms. The peri-implant microbiome differs significantly from the periodontal community in both health and disease. Peri-implantitis is a microbially heterogeneous infection with predominantly gram-negative species, and is less complex than periodontitis. © 2012 John Wiley & Sons A/S.

  18. 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

  19. The genome sequence of Atlantic cod reveals a unique immune system.

    PubMed

    Star, Bastiaan; Nederbragt, Alexander J; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone F; Rounge, Trine B; Paulsen, Jonas; Solbakken, Monica H; Sharma, Animesh; Wetten, Ola F; Lanzén, Anders; Winer, Roger; Knight, James; Vogel, Jan-Hinnerk; Aken, Bronwen; Andersen, Oivind; Lagesen, Karin; Tooming-Klunderud, Ave; Edvardsen, Rolf B; Tina, Kirubakaran G; Espelund, Mari; Nepal, Chirag; Previti, Christopher; Karlsen, Bård Ove; Moum, Truls; Skage, Morten; Berg, Paul R; Gjøen, Tor; Kuhl, Heiner; Thorsen, Jim; Malde, Ketil; Reinhardt, Richard; Du, Lei; Johansen, Steinar D; Searle, Steve; Lien, Sigbjørn; Nilsen, Frank; Jonassen, Inge; Omholt, Stig W; Stenseth, Nils Chr; Jakobsen, Kjetill S

    2011-08-10

    Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.

  20. Chronological Analysis With Fluorescent Timer Reveals Unique Features of Newly Generated β-Cells

    PubMed Central

    Matsuoka, Taka-aki; Sasaki, Shugo; Kubo, Fumiyo; Shimomura, Iichiro; Watada, Hirotaka; German, Michael S.; Hara, Manami

    2014-01-01

    Although numerous studies have uncovered the molecular mechanisms regulating pancreas development, it remains to be clarified how β-cells arise from progenitors and how recently specified β-cells are different from preexisting β-cells. To address these questions, we developed a mouse model in which the insulin 1 promoter drives DsRed-E5 Timer fluorescence that shifts its spectrum over time. In transgenic embryos, green fluorescent β-cells were readily detected by FACS and could be distinguished from mature β-cells only until postnatal day 0, suggesting that β-cell neogenesis occurs exclusively during embryogenesis. Transcriptome analysis with green fluorescent cells sorted by FACS demonstrated that newly differentiated β-cells highly expressed progenitor markers, such as Sox9, Neurog3, and Pax4, showing the progenitor-like features of newborn β-cells. Flow cytometric analysis of cell cycle dynamics showed that green fluorescent cells were mostly quiescent, and differentiated β-cells were mitotically active. Thus, the precise temporal resolution of this model enables us to dissect the unique features of newly specified insulin-producing cells, which could enhance our understanding of β-cell neogenesis for future cell therapy. PMID:24834978

  1. Chronological analysis with fluorescent timer reveals unique features of newly generated β-cells.

    PubMed

    Miyatsuka, Takeshi; Matsuoka, Taka-aki; Sasaki, Shugo; Kubo, Fumiyo; Shimomura, Iichiro; Watada, Hirotaka; German, Michael S; Hara, Manami

    2014-10-01

    Although numerous studies have uncovered the molecular mechanisms regulating pancreas development, it remains to be clarified how β-cells arise from progenitors and how recently specified β-cells are different from preexisting β-cells. To address these questions, we developed a mouse model in which the insulin 1 promoter drives DsRed-E5 Timer fluorescence that shifts its spectrum over time. In transgenic embryos, green fluorescent β-cells were readily detected by FACS and could be distinguished from mature β-cells only until postnatal day 0, suggesting that β-cell neogenesis occurs exclusively during embryogenesis. Transcriptome analysis with green fluorescent cells sorted by FACS demonstrated that newly differentiated β-cells highly expressed progenitor markers, such as Sox9, Neurog3, and Pax4, showing the progenitor-like features of newborn β-cells. Flow cytometric analysis of cell cycle dynamics showed that green fluorescent cells were mostly quiescent, and differentiated β-cells were mitotically active. Thus, the precise temporal resolution of this model enables us to dissect the unique features of newly specified insulin-producing cells, which could enhance our understanding of β-cell neogenesis for future cell therapy. © 2014 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. A domain-centric analysis of oomycete plant pathogen genomes reveals unique protein organization.

    PubMed

    Seidl, Michael F; Van den Ackerveken, Guido; Govers, Francine; Snel, Berend

    2011-02-01

    Oomycetes comprise a diverse group of organisms that morphologically resemble fungi but belong to the stramenopile lineage within the supergroup of chromalveolates. Recent studies have shown that plant pathogenic oomycetes have expanded gene families that are possibly linked to their pathogenic lifestyle. We analyzed the protein domain organization of 67 eukaryotic species including four oomycete and five fungal plant pathogens. We detected 246 expanded domains in fungal and oomycete plant pathogens. The analysis of genes differentially expressed during infection revealed a significant enrichment of genes encoding expanded domains as well as signal peptides linking a substantial part of these genes to pathogenicity. Overrepresentation and clustering of domain abundance profiles revealed domains that might have important roles in host-pathogen interactions but, as yet, have not been linked to pathogenicity. The number of distinct domain combinations (bigrams) in oomycetes was significantly higher than in fungi. We identified 773 oomycete-specific bigrams, with the majority composed of domains common to eukaryotes. The analyses enabled us to link domain content to biological processes such as host-pathogen interaction, nutrient uptake, or suppression and elicitation of plant immune responses. Taken together, this study represents a comprehensive overview of the domain repertoire of fungal and oomycete plant pathogens and points to novel features like domain expansion and species-specific bigram types that could, at least partially, explain why oomycetes are such remarkable plant pathogens.

  8. Molecular Dynamics Simulation Reveals Unique Interplays Between a Tarantula Toxin and Lipid Membranes.

    PubMed

    Wu, Lei; Xie, Si-Si; Meng, Er; Li, Wen-Ying; Liu, Long; Zhang, Dong-Yi

    2017-06-01

    Tarantula toxins compose an important class of spider toxins that target ion channels, and some are known to interact with lipid membranes. In this study, we focus on a tarantula toxin, Jingzhaotoxin-III (JZTx-III) that specifically targets the cardiac voltage-gated sodium channel Na[Formula: see text]1.5 and is suspected to be able to interact with lipid membranes. Here, we use an all-atom model and long-term molecular dynamics simulations to investigate the interactions between JZTx-III and lipid membranes of different compositions. Trajectory analyses show that JZTx-III has no substantial interaction with the neutral 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids, but binds to membranes containing negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (POPG). The most intriguing observations in our simulation are the different interactions between the toxin and the membrane in the mixed and pure POPG membrane systems. The POPC/POPG mixed membrane undergoes a phase transition to a rippled phase upon binding of the toxin, while the pure POPG membrane has no apparent change. Moreover, the binding of JZTx-III to both of the mixture and the pure POPG membrane systems induce small conformational changes. The sequence alignment shows that JZTx-III may not partition into the lipid bilayer due to the mutations of a C-terminal hydrophobic residue and some charged residues that affect toxin orientation. Taken together, JZTx-III and lipid membranes have unique effects on each other that may facilitate the specific binding of JZTx-III to Na[Formula: see text]1.5. This computational study also enriches our understanding of the potential complex interactions between spider toxins and lipid membranes.

  9. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition.

    PubMed

    Flyamer, Ilya M; Gassler, Johanna; Imakaev, Maxim; Brandão, Hugo B; Ulianov, Sergey V; Abdennur, Nezar; Razin, Sergey V; Mirny, Leonid A; Tachibana-Konwalski, Kikuë

    2017-04-06

    Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism. The maternal genome inherited from the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in the zygote. How these two epigenetically distinct genomes are spatially organized is poorly understood. Existing chromosome conformation capture-based methods are not applicable to oocytes and zygotes owing to a paucity of material. To study three-dimensional chromatin organization in rare cell types, we developed a single-nucleus Hi-C (high-resolution chromosome conformation capture) protocol that provides greater than tenfold more contacts per cell than the previous method. Here we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition in mice and is distinct in paternal and maternal nuclei within single-cell zygotes. Features of genomic organization including compartments, topologically associating domains (TADs) and loops are present in individual oocytes when averaged over the genome, but the presence of each feature at a locus varies between cells. At the sub-megabase level, we observed stochastic clusters of contacts that can occur across TAD boundaries but average into TADs. Notably, we found that TADs and loops, but not compartments, are present in zygotic maternal chromatin, suggesting that these are generated by different mechanisms. Our results demonstrate that the global chromatin organization of zygote nuclei is fundamentally different from that of other interphase cells. An understanding of this zygotic chromatin 'ground state' could potentially provide insights into reprogramming cells to a state of totipotency.

  10. Molecular Genetic Features of Polyploidization and Aneuploidization Reveal Unique Patterns for Genome Duplication in Diploid Malus

    PubMed Central

    Considine, Michael J.; Wan, Yizhen; D'Antuono, Mario F.; Zhou, Qian; Han, Mingyu; Gao, Hua; Wang, Man

    2012-01-01

    Polyploidization results in genome duplication and is an important step in evolution and speciation. The Malus genome confirmed that this genus was derived through auto-polyploidization, yet the genetic and meiotic mechanisms for polyploidization, particularly for aneuploidization, are unclear in this genus or other woody perennials. In fact the contribution of aneuploidization remains poorly understood throughout Plantae. We add to this knowledge by characterization of eupolyploidization and aneuploidization in 27,542 F1 seedlings from seven diploid Malus populations using cytology and microsatellite markers. We provide the first evidence that aneuploidy exceeds eupolyploidy in the diploid crosses, suggesting aneuploidization is a leading cause of genome duplication. Gametes from diploid Malus had a unique combinational pattern; ova preserved euploidy exclusively, while spermatozoa presented both euploidy and aneuploidy. All non-reduced gametes were genetically heterozygous, indicating first-division restitution was the exclusive mode for Malus eupolyploidization and aneuploidization. Chromosome segregation pattern among aneuploids was non-uniform, however, certain chromosomes were associated for aneuploidization. This study is the first to provide molecular evidence for the contribution of heterozygous non-reduced gametes to fitness in polyploids and aneuploids. Aneuploidization can increase, while eupolyploidization may decrease genetic diversity in their newly established populations. Auto-triploidization is important for speciation in the extant Malus. The features of Malus polyploidization confer genetic stability and diversity, and present heterozygosity, heterosis and adaptability for evolutionary selection. A protocol using co-dominant markers was proposed for accelerating apple triploid breeding program. A path was postulated for evolution of numerically odd basic chromosomes. The model for Malus derivation was considerably revised. Impacts of

  11. Unique Features of the Folding Landscape of a Repeat Protein Revealed by Pressure Perturbation

    PubMed Central

    Rouget, Jean-Baptiste; Schroer, Martin A.; Jeworrek, Christoph; Pühse, Matthias; Saldana, Jean-Louis; Bessin, Yannick; Tolan, Metin; Barrick, Doug; Winter, Roland; Royer, Catherine A.

    2010-01-01

    Abstract The volumetric properties of proteins yield information about the changes in packing and hydration between various states along the folding reaction coordinate and are also intimately linked to the energetics and dynamics of these conformations. These volumetric characteristics can be accessed via pressure perturbation methods. In this work, we report high-pressure unfolding studies of the ankyrin domain of the Notch receptor (Nank1–7) using fluorescence, small-angle x-ray scattering, and Fourier transform infrared spectroscopy. Both equilibrium and pressure-jump kinetic fluorescence experiments were consistent with a simple two-state folding/unfolding transition under pressure, with a rather small volume change for unfolding compared to proteins of similar molecular weight. High-pressure fluorescence, Fourier transform infrared spectroscopy, and small-angle x-ray scattering measurements revealed that increasing urea over a very small range leads to a more expanded pressure unfolded state with a significant decrease in helical content. These observations underscore the conformational diversity of the unfolded-state basin. The temperature dependence of pressure-jump fluorescence relaxation measurements demonstrated that at low temperatures, the folding transition state ensemble (TSE) lies close in volume to the folded state, consistent with significant dehydration at the barrier. In contrast, the thermal expansivity of the TSE was found to be equivalent to that of the unfolded state, indicating that the interactions that constrain the folded-state thermal expansivity have not been established at the folding barrier. This behavior reveals a high degree of plasticity of the TSE of Nank1–7. PMID:20513416

  12. Unique features of the folding landscape of a repeat protein revealed by pressure perturbation.

    PubMed

    Rouget, Jean-Baptiste; Schroer, Martin A; Jeworrek, Christoph; Pühse, Matthias; Saldana, Jean-Louis; Bessin, Yannick; Tolan, Metin; Barrick, Doug; Winter, Roland; Royer, Catherine A

    2010-06-02

    The volumetric properties of proteins yield information about the changes in packing and hydration between various states along the folding reaction coordinate and are also intimately linked to the energetics and dynamics of these conformations. These volumetric characteristics can be accessed via pressure perturbation methods. In this work, we report high-pressure unfolding studies of the ankyrin domain of the Notch receptor (Nank1-7) using fluorescence, small-angle x-ray scattering, and Fourier transform infrared spectroscopy. Both equilibrium and pressure-jump kinetic fluorescence experiments were consistent with a simple two-state folding/unfolding transition under pressure, with a rather small volume change for unfolding compared to proteins of similar molecular weight. High-pressure fluorescence, Fourier transform infrared spectroscopy, and small-angle x-ray scattering measurements revealed that increasing urea over a very small range leads to a more expanded pressure unfolded state with a significant decrease in helical content. These observations underscore the conformational diversity of the unfolded-state basin. The temperature dependence of pressure-jump fluorescence relaxation measurements demonstrated that at low temperatures, the folding transition state ensemble (TSE) lies close in volume to the folded state, consistent with significant dehydration at the barrier. In contrast, the thermal expansivity of the TSE was found to be equivalent to that of the unfolded state, indicating that the interactions that constrain the folded-state thermal expansivity have not been established at the folding barrier. This behavior reveals a high degree of plasticity of the TSE of Nank1-7. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  13. 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

  14. A Unique Late Triassic Dinosauromorph Assemblage Reveals Dinosaur Ancestral Anatomy and Diet.

    PubMed

    Cabreira, Sergio Furtado; Kellner, Alexander Wilhelm Armin; Dias-da-Silva, Sérgio; Roberto da Silva, Lúcio; Bronzati, Mario; Marsola, Júlio Cesar de Almeida; Müller, Rodrigo Temp; Bittencourt, Jonathas de Souza; Batista, Brunna Jul'Armando; Raugust, Tiago; Carrilho, Rodrigo; Brodt, André; Langer, Max Cardoso

    2016-11-21

    Dinosauromorpha includes dinosaurs and other much less diverse dinosaur precursors of Triassic age, such as lagerpetids [1]. Joint occurrences of these taxa with dinosaurs are rare but more common during the latest part of that period (Norian-Rhaetian, 228-201 million years ago [mya]) [2, 3]. In contrast, the new lagerpetid and saurischian dinosaur described here were unearthed from one of the oldest rock units with dinosaur fossils worldwide, the Carnian (237-228 mya) Santa Maria Formation of south Brazil [4], a record only matched in age by much more fragmentary remains from Argentina [5]. This is the first time nearly complete dinosaur and non-dinosaur dinosauromorph remains are found together in the same excavation, clearly showing that these animals were contemporaries since the first stages of dinosaur evolution. The new lagerpetid preserves the first skull, scapular and forelimb elements, plus associated vertebrae, known for the group, revealing how dinosaurs acquired several of their typical anatomical traits. Furthermore, a novel phylogenetic analysis shows the new dinosaur as the most basal Sauropodomorpha. Its plesiomorphic teeth, strictly adapted to faunivory, provide crucial data to infer the feeding behavior of the first dinosaurs.

  15. Comparison of Models for Bubonic Plague Reveals Unique Pathogen Adaptations to the Dermis.

    PubMed

    Gonzalez, Rodrigo J; Weening, Eric H; Lane, M Chelsea; Miller, Virginia L

    2015-07-01

    Vector-borne pathogens are inoculated in the skin of mammals, most likely in the dermis. Despite this, subcutaneous (s.c.) models of infection are broadly used in many fields, including Yersinia pestis pathogenesis. We expand on a previous report where we implemented intradermal (i.d.) inoculations to study bacterial dissemination during bubonic plague and compare this model with an s.c. We found that i.d. inoculations result in faster kinetics of infection and that bacterial dose influenced mouse survival after i.d. but not s.c. inoculation. Moreover, a deletion mutant of rovA, previously shown to be moderately attenuated in the s.c. model, was severely attenuated in the i.d. Lastly, based on previous observations where a population bottleneck from the skin to lymph nodes was observed after i.d., but not after s.c., inoculations, we used the latter model as a strategy to identify an additional bottleneck in bacterial dissemination from lymph nodes to the bloodstream. Our data indicate that the more biologically relevant i.d. model of bubonic plague differs significantly from the s.c. model in multiple aspects of infection. These findings reveal adaptations of Y. pestis to the dermis and how these adaptations can define the progression of disease. They also emphasize the importance of using a relevant route of infection when addressing host-pathogen interactions. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  16. 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

  17. Neurobiology of mood, anxiety, and emotions as revealed by studies of a unique antidepressant: tianeptine.

    PubMed

    McEwen, B S; Olié, J P

    2005-06-01

    Recent studies have provided evidence that structural remodeling of certain brain regions is a feature of depressive illness, and the postulated underlying mechanisms contribute to the idea that there is more to antidepressant actions that can be explained exclusively by a monoaminergic hypothesis. This review summarizes recent neurobiological studies on the antidepressant, tianeptine (S-1574, [3-chloro-6-methyl-5,5-dioxo-6,11-dihydro-(c,f)-dibenzo-(1,2-thiazepine)-11-yl) amino]-7 heptanoic acid, sodium salt), a compound with structural similarities to the tricyclic antidepressant agents, the efficacy and good tolerance of which have been clearly established. These studies have revealed that the neurobiological properties of tianeptine involve the dynamic interplay between numerous neurotransmitter systems, as well as a critical role of structural and functional plasticity in the brain regions that permit the full expression of emotional learning. Although the story is far from complete, the schema underlying the effect of tianeptine on central plasticity is the most thoroughly studied of any antidepressants. Effects of tianeptine on neuronal excitability, neuroprotection, anxiety, and memory have also been found. Together with clinical data on the efficacy of tianeptine as an antidepressant, these actions offer insights into how compounds like tianeptine may be useful in the treatment of neurobiological features of depressive disorders.

  18. The biology of interleukin-27 reveals unique pro- and anti-inflammatory functions in immunity.

    PubMed

    Aparicio-Siegmund, Samadhi; Garbers, Christoph

    2015-10-01

    Interleukin (IL)-27 is a multifaceted heterodimeric cytokine with pronounced pro- and anti-inflammatory as well as immunoregulatory functions. It consists of the two subunits p28/IL-30 and Epstein Bar virus-induced protein 3 (EBI3). EBI3 functions as a soluble α-receptor, and IL-27 can therefore directly activate its target cells through a heterodimer of glycoprotein 130 (gp130) and WSX-1. Being a heterodimeric cytokine that signals through gp130, IL-27 is either grouped into the IL-6 or the IL-12 family of cytokines. Originally identified as an IL-12-like cytokine that induces proliferation of CD4+ T cells and production of IFN-γ more than ten years ago, subsequent research revealed a much broader role of IL-27 in inflammation, cancer development and regulation and differentiation of immune cells. In this review, we summarize the current biochemical and molecular knowledge about the signal transduction of IL-27. Based on this, we highlight functional overlaps and plasticity with other cytokines and cytokine receptors of the IL-6/IL-12 superfamily, and describe the important role of IL-27 with regard to the differentiation of T cells, infections and cancer development. We further discuss IL-27 as a therapeutic target and how specific blockade of this cytokine could be achieved. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Unique Ligand Binding Patterns Between Estrogen Receptor α and β Revealed by Hydrogen/Deuterium Exchange

    PubMed Central

    Dai, Susie Y.; Burris, Thomas P.; Dodge, Jeffrey A.; Montrose-Rafizadeh, Chahrzad; Wang, Yong; Pascal, Bruce D.; Chalmers, Michael J.; Griffin, Patrick R.

    2009-01-01

    Here we present the use of hydrogen/deuterium exchange (HDX) mass spectrometry to analyze the estrogen receptor β ligand binding domain (ERβLBD) in the absence and presence of a variety of chemical compounds with different binding modes and pharmacological properties. Previously, we reported the use of HDX as a method to predict the tissue selectivity of ERα ligands. HDX profiles of ERαLBD in complex with ligand could differentiate compounds of the same chemotype. In contrast, similar analysis of ERβLBD showed correlation to the compound chemical structures but little correlation with compound tissue selectivity. The different HDX patterns observed for ERβLBD when compared to ERαLBD bound to the same chemical compounds serves as an indication that ERβLBD undergoes a different structural response to the same ligand when compared to ERαLBD. The conformational dynamics revealed by HDX forz ERβLBD together with those for ERαLBD shed light into ER ligand interactions and offer new structural insights. The compound specific perturbations in HDX kinetics observed for each of the two isoforms should aid the development of subtype selective ER ligands. PMID:19739677

  20. Unique surface gene variants of hepatitis B virus isolated from patients in the Philippines.

    PubMed

    Baclig, Michael O; Alvarez, May R; Gopez-Cervantes, Juliet; Natividad, Filipinas F

    2014-02-01

    Point mutations and multiple variants across the "a" determinant can destroy the antigenicity and immunogenicity of hepatitis B virus (HBV) leading to false negative assay and vaccine escape. In this study, the presence of surface gene variants of HBV was investigated among patients clinically diagnosed with chronic hepatitis B and positive for HBV DNA from 2002 to 2009. Sequence analysis of the surface gene of HBV showed that 23 (43%) of the 53 isolates had variations. Out of the 23 isolates, 15 (65%) exhibited single or multiple substitutions, which resulted to specific amino acid changes. The remaining 8 (35%) isolates had silent mutations. The amino acid substitution M133T which was associated with failure of HBsAg detection was found in one isolate (7%, 1/15), while the amino acid substitution D144A which was associated with vaccine escape was observed in one isolate (7%, 1/15). No G145R mutation was observed. Of the 15 isolates with identified single or multiple substitutions, 6 (40%) were found to have unique sequences which caused changes in the hydrophobicity profile in the protein. Unique sequence variants at amino acid positions M103I, L109P, S117R, F134I, and S136L found in this study have not yet been reported. These data should be taken into account when developing next generation HBV assays to detect both common and unique variants, and when new HBV vaccines will be designed.

  1. Unique Features of Hepatitis C Virus Capsid Formation Revealed by De Novo Cell-Free Assembly

    PubMed Central

    Klein, Kevin C.; Polyak, Stephen J.; Lingappa, Jaisri R.

    2004-01-01

    The assembly of hepatitis C virus (HCV) is poorly understood, largely due to the lack of mammalian cell culture systems that are easily manipulated and produce high titers of virus. This problem is highlighted by the inability of the recently established HCV replicon systems to support HCV capsid assembly despite high levels of structural protein synthesis. Here we demonstrate that up to 80% of HCV core protein synthesized de novo in cell-free systems containing rabbit reticulocyte lysate or wheat germ extracts assembles into HCV capsids. This contrasts with standard primate cell culture systems, in which almost no core assembles into capsids. Cell-free HCV capsids, which have a sedimentation value of ≈100S, have a buoyant density (1.28 g/ml) on cesium chloride similar to that of HCV capsids from other systems. Capsids produced in cell-free systems are also indistinguishable from capsids isolated from HCV-infected patient serum when analyzed by transmission electron microscopy. Using these cell-free systems, we show that HCV capsid assembly is independent of signal sequence cleavage, is dependent on the N terminus but not the C terminus of HCV core, proceeds at very low nascent chain concentrations, is independent of intact membrane surfaces, and is partially inhibited by cultured liver cell lysates. By allowing reproducible and quantitative assessment of viral and cellular requirements for capsid formation, these cell-free systems make a mechanistic dissection of HCV capsid assembly possible. PMID:15308720

  2. Structure of protein O-mannose kinase reveals a unique active site architecture

    PubMed Central

    Zhu, Qinyu; Venzke, David; Walimbe, Ameya S; Anderson, Mary E; Fu, Qiuyu; Kinch, Lisa N; Wang, Wei; Chen, Xing; Grishin, Nick V; Huang, Niu; Yu, Liping; Dixon, Jack E; Campbell, Kevin P; Xiao, Junyu

    2016-01-01

    The ‘pseudokinase’ SgK196 is a protein O-mannose kinase (POMK) that catalyzes an essential phosphorylation step during biosynthesis of the laminin-binding glycan on α-dystroglycan. However, the catalytic mechanism underlying this activity remains elusive. Here we present the crystal structure of Danio rerio POMK in complex with Mg2+ ions, ADP, aluminum fluoride, and the GalNAc-β3-GlcNAc-β4-Man trisaccharide substrate, thereby providing a snapshot of the catalytic transition state of this unusual kinase. The active site of POMK is established by residues located in non-canonical positions and is stabilized by a disulfide bridge. GalNAc-β3-GlcNAc-β4-Man is recognized by a surface groove, and the GalNAc-β3-GlcNAc moiety mediates the majority of interactions with POMK. Expression of various POMK mutants in POMK knockout cells further validated the functional requirements of critical residues. Our results provide important insights into the ability of POMK to function specifically as a glycan kinase, and highlight the structural diversity of the human kinome. DOI: http://dx.doi.org/10.7554/eLife.22238.001 PMID:27879205

  3. 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 A.; 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 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. PMID:25864384

  4. 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.

  5. Rapid transport from the surface to wells in fractured rock: a unique infiltration tracer experiment.

    PubMed

    Levison, Jana K; Novakowski, Kent S

    2012-04-01

    A unique infiltration tracer experiment was performed whereby a fluorescent dye was applied to the land surface in an agricultural field, near Perth, Ontario, Canada, to simulate the transport of solutes to two pumped monitoring wells drilled into the granitic gneiss aquifer. This experiment, interpreted using the discrete-fracture capability of the numerical model HydroGeoSphere, showed that solute transport from the surface through thin soil (less than 2m) to wells in fractured bedrock can be extremely rapid (on the order of hours). Also, it was demonstrated that maximum concentrations of contaminants originating from the ground surface will not necessarily be the highest in the shallow aquifer horizon. These are important considerations for both private and government-owned drinking water systems that draw water from shallow fractured bedrock aquifers. This research illustrates the extreme importance of protecting drinking water at the source.

  6. Common and unique mechanisms of Chinese herbal remedies on ischemic stroke mice revealed by transcriptome analyses.

    PubMed

    Shen, Yuh-Chiang; Lu, Chung-Kuang; Liou, Kuo-Tong; Hou, Yu-Chang; Lin, Yun-Lan; Wang, Yea-Hwey; Sun, Hsing-Jen; Liao, Ko-Hsun; Wang, Hsei-Wei

    2015-09-15

    Four traditional Chinese herbal remedies (CHR) including Buyang Huanwu decoction (BHD), Xuefu Zhuyu decoction (XZD), Tianma Gouteng decoction (TGD) and Shengyu decoction (SYD) are popular used in treating brain-related dysfunction clinically with different syndrome/pattern based on traditional Chinese medicine (TCM) principles, yet their neuroprotective mechanisms are still unclear. Mice were subjected to an acute ischemic stroke to examine the efficacy and molecular mechanisms of action underlying these CHR. CHR treatment significantly enhanced the survival rate of stroke mice, with BHD being the most effective CHR. All CHR were superior to recombinant tissue-type plasminogen activator (rt-PA) treatment in successfully ameliorating brain function, infarction, and neurological deficits in stroke mice that also paralleled to improvements in blood-brain barrier damage, inflammation, apoptosis, and neurogenesis. Transcriptome analyses reveals that a total of 774 ischemia-induced probe sets were significantly modulated by four CHR, including 52 commonly upregulated genes and 54 commonly downregulated ones. Among them, activation of neurogenesis-associated signaling pathways and down-regulating inflammation and apoptosis pathways are key common mechanisms in ischemic stroke protection by all CHR. Besides, levels of plasma CX3CL1 and S100a9 in patients could be used as biomarkers for therapeutic evaluation before functional recovery could be observed. Our results suggest that using CHR, a combinatory cocktail therapy, is a better way than rt-PA for treating cerebral ischemic-associated diseases through modulating a common as well as a specific group of genes/pathways that may partially explain the syndrome differentiation and treatment principle in TCM. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  7. 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.

  8. A unique physical-chemistry approach for fabricating cell friendly surfaces.

    PubMed

    Irvine, Scott; Sullivan, Alice C; McEwan, Jean R; Jayasinghe, Suwan N

    2008-01-01

    Recent interests in the fabrication of bio/cell-friendly surfaces are consistently gaining much scientific coverage as these methods could be explored as novel regenerative and therapeutic medicinal protocols. Essentially two main components govern this aspect, the processing methodology possessing the required robustness to fabricate a wide range of materials and, not least, the synthesised materials that need to be cell-compatible both in the short and long term after processing. In the study reported here we have combined one such robust jetting approach with a specially formulated siloxane sol. This has several unique properties in itself, and these have been demonstrated here to have a positive effect on the seeded cells. The current work demonstrates that this approach has great promise as a novel methodology for surface engineering for a wide range of applications spanning the physical to the life science areas of research.

  9. Haemophilus influenzae surface fibril (Hsf) is a unique twisted hairpin-like trimeric autotransporter.

    PubMed

    Singh, Birendra; Jubair, Tamim Al; Mörgelin, Matthias; Sundin, Anders; Linse, Sara; Nilsson, Ulf J; Riesbeck, Kristian

    2015-01-01

    The Haemophilus surface fibril (Hsf) is an extraordinary large (2413 amino acids) trimeric autotransporter, present in all encapsulated Haemophilus influenzae. It contributes to virulence by directly functioning as an adhesin. Furthermore, Hsf recruits the host factor vitronectin thereby inhibiting the host innate immune response resulting in enhanced survival in serum. Here we observed by electron microscopy that Hsf appears as an 100 nm long fibril at the bacterial surface albeit the length is approximately 200 nm according to a bioinformatics based model. To unveil this discrepancy, we denaturated Hsf at the surface of Hib by using guanidine hydrochloride (GuHCl). Partial denaturation induced in the presence of GuHCl unfolded the Hsf molecules, and resulted in an increased length of fibres in comparison to the native trimeric form. Importantly, our findings were also verified by E. coli expressing Hsf at its surface. In addition, a set of Hsf-specific peptide antibodies also indicated that the N-terminal of Hsf is located near the C-terminal at the base of the fibril. Taken together, our results demonstrated that Hsf is not a straight molecule but is folded and doubled over. This is the first report that provides the unique structural features of the trimeric autotransporter Hsf.

  10. 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

  11. Surface Morphology of Chalkboard Tips Captures the Uniqueness of the User's Hand Strokes

    NASA Astrophysics Data System (ADS)

    Monterola, Christopher; Crisologo, Irene; Tugaff, Jeric; Batac, Rene; Longjas, Anthony

    Penmanship has a high degree of uniqueness as exemplified by the standard use of hand signature as identifier in contract validations and property ownerships. In this work, we demonstrate that the distinctiveness of one's writing patterns is possibly embedded in the molding of chalk tips. Using conventional photometric stereo method, the three-dimensional surface features of blackboard chalk tips used in Math and Physics lectures are microscopically resolved. Principal component analysis (PCA) and neural networks (NN) are then combined in identifying the chalk user based on the extracted topography. We show that NN approach applied to eight lecturers allow average classification accuracy (ΦNN) equal to 100% and 71.5 ± 2.7% for the training and test sets, respectively. Test sets are chalks not seen previously by the trained NN and represent 25% or 93 of the 368 chalk samples used. We note that the NN test set prediction is more than five-fold higher than the proportional chance criterion (PCC, ΦPCC = 12.9%), strongly hinting to a high degree of unique correlation between the user's hand strokes and the chalk tip features. The result of NN is also about three-fold better than the standard methods of linear discriminant analysis (LDA, ΦLDA = 27.0 ± 4.2%) or classification and regression trees (CART, ΦCART = 17.3 ± 3.7%). While the procedure discussed is far from becoming a practical biometric tool, our work offers a fundamental perspective to the extent on which the uniqueness of hand strokes of humans can be exhibited.

  12. 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

  13. 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.

  14. Cell surface enzyme attachment is mediated by family 37 carbohydrate-binding modules, unique to Ruminococcus albus.

    PubMed

    Ezer, Anat; Matalon, Erez; Jindou, Sadanari; Borovok, Ilya; Atamna, Nof; Yu, Zhongtang; Morrison, Mark; Bayer, Edward A; Lamed, Raphael

    2008-12-01

    The rumen bacterium Ruminococcus albus binds to and degrades crystalline cellulosic substrates via a unique cellulose degradation system. A unique family of carbohydrate-binding modules (CBM37), located at the C terminus of different glycoside hydrolases, appears to be responsible both for anchoring these enzymes to the bacterial cell surface and for substrate binding.

  15. Cell Surface Enzyme Attachment Is Mediated by Family 37 Carbohydrate-Binding Modules, Unique to Ruminococcus albus▿ ‡

    PubMed Central

    Ezer, Anat; Matalon, Erez; Jindou, Sadanari; Borovok, Ilya; Atamna, Nof; Yu, Zhongtang; Morrison, Mark; Bayer, Edward A.; Lamed, Raphael

    2008-01-01

    The rumen bacterium Ruminococcus albus binds to and degrades crystalline cellulosic substrates via a unique cellulose degradation system. A unique family of carbohydrate-binding modules (CBM37), located at the C terminus of different glycoside hydrolases, appears to be responsible both for anchoring these enzymes to the bacterial cell surface and for substrate binding. PMID:18931104

  16. 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.

  17. 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.

  18. 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

  19. Characterization of Panglial Gap Junction Networks in the Thalamus, Neocortex, and Hippocampus Reveals a Unique Population of Glial Cells

    PubMed Central

    Griemsmann, Stephanie; Höft, Simon P.; Bedner, Peter; Zhang, Jiong; von Staden, Elena; Beinhauer, Anna; Degen, Joachim; Dublin, Pavel; Cope, David W.; Richter, Nadine; Crunelli, Vincenzo; Jabs, Ronald; Willecke, Klaus; Theis, Martin; Seifert, Gerald; Kettenmann, Helmut; Steinhäuser, Christian

    2015-01-01

    The thalamus plays important roles as a relay station for sensory information in the central nervous system (CNS). Although thalamic glial cells participate in this activity, little is known about their properties. In this study, we characterized the formation of coupled networks between astrocytes and oligodendrocytes in the murine ventrobasal thalamus and compared these properties with those in the hippocampus and cortex. Biocytin filling of individual astrocytes or oligodendrocytes revealed large panglial networks in all 3 gray matter regions. Combined analyses of mice with cell type-specific deletion of connexins (Cxs), semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) and western blotting showed that Cx30 is the dominant astrocytic Cx in the thalamus. Many thalamic astrocytes even lack expression of Cx43, while in the hippocampus astrocytic coupling is dominated by Cx43. Deletion of Cx30 and Cx47 led to complete loss of panglial coupling, which was restored when one allele of either Cxs was present. Immunohistochemistry revealed a unique antigen profile of thalamic glia and identified an intermediate cell type expressing both Olig2 and Cx43. Our findings further the emerging concept of glial heterogeneity across brain regions. PMID:25037920

  20. Characterization of Panglial Gap Junction Networks in the Thalamus, Neocortex, and Hippocampus Reveals a Unique Population of Glial Cells.

    PubMed

    Griemsmann, Stephanie; Höft, Simon P; Bedner, Peter; Zhang, Jiong; von Staden, Elena; Beinhauer, Anna; Degen, Joachim; Dublin, Pavel; Cope, David W; Richter, Nadine; Crunelli, Vincenzo; Jabs, Ronald; Willecke, Klaus; Theis, Martin; Seifert, Gerald; Kettenmann, Helmut; Steinhäuser, Christian

    2015-10-01

    The thalamus plays important roles as a relay station for sensory information in the central nervous system (CNS). Although thalamic glial cells participate in this activity, little is known about their properties. In this study, we characterized the formation of coupled networks between astrocytes and oligodendrocytes in the murine ventrobasal thalamus and compared these properties with those in the hippocampus and cortex. Biocytin filling of individual astrocytes or oligodendrocytes revealed large panglial networks in all 3 gray matter regions. Combined analyses of mice with cell type-specific deletion of connexins (Cxs), semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) and western blotting showed that Cx30 is the dominant astrocytic Cx in the thalamus. Many thalamic astrocytes even lack expression of Cx43, while in the hippocampus astrocytic coupling is dominated by Cx43. Deletion of Cx30 and Cx47 led to complete loss of panglial coupling, which was restored when one allele of either Cxs was present. Immunohistochemistry revealed a unique antigen profile of thalamic glia and identified an intermediate cell type expressing both Olig2 and Cx43. Our findings further the emerging concept of glial heterogeneity across brain regions.

  1. 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

  2. Unique secreted-surface protein complex of Lactobacillus rhamnosus, identified by phage display.

    PubMed

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

    2013-02-01

    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. © 2012 The Authors. Published by Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

  3. 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

  4. A unique carbon with a high specific surface area produced by the carbonization of agar in the presence of graphene.

    PubMed

    Xie, Tingting; Lv, Wei; Wei, Wei; Li, Zhengjie; Li, Baohua; Kang, Feiyu; Yang, Quan-Hong

    2013-11-14

    A unique carbon with a high specific surface area was prepared by carbonization of a polymer-based precursor, agar, in the presence of graphene. Graphene prevents the shrinkage and aggregation of the carbonized particles, resulting in extraordinarily large external surface area (∼1200 m(2) g(-1)) of the carbon, which shows a high rate performance as a supercapacitor electrode.

  5. Unique charge distribution in surface loops confers high velocity on the fast motor protein Chara myosin.

    PubMed

    Ito, Kohji; Yamaguchi, Yukie; Yanase, Kenji; Ichikawa, Yousuke; Yamamoto, Keiichi

    2009-12-22

    Most myosins have a positively charged loop 2 with a cluster of lysine residues that bind to the negatively charged N-terminal segment of actin. However, the net charge of loop 2 of very fast Chara myosin is zero and there is no lysine cluster in it. In contrast, Chara myosin has a highly positively charged loop 3. To elucidate the role of these unique surface loops of Chara myosin in its high velocity and high actin-activated ATPase activity, we have undertaken mutational analysis using recombinant Chara myosin motor domain. It was found that net positive charge in loop 3 affected V(max) and K(app) of actin activated ATPase activity, while it affected the velocity only slightly. The net positive charge in loop 2 affected K(app) and the velocity, although it did not affect V(max). Our results suggested that Chara myosin has evolved to have highly positively charged loop 3 for its high ATPase activity and have less positively charged loop 2 for its high velocity. Since high positive charge in loop 3 and low positive charge in loop 2 seem to be one of the reasons for Chara myosin's high velocity, we manipulated charge contents in loops 2 and 3 of Dictyostelium myosin (class II). Removing positive charge from loop 2 and adding positive charge to loop 3 of Dictyostelium myosin made its velocity higher than that of the wild type, suggesting that the charge strategy in loops 2 and 3 is widely applicable.

  6. Salivary Gland Proteome Analysis Reveals Modulation of Anopheline Unique Proteins in Insensitive Acetylcholinesterase Resistant Anopheles gambiae Mosquitoes

    PubMed Central

    Cornelie, Sylvie; Rossignol, Marie; Seveno, Martial; Demettre, Edith; Mouchet, François; Djègbè, Innocent; Marin, Philippe; Chandre, Fabrice; Corbel, Vincent; Remoué, Franck; Mathieu-Daudé, Françoise

    2014-01-01

    Insensitive acetylcholinesterase resistance due to a mutation in the acetylcholinesterase (ace) encoding ace-1 gene confers cross-resistance to organophosphate and carbamate insecticides in Anopheles gambiae populations from Central and West Africa. This mutation is associated with a strong genetic cost revealed through alterations of some life history traits but little is known about the physiological and behavioural changes in insects bearing the ace-1R allele. Comparative analysis of the salivary gland contents between An. gambiae susceptible and ace-1R resistant strains was carried out to charaterize factors that could be involved in modifications of blood meal process, trophic behaviour or pathogen interaction in the insecticide-resistant mosquitoes. Differential analysis of the salivary gland protein profiles revealed differences in abundance for several proteins, two of them showing major differences between the two strains. These two proteins identified as saglin and TRIO are salivary gland-1 related proteins, a family unique to anopheline mosquitoes, one of them playing a crucial role in salivary gland invasion by Plasmodium falciparum sporozoites. Differential expression of two other proteins previously identified in the Anopheles sialome was also observed. The differentially regulated proteins are involved in pathogen invasion, blood feeding process, and protection against oxidation, relevant steps in the outcome of malaria infection. Further functional studies and insect behaviour experiments would confirm the impact of the modification of the sialome composition on blood feeding and pathogen transmission abilities of the resistant mosquitoes. The data supports the hypothesis of alterations linked to insecticide resistance in the biology of the primary vector of human malaria in Africa. PMID:25102176

  7. Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis.

    PubMed

    Christopherson, Melissa R; Dawson, John A; Stevenson, David M; Cunningham, Andrew C; Bramhacharya, Shanti; Weimer, Paul J; Kendziorski, Christina; Suen, Garret

    2014-12-04

    Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. Moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro. The mechanism of cellulose degradation by R. albus 7 is not well-defined and is thought to involve pilin-like proteins, unique carbohydrate-binding domains, a glycocalyx, and cellulosomes. Here, we used a combination of comparative genomics, fermentation analyses, and transcriptomics to further clarify the cellulolytic and fermentative potential of R. albus 7. A comparison of the R. albus 7 genome sequence against the genome sequences of related bacteria that either encode or do not encode cellulosomes revealed that R. albus 7 does not encode for most canonical cellulosomal components. Fermentation analysis of R. albus 7 revealed the ability to produce ethanol and acetate on a wide range of fibrous substrates in vitro. Global transcriptomic analysis of R. albus 7 grown at identical dilution rates on cellulose and cellobiose in a chemostat showed that this bacterium, when growing on cellulose, utilizes a carbohydrate-degrading strategy that involves increased transcription of the rare carbohydrate-binding module (CBM) family 37 domain and the tryptophan biosynthetic operon. Our data suggest that R. albus 7 does not use canonical cellulosomal components to degrade cellulose, but rather up-regulates the expression of CBM37-containing enzymes and tryptophan biosynthesis. This study contributes to a revised model of carbohydrate degradation by this key member of the rumen ecosystem.

  8. Structure of the PSD-95/MAP1A complex reveals a unique target recognition mode of the MAGUK GK domain.

    PubMed

    Xia, Yitian; Shang, Yuan; Zhang, Rongguang; Zhu, Jinwei

    2017-08-10

    The PSD-95 family of membrane-associated guanylate kinases (MAGUKs) are major synaptic scaffold proteins and play crucial roles in the dynamic regulation of dendritic remodelling, which is understood to be the foundation of synaptogenesis and synaptic plasticity. The guanylate kinase (GK) domain of MAGUK family proteins functions as a phosphor-peptide binding module. However, the GK domain of PSD-95 has been found to directly bind to a peptide sequence within the C-terminal region of neuronal-specific microtubule-associated protein 1A (MAP1A), although the detailed molecular mechanism governing this phosphorylation-independent interaction at the atomic level is missing. In the present study, we determine the crystal structure of PSD-95 GK in complex with the MAP1A peptide at 2.6-Å resolution. The complex structure reveals that, unlike a linear and elongated conformation in the phosphor-peptide/GK complexes, the MAP1A peptide adopts a unique conformation with a stretch of hydrophobic residues far from each other in the primary sequence clustering and interacting with the 'hydrophobic site' of PSD-95 GK and a highly conserved aspartic acid of MAP1A (D2117) mimicking the phosphor-serine/threonine in binding to the 'phosphor-site' of PSD-95 GK. We demonstrate that the MAP1A peptide may undergo a conformational transition upon binding to PSD-95 GK. Further structural comparison of known DLG GK-mediated complexes reveals the target recognition specificity and versatility of DLG GKs. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  9. New sedimentary evidence reveals a unique history of C4 biomass in continental East Asia since the early Miocene.

    PubMed

    Zhou, Bin; Bird, Michael; Zheng, Hongbo; Zhang, Enlou; Wurster, Christopher M; Xie, Luhua; Taylor, David

    2017-03-13

    Pyrogenic carbon (PyC) and n-alkane data from sediments in the northern South China Sea reveal variations in material from C4 plants in East Asia over the last ~19 Ma. These data indicate the likely presence of C4 taxa during the earliest part of the record analysed, with C4 species also prominent during the mid and late Miocene and especially the mid Quaternary. Notably the two records diverge after the mid Quaternary, when PyC data indicate a reduced contribution of C4 taxa to biomass burning, whereas plant-derived n-alkanes indicate a greater abundance of C4 plants. This divergence likely reflects differences in the predominant source areas of organic materials accumulating at the coring site, with PyC representing a larger source area that includes material transported in the atmosphere from more temperate (relatively cooler and drier) parts of East Asia. Variations in the relative abundances of C3 and C4 taxa appear to be linked to a combination of environmental factors that have varied temporally and geographically and that are unique to East Asia. A major expansion of C4 biomass in warmer subtropical parts of eastern Asia from ~1 Ma and particularly from ~0.4 Ma is later than other parts of the world.

  10. 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

  11. Light and electron microscopy of the European beaver (Castor fiber) stomach reveal unique morphological features with possible general biological significance.

    PubMed

    Ziółkowska, Natalia; Lewczuk, Bogdan; 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.

  12. Proteomic and functional analyses reveal a unique lifestyle for Acinetobacter baumannii biofilms and a key role for histidine metabolism.

    PubMed

    Cabral, Maria P; Soares, Nelson C; Aranda, Jesús; Parreira, José R; Rumbo, Carlos; Poza, Margarita; Valle, Jaione; Calamia, Valentina; Lasa, Iñigo; Bou, Germán

    2011-08-05

    Biofilm formation is one of the main causes for the persistence of Acinetobacter baumannii, a pathogen associated with severe infections and outbreaks in hospitals. Here, we performed comparative proteomic analyses (2D-DIGE and MALDI-TOF/TOF and iTRAQ/SCX-LC-MS/MS) of cells at three different conditions: exponential, late stationary phase, and biofilms. These results were compared with alterations in the proteome resulting from exposure to a biofilm inhibitory compound (salicylate). Using this multiple-approach strategy, proteomic patterns showed a unique lifestyle for A. baumannii biofilms and novel associated proteins. Several cell surface proteins (such as CarO, OmpA, OprD-like, DcaP-like, PstS, LysM, and Omp33), as well as those involved in histidine metabolism (like Urocanase), were found to be implicated in biofilm formation, this being confirmed by gene disruption. Although l-His uptake triggered biofilms efficiently in wild-type A. baumannii, no effect was observed in Urocanase and OmpA mutants, while a slight increase was observed in a CarO deficient strain. We conclude that Urocanase plays a crucial role in histidine metabolism leading to biofilm formation and that OmpA and CarO can act as channels for L-His uptake. Finally, we propose a model in which novel proteins are suggested for the first time as targets for preventing the formation of A. baumannii biofilms.

  13. 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

  14. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities

    PubMed Central

    Rai, Richa; Chauhan, Sudhir Kumar; Singh, Vikas Vikram; Rai, Madhukar; Rai, Geeta

    2016-01-01

    Systemic lupus erythematosus (SLE) patients exhibit immense heterogeneity which is challenging from the diagnostic perspective. Emerging high throughput sequencing technologies have been proved to be a useful platform to understand the complex and dynamic disease processes. SLE patients categorised based on autoantibody specificities are reported to have differential immuno-regulatory mechanisms. Therefore, we performed RNA-seq analysis to identify transcriptomics of SLE patients with distinguished autoantibody specificities. The SLE patients were segregated into three subsets based on the type of autoantibodies present in their sera (anti-dsDNA+ group with anti-dsDNA autoantibody alone; anti-ENA+ group having autoantibodies against extractable nuclear antigens (ENA) only, and anti-dsDNA+ENA+ group having autoantibodies to both dsDNA and ENA). Global transcriptome profiling for each SLE patients subsets was performed using Illumina® Hiseq-2000 platform. The biological relevance of dysregulated transcripts in each SLE subsets was assessed by ingenuity pathway analysis (IPA) software. We observed that dysregulation in the transcriptome expression pattern was clearly distinct in each SLE patients subsets. IPA analysis of transcripts uniquely expressed in different SLE groups revealed specific biological pathways to be affected in each SLE subsets. Multiple cytokine signaling pathways were specifically dysregulated in anti-dsDNA+ patients whereas Interferon signaling was predominantly dysregulated in anti-ENA+ patients. In anti-dsDNA+ENA+ patients regulation of actin based motility by Rho pathway was significantly affected. The granulocyte gene signature was a common feature to all SLE subsets; however, anti-dsDNA+ group showed relatively predominant expression of these genes. Dysregulation of Plasma cell related transcripts were higher in anti-dsDNA+ and anti-ENA+ patients as compared to anti-dsDNA+ ENA+. Association of specific canonical pathways with the uniquely

  16. Structural and Biochemical Characterization of Plasmodium falciparum 12 (Pf12) Reveals a Unique Interdomain Organization and the Potential for an Antiparallel Arrangement with Pf41*

    PubMed Central

    Tonkin, Michelle L.; Arredondo, Silvia A.; Loveless, Bianca C.; Serpa, Jason J.; Makepeace, Karl A. T.; Sundar, Natarajan; Petrotchenko, Evgeniy V.; Miller, Louis H.; Grigg, Michael E.; Boulanger, Martin J.

    2013-01-01

    Plasmodium falciparum is the most devastating agent of human malaria. A major contributor to its virulence is a complex lifecycle with multiple parasite forms, each presenting a different repertoire of surface antigens. Importantly, members of the 6-Cys s48/45 family of proteins are found on the surface of P. falciparum in every stage, and several of these antigens have been investigated as vaccine targets. Pf12 is the archetypal member of the 6-Cys protein family, containing just two s48/45 domains, whereas other members have up to 14 of these domains. Pf12 is strongly recognized by immune sera from naturally infected patients. Here we show that Pf12 is highly conserved and under purifying selection. Immunofluorescence data reveals a punctate staining pattern with an apical organization in late schizonts. Together, these data are consistent with an important functional role for Pf12 in parasite-host cell attachment or invasion. To infer the structural and functional diversity between Pf12 and the other 11 6-Cys domain proteins, we solved the 1.90 Å resolution crystal structure of the Pf12 ectodomain. Structural analysis reveals a unique organization between the membrane proximal and membrane distal domains and clear homology with the SRS-domain containing proteins of Toxoplasma gondii. Cross-linking and mass spectrometry confirm the previously identified Pf12-Pf41 heterodimeric complex, and analysis of individual cross-links supports an unexpected antiparallel organization. Collectively, the localization and structure of Pf12 and details of its interaction with Pf41 reveal important insight into the structural and functional properties of this archetypal member of the 6-Cys protein family. PMID:23511632

  17. 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

  18. Visualization of a neurotropic flavivirus infection in mouse reveals unique viscerotropism controlled by host type I interferon signaling

    PubMed Central

    Li, Xiao-Feng; Li, Xiao-Dan; Deng, Cheng-Lin; Dong, Hao-Long; Zhang, Qiu-Yan; Ye, Qing; Ye, Han-Qing; Huang, Xing-Yao; Deng, Yong-Qiang; Zhang, Bo; Qin, Cheng-Feng

    2017-01-01

    Flavivirus includes a large group of human pathogens with medical importance. Especially, neurotropic flaviviruses capable of invading central and peripheral nervous system, e.g. Japanese encephalitis virus (JEV) and Zika virus (ZIKV), are highly pathogenic to human and constitute major global health problems. However, the dynamic dissemination and pathogenesis of neurotropic flavivirus infections remain largely unknown. Here, using JEV as a model, we rationally designed and constructed a recombinant reporter virus that stably expressed Renilla luciferase (Rluc). The resulting JEV reporter virus (named Rluc-JEV) and parental JEV exhibited similar replication and infection characteristics, and the magnitude of Rluc activity correlated well with progeny viral production in vitro and in vivo. By using in vivo bioluminescence imaging (BLI) technology, we dissected the replication and dissemination dynamics of JEV infection in mice upon different inoculation routes. Interestingly, besides replicating in mouse brain, Rluc-JEV predominantly invaded the abdominal organs in mice with typical viscerotropism. Further tests in mice deficient in type I interferon (IFN) receptors demonstrated robust and prolonged viral replication in the intestine, spleen, liver, kidney and other abdominal organs. Combined with histopathological and immunohistochemical results, the host type I IFN signaling was evidenced as the major barrier to the viscerotropism and pathogenicity of this neurotropic flavivirus. Additionally, the Rluc-JEV platform was readily adapted for efficacy assay of known antiviral compounds and a live JE vaccine. Collectively, our study revealed abdominal organs as important targets of JEV infection in mice and profiled the unique viscerotropism trait controlled by the host type I IFN signaling. This in vivo visualization technology described here provides a powerful tool for testing antiviral agents and vaccine candidates for flaviviral infection. PMID:28382163

  19. 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

    2014-11-07

    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.

  20. 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.

  1. 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

  2. The Sea of Japan and Its Unique Chemistry Revealed by Time-Series Observations over the Last 30 Years

    NASA Astrophysics Data System (ADS)

    Gamo, T.; Nakayama, N.; Takahata, N.; Sano, Y.; Zhang, J.; Yamazaki, E.; Taniyasu, S.; Yamashita, N.

    2014-02-01

    Chemical tracers in seawater, as well as physical parameters such as temperature and salinity, have been measured to better characterize the dynamics of water convection and its spatiotemporal changes in the Sea of Japan (also called the Japan Sea), a semi-closed, hyperoxic marginal sea (maximum depth: ˜3,800 m) in the northwestern corner of the Pacific Ocean. Repeated conductivity, temperature, and depth (CTD) observations and measurements of dissolved oxygen, for more than 30 years, have confirmed that the bottom layer of the Japan Sea, with a thickness of ˜1 km below the boundary at a depth of ˜2,500 m, is characterized by vertical homogeneity with fluctuations of potential temperature and dissolved oxygen of <0.001°C and <0.5 μmol kg-1, respectively. The timescale of the abyssal circulation in the Japan Sea has been estimated to be 100-300 years, using 14C and other chemical tracers. Stable isotope analyses for dissolved He, O2 and CH4 have given us information on their unique geochemical cycles in the Japan Sea. Profiles of the short-lived radioisotope 222Rn just above the sea bottom have brought new insights into the short-term lateral water movement with a timescale of several days in the Japan Sea bottom water. It is of special concern that the gradual deoxygenation and warming of the bottom water over the last 30 years have resulted in an ˜10% decrease in dissolved oxygen and ˜0.04°C increase in potential temperature, suggesting a change of the deep convection system in the Japan Sea. The temporal changes in the vertical profiles of tritium from 1984 to 1998 have suggested a shift of the abyssal circulation pattern from a ``total (overall) convection mode" to a ``shallow (partial) convection mode". It is likely that the global warming since the last century has hindered the formation of dense surface seawater and its ability to sink down to the bottom, isolating the bottom layer from the deep convection loop that is indispensable as the source of

  3. 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.

  4. 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

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

    PubMed

    Larroque, Mathieu; Barriot, Roland; Bottin, Arnaud; Barre, Annick; Rougé, Pierre; Dumas, Bernard; Gaulin, Elodie

    2012-11-09

    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. 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. This study provides insight into the evolution and biological roles of

  6. The interior structure of Ceres as revealed by surface topography

    NASA Astrophysics Data System (ADS)

    Fu, Roger R.; Ermakov, Anton I.; Marchi, Simone; Castillo-Rogez, Julie C.; Raymond, Carol A.; Hager, Bradford H.; Zuber, Maria T.; King, Scott D.; Bland, Michael T.; Cristina De Sanctis, Maria; Preusker, Frank; Park, Ryan S.; Russell, Christopher T.

    2017-10-01

    Ceres, the largest body in the asteroid belt (940 km diameter), provides a unique opportunity to study the interior structure of a volatile-rich dwarf planet. Variations in a planetary body's subsurface rheology and density affect the rate of topographic relaxation. Preferential attenuation of long wavelength topography (≥150 km) on Ceres suggests that the viscosity of its crust decreases with increasing depth. We present finite element (FE) geodynamical simulations of Ceres to identify the internal structures and compositions that best reproduce its topography as observed by the NASA Dawn mission. We infer that Ceres has a mechanically strong crust with maximum effective viscosity ∼1025 Pa s. Combined with density constraints, this rheology suggests a crustal composition of carbonates or phyllosilicates, water ice, and at least 30 volume percent (vol.%) low-density, high-strength phases most consistent with salt and/or clathrate hydrates. The inference of these crustal materials supports the past existence of a global ocean, consistent with the observed surface composition. Meanwhile, we infer that the uppermost ≥60 km of the silicate-rich mantle is mechanically weak with viscosity <1021 Pa s, suggesting the presence of liquid pore fluids in this region and a low temperature history that avoided igneous differentiation due to late accretion or efficient heat loss through hydrothermal processes.

  7. Common and unique neural networks for proactive and reactive response inhibition revealed by independent component analysis of functional MRI data.

    PubMed

    van Belle, Janna; Vink, Matthijs; Durston, Sarah; Zandbelt, Bram B

    2014-12-01

    Response inhibition involves proactive and reactive modes. Proactive inhibition is goal-directed, triggered by warning cues, and serves to restrain actions. Reactive inhibition is stimulus-driven, triggered by salient stop-signals, and used to stop actions completely. Functional MRI studies have identified brain regions that activate during proactive and reactive inhibition. It remains unclear how these brain regions operate in functional networks, and whether proactive and reactive inhibition depend on common networks, unique networks, or a combination. To address this we analyzed a large fMRI dataset (N=65) of a stop-signal task designed to measure proactive and reactive inhibition, using independent component analysis (ICA). We found 1) three frontal networks that were associated with both proactive and reactive inhibition, 2) one network in the superior parietal lobe, which also included dorsal premotor cortex and left putamen, that was specifically associated with proactive inhibition, and 3) two right-lateralized frontal and fronto-parietal networks, including the right inferior frontal gyrus and temporoparietal junction as well as a bilateral fronto-temporal network that were uniquely associated with reactive inhibition. Overlap between networks was observed in dorsolateral prefrontal and parietal cortices. Taken together, we offer a new perspective on the neural underpinnings of inhibitory control, by showing that proactive inhibition and reactive inhibition are supported by a group of common and unique networks that appear to integrate and interact in frontoparietal areas.

  8. 3 Neutrino mass experiments fit a strange 3 + 3 model, but will KATRIN reveal the model's unique 3-part signature?

    NASA Astrophysics Data System (ADS)

    Ehrlich, R.

    2016-12-01

    Evidence is presented in support of an unconventional 3 + 3 model of the neutrino mass eigenstates with specific m2 > 0 and m2 < 0 masses. The two large m2 > 0 masses of the model were originally suggested based on a SN 1987A analysis, and they were further supported by several dark matter fits. The new evidence for one of the m2 > 0 mass values comes from an analysis of published data from the three most precise tritium β - decay experiments. The KATRIN experiment by virtue of a unique 3-part signature should either confirm or reject the model in its entirety.

  9. Unique activity of Pd monomers: hydrogen evolution at AuPd(111) surface alloys.

    PubMed

    Pluntke, Y; Kibler, L A; Kolb, D M

    2008-07-07

    Well-defined Au/Pd(111) alloy films have been prepared on a Ru(0001) substrate by electrochemical metal deposition and subsequent heating up to 700 degrees C. The electrochemical behaviour of the 20 monolayers thick epitaxially-grown films is in excellent agreement with both equilibrium surface composition and distribution for Au/Pd alloys on Mo(110) as previously reported (D. W. Goodman et al., J. Phys. Chem., 2005, B109, 18535). The electrocatalytic activity of the AuPd(111) surface alloys was studied for the hydrogen evolution in 0.1 M H(2)SO(4) as a function of surface composition. Maximum activities were found for Pd fractions of 0.2 +/- 0.1, where the population of Pd atoms surrounded by Au has its maximum. These Pd monomers are found to be about 20 times more active than Pd atoms in the Pd overlayer.

  10. Crystalline Structure and Surface Reactivity: Atomistic models are unique tools for dealing with the chemical and physical properties of surfaces.

    PubMed

    Gatos, H C

    1962-08-03

    The role of crystalline structure in the surface reactivity of predominantly covalent materials has been examined in terms of chemical bonding concepts. In this context a solid surface can be viewed as a giant lattice defect characterized by dangling bonds. Although it is difficult, at the present stage of development of the quantum mechanical approach to surfaces, to define precisely the perturbations resulting from the abrupt termination of the lattice at the surface, a host of experimental observations can be understood by assuming displacements of surface atoms and distortions of bonding configurations in accordance with simple chemical bonding principles. A purely atomistic approach has been shown to account not only for the chemical behavior but also for certain structural and electrical characteristics of the surfaces considered. A number of phenomena, such as crystal growth and the behavior of certain lattice defects (for example, dislocations), are intimately related to the presence of dangling bonds and the associated distortions of the lattice at the surface (32).

  11. The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes.

    PubMed

    Änkö, Minna-Liisa; Müller-McNicoll, Michaela; Brandl, Holger; Curk, Tomaz; Gorup, Crtomir; Henry, Ian; Ule, Jernej; Neugebauer, Karla M

    2012-01-01

    The SR proteins comprise a family of essential, structurally related RNA binding proteins. The complexity of their RNA targets and specificity of RNA recognition in vivo is not well understood. Here we use iCLIP to globally analyze and compare the RNA binding properties of two SR proteins, SRSF3 and SRSF4, in murine cells. SRSF3 and SRSF4 binding sites mapped to largely non-overlapping target genes, and in vivo consensus binding motifs were distinct. Interactions with intronless and intron-containing mRNAs as well as non-coding RNAs were detected. Surprisingly, both SR proteins bound to the 3' ends of the majority of intronless histone transcripts, implicating SRSF3 and SRSF4 in histone mRNA metabolism. In contrast, SRSF3 but not SRSF4 specifically bound transcripts encoding numerous RNA binding proteins. Remarkably, SRSF3 was shown to modulate alternative splicing of its own as well as three other transcripts encoding SR proteins. These SRSF3-mediated splicing events led to downregulation of heterologous SR proteins via nonsense-mediated decay. SRSF3 and SRSF4 display unique RNA binding properties underlying diverse cellular regulatory mechanisms, with shared as well as unique coding and non-coding targets. Importantly, CLIP analysis led to the discovery that SRSF3 cross-regulates the expression of other SR protein family members.

  12. Comprehensive analysis of The Cancer Genome Atlas reveals a unique gene and non-coding RNA signature of fibrolamellar carcinoma

    PubMed Central

    Dinh, Timothy A.; Vitucci, Eva C. M.; Wauthier, Eliane; Graham, Rondell P.; Pitman, Wendy A.; Oikawa, Tsunekazu; Chen, Mengjie; Silva, Grace O.; Greene, Kevin G.; Torbenson, Michael S.; Reid, Lola M.; Sethupathy, Praveen

    2017-01-01

    Fibrolamellar carcinoma (FLC) is a unique liver cancer primarily affecting young adults and characterized by a fusion event between DNAJB1 and PRKACA. By analyzing RNA-sequencing data from The Cancer Genome Atlas (TCGA) for >9,100 tumors across ~30 cancer types, we show that the DNAJB1-PRKACA fusion is specific to FLCs. We demonstrate that FLC tumors (n = 6) exhibit distinct messenger RNA (mRNA) and long intergenic non-coding RNA (lincRNA) profiles compared to hepatocellular carcinoma (n = 263) and cholangiocarcinoma (n = 36), the two most common liver cancers. We also identify a set of mRNAs (n = 16) and lincRNAs (n = 4), including LINC00473, that distinguish FLC from ~25 other liver and non-liver cancer types. We confirm this unique FLC signature by analysis of two independent FLC cohorts (n = 20 and 34). Lastly, we validate the overexpression of one specific gene in the FLC signature, carbonic anhydrase XII (CA12), at the protein level by western blot and immunohistochemistry. Both the mRNA and lincRNA signatures support a major role for protein kinase A (PKA) signaling in shaping the FLC gene expression landscape, and present novel candidate FLC oncogenes that merit further investigation. PMID:28304380

  13. The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

    PubMed Central

    2012-01-01

    Background The SR proteins comprise a family of essential, structurally related RNA binding proteins. The complexity of their RNA targets and specificity of RNA recognition in vivo is not well understood. Here we use iCLIP to globally analyze and compare the RNA binding properties of two SR proteins, SRSF3 and SRSF4, in murine cells. Results SRSF3 and SRSF4 binding sites mapped to largely non-overlapping target genes, and in vivo consensus binding motifs were distinct. Interactions with intronless and intron-containing mRNAs as well as non-coding RNAs were detected. Surprisingly, both SR proteins bound to the 3' ends of the majority of intronless histone transcripts, implicating SRSF3 and SRSF4 in histone mRNA metabolism. In contrast, SRSF3 but not SRSF4 specifically bound transcripts encoding numerous RNA binding proteins. Remarkably, SRSF3 was shown to modulate alternative splicing of its own as well as three other transcripts encoding SR proteins. These SRSF3-mediated splicing events led to downregulation of heterologous SR proteins via nonsense-mediated decay. Conclusions SRSF3 and SRSF4 display unique RNA binding properties underlying diverse cellular regulatory mechanisms, with shared as well as unique coding and non-coding targets. Importantly, CLIP analysis led to the discovery that SRSF3 cross-regulates the expression of other SR protein family members. PMID:22436691

  14. Improved vacuum surface flashover performance of polymer insulators by the use of unique triple junction designs

    SciTech Connect

    Smith, J.D.; Kahaian, D.J.; Honig, E.M.; Montoya, R.E.; Rosocha, L.A.; Allen, G.R. ); Aaron, W.F. III . Plasma Lab.)

    1991-01-01

    Previous research and theories about surface flashover in vacuum indicate that the triple junction region plays a critical role in the insulator flashover process. To attempt to improve upon the performance of the standard 45-degree frustum insulator, three different insulator geometries with modified triple junction regions were investigated. Two samples of each geometry, each 2 cm thick, were tested to obtain the flashover voltage levels in a low 10{sup {minus}5} Torr vacuum using a 1.2-microsecond risetime voltage pulse. Each sample was tested five times with 20 shots per test for a total of 200 shots per geometry. Test results and comparisons of the flashover voltage levels for the four geometries are presented. One geometry showed an improvement in flashover voltage of about 40% over the standard 45-degree frustum. It also showed significantly less susceptibility to low-voltage flashover due to surface damage, suggesting a correlation between surface damage and the development of conductive paths along the surface.

  15. Cell surface antigens of human trophoblast: definition of an apparently unique system with a monoclonal antibody.

    PubMed Central

    Mueller, U W; Hawes, C S; Jones, W R

    1986-01-01

    An epitope with apparent specificity for the surface of human syncytiotrophoblast was defined by a murine monoclonal antibody, FDO46B (IgG1, kappa). The epitope was predominantly expressed during the first trimester of pregnancy. Binding was detected on frozen tissue sections and on cultured trophoblast by the immunoperoxidase technique. It was also detected on the surface of a small percentage (less than 10%) of cultured choriocarcinoma cells (JEG-3). A panel of human tissues was negative, as were normal and malignant human lymphocytes. The antigen bearing the FDO46B epitope was still expressed by trophoblast after culture in the presence of tunicamycin, indicating that it is possibly protein in nature. This antigen may have potential utility as a target for a contraceptive vaccine. Images Figure 1 Figure 2 Figure 3 PMID:2428734

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

    PubMed

    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

    2009-06-02

    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-kappaB1)/p105. This represents the first direct interaction between a pathogen-encoded protein and NF-kappaB1/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-kappaB signaling in human cells. Thus, proteomic screening of variola virus has the potential to uncover modulators of the human innate antiviral responses.

  17. Cell-material interactions revealed via material techniques of surface patterning.

    PubMed

    Yao, Xiang; Peng, Rong; Ding, Jiandong

    2013-10-04

    Cell-material interactions constitute a key fundamental topic in biomaterials study. Various cell cues and matrix cues as well as soluble factors regulate cell behaviors on materials. These factors are coupled with each other as usual, and thus it is very difficult to unambiguously elucidate the role of each regulator. The recently developed material techniques of surface patterning afford unique ways to reveal the underlying science. This paper reviews the pertinent material techniques to fabricate patterns of microscale and nanoscale resolutions, and corresponding cell studies. Some issues are emphasized, such as cell localization on patterned surfaces of chemical contrast, and effects of cell shape, cell size, cell-cell contact, and seeding density on differentiation of stem cells. Material cues to regulate cell adhesion, cell differentiation and other cell events are further summed up. Effects of some physical properties, such as surface topography and matrix stiffness, on cell behaviors are also discussed; nanoscaled features of substrate surfaces to regulate cell fate are summarized as well. The pertinent work sheds new insight into the cell-material interactions, and is stimulating for biomaterial design in regenerative medicine, tissue engineering, and high-throughput detection, diagnosis, and drug screening. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. 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

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

    PubMed

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

    2013-10-22

    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.

  20. 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

  1. 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

  2. Breakpoint structure reveals the unique origin of an interspecific chromosomal inversion (2La) in the Anopheles gambiae complex

    PubMed Central

    Sharakhov, Igor V.; White, Bradley J.; Sharakhova, Maria V.; Kayondo, Jonathan; Lobo, Neil F.; Santolamazza, Federica; della Torre, Alessandra; Simard, Frédéric; Collins, Frank H.; Besansky, Nora J.

    2006-01-01

    Paracentric chromosomal inversions are major architects of organismal evolution and have been associated with adaptations relevant to malaria transmission in anopheline mosquitoes. The processes responsible for their origin and maintenance, still poorly understood, can be illuminated by analysis of inversion breakpoint sequences. Here, we report the breakpoint structure of chromosomal inversion 2La from the principal malaria vector Anopheles gambiae and its relatives in the A. gambiae complex. The distal and proximal breakpoints of the standard (2L+a) arrangement contain gene duplications: full-length genes and their truncated copies at opposite ends. Intact genes without pseudogene copies in the alternative arrangement (2La) imply that 2L+a is derived and was viable despite damage to genes, because duplication preserved gene function. A unique origin for the interspecific 2La inversion was challenged previously by indirect genetic evidence, but breakpoint sequences determined from members of the A. gambiae complex strongly suggest their descent from a single event. The derived position of 2L+a, long considered ancestral in this medically important group, has significant implications for the phylogenetic history and the evolution of vectorial capacity in the A. gambiae complex. PMID:16606844

  3. 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

  4. Iapetus: unique surface properties and a global color dichotomy from Cassini imaging.

    PubMed

    Denk, Tilmann; Neukum, Gerhard; Roatsch, Thomas; Porco, Carolyn C; Burns, Joseph A; Galuba, Götz G; Schmedemann, Nico; Helfenstein, Paul; Thomas, Peter C; Wagner, Roland J; West, Robert A

    2010-01-22

    Since 2004, Saturn's moon Iapetus has been observed repeatedly with the Imaging Science Subsystem of the Cassini spacecraft. The images show numerous impact craters down to the resolution limit of approximately 10 meters per pixel. Small, bright craters within the dark hemisphere indicate a dark blanket thickness on the order of meters or less. Dark, equator-facing and bright, poleward-facing crater walls suggest temperature-driven water-ice sublimation as the process responsible for local albedo patterns. Imaging data also reveal a global color dichotomy, wherein both dark and bright materials on the leading side have a substantially redder color than the respective trailing-side materials. This global pattern indicates an exogenic origin for the redder leading-side parts and suggests that the global color dichotomy initiated the thermal formation of the global albedo dichotomy.

  5. 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

  6. NOX4 activity is determined by mRNA levels and reveals a unique pattern of ROS generation

    PubMed Central

    Serrander, Lena; Cartier, Laetitia; Bedard, Karen; Banfi, Botond; Lardy, Bernard; Plastre, Olivier; Sienkiewicz, Andrzej; Fórró, Lászlo; Schlegel, Werner; Krause, Karl-Heinz

    2007-01-01

    NOX4 is an enigmatic member of the NOX (NADPH oxidase) family of ROS (reactive oxygen species)-generating NADPH oxidases. NOX4 has a wide tissue distribution, but the physiological function and activation mechanisms are largely unknown, and its pharmacology is poorly understood. We have generated cell lines expressing NOX4 upon tetracycline induction. Tetracycline induced a rapid increase in NOX4 mRNA (1 h) followed closely (2 h) by a release of ROS. Upon tetracycline withdrawal, NOX4 mRNA levels and ROS release decreased rapidly (<24 h). In membrane preparations, NOX4 activity was selective for NADPH over NADH and did not require the addition of cytosol. The pharmacological profile of NOX4 was distinct from other NOX isoforms: DPI (diphenyleneiodonium chloride) and thioridazine inhibited the enzyme efficiently, whereas apocynin and gliotoxin did not (IC50>100 μM). The pattern of NOX4-dependent ROS generation was unique: (i) ROS release upon NOX4 induction was spontaneous without need for a stimulus, and (ii) the type of ROS released from NOX4-expressing cells was H2O2, whereas superoxide (O2−) was almost undetectable. Probes that allow detection of intracellular O2− generation yielded differential results: DHE (dihydroethidium) fluorescence and ACP (1-acetoxy-3-carboxy-2,2,5,5-tetramethylpyrrolidine) ESR measurements did not detect any NOX4 signal, whereas a robust signal was observed with NBT. Thus NOX4 probably generates O2− within an intracellular compartment that is accessible to NBT (Nitro Blue Tetrazolium), but not to DHE or ACP. In conclusion, NOX4 has a distinct pharmacology and pattern of ROS generation. The close correlation between NOX4 mRNA and ROS generation might hint towards a function as an inducible NOX isoform. PMID:17501721

  7. NOX4 activity is determined by mRNA levels and reveals a unique pattern of ROS generation.

    PubMed

    Serrander, Lena; Cartier, Laetitia; Bedard, Karen; Banfi, Botond; Lardy, Bernard; Plastre, Olivier; Sienkiewicz, Andrzej; Fórró, Lászlo; Schlegel, Werner; Krause, Karl-Heinz

    2007-08-15

    NOX4 is an enigmatic member of the NOX (NADPH oxidase) family of ROS (reactive oxygen species)-generating NADPH oxidases. NOX4 has a wide tissue distribution, but the physiological function and activation mechanisms are largely unknown, and its pharmacology is poorly understood. We have generated cell lines expressing NOX4 upon tetracycline induction. Tetracycline induced a rapid increase in NOX4 mRNA (1 h) followed closely (2 h) by a release of ROS. Upon tetracycline withdrawal, NOX4 mRNA levels and ROS release decreased rapidly (<24 h). In membrane preparations, NOX4 activity was selective for NADPH over NADH and did not require the addition of cytosol. The pharmacological profile of NOX4 was distinct from other NOX isoforms: DPI (diphenyleneiodonium chloride) and thioridazine inhibited the enzyme efficiently, whereas apocynin and gliotoxin did not (IC(50)>100 muM). The pattern of NOX4-dependent ROS generation was unique: (i) ROS release upon NOX4 induction was spontaneous without need for a stimulus, and (ii) the type of ROS released from NOX4-expressing cells was H(2)O(2), whereas superoxide (O(2)(-)) was almost undetectable. Probes that allow detection of intracellular O(2)(-) generation yielded differential results: DHE (dihydroethidium) fluorescence and ACP (1-acetoxy-3-carboxy-2,2,5,5-tetramethylpyrrolidine) ESR measurements did not detect any NOX4 signal, whereas a robust signal was observed with NBT. Thus NOX4 probably generates O(2)(-) within an intracellular compartment that is accessible to NBT (Nitro Blue Tetrazolium), but not to DHE or ACP. In conclusion, NOX4 has a distinct pharmacology and pattern of ROS generation. The close correlation between NOX4 mRNA and ROS generation might hint towards a function as an inducible NOX isoform.

  8. 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.

  9. 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.

  10. Comparative Subcellular Localization Analysis of Magnetosome Proteins Reveals a Unique Localization Behavior of Mms6 Protein onto Magnetite Crystals.

    PubMed

    Arakaki, Atsushi; Kikuchi, Daiki; Tanaka, Masayoshi; Yamagishi, Ayana; Yoda, Takuto; Matsunaga, Tadashi

    2016-10-15

    The magnetosome is an organelle specialized for inorganic magnetite crystal synthesis in magnetotactic bacteria. The complex mechanism of magnetosome formation is regulated by magnetosome proteins in a stepwise manner. Protein localization is a key step for magnetosome development; however, a global study of magnetosome protein localization remains to be conducted. Here, we comparatively analyzed the subcellular localization of a series of green fluorescent protein (GFP)-tagged magnetosome proteins. The protein localizations were categorized into 5 groups (short-length linear, middle-length linear, long-length linear, cell membrane, and intracellular dispersing), which were related to the protein functions. Mms6, which regulates magnetite crystal growth, localized along magnetosome chain structures under magnetite-forming (microaerobic) conditions but was dispersed in the cell under nonforming (aerobic) conditions. Correlative fluorescence and electron microscopy analyses revealed that Mms6 preferentially localized to magnetosomes enclosing magnetite crystals. We suggest that a highly organized spatial regulation mechanism controls magnetosome protein localization during magnetosome formation in magnetotactic bacteria. Magnetotactic bacteria synthesize magnetite (Fe3O4) nanocrystals in a prokaryotic organelle called the magnetosome. This organelle is formed using various magnetosome proteins in multiple steps, including vesicle formation, magnetosome alignment, and magnetite crystal formation, to provide compartmentalized nanospaces for the regulation of iron concentrations and redox conditions, enabling the synthesis of a morphologically controlled magnetite crystal. Thus, to rationalize the complex organelle development, the localization of magnetosome proteins is considered to be highly regulated; however, the mechanisms remain largely unknown. Here, we performed comparative localization analysis of magnetosome proteins that revealed the presence of a spatial

  11. Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth

    PubMed Central

    Ortiz-Morea, Fausto A.; Vicentini, Renato; Silva, Geraldo F.F.; Silva, Eder M.; Carrer, Helaine; Rodrigues, Ana P.; Nogueira, Fabio T.S.

    2013-01-01

    Axillary bud outgrowth determines shoot architecture and is under the control of endogenous hormones and a fine-tuned gene-expression network, which probably includes small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets within axillary buds are largely unknown. Here, we employed sRNA next-generation sequencing as well as computational and gene-expression analysis to identify and quantify sRNAs and their targets in vegetative axillary buds of the biofuel crop sugarcane (Saccharum spp.). Computational analysis allowed the identification of 26 conserved miRNA families and two putative novel miRNAs, as well as a number of trans-acting small interfering RNAs. sRNAs associated with transposable elements and protein-encoding genes were similarly represented in both inactive and developing bud libraries. Conversely, sequencing and quantitative reverse transcription-PCR results revealed that specific miRNAs were differentially expressed in developing buds, and some correlated negatively with the expression of their targets at specific stages of axillary bud development. For instance, the expression patterns of miR159 and its target GAMYB suggested that they may play roles in regulating abscisic acid-signalling pathways during sugarcane bud outgrowth. Our work reveals, for the first time, differences in the composition and expression profiles of diverse sRNAs and targets between inactive and developing vegetative buds that, together with the endogenous balance of specific hormones, may be important in regulating axillary bud outgrowth. PMID:23564956

  12. Comparative Subcellular Localization Analysis of Magnetosome Proteins Reveals a Unique Localization Behavior of Mms6 Protein onto Magnetite Crystals

    PubMed Central

    Arakaki, Atsushi; Kikuchi, Daiki; Tanaka, Masayoshi; Yamagishi, Ayana; Yoda, Takuto

    2016-01-01

    ABSTRACT The magnetosome is an organelle specialized for inorganic magnetite crystal synthesis in magnetotactic bacteria. The complex mechanism of magnetosome formation is regulated by magnetosome proteins in a stepwise manner. Protein localization is a key step for magnetosome development; however, a global study of magnetosome protein localization remains to be conducted. Here, we comparatively analyzed the subcellular localization of a series of green fluorescent protein (GFP)-tagged magnetosome proteins. The protein localizations were categorized into 5 groups (short-length linear, middle-length linear, long-length linear, cell membrane, and intracellular dispersing), which were related to the protein functions. Mms6, which regulates magnetite crystal growth, localized along magnetosome chain structures under magnetite-forming (microaerobic) conditions but was dispersed in the cell under nonforming (aerobic) conditions. Correlative fluorescence and electron microscopy analyses revealed that Mms6 preferentially localized to magnetosomes enclosing magnetite crystals. We suggest that a highly organized spatial regulation mechanism controls magnetosome protein localization during magnetosome formation in magnetotactic bacteria. IMPORTANCE Magnetotactic bacteria synthesize magnetite (Fe3O4) nanocrystals in a prokaryotic organelle called the magnetosome. This organelle is formed using various magnetosome proteins in multiple steps, including vesicle formation, magnetosome alignment, and magnetite crystal formation, to provide compartmentalized nanospaces for the regulation of iron concentrations and redox conditions, enabling the synthesis of a morphologically controlled magnetite crystal. Thus, to rationalize the complex organelle development, the localization of magnetosome proteins is considered to be highly regulated; however, the mechanisms remain largely unknown. Here, we performed comparative localization analysis of magnetosome proteins that revealed the

  13. Fourier transform infrared microspectroscopy reveals unique phenotypes for human embryonic and induced pluripotent stem cell lines and their progeny.

    PubMed

    Cao, Julie; Ng, Elizabeth S; McNaughton, Don; Stanley, Edouard G; Elefanty, Andrew G; Tobin, Mark J; Heraud, Philip

    2014-10-01

    Fourier transform infrared (FTIR) microspectroscopy was employed to elucidate the macromolecular phenotype of human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) and their differentiated progeny. Undifferentiated hESCs and hiPSC lines were found to be not clearly distinguishable from each other. However, although both hESC and hiPSC variants appeared to undergo similar changes during differentiation in terms of cell surface antigens, the derived cell types from all cell lines could be discriminated using FTIR spectroscopy. We foresee a possible future role for FTIR microspectroscopy as a powerful and objective investigative and quality control tool in regenerative medicine. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

    PubMed Central

    Thole, Sebastian; Kalhoefer, Daniela; Voget, Sonja; Berger, Martine; Engelhardt, Tim; Liesegang, Heiko; Wollherr, Antje; Kjelleberg, Staffan; Daniel, Rolf; Simon, Meinhard; Thomas, Torsten; Brinkhoff, Thorsten

    2012-01-01

    Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts. PMID:22717884

  15. Unique region of the minor capsid protein of human parvovirus B19 is exposed on the virion surface.

    PubMed Central

    Rosenfeld, S J; Yoshimoto, K; Kajigaya, S; Anderson, S; Young, N S; Field, A; Warrener, P; Bansal, G; Collett, M S

    1992-01-01

    Capsids of the B19 parvovirus are composed of major (VP2; 58 kD) and minor (VP1; 83 kD) structural proteins. These proteins are identical except for a unique 226 amino acid region at the amino terminus of VP1. Previous immunization studies with recombinant empty capsids have demonstrated that the presence of VP1 was required to elicit virus-neutralizing antibody activity. However, to date, neutralizing epitopes have been identified only on VP2. Crystallographic studies of a related parvovirus (canine parvovirus) suggested the unique amino-terminal portion of VP1 assumed an internal position within the viral capsid. To determine the position of VP1 in both empty capsids and virions, we expressed a fusion protein containing the unique region of VP1. Antisera raised to this protein recognized recombinant empty capsids containing VP1 and VP2, but not those containing VP2 alone, in an enzyme-linked immunosorbent assay. The antisera immunoprecipitated both recombinant empty capsids and human plasma-derived virions, and agglutinated the latter as shown by immune electron microscopy. The sera contained potent neutralizing activity for virus infectivity in vitro. These data indicate that a portion of the amino terminus of VP1 is located on the virion surface, and that this region contains intrinsic neutralizing determinants. The external location of the VP1-specific tail may provide a site for engineered heterologous epitope presentation in novel recombinant vaccines. Images PMID:1376332

  16. Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds.

    PubMed

    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.

  17. 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

    2016-03-08

    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.

  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 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

  20. 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

  1. Deficient Tryptophan Catabolism along the Kynurenine Pathway Reveals That the Epididymis Is in a Unique Tolerogenic State*

    PubMed Central

    Jrad-Lamine, Aicha; Henry-Berger, Joelle; Gourbeyre, Pascal; Damon-Soubeyrand, Christelle; Lenoir, Alain; Combaret, Lydie; Saez, Fabrice; Kocer, Ayhan; Tone, Shigenobu; Fuchs, Dietmar; Zhu, Wentao; Oefner, Peter J.; Munn, David H.; Mellor, Andrew L.; Gharbi, Najoua; Cadet, Rémi; Aitken, R. John; Drevet, Joël R.

    2011-01-01

    Indoleamine 2,3-dioxygenase (IDO) is the first and rate-limiting enzyme of tryptophan catabolism through the kynurenine pathway. Intriguingly, IDO is constitutively and highly expressed in the mammalian epididymis in contrast to most other tissues where IDO is induced by proinflammatory cytokines, such as interferons. To gain insight into the role of IDO in the physiology of the mammalian epididymis, we studied both wild type and Ido1−/−-deficient mice. In the caput epididymis of Ido1−/− animals, the lack of IDO activity was not compensated by other tryptophan-catabolizing enzymes and led to the loss of kynurenine production. The absence of IDO generated an inflammatory state in the caput epididymis as revealed by an increased accumulation of various inflammation markers. The absence of IDO also increased the tryptophan content of the caput epididymis and generated a parallel increase in caput epididymal protein content as a consequence of deficient proteasomal activity. Surprisingly, the lack of IDO expression had no noticeable impact on overall male fertility but did induce highly significant increases in both the number and the percentage of abnormal spermatozoa. These changes coincided with a significant decrease in white blood cell count in epididymal fluid compared with wild type mice. These data provide support for IDO playing a hitherto unsuspected role in sperm quality control in the epididymis involving the ubiquitination of defective spermatozoa and their subsequent removal. PMID:21189261

  2. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis

    PubMed Central

    Broddrick, Jared T.; Rubin, Benjamin E.; Welkie, David G.; Du, Niu; Mih, Nathan; Diamond, Spencer; Lee, Jenny J.; Golden, Susan S.; Palsson, Bernhard O.

    2016-01-01

    The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable obligate phototroph that is being developed for the bioproduction of high-value chemicals. Genome-scale models (GEMs) have been successfully used to assess and engineer cellular metabolism; however, GEMs of phototrophic metabolism have been limited by the lack of experimental datasets for model validation and the challenges of incorporating photon uptake. Here, we develop a GEM of metabolism in S. elongatus using random barcode transposon site sequencing (RB-TnSeq) essential gene and physiological data specific to photoautotrophic metabolism. The model explicitly describes photon absorption and accounts for shading, resulting in the characteristic linear growth curve of photoautotrophs. GEM predictions of gene essentiality were compared with data obtained from recent dense-transposon mutagenesis experiments. This dataset allowed major improvements to the accuracy of the model. Furthermore, discrepancies between GEM predictions and the in vivo dataset revealed biological characteristics, such as the importance of a truncated, linear TCA pathway, low flux toward amino acid synthesis from photorespiration, and knowledge gaps within nucleotide metabolism. Coupling of strong experimental support and photoautotrophic modeling methods thus resulted in a highly accurate model of S. elongatus metabolism that highlights previously unknown areas of S. elongatus biology. PMID:27911809

  3. 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

  4. A unique cell-surface protein phenotype distinguishes human small-cell from non-small-cell lung cancer

    SciTech Connect

    Baylin, S.B.; Gazdar, A.F.; Minna, J.D.; Bernal, S.D.; Sharper, J.H.

    1982-08-01

    Radioiodination (/sup 125/I) and two-dimensional polyacrylamide gel electrophoresis was used to determine that small-(oat) cell lung carcinoma (SCC)-a tumor with neuroedocrine features-possesses a surface protein pattern distinct from the other types of lung cancer cells (squamous, adeno-, and large-cell undifferentiated carcinoma). Twelve distinguishing proteins, 40 to 70 kilodaltons (kDal), characterized four separate lines of SCC; three of these, designated E (60 kDal; pI = 7.3), S (30 kDal; pI = 6.0), and U 57 kDal; pI = 5.6), may be unique SCC gene products and were identified only in (/sup 35/S)methionine labeling of SCC and not in non-SCC or human fibroblasts. Two lines of adeno-, one of squamous, and one of undifferentiated large-cell lung carcinoma exhibited similar surface protein patterns to one another. Nine distinguishing proteins (40 to 100 kDal) and at least five large proteins (>100 kDal) were unique to these lines. The surface protein phenotypes for SCC and non-SCC were distinct from those for human lymphoblastoid cells and fibroblasts. However, the neuroendocrine features of SCC were further substantiated because 6 of the 12 distinguishing SCC surface proteins, including E and U, were identified on human neuroblastoma cells. The proteins identified should (i) help define differentiation steps for normal and neoplastic bronchial epithelial cells, (ii) prove useful in better classifying lung cancers, and (iii) be instrumental in tracing formation of neuroendocrine cells.

  5. Flood damage claims reveal insights about surface runoff in Switzerland

    NASA Astrophysics Data System (ADS)

    Bernet, D. B.; Prasuhn, V.; Weingartner, R.

    2015-12-01

    A few case studies in Switzerland exemplify that not only overtopping water bodies frequently cause damages to buildings. Reportedly, a large share of the total loss due to flooding in Switzerland goes back to surface runoff that is formed and is propagating outside of regular watercourses. Nevertheless, little is known about when, where and why such surface runoff occurs. The described process encompasses surface runoff formation, followed by unchannelised overland flow until a water body is reached. It is understood as a type of flash flood, has short response times and occurs diffusely in the landscape. Thus, the process is difficult to observe and study directly. A promising source indicating surface runoff indirectly are houseowners' damage claims recorded by Swiss Public Insurance Companies for Buildings (PICB). In most of Switzerland, PICB hold a monopoly position and insure (almost) every building. Consequently, PICB generally register all damages to buildings caused by an insured natural hazard (including surface runoff) within the respective zones. We have gathered gapless flood related claim records of most of all Swiss PICB covering more than the last two decades on average. Based on a subset, we have developed a methodology to differentiate claims related to surface runoff from other causes. This allows us to assess the number of claims as well as total loss related to surface runoff and compare these to the numbers of overtopping watercourses. Furthermore, with the good data coverage, we are able to analyze surface runoff related claims in space and time, from which we can infer spatial and temporal characteristics of surface runoff. Although the delivered data of PICB are heterogeneous and, consequently, time-consuming to harmonize, our first results show that exploiting these damage claim records is feasible and worthwhile to learn more about surface runoff in Switzerland.

  6. 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. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Immunohistochemical Characterization of the Chemosensory Pulmonary Neuroepithelial Bodies in the Naked Mole-Rat Reveals a Unique Adaptive Phenotype

    PubMed Central

    Pan, Jie; Park, Thomas J.; Cutz, Ernest; Yeger, Herman

    2014-01-01

    The pulmonary neuroepithelial bodies (NEBs) constitute polymodal airway chemosensors for monitoring and signaling ambient gas concentrations (pO2, pCO2/H+) via complex innervation to the brain stem controlling breathing. NEBs produce the bioactive amine, serotonin (5-HT), and a variety of peptides with multiple effects on lung physiology and other organ systems. NEBs in mammals appear prominent and numerous during fetal and neonatal periods, and decline in the post-natal period suggesting an important role during perinatal adaptation. The naked mole-rat (NMR), Heterocephalus glaber, has adapted to the extreme environmental conditions of living in subterranean burrows in large colonies (up to 300 colony mates). The crowded, unventilated burrows are environments of severe hypoxia and hypercapnia. However, NMRs adjust readily to above ground conditions. The chemosensory NEBs of this species were characterized and compared to those of the conventional Wistar rat (WR) to identify similarities and differences that could explain the NMR’s adaptability to environments. A multilabel immunohistochemical analysis combined with confocal microscopy revealed that the expression patterns of amine, peptide, neuroendocrine, innervation markers and chemosensor component proteins in NEBs of NMR were similar to that of WR. However, we found the following differences: 1) NEBs in both neonatal and adult NMR lungs were significantly larger and more numerous as compared to WR; 2) NEBs in NMR had a more variable compact cell organization and exhibited significant differences in the expression of adhesion proteins; 3) NMR NEBs showed a significantly greater ratio of 5-HT positive cells with an abundance of 5-HT; 4) NEBs in NMR expressed the proliferating cell nuclear antigen (PCNA) and the neurogenic gene (MASH1) indicating active proliferation and a state of persistent differentiation. Taken together our findings suggest that NEBs in lungs of NMR are in a hyperactive, functional and

  8. 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

  9. 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.

  10. 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

  11. Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode

    PubMed Central

    Qian, Tianle; Wo, Jing; Zhang, Yan; Song, Quanwei; Feng, Guoqiang; Luo, Ray; Lin, Shuangjin; Wu, Geng; Chen, Hai-Feng

    2017-01-01

    Streptonigrin methylesterase A (StnA) is one of the tailoring enzymes that modify the aminoquinone skeleton in the biosynthesis pathway of Streptomyces species. Although StnA has no significant sequence homology with the reported α/β-fold hydrolases, it shows typical hydrolytic activity in vivo and in vitro. In order to reveal its functional characteristics, the crystal structures of the selenomethionine substituted StnA (SeMet-StnA) and the complex (S185A mutant) with its substrate were resolved to the resolution of 2.71 Å and 2.90 Å, respectively. The overall structure of StnA can be described as an α-helix cap domain on top of a common α/β hydrolase domain. The substrate methyl ester of 10′-demethoxystreptonigrin binds in a hydrophobic pocket that mainly consists of cap domain residues and is close to the catalytic triad Ser185-His349-Asp308. The transition state is stabilized by an oxyanion hole formed by the backbone amides of Ala102 and Leu186. The substrate binding appears to be dominated by interactions with several specific hydrophobic contacts and hydrogen bonds in the cap domain. The molecular dynamics simulation and site-directed mutagenesis confirmed the important roles of the key interacting residues in the cap domain. Structural alignment and phylogenetic tree analysis indicate that StnA represents a new subfamily of lipolytic enzymes with the specific binding pocket located at the cap domain instead of the interface between the two domains. PMID:28074848

  12. An Ultra-specific Avian Antibody to Phosphorylated Tau Protein Reveals a Unique Mechanism for Phosphoepitope Recognition

    PubMed Central

    Shih, Heather H.; Tu, Chao; Cao, Wei; Klein, Anne; Ramsey, Renee; Fennell, Brian J.; Lambert, Matthew; Ní Shúilleabháin, Deirdre; Autin, Bénédicte; Kouranova, Eugenia; Laxmanan, Sri; Braithwaite, Steven; Wu, Leeying; Ait-Zahra, Mostafa; Milici, Anthony J.; Dumin, Jo Ann; LaVallie, Edward R.; Arai, Maya; Corcoran, Christopher; Paulsen, Janet E.; Gill, Davinder; Cunningham, Orla; Bard, Joel; Mosyak, Lydia; Finlay, William J. J.

    2012-01-01

    Highly specific antibodies to phosphoepitopes are valuable tools to study phosphorylation in disease states, but their discovery is largely empirical, and the molecular mechanisms mediating phosphospecific binding are poorly understood. Here, we report the generation and characterization of extremely specific recombinant chicken antibodies to three phosphoepitopes on the Alzheimer disease-associated protein tau. Each antibody shows full specificity for a single phosphopeptide. The chimeric IgG pT231/pS235_1 exhibits a KD of 0.35 nm in 1:1 binding to its cognate phosphopeptide. This IgG is murine ortholog-cross-reactive, specifically recognizing the pathological form of tau in brain samples from Alzheimer patients and a mouse model of tauopathy. To better understand the underlying binding mechanisms allowing such remarkable specificity, we determined the structure of pT231/pS235_1 Fab in complex with its cognate phosphopeptide at 1.9 Å resolution. The Fab fragment exhibits novel complementarity determining region (CDR) structures with a “bowl-like” conformation in CDR-H2 that tightly and specifically interacts with the phospho-Thr-231 phosphate group, as well as a long, disulfide-constrained CDR-H3 that mediates peptide recognition. This binding mechanism differs distinctly from either peptide- or hapten-specific antibodies described to date. Surface plasmon resonance analyses showed that pT231/pS235_1 binds a truly compound epitope, as neither phosphorylated Ser-235 nor free peptide shows any measurable binding affinity. PMID:23148212

  13. A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment

    PubMed Central

    2013-01-01

    Background Propionibacterium freudenreichii is a food grade bacterium consumed both in cheeses and in probiotic preparations. Its promising probiotic potential, relying largely on the active release of beneficial metabolites within the gut as well as the expression of key surface proteins involved in immunomodulation, deserves to be explored more deeply. Adaptation to the colon environment is requisite for the active release of propionibacterial beneficial metabolites and constitutes a bottleneck for metabolic activity in vivo. Mechanisms allowing P. freudenreichii to adapt to digestive stresses have been only studied in vitro so far. Our aim was therefore to study P. freudenreichii metabolic adaptation to intra-colonic conditions in situ. Results We maintained a pure culture of the type strain P. freudenreichii CIRM BIA 1, contained in a dialysis bag, within the colon of vigilant piglets during 24 hours. A transcriptomic analysis compared gene expression to identify the metabolic pathways induced by this environment, versus control cultures maintained in spent culture medium. We observed drastic changes in the catabolism of sugars and amino-acids. Glycolysis, the Wood-Werkman cycle and the oxidative phosphorylation pathways were down-regulated but induction of specific carbohydrate catabolisms and alternative pathways were induced to produce NADH, NADPH, ATP and precursors (utilizing of propanediol, gluconate, lactate, purine and pyrimidine and amino-acids). Genes involved in stress response were down-regulated and genes specifically expressed during cell division were induced, suggesting that P. freudenreichii adapted its metabolism to the conditions encountered in the colon. Conclusions This study constitutes the first molecular demonstration of P. freudenreichii activity and physiological adaptation in vivo within the colon. Our data are likely specific to our pig microbiota composition but opens an avenue towards understanding probiotic action within the gut

  14. 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.

  15. The structure of cardiac troponin C regulatory domain with bound Cd2+ reveals a closed conformation and unique ion coordination.

    PubMed

    Zhang, Xiaolu Linda; Tibbits, Glen F; Paetzel, Mark

    2013-05-01

    The amino-terminal domain of cardiac troponin C (cNTnC) is an essential Ca(2+) sensor found in cardiomyocytes. It undergoes a conformational change upon Ca(2+) binding and transduces the signal to the rest of the troponin complex to initiate cardiac muscle contraction. Two classical EF-hand motifs (EF1 and EF2) are present in cNTnC. Under physiological conditions, only EF2 binds Ca(2+); EF1 is a vestigial site that has lost its function in binding Ca(2+) owing to amino-acid sequence changes during evolution. Proteins with EF-hand motifs are capable of binding divalent cations other than calcium. Here, the crystal structure of wild-type (WT) human cNTnC in complex with Cd(2+) is presented. The structure of Cd(2+)-bound cNTnC with the disease-related mutation L29Q, as well as a structure with the residue differences D2N, V28I, L29Q and G30D (NIQD), which have been shown to have functional importance in Ca(2+) sensing at lower temperatures in ectothermic species, have also been determined. The structures resemble the overall conformation of NMR structures of Ca(2+)-bound cNTnC, but differ significantly from a previous crystal structure of Cd(2+)-bound cNTnC in complex with deoxycholic acid. The subtle structural changes observed in the region near the mutations may play a role in the increased Ca(2+) affinity. The 1.4 Å resolution WT cNTnC structure, which is the highest resolution structure yet obtained for cardiac troponin C, reveals a Cd(2+) ion coordinated in the canonical pentagonal bipyramidal geometry in EF2 despite three residues in the loop being disordered. A Cd(2+) ion found in the vestigial ion-binding site of EF1 is coordinated in a noncanonical `distorted' octahedral geometry. A comparison of the ion coordination observed within EF-hand-containing proteins for which structures have been solved in the presence of Cd(2+) is presented. A refolded WT cNTnC structure is also presented.

  16. Advances in cell surface glycoengineering reveal biological function.

    PubMed

    Nischan, Nicole; Kohler, Jennifer J

    2016-08-01

    Cell surface glycans are critical mediators of cell-cell, cell-ligand, and cell-pathogen interactions. By controlling the set of glycans displayed on the surface of a cell, it is possible to gain insight into the biological functions of glycans. Moreover, control of glycan expression can be used to direct cellular behavior. While genetic approaches to manipulate glycosyltransferase gene expression are available, their utility in glycan engineering has limitations due to the combinatorial nature of glycan biosynthesis and the functional redundancy of glycosyltransferase genes. Biochemical and chemical strategies offer valuable complements to these genetic approaches, notably by enabling introduction of unnatural functionalities, such as fluorophores, into cell surface glycans. Here, we describe some of the most recent developments in glycoengineering of cell surfaces, with an emphasis on strategies that employ novel chemical reagents. We highlight key examples of how these advances in cell surface glycan engineering enable study of cell surface glycans and their function. Exciting new technologies include synthetic lipid-glycans, new chemical reporters for metabolic oligosaccharide engineering to allow tandem and in vivo labeling of glycans, improved chemical and enzymatic methods for glycoproteomics, and metabolic glycosyltransferase inhibitors. Many chemical and biochemical reagents for glycan engineering are commercially available, facilitating their adoption by the biological community.

  17. A review of pollutants in the sea-surface microlayer (SML): a unique habitat for marine organisms.

    PubMed

    Wurl, Oliver; Obbard, Jeffrey Phillip

    2004-06-01

    Boundary layers between different environmental compartments represent critical interfaces for biological, chemical and physical processes. The sea-surface microlayer (uppermost 1-1000 microm layer) forms the boundary layer interface between the atmosphere and ocean. Environmental processes are controlled by the SML, and it is known to play a key role in the global distribution of anthropogenic pollutants. Due to its unique chemical composition, the upper organic film of the SML represents both a sink and a source for a range of pollutants including chlorinated hydrocarbons, organotin compounds, petroleum hydrocarbons, polycyclic aromatic hydrocarbons (PAH) and heavy metals. These pollutants can be enriched in the SML by up to 500 times relative to concentrations occurring in the underlying bulk water column. The SML is also a unique ecosystem, serving as an important habitat for fish eggs and larvae. Concentration ranges and enrichment factors of pollutants in the SML in different areas of the world's oceans have been critically reviewed, together with available toxicity data for marine biota found within the SML. Overall, the SML is highly contaminated in many urban and industrialized areas of the world, resulting in severe ecotoxicological impacts. Such impacts may lead to drastic effects on the marine food web and to fishery recruitment in coastal waters. Studies of the toxicity of fish eggs and larvae exposed to the SML contaminants have shown that the SML in polluted areas leads to significantly higher rates of mortality and abnormality of fish embryos and larvae.

  18. 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.

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

    PubMed Central

    Drennan, Catherine L.; Nonato, M. Cristina

    2016-01-01

    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

  20. 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.

  1. Effort towards symmetric removal and surface smoothening of 1.3-GHz niobium single-cell cavity in vertical electropolishing using a unique cathode

    NASA Astrophysics Data System (ADS)

    Chouhan, Vijay; Kato, Shigeki; Nii, Keisuke; Yamaguchi, Takanori; Sawabe, Motoaki; Hayano, Hitoshi; Ida, Yoshiaki

    2017-08-01

    A detailed study on vertical electropolishing (VEP) of a 1.3-GHz single-cell niobium coupon cavity, which contains six coupons and four viewports at different positions, is reported. The cavity was vertically electropolished using a conventional rod and three types of unique cathodes named as Ninja cathodes, which were designed to have four retractable blades made of either an insulator or a metal or a combination of both. This study reveals the effect of the cathodes and their rotation speed on uniformity in removal thickness and surface morphology at different positions inside the cavity. Removal thickness was measured at several positions of the cavity using an ultrasonic thickness gauge and the surface features of the coupons were examined by an optical microscope and a surface profiler. The Ninja cathode with partial metallic blades was found to be effective not only in reducing asymmetric removal, which is one of the major problems in VEP and might be caused by the accumulation of hydrogen (H2 ) gas bubbles on the top iris of the cavity, but also in yielding a smooth surface of the entire cavity. A higher rotation speed of the Ninja cathode prevents bubble accumulation on the upper iris, and might result in a viscous layer of similar thickness in the cavity cell. Moreover, a higher electric field at the equator owing to the proximity of partial metallic blades to the equator surface resulted in a smooth surface. The effects of H2 gas bubbles and stirring were also observed in lab EP experiments.

  2. 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.

  3. Non-uniqueness of quantum transition state theory and general dividing surfaces in the path integral space.

    PubMed

    Jang, Seogjoo; Voth, Gregory A

    2017-05-07

    Despite the fact that quantum mechanical principles do not allow the establishment of an exact quantum analogue of the classical transition state theory (TST), the development of a quantum TST (QTST) with a proper dynamical justification, while recovering the TST in the classical limit, has been a long standing theoretical challenge in chemical physics. One of the most recent efforts of this kind was put forth by Hele and Althorpe (HA) [J. Chem. Phys. 138, 084108 (2013)], which can be specified for any cyclically invariant dividing surface defined in the space of the imaginary time path integral. The present work revisits the issue of the non-uniqueness of QTST and provides a detailed theoretical analysis of HA-QTST for a general class of such path integral dividing surfaces. While we confirm that HA-QTST reproduces the result based on the ring polymer molecular dynamics (RPMD) rate theory for dividing surfaces containing only a quadratic form of low frequency Fourier modes, we find that it produces different results for those containing higher frequency imaginary time paths which accommodate greater quantum fluctuations. This result confirms the assessment made in our previous work [Jang and Voth, J. Chem. Phys. 144, 084110 (2016)] that HA-QTST does not provide a derivation of RPMD-TST in general and points to a new ambiguity of HA-QTST with respect to its justification for general cyclically invariant dividing surfaces defined in the space of imaginary time path integrals. Our analysis also offers new insights into similar path integral based QTST approaches.

  4. A High-Resolution Crystal Structure of a Psychrohalophilic α–Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface

    PubMed Central

    Somalinga, Vijayakumar; Buhrman, Greg; Arun, Ashikha; Rose, Robert B.

    2016-01-01

    Bacterial α–carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, Photobacterium profundum. Size exclusion chromatography of the purified P. profundum α–CA (PprCA) reveals that the protein is a heterogeneous mix of monomers and dimers. Furthermore, an “in-gel” carbonic anhydrase activity assay, also known as protonography, revealed two distinct bands corresponding to monomeric and dimeric forms of PprCA that are catalytically active. The crystal structure of PprCA was determined in its native form and reveals a highly conserved “knot-topology” that is characteristic of α–CA’s. Similar to other bacterial α–CA’s, PprCA also crystallized as a dimer. Furthermore, dimer interface analysis revealed the presence of a chloride ion (Cl-) in the interface which is unique to PprCA and has not been observed in any other α–CA’s characterized so far. Molecular dynamics simulation and chloride ion occupancy analysis shows 100% occupancy for the Cl- ion in the dimer interface. Zinc coordinating triple histidine residues, substrate binding hydrophobic patch residues, and the hydrophilic proton wire residues are highly conserved in PprCA and are identical to other well-studied α–CA’s. PMID:27936100

  5. A High-Resolution Crystal Structure of a Psychrohalophilic α–Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface

    SciTech Connect

    Somalinga, Vijayakumar; Buhrman, Greg; Arun, Ashikha; Rose, Robert B.; Grunden, Amy M.; Hofmann, Andreas

    2016-12-09

    Bacterial α–carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, Photobacterium profundum. Size exclusion chromatography of the purified P. profundum α–CA (PprCA) reveals that the protein is a heterogeneous mix of monomers and dimers. Furthermore, an “in-gel” carbonic anhydrase activity assay, also known as protonography, revealed two distinct bands corresponding to monomeric and dimeric forms of PprCA that are catalytically active. The crystal structure of PprCA was determined in its native form and reveals a highly conserved “knot-topology” that is characteristic of α–CA’s. Similar to other bacterial α–CA’s, PprCA also crystallized as a dimer. Furthermore, dimer interface analysis revealed the presence of a chloride ion (Cl-) in the interface which is unique to PprCA and has not been observed in any other α–CA’s characterized so far. Molecular dynamics simulation and chloride ion occupancy analysis shows 100% occupancy for the Cl- ion in the dimer interface. Zinc coordinating triple histidine residues, substrate binding hydrophobic patch residues, and the hydrophilic proton wire residues are highly conserved in PprCA and are identical to other well-studied α–CA’s.

  6. Comprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome Reveals a Compartmentalization Bias toward the Bacterial Surface

    PubMed Central

    Dowdell, Alexander S.; Murphy, Maxwell D.; Azodi, Christina; Swanson, Selene K.; Florens, Laurence

    2017-01-01

    ABSTRACT The Lyme disease spirochete Borrelia burgdorferi is unique among bacteria in its large number of lipoproteins that are encoded by a small, exceptionally fragmented, and predominantly linear genome. Peripherally anchored in either the inner or outer membrane and facing either the periplasm or the external environment, these lipoproteins assume varied roles. A prominent subset of lipoproteins functioning as the apparent linchpins of the enzootic tick-vertebrate infection cycle have been explored as vaccine targets. Yet, most of the B. burgdorferi lipoproteome has remained uncharacterized. Here, we comprehensively and conclusively localize the B. burgdorferi lipoproteome by applying established protein localization assays to a newly generated epitope-tagged lipoprotein expression library and by validating the obtained individual protein localization results using a sensitive global mass spectrometry approach. The derived consensus localization data indicate that 86 of the 125 analyzed lipoproteins encoded by B. burgdorferi are secreted to the bacterial surface. Thirty-one of the remaining 39 periplasmic lipoproteins are retained in the inner membrane, with only 8 lipoproteins being anchored in the periplasmic leaflet of the outer membrane. The localization of 10 lipoproteins was further defined or revised, and 52 surface and 23 periplasmic lipoproteins were newly localized. Cross-referencing prior studies revealed that the borrelial surface lipoproteome contributing to the host-pathogen interface is encoded predominantly by plasmids. Conversely, periplasmic lipoproteins are encoded mainly by chromosomal loci. These studies close a gap in our understanding of the functional lipoproteome of an important human pathogen and set the stage for more in-depth studies of thus-far-neglected spirochetal lipoproteins. IMPORTANCE The small and exceptionally fragmented genome of the Lyme disease spirochete Borrelia burgdorferi encodes over 120 lipoproteins. Studies in the

  7. 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

  8. A computer-assisted 3D model for analyzing the aggregation of tumorigenic cells reveals specialized behaviors and unique cell types that facilitate aggregate coalescence.

    PubMed

    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.

  9. 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.

  10. Use of a micro- to nanochannel for the characterization of surface-enhanced Raman spectroscopy signals from unique functionalized nanoparticles

    NASA Astrophysics Data System (ADS)

    Walton, Brian M.; Huang, Po-Jung; Kameoka, Jun; Cote, Gerard L.

    2016-08-01

    A micro- to nanochannel nanoparticle aggregating device that does not require any input energy to organize the particles to a specific location, i.e., no pumps, plugs, heat, or magnets, has been designed and used to characterize the surface-enhanced Raman spectroscopy (SERS) signal from four unique functionalized nanoparticles (gold, silver-gold nanocages, silver nanocubes, and silica-gold nanoshells). The SERS signal was assessed in terms of the peak signal strength from the four different Raman reporter functionalized nanoparticles to determine which nanoparticle had better utility in the channel to provide the most robust platform for a future biological analyte detection device. The innovation used to fabricate the micro- to nanochannel device is described; the TEM images of the nanoparticles are shown; the absorption data for the nanoparticles are given; and the spectral data for the Raman reporter, mercaptobenzoic acid (MBA), are depicted. In the micro- to nanochannel described in this work, 5 μl of 22.3 μM MBA functionalized silver nanocubes were determined to have the strongest SERS enhancement.

  11. A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and Genomic Differences between the Monocot Orders Asparagales and PoalesW⃞

    PubMed Central

    Kuhl, Joseph C.; Cheung, Foo; Yuan, Qiaoping; Martin, William; Zewdie, Yayeh; McCallum, John; Catanach, Andrew; Rutherford, Paul; Sink, Kenneth C.; Jenderek, Maria; Prince, James P.; Town, Christopher D.; Havey, Michael J.

    2004-01-01

    Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not clear how representative the Poales are for the monocots as a whole. The Asparagales are a monophyletic order sister to the lineage carrying the Poales and possess economically important plants such as asparagus, garlic, and onion. To assess the genomic differences between the Asparagales and Poales, we generated 11,008 unique ESTs from a normalized cDNA library of onion. Sequence analyses of these ESTs revealed microsatellite markers, single nucleotide polymorphisms, and homologs of transposable elements. Mean nucleotide similarity between rice and the Asparagales was 78% across coding regions. Expressed sequence and genomic comparisons revealed strong differences between the Asparagales and Poales for codon usage and mean GC content, GC distribution, and relative GC content at each codon position, indicating that genomic characteristics are not uniform across the monocots. The Asparagales were more similar to eudicots than to the Poales for these genomic characteristics. PMID:14671025

  12. Amygdala subnuclei connectivity in response to violence reveals unique influences of individual differences in psychopathic traits in a non-forensic sample

    PubMed Central

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

    2016-01-01

    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 non-forensic sample are linked to amygdala response to violence, the current 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

  13. IlsA, a unique surface protein of Bacillus cereus required for iron acquisition from heme, hemoglobin and ferritin.

    PubMed

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

    2009-11-01

    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.

  14. Surface Structure of Azotobacter vinelandii Cysts as Revealed by Freeze-Cleaving1

    PubMed Central

    Koo, Victoria M.; Lin, L. P.; Sadoff, H. L.

    1969-01-01

    Micrographs of freeze-cleaved Azotobacter vinelandii cysts reveal that the surface is composed of several overlapping layers. This observation is consistent with the previously proposed structure of the outer cyst coat. Images PMID:5359611

  15. 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

    governing the distribution? Detailed aspects of the local climate warranted more investigation. Chapter 4 investigates the climate associated with the frequent cloud formation over the western slopes of the southern Sierra Nevada: the "sequoia belt". This region is climatically distinct in a number of ways, all of which could be factors in influencing the distribution of giant sequoia and other species. Satellite and micrometeorological flux tower data reveal characteristics of the sequoia belt that were not evident with surface climate measurements and maps derived from them. Results have implications for species distributions everywhere, but especially in rugged mountains, where climates are complex and poorly mapped. Chapter 5 summarizes some of the main conclusions from the work and suggests directions for related future research. (Abstract shortened by UMI.).

  16. 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.

  17. Local Environment and Interactions of Liquid and Solid Interfaces Revealed by Spectral Line Shape of Surface Selective Nonlinear Vibrational Probe

    SciTech Connect

    Chen, Shun-Li; Fu, Li; Chase, Zizwe A.; Gan, Wei; Wang, Hong-Fei

    2016-11-10

    Vibrational spectral lineshape contains important detailed information of molecular vibration and reports its specific interactions and couplings to its local environment. In this work, recently developed sub-1 cm-1 high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) was used to measure the -C≡N stretch vibration in the 4-n-octyl-4’-cyanobiphenyl (8CB) Langmuir or Langmuir-Blodgett (LB) monolayer as a unique vibrational probe, and the spectral lineshape analysis revealed the local environment and interactions at the air/water, air/glass, air/calcium fluoride and air/-quartz interfaces for the first time. The 8CB Langmuir or LB film is uniform and the vibrational spectral lineshape of its -C≡N group has been well characterized, making it a good choice as the surface vibrational probe. Lineshape analysis of the 8CB -C≡N stretch SFG vibrational spectra suggests the coherent vibrational dynamics and the structural and dynamic inhomogeneity of the -C≡N group at each interface are uniquely different. In addition, it is also found that there are significantly different roles for water molecules in the LB films on different substrate surfaces. These results demonstrated the novel capabilities of the surface nonlinear spectroscopy in characterization and in understanding the specific structures and chemical interactions at the liquid and solid interfaces in general.

  18. 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

    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.

  19. Molecular analysis of phosphomannomutase (PMM) genes reveals a unique PMM duplication event in diverse Triticeae species and the main PMM isozymes in bread wheat tissues.

    PubMed

    Yu, Chunmei; Li, Yiwen; Li, Bin; Liu, Xin; Hao, Lifang; Chen, Jing; Qian, Weiqiang; Li, Shiming; Wang, Guanfeng; Bai, Shiwei; Ye, Hua; Qin, Huanju; Shen, Qianhua; Chen, Liangbiao; Zhang, Aimin; Wang, Daowen

    2010-10-05

    Phosphomannomutase (PMM) is an essential enzyme in eukaryotes. However, little is known about PMM gene and function in crop plants. Here, we report molecular evolutionary and biochemical analysis of PMM genes in bread wheat and related Triticeae species. Two sets of homologous PMM genes (TaPMM-1 and 2) were found in bread wheat, and two corresponding PMM genes were identified in the diploid progenitors of bread wheat and many other diploid Triticeae species. The duplication event yielding PMM-1 and 2 occurred before the radiation of diploid Triticeae genomes. The PMM gene family in wheat and relatives may evolve largely under purifying selection. Among the six TaPMM genes, the transcript levels of PMM-1 members were comparatively high and their recombinant proteins were all enzymatically active. However, PMM-2 homologs exhibited lower transcript levels, two of which were also inactive. TaPMM-A1, B1 and D1 were probably the main active isozymes in bread wheat tissues. The three isozymes differed from their counterparts in barley and Brachypodium distachyon in being more tolerant to elevated test temperatures. Our work identified the genes encoding PMM isozymes in bread wheat and relatives, uncovered a unique PMM duplication event in diverse Triticeae species, and revealed the main active PMM isozymes in bread wheat tissues. The knowledge obtained here improves the understanding of PMM evolution in eukaryotic organisms, and may facilitate further investigations of PMM function in the temperature adaptability of bread wheat.

  20. Genome-wide gene expression analyses reveal unique cellular characteristics related to the amenability of HPC/HSCs into high-quality induced pluripotent stem cells.

    PubMed

    Gao, Shuai; Tao, Li; Hou, Xinfeng; Xu, Zijian; Liu, Wenqiang; Zhao, Kun; Guo, Mingyue; Wang, Hong; Cai, Tao; Tian, Jianhui; Gao, Shaorong; Chang, Gang

    2016-03-15

    Transcription factor-mediated reprogramming can efficiently convert differentiated cells into induced pluripotent stem cells (iPSCs). Furthermore, many cell types have been shown to be amenable to reprogramming into iPSCs, such as neural stem cells, hematopoietic progenitor and stem cells (HPC/HSCs). However, the mechanisms related to the amenability of these cell types to be reprogrammed are still unknown. Herein, we attempt to elucidate the mechanisms of HPC/HSC reprogramming using the sequential reprogramming system that we have previously established. We found that HPC/HSCs were amenable to transcription factor-mediated reprogramming, which yielded a high frequency of fully reprogrammed HPC/HSC-iPSCs. Genome-wide gene expression analyses revealed select down-regulated tumor suppressor and mesenchymal genes as well as up-regulated oncogenes in HPC/HSCs compared with mouse embryonic fibroblasts (MEFs), indicating that these genes may play important roles during the reprogramming of HPC/HSCs. Additional studies provided insights into the contribution of select tumor suppressor genes (p21, Ink4a and Arf) and an epithelial-to-mesenchymal transition (EMT) factor (Snail1) to the reprogramming process of HPC/HSCs. Our findings demonstrate that HPC/HSCs carry unique cellular characteristics, which determine the amenability of HPC/HSCs to be reprogrammed into high-quality iPSCs.

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

    DOE PAGES

    Oulas, Anastasis; Polymenakou, Paraskevi N.; Seshadri, Rekha; ...

    2015-12-21

    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 significantmore » 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.« less

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

    SciTech Connect

    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.

    2015-12-21

    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.

  3. Structure of the Human Angiotensin II Type 1 (AT1) Receptor Bound to Angiotensin II from Multiple Chemoselective Photoprobe Contacts Reveals a Unique Peptide Binding Mode*

    PubMed Central

    Fillion, Dany; Cabana, Jérôme; Guillemette, Gaétan; Leduc, Richard; Lavigne, Pierre; Escher, Emanuel

    2013-01-01

    Breakthroughs in G protein-coupled receptor structure determination based on crystallography have been mainly obtained from receptors occupied in their transmembrane domain core by low molecular weight ligands, and we have only recently begun to elucidate how the extracellular surface of G protein-coupled receptors (GPCRs) allows for the binding of larger peptide molecules. In the present study, we used a unique chemoselective photoaffinity labeling strategy, the methionine proximity assay, to directly identify at physiological conditions a total of 38 discrete ligand/receptor contact residues that form the extracellular peptide-binding site of an activated GPCR, the angiotensin II type 1 receptor. This experimental data set was used in homology modeling to guide the positioning of the angiotensin II (AngII) peptide within several GPCR crystal structure templates. We found that the CXC chemokine receptor type 4 accommodated the results better than the other templates evaluated; ligand/receptor contact residues were spatially grouped into defined interaction clusters with AngII. In the resulting receptor structure, a β-hairpin fold in extracellular loop 2 in conjunction with two extracellular disulfide bridges appeared to open and shape the entrance of the ligand-binding site. The bound AngII adopted a somewhat vertical binding mode, allowing concomitant contacts across the extracellular surface and deep within the transmembrane domain core of the receptor. We propose that such a dualistic nature of GPCR interaction could be well suited for diffusible linear peptide ligands and a common feature of other peptidergic class A GPCRs. PMID:23386604

  4. Structure of the human angiotensin II type 1 (AT1) receptor bound to angiotensin II from multiple chemoselective photoprobe contacts reveals a unique peptide binding mode.

    PubMed

    Fillion, Dany; Cabana, Jérôme; Guillemette, Gaétan; Leduc, Richard; Lavigne, Pierre; Escher, Emanuel

    2013-03-22

    Breakthroughs in G protein-coupled receptor structure determination based on crystallography have been mainly obtained from receptors occupied in their transmembrane domain core by low molecular weight ligands, and we have only recently begun to elucidate how the extracellular surface of G protein-coupled receptors (GPCRs) allows for the binding of larger peptide molecules. In the present study, we used a unique chemoselective photoaffinity labeling strategy, the methionine proximity assay, to directly identify at physiological conditions a total of 38 discrete ligand/receptor contact residues that form the extracellular peptide-binding site of an activated GPCR, the angiotensin II type 1 receptor. This experimental data set was used in homology modeling to guide the positioning of the angiotensin II (AngII) peptide within several GPCR crystal structure templates. We found that the CXC chemokine receptor type 4 accommodated the results better than the other templates evaluated; ligand/receptor contact residues were spatially grouped into defined interaction clusters with AngII. In the resulting receptor structure, a β-hairpin fold in extracellular loop 2 in conjunction with two extracellular disulfide bridges appeared to open and shape the entrance of the ligand-binding site. The bound AngII adopted a somewhat vertical binding mode, allowing concomitant contacts across the extracellular surface and deep within the transmembrane domain core of the receptor. We propose that such a dualistic nature of GPCR interaction could be well suited for diffusible linear peptide ligands and a common feature of other peptidergic class A GPCRs.

  5. Gated Hall effect of nanoplate devices reveals surface-state-induced surface inversion in iron pyrite semiconductor.

    PubMed

    Liang, Dong; Cabán-Acevedo, Miguel; Kaiser, Nicholas S; Jin, Song

    2014-12-10

    Understanding semiconductor surface states is critical for their applications, but fully characterizing surface electrical properties is challenging. Such a challenge is especially crippling for semiconducting iron pyrite (FeS2), whose potential for solar energy conversion has been suggested to be held back by rich surface states. Here, by taking advantage of the high surface-to-bulk ratio in nanostructures and effective electrolyte gating, we develop a general method to fully characterize both the surface inversion and bulk electrical transport properties for the first time through electrolyte-gated Hall measurements of pyrite nanoplate devices. Our study shows that pyrite is n-type in the bulk and p-type near the surface due to strong inversion and yields the concentrations and mobilities of both bulk electrons and surface holes. Further, solutions of the Poisson equation reveal a high-density of surface holes accumulated in a 1.3 nm thick strong inversion layer and an upward band bending of 0.9-1.0 eV. This work presents a general methodology for using transport measurements of nanostructures to study both bulk and surface transport properties of semiconductors. It also suggests that high-density of surface states are present on surface of pyrite, which partially explains the universal p-type conductivity and lack of photovoltage in polycrystalline pyrite.

  6. 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.

  7. 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.

  8. Gene Expression Analysis of Early Stage Endometrial Cancers Reveals Unique Transcripts Associated with Grade and Histology but Not Depth of Invasion

    PubMed Central

    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

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

    PubMed Central

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

    2015-01-01

    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 (kcatapp/Kmapp = (1.7 × 107) 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 Asp220 and Arg327 are found necessary for compound I formation, His312 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 His312 and Arg327 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

  10. 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. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Genetic analysis of the Replication Protein A large subunit family in Arabidopsis reveals unique and overlapping roles in DNA repair, meiosis and DNA replication

    PubMed Central

    Aklilu, Behailu B.; Soderquist, Ryan S.; Culligan, Kevin M.

    2014-01-01

    Replication Protein A (RPA) is a heterotrimeric protein complex that binds single-stranded DNA. In plants, multiple genes encode the three RPA subunits (RPA1, RPA2 and RPA3), including five RPA1-like genes in Arabidopsis. Phylogenetic analysis suggests two distinct groups composed of RPA1A, RPA1C, RPA1E (ACE group) and RPA1B, RPA1D (BD group). ACE-group members are transcriptionally induced by ionizing radiation, while BD-group members show higher basal transcription and are not induced by ionizing radiation. Analysis of rpa1 T-DNA insertion mutants demonstrates that although each mutant line is likely null, all mutant lines are viable and display normal vegetative growth. The rpa1c and rpa1e single mutants however display hypersensitivity to ionizing radiation, and combination of rpa1c and rpa1e results in additive hypersensitivity to a variety of DNA damaging agents. Combination of the partially sterile rpa1a with rpa1c results in complete sterility, incomplete synapsis and meiotic chromosome fragmentation, suggesting an early role for RPA1C in promoting homologous recombination. Combination of either rpa1c and/or rpa1e with atr revealed additive hypersensitivity phenotypes consistent with each functioning in unique repair pathways. In contrast, rpa1b rpa1d double mutant plants display slow growth and developmental defects under non-damaging conditions. We show these defects in the rpa1b rpa1d mutant are likely the result of defective DNA replication leading to reduction in cell division. PMID:24335281

  12. 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

  13. 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

  14. Kinetic interaction analysis of human interleukin 5 receptor alpha mutants reveals a unique binding topology and charge distribution for cytokine recognition.

    PubMed

    Ishino, Tetsuya; Pasut, Gianfranco; Scibek, Jeffery; Chaiken, Irwin

    2004-03-05

    Human interleukin 5 receptor alpha (IL5Ralpha) comprises three fibronectin type III domains (D1, D2, and D3) in the extracellular region. Previous results have indicated that residues in the D1D2 domains are crucial for high affinity interaction with human interleukin 5 (IL5). Yet, it is the D2D3 domains that have sequence homology with the classic cytokine recognition motif that is generally assumed to be the minimum cytokine-recognizing unit. In the present study, we used kinetic interaction analysis of alanine-scanning mutational variants of IL5Ralpha to define the residues involved in IL5 recognition. Soluble forms of IL5Ralpha variants were expressed in S2 cells, selectively captured via their C-terminal V5 tag by anti-V5 tag antibody immobilized onto the sensor chip and examined for IL5 interaction by using a sandwich surface plasmon resonance biosensor method. Marked effects on the interaction kinetics were observed not only in D1 (Asp(55), Asp(56), and Glu(58)) and D2 (Lys(186) and Arg(188)) domains, but also in the D3 (Arg(297)) domain. Modeling of the tertiary structure of IL5Ralpha indicated that these binding residues fell into two clusters. The first cluster consists of D1 domain residues that form a negatively charged patch, whereas the second cluster consists of residues that form a positively charged patch at the interface of D2 and D3 domains. These results suggest that the IL5 x IL5Ralpha system adopts a unique binding topology, in which the cytokine is recognized by a D2D3 tandem domain combined with a D1 domain, to form an extended cytokine recognition interface.

  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. © 2016 Wiley Periodicals, Inc.

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

    SciTech Connect

    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 reconstruction 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.

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

    DOE PAGES

    Amos, Charles D.; Roldan, Manuel A.; Varela, Maria; ...

    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

  18. 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

    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.

  19. 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

  20. 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

  1. Peptide profiling of bovine kefir reveals 236 unique peptides released from caseins during its production by starter culture or kefir grains.

    PubMed

    Ebner, Jennifer; Aşçı Arslan, Ayşe; Fedorova, Maria; Hoffmann, Ralf; Küçükçetin, Ahmet; Pischetsrieder, Monika

    2015-03-18

    Kefir has a long tradition in human nutrition due to its presupposed health promoting effects. To investigate the potential contribution of bioactive peptides to the physiological effects of kefir, comprehensive analysis of the peptide profile was performed by nano-ESI-LTQ-Orbitrap MS coupled to nano-ultrahigh-performance liquid chromatography. Thus, 257 peptides were identified, mainly released from β-casein, followed by αS1-, κ-, and αS2-casein. Most (236) peptides were uniquely detected in kefir, but not in raw milk indicating that the fermentation step does not only increase the proteolytic activity 1.7- to 2.4-fold compared to unfermented milk, but also alters the composition of the peptide fraction. The influence of the microflora was determined by analyzing kefir produced from traditional kefir grains or commercial starter culture. Kefir from starter culture featured 230 peptide sequences and showed a significantly, 1.4-fold higher proteolytic activity than kefir from kefir grains with 127 peptides. A match of 97 peptides in both varieties indicates the presence of a typical kefir peptide profile that is not influenced by the individual composition of the microflora. Sixteen of the newly identified peptides were previously described as bioactive, including angiotensin-converting enzyme (ACE)-inhibitory, antimicrobial, immunomodulating, opioid, mineral binding, antioxidant, and antithrombotic effects. The present study describes a comprehensive peptide profile of kefir comprising 257 sequences. The peptide list was used to identify 16 bioactive peptides with ACE-inhibitory, antioxidant, antithrombotic, mineral binding, antimicrobial, immunomodulating and opioid activity in kefir. Furthermore, it was shown that a majority of the kefir peptides were not endogenously present in the raw material milk, but were released from milk caseins by proteases of the microbiota and are therefore specific for the product. Consequently, the proteolytic activity and the

  2. 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.

  3. A deformable nanoplasmonic membrane reveals universal correlations between plasmon resonance and surface enhanced Raman scattering.

    PubMed

    Kang, Minhee; Kim, Jae-Jun; Oh, Young-Jae; Park, Sang-Gil; Jeong, Ki-Hun

    2014-07-09

    A quantitative correlation between plasmon resonance and surface enhanced Raman scattering (SERS) signals is revealed by using a novel active plasmonic method, that is, a deformable nanoplasmonic membrane. A single SERS peak has the maximum gain at the corresponding plasmon resonance wavelength, which has the maximum extinction product of an excitation and the corresponding Raman scattering wavelengths.

  4. Surface phenomena revealed by in situ imaging: studies from adhesion, wear and cutting

    NASA Astrophysics Data System (ADS)

    Viswanathan, Koushik; Mahato, Anirban; Yeung, Ho; Chandrasekar, Srinivasan

    2017-03-01

    Surface deformation and flow phenomena are ubiquitous in mechanical processes. In this work we present an in situ imaging framework for studying a range of surface mechanical phenomena at high spatial resolution and across a range of time scales. The in situ framework is capable of resolving deformation and flow fields quantitatively in terms of surface displacements, velocities, strains and strain rates. Three case studies are presented demonstrating the power of this framework for studying surface deformation. In the first, the origin of stick-slip motion in adhesive polymer interfaces is investigated, revealing a intimate link between stick-slip and surface wave propagation. Second, the role of flow in mediating formation of surface defects and wear particles in metals is analyzed using a prototypical sliding process. It is shown that conventional post-mortem observation and inference can lead to erroneous conclusions with regard to formation of surface cracks and wear particles. The in situ framework is shown to unambiguously capture delamination wear in sliding. Third, material flow and surface deformation in a typical cutting process is analyzed. It is shown that a long-standing problem in the cutting of annealed metals is resolved by the imaging, with other benefits such as estimation of energy dissipation and power from the flow fields. In closure, guidelines are provided for profitably exploiting in situ observations to study large-strain deformation, flow and friction phenomena at surfaces that display a variety of time-scales.

  5. 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.

  6. Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms

    SciTech Connect

    Kober, Daniel L.; Alexander-Brett, Jennifer M.; Karch, Celeste M.; Cruchaga, Carlos; Colonna, Marco; Holtzman, Michael J.; Brett, Thomas J.

    2016-12-20

    Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3.1 Å TREM2 crystal structure revealed that mutations found in Nasu-Hakola disease are buried whereas Alzheimer’s disease risk variants are found on the surface, suggesting that these mutations have distinct effects on TREM2 function. Biophysical and cellular methods indicate that Nasu-Hakola mutations impact protein stability and decrease folded TREM2 surface expression, whereas Alzheimer’s risk variants impact binding to a TREM2 ligand. Additionally, the Alzheimer’s risk variants appear to epitope map a functional surface on TREM2 that is unique within the larger TREM family. These findings provide a guide to structural and functional differences among genetic variants of TREM2, indicating that therapies targeting the TREM2 pathway should be tailored to these genetic and functional differences with patient-specific medicine approaches for neurodegenerative disorders.

  7. Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms

    PubMed Central

    Kober, Daniel L; Alexander-Brett, Jennifer M; Karch, Celeste M; Cruchaga, Carlos; Colonna, Marco; Holtzman, Michael J; Brett, Thomas J

    2016-01-01

    Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3.1 Å TREM2 crystal structure revealed that mutations found in Nasu-Hakola disease are buried whereas Alzheimer’s disease risk variants are found on the surface, suggesting that these mutations have distinct effects on TREM2 function. Biophysical and cellular methods indicate that Nasu-Hakola mutations impact protein stability and decrease folded TREM2 surface expression, whereas Alzheimer’s risk variants impact binding to a TREM2 ligand. Additionally, the Alzheimer’s risk variants appear to epitope map a functional surface on TREM2 that is unique within the larger TREM family. These findings provide a guide to structural and functional differences among genetic variants of TREM2, indicating that therapies targeting the TREM2 pathway should be tailored to these genetic and functional differences with patient-specific medicine approaches for neurodegenerative disorders. DOI: http://dx.doi.org/10.7554/eLife.20391.001 PMID:27995897

  8. Unique residues on the H2A.Z containing nucleosome surface are important for Xenopus laevis development.

    PubMed

    Ridgway, Patricia; Brown, Karl D; Rangasamy, Danny; Svensson, Ulrica; Tremethick, David J

    2004-10-15

    Critical to vertebrate development is a complex program of events that establishes specialized tissues and organs from a single fertilized cell. Transitions in chromatin architecture, through alterations in its composition and modification markings, characterize early development. A variant of the H2A core histone, H2A.Z, is essential for development of both Drosophila and mice. We recently showed that H2A.Z is required for proper chromosome segregation. Whether H2A.Z has additional specific functions during early development remains unknown. Here we demonstrate that depletion of H2A.Z by RNA interference perturbs Xenopus laevis development at gastrulation leading to embryos with malformed, shortened trunks. Consistent with this result, whole embryo in situ hybridization indicates that endogenous expression of H2A.Z is highly enriched in the notochord. H2A.Z modifies the surface of a canonical nucleosome by creating an extended acidic patch and a metal ion-binding site stabilized by two histidine residues. To examine the significance of these specific surface regions in vivo, we investigated the consequences of overexpressing H2A.Z and mutant proteins during X. laevis development. Overexpression of H2A.Z slowed development following gastrulation. Altering the extended acidic patch of H2A.Z reversed this effect. Remarkably, modification of a single stabilizing histidine residue located on the exposed surface of an H2A.Z containing nucleosome was sufficient to disrupt normal trunk formation mimicking the effect observed by RNA interference. Taken together, these results argue that key determinants located on the surface of an H2A.Z nucleosome play an important specific role during embryonic patterning and provide a link between a chromatin structural modification and normal vertebrate development.

  9. The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages.

    PubMed

    Asha, Srinivasan; Soniya, E V

    2017-02-01

    Small RNAs derived from ribosomal RNAs (srRNAs) are rarely explored in the high-throughput data of plant systems. Here, we analyzed srRNAs from the deep-sequenced small RNA libraries of Piper nigrum, a unique magnoliid plant. The 5' end of the putative long form of 5.8S rRNA (5.8SLrRNA) was identified as the site for biogenesis of highly abundant srRNAs that are unique among the Piperaceae family of plants. A subsequent comparative analysis of the ninety-seven sRNAomes of diverse plants successfully uncovered the abundant existence and precise cleavage of unique rRF signature small RNAs upstream of a novel 5' consensus sequence of the 5.8S rRNA. The major cleavage process mapped identically among the different tissues of the same plant. The differential expression and cleavage of 5'5.8S srRNAs in Phytophthora capsici infected P. nigrum tissues indicated the critical biological functions of these srRNAs during stress response. The non-canonical short hairpin precursor structure, the association with Argonaute proteins, and the potential targets of 5'5.8S srRNAs reinforced their regulatory role in the RNAi pathway in plants. In addition, this novel lineage specific small RNAs may have tremendous biological potential in the taxonomic profiling of plants.

  10. The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages

    PubMed Central

    Asha, Srinivasan; Soniya, E. V.

    2017-01-01

    Small RNAs derived from ribosomal RNAs (srRNAs) are rarely explored in the high-throughput data of plant systems. Here, we analyzed srRNAs from the deep-sequenced small RNA libraries of Piper nigrum, a unique magnoliid plant. The 5′ end of the putative long form of 5.8S rRNA (5.8SLrRNA) was identified as the site for biogenesis of highly abundant srRNAs that are unique among the Piperaceae family of plants. A subsequent comparative analysis of the ninety-seven sRNAomes of diverse plants successfully uncovered the abundant existence and precise cleavage of unique rRF signature small RNAs upstream of a novel 5′ consensus sequence of the 5.8S rRNA. The major cleavage process mapped identically among the different tissues of the same plant. The differential expression and cleavage of 5′5.8S srRNAs in Phytophthora capsici infected P. nigrum tissues indicated the critical biological functions of these srRNAs during stress response. The non-canonical short hairpin precursor structure, the association with Argonaute proteins, and the potential targets of 5′5.8S srRNAs reinforced their regulatory role in the RNAi pathway in plants. In addition, this novel lineage specific small RNAs may have tremendous biological potential in the taxonomic profiling of plants. PMID:28145468

  11. Revealing Surface States in In-Doped SnTe Nanoplates with Low Bulk Mobility.

    PubMed

    Shen, Jie; Xie, Yujun; Cha, Judy J

    2015-06-10

    Indium (In) doping in topological crystalline insulator SnTe induces superconductivity, making In-doped SnTe a candidate for a topological superconductor. SnTe nanostructures offer well-defined nanoscale morphology and high surface-to-volume ratios to enhance surface effects. Here, we study In-doped SnTe nanoplates, In(x)Sn(1-x)Te, with x ranging from 0 to 0.1 and show they superconduct. More importantly, we show that In doping reduces the bulk mobility of In(x)Sn(1-x)Te such that the surface states are revealed in magnetotransport despite the high bulk carrier density. This is manifested by two-dimensional linear magnetoresistance in high magnetic fields, which is independent of temperature up to 10 K. Aging experiments show that the linear magnetoresistance is sensitive to ambient conditions, further confirming its surface origin. We also show that the weak antilocalization observed in In(x)Sn(1-x)Te nanoplates is a bulk effect. Thus, we show that nanostructures and reducing the bulk mobility are effective strategies to reveal the surface states and test for topological superconductors.

  12. 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.

  13. 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

  14. Additively manufactured metallic porous biomaterials based on minimal surfaces: A unique combination of topological, mechanical, and mass transport properties.

    PubMed

    Bobbert, F S L; Lietaert, K; Eftekhari, A A; Pouran, B; Ahmadi, S M; Weinans, H; Zadpoor, A A

    2017-02-16

    Porous biomaterials that simultaneously mimic the topological, mechanical, and mass transport properties of bone are in great demand but are rarely found in the literature. In this study, we rationally designed and additively manufactured (AM) porous metallic biomaterials based on four different types of triply periodic minimal surfaces (TPMS) that mimic the properties of bone to an unprecedented level of multi-physics detail. Sixteen different types of porous biomaterials were rationally designed and fabricated using selective laser melting (SLM) from a titanium alloy (Ti-6Al-4V). The topology, quasi-static mechanical properties, fatigue resistance, and permeability of the developed biomaterials were then characterized. In terms of topology, the biomaterials resembled the morphological properties of trabecular bone including mean surface curvatures close to zero. The biomaterials showed a favorable but rare combination of relatively low elastic properties in the range of those observed for trabecular bone and high yield strengths exceeding those reported for cortical bone. This combination allows for simultaneously avoiding stress shielding, while providing ample mechanical support for bone tissue regeneration and osseointegration. Furthermore, as opposed to other AM porous biomaterials developed to date for which the fatigue endurance limit has been found to be ≈20% of their yield (or plateau) stress, some of the biomaterials developed in the current study show extremely high fatigue resistance with endurance limits up to 60% of their yield stress. It was also found that the permeability values measured for the developed biomaterials were in the range of values reported for trabecular bone. In summary, the developed porous metallic biomaterials based on TPMS mimic the topological, mechanical, and physical properties of trabecular bone to a great degree. These properties make them potential candidates to be applied as parts of orthopedic implants and/or as bone

  15. Multi-modal analysis of functional connectivity and cerebral blood flow reveals shared and unique effects of propofol in large-scale brain networks.

    PubMed

    Qiu, Maolin; Scheinost, Dustin; Ramani, Ramachandran; Constable, R Todd

    2017-03-01

    Anesthesia-induced changes in functional connectivity and cerebral blow flow (CBF) in large-scale brain networks have emerged as key markers of reduced consciousness. However, studies of functional connectivity disagree on which large-scale networks are altered or preserved during anesthesia, making it difficult to find a consensus amount studies. Additionally, pharmacological alterations in CBF could amplify or occlude changes in connectivity due to the shared variance between CBF and connectivity. Here, we used data-driven connectivity methods and multi-modal imaging to investigate shared and unique neural correlates of reduced consciousness for connectivity in large-scale brain networks. Rs-fMRI and CBF data were collected from the same subjects during an awake and deep sedation condition induced by propofol. We measured whole-brain connectivity using the intrinsic connectivity distribution (ICD), a method not reliant on pre-defined seed regions, networks of interest, or connectivity thresholds. The shared and unique variance between connectivity and CBF were investigated. Finally, to account for shared variance, we present a novel extension to ICD that incorporates cerebral blood flow (CBF) as a scaling factor in the calculation of global connectivity, labeled CBF-adjusted ICD). We observed altered connectivity in multiple large-scale brain networks including the default mode (DMN), salience, visual, and motor networks and reduced CBF in the DMN, frontoparietal network, and thalamus. Regional connectivity and CBF were significantly correlated during both the awake and propofol condition. Nevertheless changes in connectivity and CBF between the awake and deep sedation condition were only significantly correlated in a subsystem of the DMN, suggesting that, while there is significant shared variance between the modalities, changes due to propofol are relatively unique. Similar, but less significant, results were observed in the CBF-adjusted ICD analysis, providing

  16. Ultrafast vibrational energy transfer at the water/air interface revealed by two-dimensional surface vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Zhen; Piatkowski, Lukasz; Bakker, Huib J.; Bonn, Mischa

    2011-11-01

    Water is very different from liquids of similar molecular weight, and one of its unique properties is the very efficient transfer of vibrational energy between molecules, which arises as a result of strong dipole-dipole interactions between the O-H oscillators. Although we have a sound understanding of such energy transfer in bulk water, we know less about how, and how quickly, transfer occurs at its interface with a hydrophobic phase, because specifically addressing the outermost monolayer is difficult. Here, we use ultrafast two-dimensional surface-specific vibrational spectroscopy to probe the interfacial energy dynamics of heavy water (D2O) at the water/air interface. The measurements reveal the presence of surprisingly rapid energy transfer, both between hydrogen-bonded interfacial water molecules (intermolecular), and between O-D groups sticking out from the water surface and those located on the same molecule and pointing towards the water bulk (intramolecular). Vibrational energy transfer occurs on sub-picosecond timescales, and its rates and pathways can be quantified directly.

  17. 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.

  18. Ultrafast vibrational energy transfer at the water/air interface revealed by two-dimensional surface vibrational spectroscopy.

    PubMed

    Zhang, Zhen; Piatkowski, Lukasz; Bakker, Huib J; Bonn, Mischa

    2011-10-02

    Water is very different from liquids of similar molecular weight, and one of its unique properties is the very efficient transfer of vibrational energy between molecules, which arises as a result of strong dipole-dipole interactions between the O-H oscillators. Although we have a sound understanding of such energy transfer in bulk water, we know less about how, and how quickly, transfer occurs at its interface with a hydrophobic phase, because specifically addressing the outermost monolayer is difficult. Here, we use ultrafast two-dimensional surface-specific vibrational spectroscopy to probe the interfacial energy dynamics of heavy water (D(2)O) at the water/air interface. The measurements reveal the presence of surprisingly rapid energy transfer, both between hydrogen-bonded interfacial water molecules (intermolecular), and between O-D groups sticking out from the water surface and those located on the same molecule and pointing towards the water bulk (intramolecular). Vibrational energy transfer occurs on sub-picosecond timescales, and its rates and pathways can be quantified directly.

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

    PubMed Central

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

    2010-01-01

    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 Å 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 β-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

  20. Soil surface temperatures reveal moderation of the urban heat island effect by trees and shrubs

    PubMed Central

    Edmondson, J. L.; Stott, I.; Davies, Z. G.; Gaston, K. J.; Leake, J. R.

    2016-01-01

    Urban areas are major contributors to air pollution and climate change, causing impacts on human health that are amplified by the microclimatological effects of buildings and grey infrastructure through the urban heat island (UHI) effect. Urban greenspaces may be important in reducing surface temperature extremes, but their effects have not been investigated at a city-wide scale. Across a mid-sized UK city we buried temperature loggers at the surface of greenspace soils at 100 sites, stratified by proximity to city centre, vegetation cover and land-use. Mean daily soil surface temperature over 11 months increased by 0.6 °C over the 5 km from the city outskirts to the centre. Trees and shrubs in non-domestic greenspace reduced mean maximum daily soil surface temperatures in the summer by 5.7 °C compared to herbaceous vegetation, but tended to maintain slightly higher temperatures in winter. Trees in domestic gardens, which tend to be smaller, were less effective at reducing summer soil surface temperatures. Our findings reveal that the UHI effects soil temperatures at a city-wide scale, and that in their moderating urban soil surface temperature extremes, trees and shrubs may help to reduce the adverse impacts of urbanization on microclimate, soil processes and human health. PMID:27641002

  1. 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.

  2. Soil surface temperatures reveal moderation of the urban heat island effect by trees and shrubs.

    PubMed

    Edmondson, J L; Stott, I; Davies, Z G; Gaston, K J; Leake, J R

    2016-09-19

    Urban areas are major contributors to air pollution and climate change, causing impacts on human health that are amplified by the microclimatological effects of buildings and grey infrastructure through the urban heat island (UHI) effect. Urban greenspaces may be important in reducing surface temperature extremes, but their effects have not been investigated at a city-wide scale. Across a mid-sized UK city we buried temperature loggers at the surface of greenspace soils at 100 sites, stratified by proximity to city centre, vegetation cover and land-use. Mean daily soil surface temperature over 11 months increased by 0.6 °C over the 5 km from the city outskirts to the centre. Trees and shrubs in non-domestic greenspace reduced mean maximum daily soil surface temperatures in the summer by 5.7 °C compared to herbaceous vegetation, but tended to maintain slightly higher temperatures in winter. Trees in domestic gardens, which tend to be smaller, were less effective at reducing summer soil surface temperatures. Our findings reveal that the UHI effects soil temperatures at a city-wide scale, and that in their moderating urban soil surface temperature extremes, trees and shrubs may help to reduce the adverse impacts of urbanization on microclimate, soil processes and human health.

  3. Soil surface temperatures reveal moderation of the urban heat island effect by trees and shrubs

    NASA Astrophysics Data System (ADS)

    Edmondson, J. L.; Stott, I.; Davies, Z. G.; Gaston, K. J.; Leake, J. R.

    2016-09-01

    Urban areas are major contributors to air pollution and climate change, causing impacts on human health that are amplified by the microclimatological effects of buildings and grey infrastructure through the urban heat island (UHI) effect. Urban greenspaces may be important in reducing surface temperature extremes, but their effects have not been investigated at a city-wide scale. Across a mid-sized UK city we buried temperature loggers at the surface of greenspace soils at 100 sites, stratified by proximity to city centre, vegetation cover and land-use. Mean daily soil surface temperature over 11 months increased by 0.6 °C over the 5 km from the city outskirts to the centre. Trees and shrubs in non-domestic greenspace reduced mean maximum daily soil surface temperatures in the summer by 5.7 °C compared to herbaceous vegetation, but tended to maintain slightly higher temperatures in winter. Trees in domestic gardens, which tend to be smaller, were less effective at reducing summer soil surface temperatures. Our findings reveal that the UHI effects soil temperatures at a city-wide scale, and that in their moderating urban soil surface temperature extremes, trees and shrubs may help to reduce the adverse impacts of urbanization on microclimate, soil processes and human health.

  4. Comparative analysis of antiviral responses in Brachypodium distachyon and Setaria viridis reveals conserved and unique outcomes among C3 and C4 plant defenses.

    PubMed

    Mandadi, Kranthi K; Pyle, Jesse D; Scholthof, Karen-Beth G

    2014-11-01

    Viral diseases cause significant losses in global agricultural production, yet little is known about grass antiviral defense mechanisms. We previously reported on host immune responses triggered by Panicum mosaic virus (PMV) and its satellite virus (SPMV) in the model C3 grass Brachypodium distachyon. To aid comparative analyses of C3 and C4 grass antiviral defenses, here, we establish B. distachyon and Setaria viridis (a C4 grass) as compatible hosts for seven grass-infecting viruses, including PMV and SPMV, Brome mosaic virus, Barley stripe mosaic virus, Maize mild mottle virus, Sorghum yellow banding virus, Wheat streak mosaic virus (WSMV), and Foxtail mosaic virus (FoMV). Etiological and molecular characterization of the fourteen grass-virus pathosystems showed evidence for conserved crosstalk among salicylic acid (SA), jasmonic acid, and ethylene pathways in B. distachyon and S. viridis. Strikingly, expression of PHYTOALEXIN DEFICIENT4, an upstream modulator of SA signaling, was consistently suppressed during most virus infections in B. distachyon and S. viridis. Hierarchical clustering analyses further identified unique antiviral responses triggered by two morphologically similar viruses, FoMV and WSMV, and uncovered other host-dependent effects. Together, the results of this study establish B. distachyon and S. viridis as models for the analysis of plant-virus interactions and provide the first framework for conserved and unique features of C3 and C4 grass antiviral defenses.

  5. Interspecific comparison of constitutive ash phloem phenolic chemistry reveals compounds unique to manchurian ash, a species resistant to emerald ash borer.

    PubMed

    Whitehill, Justin G A; Opiyo, Stephen O; Koch, Jennifer L; Herms, Daniel A; Cipollini, Donald F; Bonello, Pierluigi

    2012-05-01

    The emerald ash borer (Agrilus planipennis, EAB) is an invasive wood-borer indigenous to Asia and is responsible for widespread ash (Fraxinus spp.) mortality in the U.S. and Canada. Resistance and susceptibility to EAB varies among Fraxinus spp., which is a result of their co-evolutionary history with the pest. We characterized constitutive phenolic profiles and lignin levels in the phloem of green, white, black, blue, European, and Manchurian ash. Phloem was sampled twice during the growing season, coinciding with phenology of early and late instar EAB. We identified 66 metabolites that displayed a pattern of variation, which corresponded strongly with phylogeny. Previously identified lignans and lignan derivatives were confirmed to be unique to Manchurian ash, and may contribute to its high level of resistance to EAB. Other compounds that had been considered unique to Manchurian ash, including hydroxycoumarins and the phenylethanoids calceolarioside A and B, were detected in closely related, but susceptible species, and thus are unlikely to contribute to EAB resistance of Manchurian ash. The distinct phenolic profile of blue ash may contribute to its relatively high resistance to EAB.

  6. Col-OSSOS: z-Band Photometry Reveals Three Distinct TNO Surface Types

    NASA Astrophysics Data System (ADS)

    Pike, Rosemary E.; Fraser, Wesley C.; Schwamb, Megan E.; Kavelaars, J. J.; Marsset, Michael; Bannister, Michele T.; Lehner, Matthew J.; Wang, Shiang-Yu; Alexandersen, Mike; Chen, Ying-Tung; Gladman, Brett J.; Gwyn, Stephen; Petit, Jean-Marc; Volk, Kathryn

    2017-09-01

    Several different classes of trans-Neptunian objects (TNOs) have been identified based on their optical and near-infrared colors. As part of the Colours of the Outer Solar System Origins Survey (Col-OSSOS), we have obtained g-, r-, and z-band photometry of 26 TNOs using Subaru and Gemini Observatories. Previous color surveys have not utilized z-band reflectance, and the inclusion of this band reveals significant surface reflectance variations between sub-populations. The colors of TNOs in g - r and r - z show obvious structure, and appear consistent with the previously measured bi-modality in g - r. The distribution of colors of the two dynamically excited surface types can be modeled using the two-component mixing models from Fraser & Brown. With the combination of g - r and r - z, the dynamically excited classes can be separated cleanly into red and neutral surface classes. In g - r and r - z, the two dynamically excited surface groups are also clearly distinct from the cold classical TNO surfaces, which are red, with g-r≳ 0.85 and r - z ≲ 0.6, while all dynamically excited objects with similar g - r colors exhibit redder r - z colors. The z-band photometry makes it possible for the first time to differentiate the red excited TNO surfaces from the red cold classical TNO surfaces. The discovery of different r - z colors for these cold classical TNOs makes it possible to search for cold classical surfaces in other regions of the Kuiper Belt and to completely separate cold classical TNOs from the dynamically excited population, which overlaps in orbital parameter space.

  7. 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.

  8. In situ X-ray probing reveals fingerprints of surface platinum oxide.

    PubMed

    Friebel, Daniel; Miller, Daniel J; O'Grady, Christopher P; Anniyev, Toyli; Bargar, John; Bergmann, Uwe; Ogasawara, Hirohito; Wikfeldt, Kjartan Thor; Pettersson, Lars G M; Nilsson, Anders

    2011-01-07

    In situ X-ray absorption spectroscopy (XAS) at the Pt L(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 FEFF 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.

  9. 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.

  10. Extracellular-signal regulated kinase 8 of Trypanosoma brucei uniquely phosphorylates its proliferating cell nuclear antigen homolog and reveals exploitable properties

    PubMed Central

    Valenciano, Ana L.; Knudsen, Giselle M.; Mackey, Zachary B.

    2016-01-01

    ABSTRACT The Trypanosoma brucei subspecies T. brucei gambiense and T. brucei rhodesiense are vector-borne pathogens that cause sleeping sickness also known as Human African Trypanosomiasis (HAT), which is fatal if left untreated. The drugs that treat HAT are ineffective and cause toxic side effects. One strategy for identifying safer and more effective HAT drugs is to therapeutically exploit essential gene targets in T. brucei. Genes that make up a basic mitogen-activated protein kinase (MAPK) network are present in T. brucei. Tb927.10.5140 encodes an essential MAPK that is homologous to the human extracellular-signal regulated kinase 8 (HsERK8) which forms a tight complex with the replication factor proliferating cell nuclear antigen (PCNA) to stabilize intracellular PCNA levels. Here we demonstrate that (TbPCNA) is uniquely phos-phorylated on serine (S) and threonine (T) residues in T. brucei and that TbERK8 phosphorylates TbPCNA at each of these residues. The ability of an ERK8 homolog to phosphorylate a PCNA homolog is a novel biochemical property that is first demonstrated here in T. brucei and may be unique to this pathogen. We demonstrate that the potent HsERK8 inhibitor Ro318220, has an IC50 for TbERK8 that is several hundred times higher than its reported IC50 for HsERK8. This indicated that the active sites of TbERK8 and HsERK8 can be selectively inhibited, which provides a rational basis for discovering inhibitors that specifically target this essential parasite MAPK to kill the parasite. PMID:27589575

  11. Transcriptome analysis reveals unique C4-like photosynthesis and oil body formation in an arachidonic acid-rich microalga Myrmecia incisa Reisigl H4301.

    PubMed

    Ouyang, Long-Ling; Chen, Si-Hong; Li, Yan; Zhou, Zhi-Gang

    2013-06-13

    Arachidonic acid (ArA) is important for human health because it is one of the major components of mammalian brain membrane phospholipids. The interest in ArA inspired the search for a new sustainable source, and the green microalga Myrmecia incisa Reisigl H4301 has been found a potential ArA-producer due to a high content of intracellular ArA. To gain more molecular information about metabolism pathways, including the biosynthesis of ArA in the non-model microalga, a transcriptomic analysis was performed. The 454 pyrosequencing generated 371,740 high-quality reads, which were assembled into 51,908 unique sequences consisting of 22,749 contigs and 29,159 singletons. A total of 11,873 unique sequences were annotated through BLAST analysis, and 3,733 were assigned to Gene Ontology (GO) categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis uncovered a C4-like photosynthesis pathway in M. incisa. The biosynthesis pathways of lipid particularly those of ArA and triacylglycerol (TAG) were analyzed in detail, and TAG was proposed to be accumulated in oil bodies in the cytosol with the help of caleosin or oil globule-associated proteins. In addition, the carotenoid biosynthesis pathways are discussed. This transcriptomic analysis of M. incisa enabled a global understanding of mechanisms involved in photosynthesis, de novo biosynthesis of ArA, metabolism of carotenoids, and accumulation of TAG in M. incisa. These findings provided a molecular basis for the research and possibly economic exploitation of this ArA-rich microalga.

  12. Fermi surface of underdoped cuprate revealed by quantum oscillations and Hall effect

    NASA Astrophysics Data System (ADS)

    Proust, Cyril

    2008-03-01

    Despite twenty years of research, the phase diagram of high temperature superconductors remains enigmatic. A central issue is the origin of the differences in the physical properties of these copper oxides doped to opposite sides of the superconducting region. In the overdoped regime, the material behaves as a reasonably conventional metal, with a large Fermi surface [1]. The underdoped regime, however, is highly anomalous and appears to have no coherent Fermi surface, but only disconnected `Fermi arcs' [2]. We have reported the observation of quantum oscillations in the electrical resistance of the oxygen-ordered copper oxides YBa2Cu3O6.5 [3] and YBa2Cu4O8 [4], establishing the existence of a coherent closed Fermi surface at low temperature in the underdoped side of the phase diagram of cuprates, once superconductivity is suppressed by a large magnetic field. The low oscillation frequency reveals a Fermi surface made of small pockets, in contrast to the large cylinder characteristic of the overdoped regime. Moreover, the negative sign of the Hall effect at low temperature reveals that these pockets are electron-like rather than hole-like. We propose that the Fermi surface of these Y-based cuprates consists of both electron and hole pockets, probably arising from a reconstruction of the FS [5]. Work in collaboration with N Doiron-Leyraud, D. LeBoeuf and L. Taillefer from the University of Sherbrooke, J. Levallois and B. Vignolle from the LNCMP, A. Bangura and N. Hussey from the University of Bristol and R. Liang, D. Bonn, W. Hardy from the University of British Columbia. [1] N Hussey et al, Nature 425, 814 (2003) [2] M. Norman et al, Nature 392, 157 (1998) [3] N. Doiron-Leyraud et al, Nature 447, 565 (2007) [4] A. Bangura et al, submitted to Phys. Rev. Lett (arXiv: 0707.4461) [5] D. LeBoeuf et al, Nature 450, 533 (2007)

  13. The surface and interior evolution of Ceres revealed by fractures and secondary crater chains

    NASA Astrophysics Data System (ADS)

    Scully, Jennifer E. C.; Buczkowski, Debra; Schmedemann, Nico; King, Scott; O'Brien, David P.; Castillo-Rogez, Julie; Raymond, Carol; Marchi, Simone; Russell, Christopher T.; Mitri, Giuseppe; Bland, Michael T.

    2016-10-01

    Dawn became the first spacecraft to visit and orbit Ceres, a dwarf planet and the largest body in the asteroid belt (radius ~470 km) (Russell et al., 2016). Before Dawn's arrival, telescopic observations and thermal evolution modeling indicated Ceres was differentiated, with an average density of 2,100 kg/m3 (e.g. McCord & Sotin, 2005; Castillo-Rogez & McCord, 2010). Moreover, pervasive viscous relaxation in a water-ice-rich outer layer was predicted to erase most features on Ceres' surface (Bland, 2013). However, a full understanding of Ceres' surface and interior evolution remained elusive. On the basis of global geologic mapping, we identify prevalent ≥1 km wide linear features that formed: 1) as the surface expression of subsurface fractures, and 2) as material ejected during impact-crater formation impacted and scoured the surface, forming secondary crater chains. The formation and preservation of these linear features indicates Ceres' outer layer is relatively strong, and is not dominated by viscous relaxation as predicted. The fractures also give us insights into Ceres' interior: their spacing indicates the fractured layer is ~30 km thick, and we interpret the fractures formed because of uplift and extension induced by an upwelling region, which is consistent with geodynamic modeling (King et al., 2016). In addition, we find that some secondary crater chains do not form radial patterns around their source impact craters, and are located in a different hemisphere from their source impact craters, because of Ceres' fast rotation (period of ~9 hours) and relatively small radius. Our results show Ceres has a surface and outer layer with characteristics that are different than predicted, and underwent complex surface and interior evolution. Our fuller understanding of Ceres, based on Dawn data, gives us important insights into the evolution of bodies in the asteroid belt, and provides unique constraints that can be used to evaluate predictions of the surface

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Recent acceleration in summer surface melt on the Greenland ice sheet (GrIS) has occurred concurrently with a rapidly warming Arctic and has been connected to persistent, anomalous circulation patterns over Greenland. To identify patterns that favor enhanced GrIS surface melt and their decadal changes, we first develop a summer Arctic synoptic climatology by employing a nonlinear classification technique known as the self organizing map (SOM). This is applied to daily JJA sea level pressure (SLP) and 500 hPa geopotential height fields obtained from the Modern Era Retrospective Analysis for Research and Applications (MERRA) reanalysis product from 1979 to 2014. Model output from Modèle Atmosphérique Régional (MAR) is used to relate meteorological conditions and subsequent Greenland surface melt anomalies to particular circulation regimes. Results demonstrate that circulation patterns featuring positive SLP anomalies from Greenland to the Beaufort Sea support the largest positive surface melt anomalies, particularly over western Greenland. These patterns facilitate strong meridional transport of heat and moisture, contrasted by a dominant zonal flow across the North Atlantic during periods of low surface melt. Additionally, composites of energy balance components reveal that melt events are favored under clear conditions generating positive shortwave radiation anomalies rather than increased downwelling longwave radiation occurring with increased cloud cover. Sea surface temperature anomalies suggest that there may be a linkage between surface melt and recent sea ice loss around Greenland, though a causal relationship is not established. We assess decadal shifts in the SOM nodes, finding an increased frequency of upper level patterns favoring higher 500 hPa geopotential heights primarily over Greenland. The observed increases in GrIS melt through the time period coincides with this shift in SOM node frequency.

  15. 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.

  16. Influenza H3N2 infection of the collaborative cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice.

    PubMed

    Leist, Sarah R; Pilzner, Carolin; van den Brand, Judith M A; Dengler, Leonie; Geffers, Robert; Kuiken, Thijs; Balling, Rudi; Kollmus, Heike; Schughart, Klaus

    2016-02-27

    Influenza A virus is a zoonotic pathogen that poses a major threat to human and animal health. The severe course of influenza infection is not only influenced by viral virulence factors but also by individual differences in the host response. To determine the extent to which the genetic background can modulate severity of an infection, we studied the host responses to influenza infections in the eight genetically highly diverse Collaborative Cross (CC) founder mouse strains. We observed highly divergent host responses between the CC founder strains with respect to survival, body weight loss, hematological parameters in the blood, relative lung weight and viral load. Mouse strain was the main factor with highest effect size on body weight loss after infection, demonstrating that this phenotype was highly heritable. Sex represented another significant main effect, although it was less strong. Analysis of survival rates and mean time to death suggested three groups of susceptibility phenotypes: highly susceptible (A/J, CAST/EiJ, WSB/EiJ), intermediate susceptible (C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ) and highly resistant strains (NZO/HlLtJ, PWK/PhJ). These three susceptibility groups were significantly different with respect to death/survival counts. Viral load was significantly different between susceptible and resistant strains but not between intermediate and highly susceptible strains. CAST/EiJ mice showed a unique phenotype. Despite high viral loads in their lungs, CAST/EiJ mice exhibited low counts of infiltrating granulocytes and showed increased numbers of macrophages in the lung. Histological studies of infected lungs and transcriptome analyses of peripheral blood cells and lungs confirmed an abnormal response in the leukocyte recruitment in CAST/EiJ mice. The eight CC founder strains exhibited a large diversity in their response to influenza infections. Therefore, the CC will represent an ideal mouse genetic reference population to study the influence of

  17. Characterization of brain tumours with spin-spin relaxation: pilot case study reveals unique T 2 distribution profiles of glioblastoma, oligodendroglioma and meningioma.

    PubMed

    Laule, Cornelia; Bjarnason, Thorarin A; Vavasour, Irene M; Traboulsee, Anthony L; Wayne Moore, G R; Li, David K B; MacKay, Alex L

    2017-09-11

    Prolonged spin-spin relaxation times in tumour tissue have been observed since some of the earliest nuclear magnetic resonance investigations of the brain. Over the last three decades, numerous studies have sought to characterize tumour morphology and malignancy using quantitative assessment of T 2 relaxation times, although attempts to categorize and differentiate tumours have had limited success. However, previous work must be interpreted with caution as relaxation data were typically acquired using a variety of multiple echo sequences with a range of echoes and T 2 decay curves and were frequently fit with monoexponential analysis. We defined the distribution of T 2 components in three different human brain tumours (glioblastoma, oligodendroglioma, meningioma) using a multi-echo sequence with a greater number of echoes and a longer acquisition window than previously used (48 echoes, data collection out to 1120 ms) with no a priori assumptions about the number of exponential components contributing to the T 2 decay. T 2 relaxation times were increased in tumour tissue and each tumour showed a distinct T 2 distribution profile. Tumours have complex and unique compartmentalization characteristics. Quantitative assessment of T 2 relaxation in brain cancer may be useful in evaluating different grades of brain tumours on the basis of their T 2 distribution profile, and has the potential to be a non-invasive diagnostic tool which may also be useful in monitoring therapy. Further study with a larger sample size and varying grades of tumours is warranted.

  18. The Structure of the RAGE:S100A6 Complex Reveals a Unique Mode of Homodimerization for S100 Proteins.

    PubMed

    Yatime, Laure; Betzer, Cristine; Jensen, Rasmus Kjeldsen; Mortensen, Sofia; Jensen, Poul Henning; Andersen, Gregers Rom

    2016-12-06

    S100 proteins are calcium-dependent regulators of homeostatic processes. Upon cellular response to stress, and notably during tumorigenesis, they relocalize to the extracellular environment where they induce pro-inflammatory signals by activating the receptor for advanced glycation end products (RAGE), thereby facilitating tumor growth and metastasis. Despite its importance in sustaining inflammation, the structural basis for RAGE-S100 crosstalk is still unknown. Here we report two crystal structures of the RAGE:S100A6 complex encompassing a full-length RAGE ectodomain. The structures, in combination with a comprehensive interaction analysis, suggest that the primary S100A6 binding site is formed by the RAGE C1 domain. Complex formation with S100A6 induces a unique dimeric conformation of RAGE that appears suited for signal transduction and intracellular effector recruitment. Intriguingly, S100A6 adopts a dimeric conformation radically different from all known S100 dimers. We discuss the physiological relevance of this non-canonical homodimeric form in vivo. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Nucleotide sequence of shallot virus X RNA reveals a 5'-proximal cistron closely related to those of potexviruses and a unique arrangement of the 3'-proximal cistrons.

    PubMed

    Kanyuka, K V; Vishnichenko, V K; Levay, K E; Kondrikov DYu; Ryabov, E V; Zavriev, S K

    1992-10-01

    The 8890 nucleotide RNA sequence of shallot virus X (ShVX), a new virus isolated from shallot, has been determined. The sequence contains six open reading frames (ORFs) which encode putative proteins (in the 5' to 3' direction) of M(r) 194528 (ORF1), 26333 (ORF2), 11245 (ORF3), 42209 (ORF4), 28486 (ORF5) and 14741 (ORF6). The ORF1 protein was found to be highly homologous to the putative potexvirus RNA replicases; ORF2, -3, -5 and -6 proteins also have analogues among the potex- and/or carlavirus-encoded proteins. ORF3 is followed by an AUG-lacking frame coding for an amino acid sequence homologous to that of the 7K to 8K proteins of the triple gene block of the above-mentioned viruses. The putative ORF4 protein has no reliable homology with proteins in the database. The results obtained testify that, except for the unique 42K protein gene, the ShVX genome combines a number of elements typical of both carla- and potexviruses.

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

    PubMed

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

    2015-10-01

    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.

  1. 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

  2. Mars surface diversity as revealed by the OMEGA/Mars Express observations.

    PubMed

    Bibring, Jean-Pierre; Langevin, Yves; Gendrin, Aline; Gondet, Brigitte; Poulet, François; Berthé, Michel; Soufflot, Alain; Arvidson, Ray; Mangold, Nicolas; Mustard, John; Drossart, P

    2005-03-11

    The Observatoire pour la Minéralogie, l'Eau, les Glaces, et l'Activité (OMEGA) investigation, on board the European Space Agency Mars Express mission, is mapping the surface composition of Mars at a 0.3- to 5-kilometer resolution by means of visible-near-infrared hyperspectral reflectance imagery. The data acquired during the first 9 months of the mission already reveal a diverse and complex surface mineralogy, offering key insights into the evolution of Mars. OMEGA has identified and mapped mafic iron-bearing silicates of both the northern and southern crust, localized concentrations of hydrated phyllosilicates and sulfates but no carbonates, and ices and frosts with a water-ice composition of the north polar perennial cap, as for the south cap, covered by a thin carbon dioxide-ice veneer.

  3. Revealing obliterated engraved marks on high strength aluminium alloy (AA7010) surfaces by etching technique.

    PubMed

    Bong, Yeu Uei; Kuppuswamy, R

    2010-02-25

    Restoration of obliterated engraved marks on high strength Al-Zn-Mg-Cu alloy (AA7010) surfaces by etching technique was studied. The alloy surfaces were mechanically engraved with some identification marks using "Gravograph". The marks were then erased by removing the metal to different levels up to and below the depth of engraving. Five metallographic reagents were tested on the obliterated surfaces by etching. The following two methods (i) immersion in 10% aq. phosphoric acid and (ii) alternate swabbing of 60% HCl and 40% NaOH were found to be quite effective to reveal the obliterated marks. These two procedures were also able to show effectively the marks obliterated by over-engraving and centre punching. Of the two techniques immersion in phosphoric acid provided more contrast. Interestingly, alternate swabbing of 60% HCl and 40% NaOH presented itself to be the common reagent for restoration on pure aluminium as well as its alloy surfaces. This is evident from our own current experiments and those of earlier researchers [G. Peeler, S. Gutowski, H. Wrobel, G. Dower, The restoration of impressed characters on aluminium alloy motor cycle frames, J. Forensic Ident. 58 (1) (2008) 27-32; M. Izhar M. Baharum, R. Kuppuswamy, A.A. Rahman, Restoration of engraved marks on aluminium surfaces by etching technique, Forensic Sci. Int. 177 (2008) 221-227]. The findings have assumed importance as engines and chassis of cars and frames of firearms are currently made of high strength aluminium alloys and recovery on these surfaces by current methods is not satisfactory.

  4. Nanoscale electrochemical patterning reveals the active sites for catechol oxidation at graphite surfaces.

    PubMed

    Patel, Anisha N; McKelvey, Kim; Unwin, Patrick R

    2012-12-19

    Graphite-based electrodes (graphite, graphene, and nanotubes) are used widely in electrochemistry, and there is a long-standing view that graphite step edges are needed to catalyze many reactions, with the basal surface considered to be inert. In the present work, this model was tested directly for the first time using scanning electrochemical cell microscopy reactive patterning and shown to be incorrect. For the electro-oxidation of dopamine as a model process, the reaction rate was measured at high spatial resolution across a surface of highly oriented pyrolytic graphite. Oxidation products left behind in a pattern defined by the scanned electrochemical cell served as surface-site markers, allowing the electrochemical activity to be correlated directly with the graphite structure on the nanoscale. This process produced tens of thousands of electrochemical measurements at different locations across the basal surface, unambiguously revealing it to be highly electrochemically active, with step edges providing no enhanced activity. This new model of graphite electrodes has significant implications for the design of carbon-based biosensors, and the results are additionally important for understanding electrochemical processes on related sp(2)-hybridized materials such as pristine graphene and nanotubes.

  5. Compositional variability across Mercury's surface revealed by MESSENGER measurements of variations in thermal neutron count rates

    NASA Astrophysics Data System (ADS)

    Peplowski, P. N.; Lawrence, D. J.; Goldsten, J. O.; Nittler, L. R.; Solomon, S. C.

    2013-12-01

    Measurements by MESSENGER's Gamma-Ray and Neutron Spectrometer (GRNS) have revealed variations in the flux of thermal neutrons across Mercury's northern hemisphere. These variations are interpreted to originate from spatial variations in surface elemental composition. In particular, the measurements are sensitive to the near-surface abundances of elements that absorb thermal neutrons, including major rock-forming elements such as Fe and Ti, minor elements such as Mn and Cl, and rare-earth elements such as Gd and Sm. We have constructed a map of thermal neutron variability across the surface and compared it with known variations in elemental composition and with the distribution of geologic units. Development of the map included the derivation of the macroscopic thermal neutron absorption cross section across the surface, a quantity whose value and variability provides useful constraints on the formation and geochemical evolution of Mercury's crust. Finally, by combining the thermal neutron measurements with previously reported elemental measurements from the GRNS and MESSENGER's X-Ray Spectrometer, we have derived constraints on the abundances of neutron-absorbing elements, including previously unreported limits for some minor and rare-earth elements.

  6. Zebrafish Tg(7.2mab21l2:EGFP)ucd2 transgenics reveal a unique population of retinal amacrine cells.

    PubMed

    Cederlund, Maria L; Morrissey, Maria E; Baden, Tom; Scholz, Dimitri; Vendrell, Victor; Lagnado, Leon; Connaughton, Victoria P; Kennedy, Breandán N

    2011-03-01

    Amacrine cells constitute a diverse, yet poorly characterized, cell population in the inner retina. Here, the authors sought to characterize the morphology, molecular physiology, and electrophysiology of a subpopulation of EGFP-expressing retinal amacrine cells identified in a novel zebrafish transgenic line. After 7.2 kb of the zebrafish mab21l2 promoter was cloned upstream of EGFP, it was used to create the Tg(7.2mab21l2:EGFP)ucd2 transgenic line. Transgenic EGFP expression was analyzed by fluorescence microscopy in whole mount embryos, followed by detailed analysis of EGFP-expressing amacrine cells using fluorescence microscopy, immunohistochemistry, and electrophysiology. A 7.2-kb fragment of the mab21l2 promoter region is sufficient to drive transgene expression in the developing lens and tectum. Intriguingly, EGFP was also observed in differentiated amacrine cells. EGFP-labeled amacrine cells in Tg(7.2mab21l2:EGFP)ucd2 constitute a novel GABA- and glycine-negative amacrine subpopulation. Morphologically, EGFP-expressing cells stratify in sublamina 1 to 2 (type 1 OFF) or sublamina 3 to 4 (type 1 ON) or branch diffusely (type 2). Electrophysiologically, these cells segregate into amacrine cells with somas in the vitreal part of the INL and linear responses to current injection or, alternatively, amacrine cells with somas proximal to the IPL and active oscillatory voltage signals. CONCLUSIONS; The novel transgenic line Tg(7.2mab21l2:EGFP)ucd2 uncovers a unique subpopulation of retinal amacrine cells.

  7. Mutational Analysis of the Myxococcus xanthus Ω4499 Promoter Region Reveals Shared and Unique Properties in Comparison with Other C-Signal-Dependent Promoters

    PubMed Central

    Yoder, Deborah R.; Kroos, Lee

    2004-01-01

    The bacterium Myxococcus xanthus undergoes multicellular development during times of nutritional stress and uses extracellular signals to coordinate cell behavior. C-signal affects gene expression late in development, including that of Ω4499, an operon identified by insertion of Tn5 lac into the M. xanthus chromosome. The Ω4499 promoter region has several sequences in common with those found previously to be important for expression of other C-signal-dependent promoters. To determine if these sequences are important for Ω4499 promoter activity, the effects of mutations on expression of a downstream reporter gene were tested in M. xanthus. Although the promoter resembles those recognized by Escherichia coli σ54, mutational analysis implied that a σ70-type σ factor likely recognizes the promoter. A 7-bp sequence known as a C box and a 5-bp element located 6 bp upstream of the C box have been shown to be important for expression of other C-signal-dependent promoters. The Ω4499 promoter region has C boxes centered at −33 and −55 bp, with 5-bp elements located 7 and 8 bp upstream, respectively. A multiple-base-pair mutation in any of these sequences reduced Ω4499 promoter activity more than twofold. Single base-pair mutations in the C box centered at −33 bp yielded a different pattern of effects on expression than similar mutations in other C boxes, indicating that each functions somewhat differently. An element from about −81 to −77 bp exerted a twofold positive effect on expression but did not appear to be responsible for the C-signal dependence of the Ω4499 promoter. Mutations in sigD and sigE, which are genes that encode σ factors, reduced expression from the Ω4499 promoter. The results provide further insight into the regulation of C-signal-dependent genes, demonstrating both shared and unique properties among the promoter regions so far examined. PMID:15175290

  8. Biophysical investigations of complement receptor 2 (CD21 and CR2)-ligand interactions reveal amino acid contacts unique to each receptor-ligand pair.

    PubMed

    Kovacs, James M; Hannan, Jonathan P; Eisenmesser, Elan Z; Holers, V Michael

    2010-08-27

    Human complement receptor type 2 (CR2 and CD21) is a cell membrane receptor, with 15 or 16 extracellular short consensus repeats (SCRs), that promotes B lymphocyte responses and bridges innate and acquired immunity. The most distally located SCRs, SCR1-2, mediate the interaction of CR2 with its four known ligands (C3d, EBV gp350, IFNalpha, and CD23). To ascertain specific interacting residues on CR2, we utilized NMR studies wherein gp350 and IFNalpha were titrated into (15)N-labeled SCR1-2, and chemical shift changes indicative of specific inter-molecular interactions were identified. With backbone assignments made, the chemical shift changes were mapped onto the crystal structure of SCR1-2. With regard to gp350, the binding region of CR2 is primarily focused on SCR1 and the inter-SCR linker, specifically residues Asn(11), Arg(13), Ala(22), Arg(28), Ser(32), Arg(36), Lys(41), Lys(57), Tyr(64), Lys(67), Tyr(68), Arg(83), Gly(84), and Arg(89). With regard to IFNalpha, the binding is similar to the CR2-C3d interaction with specific residues being Arg(13), Tyr(16), Arg(28), Ser(42), Lys(48), Lys(50), Tyr(68), Arg(83), Gly(84), and Arg(89). We also report thermodynamic properties of each ligand-receptor pair determined using isothermal titration calorimetry. The CR2-C3d interaction was characterized as a two-mode binding interaction with K(d) values of 0.13 and 160 microm, whereas the CR2-gp350 and CR2-IFNalpha interactions were characterized as single site binding events with affinities of 0.014 and 0.035 microm, respectively. The compilation of chemical binding maps suggests specific residues on CR2 that are uniquely important in each of these three binding interactions.

  9. Systematic Studies of Sulfation and Glucuronidation of 12 Flavonoids in the Mouse Liver S9 Fraction Reveals both Unique and Shared Positional Preferences

    PubMed Central

    Tang, Lan; Zhou, Juan; Yang, Cai-Hua; Xia, Bi-Jun; Hu, Ming; Liu, Zhong-Qiu

    2012-01-01

    Sulfation and glucuronidation are the principal metabolic pathways of flavonoids, and extensive phase II metabolism is the main reason for their poor bioavailabilities. The purpose of this study was to compare the similarities and differences in the positional preference of glucuronidation versus sulfation in the mouse liver S9 fraction. The conjugating rates of seven mono-hydroxyflavones (HFs) (i.e., 2’-, 3’-, 4’-, 3-, 5-, 6-, and 7-HF), and five di-hydroxyflavones (diHFs), (i.e., 6,7-, 4’,7-, 3,7-, 5,7-, and 3,4’-diHF) were determined in three separate enzymatic reaction systems: (A) sulfation only, (B) glucuronidation only, or (C) simultaneous sulfation and glucuronidation (i.e., Sult-Ugt co-reaction). In general, glucuronidation rates were much faster than the sulfation rates. Among the HFs, 7-HF was the best substrate for both conjugation reactions, whereas 3-HF was rapidly glucuronidated but was not sulfated. As a result, the rank order of sulfation was very different from that of glucuronidation. Among the diHFs, regiospecific glucuronidation was limited to 7-OH and 3-OH positions, whereas regiospecific sulfation was limited to 7-OH and 4’-OH positions. Other positions (i.e., 6-OH and 5-OH) in diHFs were not conjugated. The positional preferences were essentially maintained in a Sult-Ugt co-reaction system, although sulfation was surprisingly enhanced. Lastly, sulfation and glucuronidation displayed different regiospecific- and substrate-dependent characteristics. In conclusion, glucuronidation and sulfation shared the same preference for 7-OH position (of flavonoids) but displayed unique preference in other positions in that glucuronidation preferred 3-OH position whereas sulfation preferred 4’-OH position. PMID:22352802

  10. 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

  11. microRNA expression profiling of endometrial endometrioid adenocarcinomas and serous adenocarcinomas reveals profiles containing shared, unique and differentiating groups of microRNAs.

    PubMed

    Devor, Eric J; Hovey, Adriann M; Goodheart, Michael J; Ramachandran, Shyam; Leslie, Kimberly K

    2011-10-01

    microRNAs (miRNAs) control a multitude of pathways in human cancers. Differential expression of miRNAs among different histological types of tumors within the same type of tissue offers insight into the mechanism of pathogenesis and may help to direct treatment to improve prognosis. We assessed expression of 667 miRNAs in endometrial endometrioid and serous adenocarcinomas using RNA extracted from benign endometrium as well as from primary endometrial tumors. Quantitative miRNA profiling of endometrial adenocarcinomas revealed four overlapping groups of significantly overexpressed and underexpressed miRNAs. The first group was composed of 20 miRNAs significantly dysregulated in both adenocarcinoma types compared with benign endometrium, two groups were composed of miRNAs significantly dysregulated in either endometrioid adenocarcinomas or in serous adenocarcinomas compared with benign endometrium, and the fourth group was composed of 17 miRNAs that significantly distinguished between endometrioid adenocarcinomas and serous adenocarcinomas themselves. Validation of the expression levels of the selected miRNAs was carried out in a second panel composed of ten endometrioid and five serous tumors. Experimentally validated mRNA targets of these dysregulated miRNAs were identified using published sources, whereas TargetScan was used to predict targets of miRNAs in the first and fourth profile groups. These validated and potential miRNA target lists were filtered using published lists of genes displaying significant overexpression or underexpression in endometrial cancers compared to benign endometrium. Our results revealed a number of dysregulated miRNAs that are commonly found in endometrial (and other) cancers as well as several dysregulated miRNAs not previously identified in endometrial cancers. Understanding these differences may permit the development of both prognostic and diagnostic biomarkers.

  12. Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

    PubMed Central

    2011-01-01

    Background Pollen development in flowering plants requires strict control of the gene expression program and genetic information stability by mechanisms possibly including the miRNA pathway. However, our understanding of the miRNA pathway in pollen development remains limited, and the dynamic profile of miRNAs in developing pollen is unknown. Results Using next-generation sequencing technology, we pyrosequenced small RNA populations from rice uninucleate microspores to tricellular pollen and control sporophytic tissues at the genome-wide level. We identified 292 known miRNAs, including members of all 20 families conserved in plants, and 75 novel miRNAs. Of the 292 known miRNAs, 202 were expressed, with 103 enriched, in developing pollen. More than half of these novel miRNAs displayed pollen-or stage-specific expression. Furthermore, analyzing the 367 miRNAs and their predicted targets indicated that correlation in expression profiles of pollen-enriched known miRNAs and their targets significantly differs from that of sporophyte-enriched known miRNAs and their targets in some functional terms, while novel miRNAs appeared to negatively regulate their targets. Importantly, gene ontology abundance analysis demonstrated chromatin assembly and disassembly was important in the targets of bicellular pollen-expressed novel miRNAs. Principal component analysis revealed pollen of all three stages was discriminated from sporophytes, largely because of the novel and non-conserved known miRNAs. Conclusions Our study, for the first time, revealed the differences in composition and expression profiles of miRNAs between developing pollen and sporophytes, with novel and non-conserved known miRNAs the main contributors. Our results suggest the important roles of the miRNA pathway in pollen development. PMID:21679406

  13. 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

    2013-09-04

    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.

  14. Cryptic diversity in Amazonian frogs: Integrative taxonomy of the genus Anomaloglossus (Amphibia: Anura: Aromobatidae) reveals a unique case of diversification within the Guiana Shield.

    PubMed

    Vacher, Jean-Pierre; Kok, Philippe J R; Rodrigues, Miguel T; Lima, Jucivaldo Dias; Lorenzini, Andy; Martinez, Quentin; Fallet, Manon; Courtois, Elodie A; Blanc, Michel; Gaucher, Philippe; Dewynter, Maël; Jairam, Rawien; Ouboter, Paul; Thébaud, Christophe; Fouquet, Antoine

    2017-07-01

    Lack of resolution on species boundaries and distribution can hamper inferences in many fields of biology, notably biogeography and conservation biology. This is particularly true in megadiverse and under-surveyed regions such as Amazonia, where species richness remains vastly underestimated. Integrative approaches using a combination of phenotypic and molecular evidence have proved extremely successful in reducing knowledge gaps in species boundaries, especially in animal groups displaying high levels of cryptic diversity like amphibians. Here we combine molecular data (mitochondrial 16S rRNA and nuclear TYR, POMC, and RAG1) from 522 specimens of Anomaloglossus, a frog genus endemic to the Guiana Shield, including 16 of the 26 nominal species, with morphometrics, bioacoustics, tadpole development mode, and habitat use to evaluate species delineation in two lowlands species groups. Molecular data reveal the existence of 18 major mtDNA lineages among which only six correspond to described species. Combined with other lines of evidence, we confirm the existence of at least 12 Anomaloglossus species in the Guiana Shield lowlands. Anomaloglossus appears to be the only amphibian genus to have largely diversified within the eastern part of the Guiana Shield. Our results also reveal strikingly different phenotypic evolution among lineages. Within the A. degranvillei group, one subclade displays acoustic and morphological conservatism, while the second subclade displays less molecular divergence but clear phenotypic divergence. In the A. stepheni species group, a complex evolutionary diversification in tadpole development is observed, notably with two closely related lineages each displaying exotrophic and endotrophic tadpoles. Copyright © 2017 Elsevier Inc. All rights reserved.

  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. 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

  17. 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

  18. 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.

  19. Soil-surface genotoxicity of military and urban territories in Lithuania, as revealed by Tradescantia bioassays.

    PubMed

    Cesniene, Tatjana; Kleizaite, Violeta; Ursache, Robertas; Zvingila, Donatas; Radzevicius, Alfredas; Patamsyte, Jolanta; Rancelis, Vytautas

    2010-03-29

    The soil surface is a major natural system that accumulates pollutants and allows researchers to disclose the history and the present state of contamination of an area with toxic pollutants. This conclusion is based on the comparison of genotoxicity of aqueous extracts and DMSO extracts of topsoil from military territories in various locations left behind after the retreat of the Soviet Army from Lithuania, and several sites in the city of Vilnius, characterized by different history and current traffic intensity. The specific character of the soil-surface contamination was shown in a series of Tradescantia micronucleus (Trad-MN) and stamen-hair mutation (Trad-SHM) bioassays and tests. The most effective ones were the Trad-MN and, unexpectedly, the branched-hair tests. A preliminary result of the study is the somaclonal variation of individual Tradescantia plants revealed by the RAPD method of DNA analysis. A comparison of aqueous extracts and DMSO extracts of the soil showed the permanent character of the mobile forms of genotoxic pollutants in the soil surface, despite the fact that several military territories were already closed 20 years ago.

  20. The mechanics of bacterial cluster formation on plant leaf surfaces as revealed by bioreporter technology.

    PubMed

    Tecon, Robin; Leveau, Johan H J

    2012-05-01

    Bacteria that colonize the leaves of terrestrial plants often occur in clusters whose size varies from a few to thousands of cells. For the formation of such bacterial clusters, two non-mutually exclusive but very different mechanisms may be proposed: aggregation of multiple cells or clonal reproduction of a single cell. Here we assessed the contribution of both mechanisms on the leaves of bean plants that were colonized by the bacterium Pantoea agglomerans. In one approach, we used a mixture of green and red fluorescent P. agglomerans cells to populate bean leaves. We observed that this resulted in clusters made up of only one colour as well as two-colour clusters, thus providing evidence for both mechanisms. Another P. agglomerans bioreporter, designed to quantify the reproductive success of bacterial colonizers by proxy to the rate at which green fluorescent protein is diluted from dividing cells, revealed that during the first hours on the leaf surface, many bacteria were dividing, but not staying together and forming clusters, which is suggestive of bacterial relocation. Together, these findings support a dynamic model of leaf surface colonization, where both aggregative and reproductive mechanisms take place. The bioreporter-based approach we employed here should be broadly applicable towards a more quantitative and mechanistic understanding of bacterial colonization of surfaces in general. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  1. Unique genetic responses revealed in RNA-seq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat

    PubMed Central

    Van Goor, Angelica; Ashwell, Chris M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.

    2017-01-01

    Climate change and disease have large negative impacts on poultry production, but little is known about the interactions of responses to these stressors in chickens. Fayoumi (heat and disease resistant) and broiler (heat and disease susceptible) chicken lines were stimulated at 22 days of age, using a 2x2x2 factorial design including: breed (Fayoumi or broiler), inflammatory stimulus (lipopolysaccharide (LPS) or saline), and temperature (35°C or 25°C). Transcriptional changes in spleens were analyzed using RNA-sequencing on the Illumina HiSeq 2500. Thirty-two individual cDNA libraries were sequenced (four per treatment) and an average of 22 million reads were generated per library. Stimulation with LPS induced more differentially expressed genes (DEG, log2 fold change ≥ 2 and FDR ≤ 0.05) in the broiler (N = 283) than the Fayoumi (N = 85), whereas heat treatment resulted in fewer DEG in broiler (N = 22) compared to Fayoumi (N = 107). The double stimulus of LPS+heat induced the largest numbers of changes in gene expression, for which broiler had 567 DEG and Fayoumi had 1471 DEG of which 399 were shared between breeds. Further analysis of DEG revealed pathways impacted by these stressors such as Remodelling of Epithelial Adherens Junctions due to heat stress, Granulocyte Adhesion and Diapedesis due to LPS, and Hepatic Fibrosis/Hepatic Stellate Cell Activation due to LPS+heat. The genes and pathways identified provide deeper understanding of the response to the applied stressors and may serve as biomarkers for genetic selection for heat and disease tolerant chickens. PMID:28166270

  2. 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

  3. Comparative analysis of the secretomes of Schizophyllum commune and other wood-decay basidiomycetes during solid-state fermentation reveals its unique lignocellulose-degrading enzyme system.

    PubMed

    Zhu, Ning; Liu, Jiawen; Yang, Jinshui; Lin, Yujian; Yang, Yi; Ji, Lei; Li, Meng; Yuan, Hongli

    2016-01-01

    The genome of Schizophyllum commune encodes a diverse repertoire of degradative enzymes for plant cell wall breakdown. Recent comparative genomics study suggests that this wood decayer likely has a mode of biodegradation distinct from the well-established white-rot/brown-rot models. However, much about the extracellular enzyme system secreted by S. commune during lignocellulose deconstruction remains unknown and the underlying mechanism is poorly understood. In this study, extracellular proteins of S. commune colonizing Jerusalem artichoke stalk were analyzed and compared with those of two white-rot fungi Phanerochaete chrysosporium and Ceriporiopsis subvermispora and a brown-rot fungus Gloeophyllum trabeum. Under solid-state fermentation (SSF) conditions, S. commune displayed considerably higher levels of hydrolytic enzyme activities in comparison with those of P. chrysosporium, C. subvermispora and G. trabeum. During biodegradation process, this fungus modified the lignin polymer in a way which was consistent with a hydroxyl radical attack, similar to that of G. trabeum. The crude enzyme cocktail derived from S. commune demonstrated superior performance over a commercial enzyme preparation from Trichoderma longibrachiatum in the hydrolysis of pretreated lignocellulosic biomass at low enzyme loadings. Secretomic analysis revealed that compared with three other fungi, this species produced a higher diversity of carbohydrate-degrading enzymes, especially hemicellulases and pectinases acting on polysaccharide backbones and side chains, and a larger set of enzymes potentially supporting the generation of hydroxyl radicals. In addition, multiple non-hydrolytic proteins implicated in enhancing polysaccharide accessibility were identified in the S. commune secretome, including lytic polysaccharide monooxygenases (LPMOs) and expansin-like proteins. Plant lignocellulose degradation by S. commune involves a hydroxyl radical-mediated mechanism for lignocellulose modification

  4. 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

  5. An antisense microwalk reveals critical role of an intronic position linked to a unique long-distance interaction in pre-mRNA splicing

    PubMed Central

    Singh, Natalia N.; Hollinger, Katrin; Bhattacharya, Dhruva; Singh, Ravindra N.

    2010-01-01

    Here we report a novel finding of an antisense oligonucleotide (ASO) microwalk in which we examined the position-specific role of intronic residues downstream from the 5′ splice site (5′ ss) of SMN2 exon 7, skipping of which is associated with spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. Our results revealed the inhibitory role of a cytosine residue at the 10th intronic position (10C), which is neither conserved nor associated with any known splicing motif. Significance of 10C emerged from the splicing pattern of SMN2 exon 7 in presence of a 14-mer ASO (L14) that sequestered two adjacent hnRNP A1 motifs downstream from 10C and yet promoted SMN2 exon 7 skipping. Another 14-mer ASO (F14) that sequestered both, 10C and adjacent hnRNP A1 motifs, led to a strong stimulation of SMN2 exon 7 inclusion. The inhibitory role of 10C was found to be tightly linked to its unpaired status and specific positioning immediately upstream of a RNA:RNA helix formed between the targeting ASO and its intronic target. Employing a heterologous context as well as changed contexts of SMN2 intron 7, we show that the inhibitory effect of unpaired 10C is dependent upon a long-distance interaction involving downstream intronic sequences. Our report furnishes one of the rare examples in which an ASO-based approach could be applied to unravel the critical role of an intronic position that may not belong to a linear motif and yet play significant role through long-distance interactions. PMID:20413618

  6. 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

  7. Genome sequencing reveals unique mutations in characteristic metabolic pathways and the transfer of virulence genes between V. mimicus and V. cholerae.

    PubMed

    Wang, Duochun; Wang, Haiyin; 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.

  8. A unique swim bladder-inner ear connection in a teleost fish revealed by a combined high-resolution microtomographic and three-dimensional histological study

    PubMed Central

    2013-01-01

    Background In most modern bony fishes (teleosts) hearing improvement is often correlated with a close morphological relationship between the swim bladder or other gas-filled cavities and the saccule or more rarely with the utricle. A connection of an accessory hearing structure to the third end organ, the lagena, has not yet been reported. A recent study in the Asian cichlid Etroplus maculatus provided the first evidence that a swim bladder may come close to the lagena. Our study was designed to uncover the swim bladder-inner ear relationship in this species. We used a new approach by applying a combination of two high-resolution techniques, namely microtomographic (microCT) imaging and histological serial semithin sectioning, providing the basis for subsequent three-dimensional reconstructions. Prior to the morphological study, we additionally measured auditory evoked potentials at four frequencies (0.5, 1, 2, 3 kHz) to test the hearing abilities of the fish. Results E. maculatus revealed a complex swim bladder-inner ear connection in which a bipartite swim bladder extension contacts the upper as well as the lower parts of each inner ear, a condition not observed in any other teleost species studied so far. The gas-filled part of the extension is connected to the lagena via a thin bony lamella and is firmly attached to this bony lamella with connective material. The second part of the extension, a pad-like structure, approaches the posterior and horizontal semicircular canals and a recessus located posterior to the utricle. Conclusions Our study is the first detailed report of a link between the swim bladder and the lagena in a teleost species. We suggest that the lagena has an auditory function in this species because the most intimate contact exists between the swim bladder and this end organ. The specialized attachment of the saccule to the cranial bone and the close proximity of the swim bladder extension to the recessus located posterior to the utricle

  9. Unique Ecophysiology among U(VI)-Reducing Bacteria as Revealed by Evaluation of Oxygen Metabolism in Anaeromyxobacter dehalogenans Strain 2CP-C▿ †

    PubMed Central

    Thomas, Sara H.; Sanford, Robert A.; Amos, Benjamin K.; Leigh, Mary Beth; Cardenas, Erick; Löffler, Frank E.

    2010-01-01

    Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter dehalogenans cells increased approximately 5-fold from 2.2 × 107 ± 8.6 × 106 to 1.0 × 108 ± 2.2 × 107 cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3 × 104 ± 1.1 × 104 cells per liter) than sediment-associated cells, suggesting that A. dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [μ = (−0.09 × pO2) + 0.051; R2 = 0.923] was observed between the instantaneous specific growth rate μ and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations

  10. The history of hepatitis C virus (HCV): Basic research reveals unique features in phylogeny, evolution and the viral life cycle with new perspectives for epidemic control.

    PubMed

    Bukh, Jens

    2016-10-01

    The discovery of hepatitis C virus (HCV) in 1989 permitted basic research to unravel critical components of a complex life cycle for this important human pathogen. HCV is a highly divergent group of viruses classified in 7 major genotypes and a great number of subtypes, and circulating in infected individuals as a continuously evolving quasispecies destined to escape host immune responses and applied antivirals. Despite the inability to culture patient viruses directly in the laboratory, efforts to define the infectious genome of HCV resulted in development of experimental recombinant in vivo and in vitro systems, including replicons and infectious cultures in human hepatoma cell lines. And HCV has become a model virus defining new paradigms in virology, immunology and biology. For example, HCV research discovered that a virus could be completely dependent on microRNA for its replication since microRNA-122 is critical for the HCV life cycle. A number of other host molecules critical for HCV entry and replication have been identified. Thus, basic HCV research revealed important molecules for development of host targeting agents (HTA). The identification and characterization of HCV encoded proteins and their functional units contributed to the development of highly effective direct acting antivirals (DAA) against the NS3 protease, NS5A and the NS5B polymerase. In combination, these inhibitors have since 2014 permitted interferon-free therapy with cure rates above 90% among patients with chronic HCV infection; however, viral resistance represents a challenge. Worldwide control of HCV will most likely require the development of a prophylactic vaccine, and numerous candidates have been pursued. Research characterizing features critical for antibody-based virus neutralization and T cell based virus elimination from infected cells is essential for this effort. If the world community promotes an ambitious approach by applying current DAA broadly, continues to develop

  11. 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

  12. 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.

  13. The surface oxidation potential of human neuromelanin reveals a spherical architecture with a pheomelanin core and a eumelanin surface.

    PubMed

    Bush, William D; Garguilo, Jacob; Zucca, Fabio A; Albertini, Alberto; Zecca, Luigi; Edwards, Glenn S; Nemanich, Robert J; Simon, John D

    2006-10-03

    Neuromelanin (NM) isolated from the substantia nigra region of the human brain was studied by scanning probe and photoelectron emission microscopies. Atomic force microscopy reveals that NM granules are comprised of spherical structures with a diameter of approximately 30 nm, similar to that observed for Sepia cuttlefish, bovine eye, and human eye and hair melanosomes. Photoelectron microscopy images were collected at specific wavelengths of UV light between 248 and 413 nm, using the spontaneous-emission output from the Duke OK-4 free electron laser. Analysis of the data establishes a threshold photoionization potential for NM of 4.5 +/- 0.2 eV, which corresponds to an oxidation potential of -0.1 +/- 0.2 V vs. the normal hydrogen electrode (NHE). The oxidation potential of NM is within experimental error of the oxidation potential measured for human eumelanosomes (-0.2 +/- 0.2 V vs. NHE), despite the presence of a significant fraction of the red pigment, pheomelanin, which is characterized by a higher oxidation potential (+0.5 +/- 0.2 V vs. NHE). Published kinetic studies on the early chemical steps of melanogenesis show that in the case of pigments containing a mixture of pheomelanin and eumelanin, of which NM is an example, pheomelanin formation occurs first with eumelanin formation predominantly occurring only after cysteine levels are depleted. Such a kinetic model would predict a structural motif with pheomelanin at the core and eumelanin at the surface, which is consistent with the measured surface oxidation potential of the approximately 30-nm constituents of NM granules.

  14. 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

  15. Hydrogen bonding at the water surface revealed by isotopic dilution spectroscopy.

    PubMed

    Stiopkin, Igor V; Weeraman, Champika; Pieniazek, Piotr A; Shalhout, Fadel Y; Skinner, James L; Benderskii, Alexander V

    2011-06-08

    The air-water interface is perhaps the most common liquid interface. It covers more than 70 per cent of the Earth's surface and strongly affects atmospheric, aerosol and environmental chemistry. The air-water interface has also attracted much interest as a model system that allows rigorous tests of theory, with one fundamental question being just how thin it is. Theoretical studies have suggested a surprisingly short 'healing length' of about 3 ångströms (1 Å = 0.1 nm), with the bulk-phase properties of water recovered within the top few monolayers. However, direct experimental evidence has been elusive owing to the difficulty of depth-profiling the liquid surface on the ångström scale. Most physical, chemical and biological properties of water, such as viscosity, solvation, wetting and the hydrophobic effect, are determined by its hydrogen-bond network. This can be probed by observing the lineshape of the OH-stretch mode, the frequency shift of which is related to the hydrogen-bond strength. Here we report a combined experimental and theoretical study of the air-water interface using surface-selective heterodyne-detected vibrational sum frequency spectroscopy to focus on the 'free OD' transition found only in the topmost water layer. By using deuterated water and isotopic dilution to reveal the vibrational coupling mechanism, we find that the free OD stretch is affected only by intramolecular coupling to the stretching of the other OD group on the same molecule. The other OD stretch frequency indicates the strength of one of the first hydrogen bonds encountered at the surface; this is the donor hydrogen bond of the water molecule straddling the interface, which we find to be only slightly weaker than bulk-phase water hydrogen bonds. We infer from this observation a remarkably fast onset of bulk-phase behaviour on crossing from the air into the water phase.

  16. Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree.

    PubMed

    Kaewkla, Onuma; Franco, Christopher M M

    2011-04-01

    A novel strain, designated EUM 374(T), was isolated from the root of a native Australian eucalyptus tree, Eucalyptus microcarpa, and subjected to a range of morphological, phylogenetic and chemotaxonomic analyses. The strain was Gram-reaction-positive with well-developed aerial mycelia, which fragmented into rod-shaped spores that had unique knobby protrusions on the spore surface. Substrate mycelia were not present in the media used. Strain EUM 374(T) grew as a film on the surface of static liquid culture medium but did not grow under shaking conditions. Phylogenetic evaluation based on 16S rRNA gene sequences identified the new isolate as belonging to the family Pseudonocardiaceae with sequence similarities of 96.1 and 96.3 % to Pseudonocardia acaciae GMKU095(T) and Pseudonocardia spinosispora LM 141(T), respectively, and 93-96 % sequence similarity to other members of the genus Pseudonocardia. The results of comprehensive phylogenetic analyses, including physiological and biochemical tests, differentiated strain EUM 374(T) from related members of the genus Pseudonocardia. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, strain EUM 374(T) represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia eucalypti sp. nov. is proposed. The type strain is EUM 374(T) ( = DSM 45351(T)  = ACM 5285(T)).

  17. Selective Targeting of Neurons with Inorganic Nanoparticles: Revealing the Crucial Role of Nanoparticle Surface Charge.

    PubMed

    Dante, Silvia; Petrelli, Alessia; Petrini, Enrica Maria; Marotta, Roberto; Maccione, Alessandro; Alabastri, Alessandro; Quarta, Alessandra; De Donato, Francesco; Ravasenga, Tiziana; Sathya, Ayyappan; Cingolani, Roberto; Proietti Zaccaria, Remo; Berdondini, Luca; Barberis, Andrea; Pellegrino, Teresa

    2017-07-25

    Nanoparticles (NPs) are increasingly used in biomedical applications, but the factors that influence their interactions with living cells need to be elucidated. Here, we reveal the role of NP surface charge in determining their neuronal interactions and electrical responses. We discovered that negatively charged NPs administered at low concentration (10 nM) interact with the neuronal membrane and at the synaptic cleft, whereas positively and neutrally charged NPs never localize on neurons. This effect is shape and material independent. The presence of negatively charged NPs on neuronal cell membranes influences the excitability of neurons by causing an increase in the amplitude and frequency of spontaneous postsynaptic currents at the single cell level and an increase of both the spiking activity and synchronous firing at neural network level. The negatively charged NPs exclusively bind to excitable neuronal cells, and never to nonexcitable glial cells. This specific interaction was also confirmed by manipulating the electrophysiological activity of neuronal cells. Indeed, the interaction of negatively charged NPs with neurons is either promoted or hindered by pharmacological suppression or enhancement of the neuronal activity with tetrodotoxin or bicuculline, respectively. We further support our main experimental conclusions by using numerical simulations. This study demonstrates that negatively charged NPs modulate the excitability of neurons, revealing the potential use of NPs for controlling neuron activity.

  18. 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.

  19. Surface N-glycoproteome patterns reveal key proteins of neuronal differentiation.

    PubMed

    Tyleckova, Jirina; Valekova, Ivona; Zizkova, Martina; Rakocyova, Michaela; Marsala, Silvia; Marsala, Martin; Gadher, Suresh Jivan; Kovarova, Hana

    2016-01-30

    Pluripotent stem cell-derived committed neural precursors are an important source of cells to treat neurodegenerative diseases including spinal cord injury. There remains an urgency to identify markers for monitoring of neural progenitor specificity, estimation of neural fate and follow-up correlation with therapeutic effect in preclinical studies using animal disease models. Cell surface capture technology was used to uncover the cell surface exposed N-glycoproteome of neural precursor cells upon neuronal differentiation as well as post-mitotic mature hNT neurons. The data presented depict an extensive study of surfaceome during neuronal differentiation, confirming glycosylation at a particular predicted site of many of the identified proteins. Quantitative changes detected in cell surface protein levels reveal a set of proteins that highlight the complexity of the neuronal differentiation process. Several of these proteins including the cell adhesion molecules ICAM1, CHL1, and astrotactin1 as well as LAMP1 were validated by SRM. Combination of immunofluorescence staining of ICAM1 and flow cytometry indicated a possible direction for future scrutiny of such proteins as targets for enrichment of the neuronal subpopulation from mixed cultures after differentiation of neural precursor cells. These surface proteins hold an important key for development of safe strategies in cell-replacement therapies of neuronal disorders. Neural stem and/or precursor cells have a great potential for cell-replacement therapies of neuronal diseases. Availability of well characterised and expandable neural cell lineage specific populations is critical for addressing such a challenge. In our study we identified and relatively quantified several hundred surface N-glycoproteins in the course of neuronal differentiation. We further confirmed the abundant changes for several cell adhesion proteins by SRM and outlined a strategy for utilisation of such N-glycoproteins in antibody based cell

  20. Ocean Processes Revealing by Seasonal Dynamics of Surface Chlorophyll Concentration (by Satellite Data)

    NASA Astrophysics Data System (ADS)

    Shevyrnogov, Anatoly; Vysotskaya, Galina

    Continuous monitoring of phytopigment concentrations in the ocean by space-borne methods makes possible to estimate ecological condition of biocenoses in critical areas. Unlike land vege-tation, hydrological processes largely determine phytoplankton dynamics, which may be either recurrent or random. The types of chlorophyll concentration dynamics can manifest as zones quasistationary by seasonal chlorophyll dynamics, perennial variations of phytopigment con-centrations, anomalous variations, etc., that makes possible revealing of hydrological structure of the ocean. While large-scale and frequently occurring phenomena have been much studied, the seldom-occurring changes of small size may be of interest for analysis of long-term processes and rare natural variations. Along with this, the ability to reflect consequences of anthropoge-nous impact or natural ecological disasters on the ocean biota makes the anomalous variations ecologically essential. Civilization aspiring for steady development and preservation of the bio-sphere, must have the knowledge of spatial distribution, seasonal dynamics and anomalies of the primary production process on the planet. In the papers of the authors (Shevyrnogov A.P., Vysotskaya G.S., Gitelzon J.I. Quasistationary areas of chlorophyll concentration in the world ocean as observed satellite data. Adv. Space Res. Vol. 18, No. 7, pp. 129-132, 1996) existence of zones, which are quasi-stationary with similar seasonal dynamics of chlorophyll concentration at surface layer of ocean, was shown. Results were obtained on the base of pro-cessing of time series of satellite images SeaWiFS. It was shown that fronts and frontal zones coincide with dividing lines between quasi-stationary areas, especially in areas of large oceanic streams. Biota of surface oceanic layer is more stable in comparison with quickly changing sur-face temperature. It gives a possibility to circumvent influence of high-frequency component (for example, a diurnal cycle

  1. 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

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

    PubMed Central

    Kanai, Ryuta; Kar, Kalipada; Anthony, Karen; Gould, L. Hannah; Ledizet, Michel; Fikrig, Erol; Marasco, Wayne A.; Koski, Raymond A.; Modis, Yorgo

    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. PMID:16943291

  4. The genomic sequence analysis of the left and right species-specific terminal region of a cowpox virus strain reveals unique sequences and a cluster of intact ORFs for immunomodulatory and host range proteins.

    PubMed

    Shchelkunov, S N; Safronov, P F; Totmenin, A V; Petrov, N A; Ryazankina, O I; Gutorov, V V; Kotwal, G J

    1998-04-10

    Sequencing and computer analysis of the left (52,283 bp) and right (49,649 bp) variable DNA regions of the cowpox virus strain GRI-90 (CPV-GRI) has revealed 51 and 37 potential open reading frames (ORFs), respectively. Comparison of the structure-function organization of these DNA regions of CPV-GRI with those previously published for corresponding regions of genomes of vaccinia virus, strains Copenhagen (VAC-COP) and Western Reserve (VAC-WR); and variola major virus, strains India-1967 (VAR-IND), Bangladesh-1975 (VAR-BSH); and alastrim variola minor virus, strain Garcia-1966 (VAR-GAR), was performed. Within the left terminal region under study, an extended DNA sequence (14,171 bp), unique to CPV, has been found. Within the right region of the CPV-GRI genome two segments, which are unique to CPV DNA (1579 and 3585 bp) have been found. Numerous differences have been revealed in the genetic structure of CPV-GRI DNA regions, homologous to fragments of the genomes of the above-mentioned orthopoxvirus strains. A cluster of ORFs with structural similarity ot immunomodulatory and host range function of other poxviruses have also been detected. A comparison of the sequences of ORF B, crmA, crmB, crmC, IMP, and CHO hr genes of CPV Brighton strain (CPV-BRI) with the corresponding genes in strain GRI-90 have revealed an identity at the amino acid level ranging from 82 to 96% between the two strains. The findings are significant in light of the recent demonstration of CPV as an important poxvirus model system to probe the precise in vivo role(s) of the unique virally encoded immunomodulatory proteins. Also, the presence of a complete and intact repertoire of immunomodulatory proteins, ring canal proteins family, and host range genes indicates that CPV may have been the most ancient of all studied orthopoxviruses.

  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

    2015-07-08

    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.

  7. Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein.

    PubMed

    Horejs, Christine; Ristl, Robin; Tscheliessnig, Rupert; Sleytr, Uwe B; Pum, Dietmar

    2011-08-05

    Surface layers (S-layers) represent an almost universal feature of archaeal cell envelopes and are probably the most abundant bacterial cell proteins. S-layers are monomolecular crystalline structures of single protein or glycoprotein monomers that completely cover the cell surface during all stages of the cell growth cycle, thereby performing their intrinsic function under a constant intra- and intermolecular mechanical stress. In gram-positive bacteria, the individual S-layer proteins are anchored by a specific binding mechanism to polysaccharides (secondary cell wall polymers) that are linked to the underlying peptidoglycan layer. In this work, atomic force microscopy-based single-molecule force spectroscopy and a polyprotein approach are used to study the individual mechanical unfolding pathways of an S-layer protein. We uncover complex unfolding pathways involving the consecutive unfolding of structural intermediates, where a mechanical stability of 87 pN is revealed. Different initial extensibilities allow the hypothesis that S-layer proteins adapt highly stable, mechanically resilient conformations that are not extensible under the presence of a pulling force. Interestingly, a change of the unfolding pathway is observed when individual S-layer proteins interact with secondary cell wall polymers, which is a direct signature of a conformational change induced by the ligand. Moreover, the mechanical stability increases up to 110 pN. This work demonstrates that single-molecule force spectroscopy offers a powerful tool to detect subtle changes in the structure of an individual protein upon binding of a ligand and constitutes the first conformational study of surface layer proteins at the single-molecule level.

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

    PubMed

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

    2015-10-19

    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. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  9. 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.

  10. Spontaneous mutation reveals influence of exopolysaccharide on Lactobacillus johnsonii surface characteristics.

    PubMed

    Horn, Nikki; Wegmann, Udo; Dertli, Enes; Mulholland, Francis; Collins, Samuel R A; Waldron, Keith W; Bongaerts, Roy J; Mayer, Melinda J; Narbad, Arjan

    2013-01-01

    As a competitive exclusion agent, Lactobacillus johnsonii FI9785 has been shown to prevent the colonization of selected pathogenic bacteria from the chicken gastrointestinal tract. During growth of the bacterium a rare but consistent emergence of an altered phenotype was noted, generating smooth colonies in contrast to the wild type rough form. A smooth colony variant was isolated and two-dimensional gel analysis of both strains revealed a protein spot with different migration properties in the two phenotypes. The spot in both gels was identified as a putative tyrosine kinase (EpsC), associated with a predicted exopolysaccharide gene cluster. Sequencing of the epsC gene from the smooth mutant revealed a single substitution (G to A) in the coding strand, resulting in the amino acid change D88N in the corresponding gene product. A native plasmid of L. johnsonii was engineered to produce a novel vector for constitutive expression and this was used to demonstrate that expression of the wild type epsC gene in the smooth mutant produced a reversion to the rough colony phenotype. Both the mutant and epsC complemented strains had increased levels of exopolysaccharides compared to the wild type strain, indicating that the rough phenotype is not solely associated with the quantity of exopolysaccharide. Another gene in the cluster, epsE, that encoded a putative undecaprenyl-phosphate galactosephosphotransferase, was deleted in order to investigate its role in exopolysaccharide biosynthesis. The ΔepsE strain exhibited a large increase in cell aggregation and a reduction in exopolysaccharide content, while plasmid complementation of epsE restored the wild type phenotype. Flow cytometry showed that the wild type and derivative strains exhibited clear differences in their adhesive ability to HT29 monolayers in tissue culture, demonstrating an impact of EPS on surface properties and bacteria-host interactions.

  11. Synthesis of Unique Flowerlike Bi2 O2 (OH)(NO3 ) Hierarchical Microstructures with High Surface Area and Superior Photocatalytic Performance.

    PubMed

    Han, Qiaofeng; Pang, Jiawei; Wang, Xin; Wu, Xiaodong; Zhu, Junwu

    2017-03-17

    Unique flowerlike Bi2 O2 (OH)(NO3 ) (denoted as BION) hierarchical microstructures assembled by ultrathin nanosheets were hydrothermally synthesized from incomplete hydrolysis of anhydrous bismuth nitrate (Bi(NO3 )3 ) after adsorption of glacial acetic acid (HAc). The structure, composition, and optical properties of the products were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), UV/Vis spectroscopy, etc. The as-prepared flowerlike BION possessed an ultra-high surface area and thus exhibited exceptional photocatalytic activity for rhodamine B (RhB) degradation under UV light irradiation with an efficiency of about 17; 6 and 2.5 times higher than spherical, aggregated sheet-like BION and P25 TiO2 , respectively, and also superior to the reported sheet-like BION. It also showed good photocatalytic activity for crystal violet (CV) degradation. This work opens new routes for the rational design and synthesis of nontoxic basic bismuth nitrates with a facile synthetic approach, controllable morphology, and excellent photoreactivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed

    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

    2015-09-22

    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.

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

    SciTech Connect

    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 cuboctahedra 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.

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

    DOE PAGES

    Zhang, Jiawei; Winget, Sarah A.; Wu, Yiren; ...

    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. Revealing the connectivity of groundwater and surface water using electromagnetic induction measurements

    NASA Astrophysics Data System (ADS)

    Binley, A. M.; McLachlan, P.; Chambers, J. E.; Uhlemann, S.

    2016-12-01

    It is now widely recognised that hydrological and biogeochemical processes that occur at the interface of groundwater (GW) and surface water (SW) can have a significant impact on catchment water quality and ecosystem health. Significant heterogeneity in the fabric of the subsurface at the GW-SW interface can lead to complex fluid flow pathways, both of which can exert a strong control on biogeochemical cycling. Revealing such heterogeneity remains a challenge because of the limitations of traditional field experimental processes. Such traditional techniques are often invasive, which often prevents their use in ecologically sensitive environments. Furthermore, they are often limited to localised characterisation. Studies to date have thus focussed on relatively small (easily accessible) stream environments, at short reach, or plot, scales. There is a clear demand for techniques that can capture the heterogeneity of sediments and pore fluids over larger scales. Geophysical methods may offer valuable information at such scales, particularly when used in combination with traditional sampling approaches. The value of electrical methods for revealing detailed information about the heterogeneity of sediments at the GW-SW interface has been demonstrated, and in a few studies such methods have assisted tracer tests in mapping the solute pathways. However, most investigations have been confined to relatively small scale (tens of metres). There is growing (and renewed) interest in the use of frequency domain electromagnetic induction (EMI) techniques in hydrogeophysics. At the GW-SW interface these methods allow rapid, non-invasive exploration of the top few metres. Relatively recent technological developments have provided multi-coil instrumentation, permitting rapid assessment of electrical conductivity at multiple depths of investigation. Here, we demonstrate the effectiveness of EMI for revealing the heterogeneity of sediments and flow pathways at the GW-SW interface. We

  16. Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery

    PubMed Central

    Itoh, Takafumi; Hibi, Takao; Suzuki, Fumiko; Sugimoto, Ikumi; Fujiwara, Akihiro; Inaka, Koji; Tanaka, Hiroaki; Ohta, Kazunori; Fujii, Yutaka; Taketo, Akira; Kimoto, Hisashi

    2016-01-01

    The Gram-positive bacterium Paenibacillus sp. str. FPU-7 effectively hydrolyzes chitin by using a number of chitinases. A unique chitinase with two catalytic domains, ChiW, is expressed on the cell surface of this bacterium and has high activity towards various chitins, even crystalline chitin. Here, the crystal structure of ChiW at 2.1 Å resolution is presented and describes how the enzyme degrades chitin on the bacterial cell surface. The crystal structure revealed a unique multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed β-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st β/α-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd β/α-barrel catalytic domain (GH-18). The structure of the CBM-54, flexibly linked to the catalytic region of ChiW, is described here for the first time. It is similar to those of carbohydrate lyases but displayed no detectable carbohydrate degradation activities. The CBM-54 of ChiW bound to cell wall polysaccharides, such as chin, chitosan, β-1,3-glucan, xylan and cellulose. The structural and biochemical data obtained here also indicated that the enzyme has deep and short active site clefts with endo-acting character. The affinity of CBM-54 towards cell wall polysaccharides and the degradation pattern of the catalytic domains may help to efficiently decompose the cell wall chitin through the contact surface. Furthermore, we clarify that other Gram-positive bacteria possess similar cell-surface-expressed multi-modular enzymes for cell wall polysaccharide degradation. PMID:27907169

  17. Gross morphological features of the organ surface primo-vascular system revealed by hemacolor staining.

    PubMed

    Lim, Chae Jeong; Yoo, Jong-Hyun; Kim, Yongbaek; Lee, So Yeong; Ryu, Pan Dong

    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  μ m) with a remarkably low cellularity within PNs and PVs and several lines of ductules (3-5  μ m) filled with single cells or granules (~1  μ m) 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  μ m). 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.

  18. 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.

  19. 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

  20. 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.

  1. In Vitro Characterization of Thermostable CAM Rubisco Activase Reveals a Rubisco Interacting Surface Loop1[OPEN

    PubMed Central

    Shivhare, Devendra

    2017-01-01

    To maintain metabolic flux through the Calvin-Benson-Bassham cycle in higher plants, dead-end inhibited complexes of Rubisco must constantly be engaged and remodeled by the molecular chaperone Rubisco activase (Rca). In C3 plants, the thermolability of Rca is responsible for the deactivation of Rubisco and reduction of photosynthesis at moderately elevated temperatures. We reasoned that crassulacean acid metabolism (CAM) plants must possess thermostable Rca to support Calvin-Benson-Bassham cycle flux during the day when stomata are closed. A comparative biochemical characterization of rice (Oryza sativa) and Agave tequilana Rca isoforms demonstrated that the CAM Rca isoforms are approximately10°C more thermostable than the C3 isoforms. Agave Rca also possessed a much higher in vitro biochemical activity, even at low assay temperatures. Mixtures of rice and agave Rca form functional hetero-oligomers in vitro, but only the rice isoforms denature at nonpermissive temperatures. The high thermostability and activity of agave Rca mapped to the N-terminal 244 residues. A Glu-217-Gln amino acid substitution was found to confer high Rca activity to rice Rca. Further mutational analysis suggested that Glu-217 restricts the flexibility of the α4-β4 surface loop that interacts with Rubisco via Lys-216. CAM plants thus promise to be a source of highly functional, thermostable Rca candidates for thermal fortification of crop photosynthesis. Careful characterization of their properties will likely reveal further protein-protein interaction motifs to enrich our mechanistic model of Rca function. PMID:28546437

  2. Chemical states of surface oxygen during CO oxidation on Pt(110) surface revealed by ambient pressure XPS.

    PubMed

    Yu, Youngseok; Koh, Yoobin Esther; Lim, Hojoon; Jeong, Beomgyun; Isegawa, Kazuhisa; Kim, Dae Hyun; Ueda, Kohei; Kondoh, Hiroshi; Mase, Kazuhiko; Crumlin, Ethan; Ross, Philip N; Gallet, Jean-Jacques; Bournel, Fabrice; Mun, Bongjin Simon

    2017-08-25

    The study of CO oxidation on Pt(110) surface is revisited using ambient pressure x-ray photoemission spectroscopy. When the surface temperature reaches the activation temperature for CO oxidation under elevated pressure condition, both the -phase of PtO2 oxide and chemisorbed oxygen are formed simultaneously on the surface. Due to exothermic nature of CO oxidation, the temperature of Pt surface increases as CO oxidation takes places. As the CO/O2 ratio increases, the production of CO2 increases continuously and the surface temperature also increases. Interestingly, during the mass transfer limiting regions, the amount of surface oxide changes little while the chemisorbed oxygen is being reduced. . © 2017 IOP Publishing Ltd.

  3. In Vitro Characterization of Thermostable CAM Rubisco Activase Reveals a Rubisco Interacting Surface Loop.

    PubMed

    Shivhare, Devendra; Mueller-Cajar, Oliver

    2017-07-01

    To maintain metabolic flux through the Calvin-Benson-Bassham cycle in higher plants, dead-end inhibited complexes of Rubisco must constantly be engaged and remodeled by the molecular chaperone Rubisco activase (Rca). In C3 plants, the thermolability of Rca is responsible for the deactivation of Rubisco and reduction of photosynthesis at moderately elevated temperatures. We reasoned that crassulacean acid metabolism (CAM) plants must possess thermostable Rca to support Calvin-Benson-Bassham cycle flux during the day when stomata are closed. A comparative biochemical characterization of rice (Oryza sativa) and Agave tequilana Rca isoforms demonstrated that the CAM Rca isoforms are approximately10°C more thermostable than the C3 isoforms. Agave Rca also possessed a much higher in vitro biochemical activity, even at low assay temperatures. Mixtures of rice and agave Rca form functional hetero-oligomers in vitro, but only the rice isoforms denature at nonpermissive temperatures. The high thermostability and activity of agave Rca mapped to the N-terminal 244 residues. A Glu-217-Gln amino acid substitution was found to confer high Rca activity to rice Rca Further mutational analysis suggested that Glu-217 restricts the flexibility of the α4-β4 surface loop that interacts with Rubisco via Lys-216. CAM plants thus promise to be a source of highly functional, thermostable Rca candidates for thermal fortification of crop photosynthesis. Careful characterization of their properties will likely reveal further protein-protein interaction motifs to enrich our mechanistic model of Rca function. © 2017 American Society of Plant Biologists. All Rights Reserved.

  4. 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

  5. Polymer surface functionalities that control human embryoid body cell adhesion revealed by high throughput surface characterization of combinatorial material microarrays.

    PubMed

    Yang, Jing; Mei, Ying; Hook, Andrew L; Taylor, Michael; Urquhart, Andrew J; Bogatyrev, Said R; Langer, Robert; Anderson, Daniel G; Davies, Martyn C; Alexander, Morgan R

    2010-12-01

    High throughput materials discovery using combinatorial polymer microarrays to screen for new biomaterials with new and improved function is established as a powerful strategy. Here we combine this screening approach with high throughput surface characterization (HT-SC) to identify surface structure-function relationships. We explore how this combination can help to identify surface chemical moieties that control protein adsorption and subsequent cellular response. The adhesion of human embryoid body (hEB) cells to a large number (496) of different acrylate polymers synthesized in a microarray format is screened using a high throughput procedure. To determine the role of the polymer surface properties on hEB cell adhesion, detailed HT-SC of these acrylate polymers is carried out using time of flight secondary ion mass spectrometry (ToF SIMS), X-ray photoelectron spectroscopy (XPS), pico litre drop sessile water contact angle (WCA) measurement and atomic force microscopy (AFM). A structure-function relationship is identified between the ToF SIMS analysis of the surface chemistry after a fibronectin (Fn) pre-conditioning step and the cell adhesion to each spot using the multivariate analysis technique partial least squares (PLS) regression. Secondary ions indicative of the adsorbed Fn correlate with increased cell adhesion whereas glycol and other functionalities from the polymers are identified that reduce cell adhesion. Furthermore, a strong relationship between the ToF SIMS spectra of bare polymers and the cell adhesion to each spot is identified using PLS regression. This identifies a role for both the surface chemistry of the bare polymer and the pre-adsorbed Fn, as-represented in the ToF SIMS spectra, in controlling cellular adhesion. In contrast, no relationship is found between cell adhesion and wettability, surface roughness, elemental or functional surface composition. The correlation between ToF SIMS data of the surfaces and the cell adhesion demonstrates

  6. 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

    2015-10-06

    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.

  7. 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.

  8. Universal deformation of soft substrates near contact line reveals solid surface stresses

    NASA Astrophysics Data System (ADS)

    Style, Robert; Wettlaufer, John; Wilen, Larry; Dufresne, Eric

    2012-11-01

    We study how sessile droplets behave on soft substrates. Using confocal microscopy, we investigate how droplet surface tension (and Laplace pressure) deforms the substrate. We show that the near-tip shape of the wetting ridge is entirely determined by the surface tensions of the three contacting phases. In particular we can use this observation to (i) directly measure solid-vapour and solid-liquid surface tensions, (ii) resolve how out-of-plane force balance is ensured at the contact line.

  9. Nanochemistry at the atomic scale revealed in hydrogen-induced semiconductor surface metallization

    NASA Astrophysics Data System (ADS)

    Derycke, Vincent; Soukiassian, Patrick G.; Amy, Fabrice; Chabal, Yves J.; D'Angelo, Marie D.; Enriquez, Hanna B.; Silly, Mathieu G.

    2003-04-01

    Passivation of semiconductor surfaces against chemical attack can be achieved by terminating the surface-dangling bonds with a monovalent atom such as hydrogen. Such passivation invariably leads to the removal of all surface states in the bandgap, and thus to the termination of non-metallic surfaces. Here we report the first observation of semiconductor surface metallization induced by atomic hydrogen. This result, established by using photo-electron and photo-absorption spectroscopies and scanning tunnelling techniques, is achieved on a Si-terminated cubic silicon carbide (SiC) surface. It results from competition between hydrogen termination of surface-dangling bonds and hydrogen-generated steric hindrance below the surface. Understanding the ingredient for hydrogen-stabilized metallization directly impacts the ability to eliminate electronic defects at semiconductor interfaces critical for microelectronics, provides a means to develop electrical contacts on high-bandgap chemically passive materials, particularly for interfacing with biological systems, and gives control of surfaces for lubrication, for example of nanomechanical devices.

  10. Nanochemistry at the atomic scale revealed in hydrogen-induced semiconductor surface metallization.

    PubMed

    Derycke, Vincent; Soukiassian, Patrick G; Amy, Fabrice; Chabal, Yves J; D'angelo, Marie D; Enriquez, Hanna B; Silly, Mathieu G

    2003-04-01

    Passivation of semiconductor surfaces against chemical attack can be achieved by terminating the surface-dangling bonds with a monovalent atom such as hydrogen. Such passivation invariably leads to the removal of all surface states in the bandgap, and thus to the termination of non-metallic surfaces. Here we report the first observation of semiconductor surface metallization induced by atomic hydrogen. This result, established by using photo-electron and photo-absorption spectroscopies and scanning tunnelling techniques, is achieved on a Si-terminated cubic silicon carbide (SiC) surface. It results from competition between hydrogen termination of surface-dangling bonds and hydrogen-generated steric hindrance below the surface. Understanding the ingredient for hydrogen-stabilized metallization directly impacts the ability to eliminate electronic defects at semiconductor interfaces critical for microelectronics, provides a means to develop electrical contacts on high-bandgap chemically passive materials, particularly for interfacing with biological systems, and gives control of surfaces for lubrication, for example of nanomechanical devices.

  11. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation

    PubMed Central

    Miller, Mitchell D.; Aravind, L.; Bakolitsa, Constantina; Rife, Christopher L.; Carlton, Dennis; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation. PMID:20944207

  12. Short-Range Catalyst-Surface Interactions Revealed by Heterodyne Two-Dimensional Sum Frequency Generation Spectroscopy.

    PubMed

    Wang, Jiaxi; Clark, Melissa L; Li, Yingmin; Kaslan, Camille L; Kubiak, Clifford P; Xiong, Wei

    2015-11-05

    Heterodyne 2D sum frequency generation spectroscopy is used to study a model CO2 reduction catalyst, Re(diCN-bpy) (CO)3Cl, as a monolayer on a gold surface. We show that short-range interactions with the surface can cause substantial line-shape differences between vibrational bands from the same molecules. We explain this interaction as the result of couplings between CO vibrational modes of the catalyst molecules and the image dipoles on gold surface, which are sensitive to the relative distance between the molecule and the surface. Thus, by analysis of HD 2D SFG line-shape differences and polarization dependences of IR spectra, we can unambiguously determine the ensemble-averaged orientation of the molecules on the surface. The high sensitivity of HD 2D SFG spectra to short-range interactions can be applied to many other adsorbate-substrate interactions and therefore can serve as a unique tool to determine adsorbate orientations on surfaces.

  13. Using principal component analysis to capture individual differences within a unified neuropsychological model of chronic post-stroke aphasia: Revealing the unique neural correlates of speech fluency, phonology and semantics.

    PubMed

    Halai, Ajay D; Woollams, Anna M; Lambon Ralph, Matthew A

    2017-01-01

    Individual differences in the performance profiles of neuropsychologically-impaired patients are pervasive yet there is still no resolution on the best way to model and account for the variation in their behavioural impairments and the associated neural correlates. To date, researchers have generally taken one of three different approaches: a single-case study methodology in which each case is considered separately; a case-series design in which all individual patients from a small coherent group are examined and directly compared; or, group studies, in which a sample of cases are investigated as one group with the assumption that they are drawn from a homogenous category and that performance differences are of no interest. In recent research, we have developed a complementary alternative through the use of principal component analysis (PCA) of individual data from large patient cohorts. This data-driven approach not only generates a single unified model for the group as a whole (expressed in terms of the emergent principal components) but is also able to capture the individual differences between patients (in terms of their relative positions along the principal behavioural axes). We demonstrate the use of this approach by considering speech fluency, phonology and semantics in aphasia diagnosis and classification, as well as their unique neural correlates. PCA of the behavioural data from 31 patients with chronic post-stroke aphasia resulted in four statistically-independent behavioural components reflecting phonological, semantic, executive-cognitive and fluency abilities. Even after accounting for lesion volume, entering the four behavioural components simultaneously into a voxel-based correlational methodology (VBCM) analysis revealed that speech fluency (speech quanta) was uniquely correlated with left motor cortex and underlying white matter (including the anterior section of the arcuate fasciculus and the frontal aslant tract), phonological skills with

  14. 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.

  15. 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.

  16. Anatase (101)-like Structural Model Revealed for Metastable Rutile TiO2(011) Surface.

    PubMed

    Xu, Meiling; Shao, Sen; Gao, Bo; Lv, Jian; Li, Quan; Wang, Yanchao; Wang, Hui; Zhang, Lijun; Ma, Yanming

    2017-03-08

    Titanium dioxide has been widely used as an efficient transition metal oxide photocatalyst. However, its photocatalytic activity is limited to the ultraviolet spectrum range due to the large bandgap beyond 3 eV. Efforts to reduce the bandgap to achieve a broader spectrum range of light absorption have been successfully attempted via the experimental synthesis of dopant-free metastable surface structures of rutile-type TiO2 (011) 2 × 1. This new surface phase possesses a reduced bandgap of ∼2.1 eV, showing great potential for an excellent photocatalyst covering a wide range of visible light. There is a need to establish the atomistic structure of this metastable surface to understand the physical cause for the bandgap reduction and to improve the future design of photocatalysts. Here, we report computational investigations in an effort to unravel this surface structure via swarm structure-searching simulations. The established structure adopts the anatase (101)-like structure model, where the topmost 2-fold O atoms form a quasi-hexagonal surface pattern and bond with the unsaturated 5-fold and 4-fold Ti atoms in the next layer. The predicted anatase (101)-like surface model can naturally explain the experimental observation of the STM images, the electronic bandgap, and the oxidation state of Ti(4+). Dangling bonds on the anatase (101)-like surface are abundant making it a superior photocatalyst. First-principles molecular dynamics simulations have supported the high photocatalytic activity by showing that water and formic acid molecules dissociate spontaneously on the anatase (101)-like surface.

  17. Cell Surface Properties of Lactococcus lactis Reveal Milk Protein Binding Specifically Evolved in Dairy Isolates.

    PubMed

    Tarazanova, Mariya; Huppertz, Thom; Beerthuyzen, Marke; van Schalkwijk, Saskia; Janssen, Patrick; Wels, Michiel; Kok, Jan; Bachmann, Herwig

    2017-01-01

    Surface properties of bacteria are determined by the molecular composition of the cell wall and they are important for interactions of cells with their environment. Well-known examples of bacterial interactions with surfaces are biofilm formation and the fermentation of solid materials like food and feed. Lactococcus lactis is broadly used for the fermentation of cheese and buttermilk and it is primarily isolated from either plant material or the dairy environment. In this study, we characterized surface hydrophobicity, charge, emulsification properties, and the attachment to milk proteins of 55 L. lactis strains in stationary and exponential growth phases. The attachment to milk protein was assessed through a newly developed flow cytometry-based protocol. Besides finding a high degree of biodiversity, phenotype-genotype matching allowed the identification of candidate genes involved in the modification of the cell surface. Overexpression and gene deletion analysis allowed to verify the predictions for three identified proteins that altered surface hydrophobicity and attachment of milk proteins. The data also showed that lactococci isolated from a dairy environment bind higher amounts of milk proteins when compared to plant isolates. It remains to be determined whether the alteration of surface properties also has potential to alter starter culture functionalities.

  18. 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.

  19. Internal structure of normal maize starch granules revealed by chemical surface gelatinization.

    PubMed

    Pan, D D; Jane, J I

    2000-01-01

    Normal maize starch was fractionated into two sizes: large granules with diameters more than 5 microns and small granules with diameters less than 5 microns. The large granules were surface gelatinized by treating them with an aqueous LiCl solution (13 M) at 22-23 degrees C. Surface-gelatinized remaining granules were obtained by mechanical blending, and gelatinized surface starch was obtained by grinding with a mortar and a pestle. Starches of different granular sizes and radial locations, obtained after different degrees of surface gelatinization, were subjected to scanning electron microscopy, iodine potentiometric titration, gel-permeation chromatography, and amylopectin branch chain length analysis. Results showed that the remaining granules had a rough surface with a lamella structure. Amylose was more concentrated at the periphery than at the core of the granule. Amylopectin had longer long B-chains at the core than at the periphery of the granule. Greater proportions of the long B-chains were present at the core than at the periphery of the granule.

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

    PubMed

    Pottier, B; Frétigny, C; Talini, L

    2015-06-05

    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.

  1. Internal structure and physicochemical properties of corn starches as revealed by chemical surface gelatinization.

    PubMed

    Kuakpetoon, Daris; Wang, Ya-Jane

    2007-11-05

    The organization of amylose and amylopectin within starch granules is still not well elucidated. This study investigates the radial distribution of amylose and amylopectin in different corn starches varying in amylose content (waxy corn starch (WC), common corn starch (CC), and 50% and 70% amylose corn starches (AMC)). Corn starches were surface gelatinized by 13 M LiCl at room temperature to different extents (approximately 10%, 20%, 30%, and 40%). The gelatinized surface starch and remaining granules were characterized for amylose content, amylopectin chain-length distribution, thermal properties, swelling power (SP), and water solubility index (WSI). Except for the outmost 10% layer, the amylose content in CC increased slightly with increasing surface removal. In contrast, amylose was more concentrated at the periphery than at the core for 50% and 70% AMC. The proportion of amylopectin A chains generally decreased while that of B1 chains generally increased with increasing surface removal for all corn starches. The gelatinization enthalpy usually decreased, except for 70% AMC, whereas the retrogradation enthalpy relatively remained unchanged for CC but increased for WC, 50% and 70% AMC with increasing surface removal. The SP and WSI increased with increasing surface removal for all corn starches, with WC showing a significant increase in SP after the removal of the outmost 10% layer. The results of this study indicated that there were similarities and differences in the distribution of amylose and amylopectin chains along the radial location of corn starch granules with varying amylose contents. More amylose-lipid complex and amylopectin long chains were present at the periphery than at the core for amylose-containing corn starches.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. NMR reveals the surface functionalisation of Ti3C2 MXene.

    PubMed

    Hope, Michael A; Forse, Alexander C; Griffith, Kent J; Lukatskaya, Maria R; Ghidiu, Michael; Gogotsi, Yury; Grey, Clare P

    2016-02-21

    (1)H and (19)F NMR experiments have identified and quantified the internal surface terminations of Ti3C2Tx MXene. -F and -OH terminations are shown to be intimately mixed and there are found to be significantly fewer -OH terminations than -F and -O, with the proportions highly dependent on the synthesis method.

  7. Giant Rashba effect at the topological surface of PrGe revealing antiferromagnetic spintronics.

    PubMed

    Banik, Soma; Das, Pranab Kumar; Bendounan, Azzedine; Vobornik, Ivana; Arya, A; Beaulieu, Nathan; Fujii, Jun; Thamizhavel, A; Sastry, P U; Sinha, A K; Phase, D M; Deb, S K

    2017-06-23

    Rashba spin-orbit splitting in the magnetic materials opens up a new perspective in the field of spintronics. Here, we report a giant Rashba spin-orbit splitting on the PrGe [010] surface in the paramagnetic phase with Rashba coefficient α R  = 5 eVÅ. We find that α R can be tuned in this system as a function of temperature at different magnetic phases. Rashba type spin polarized surface states originates due to the strong hybridization between Pr 4f states with the conduction electrons. Significant changes observed in the spin polarized surface states across the magnetic transitions are due to the competition between Dzyaloshinsky-Moriya interaction and exchange interaction present in this system. Presence of Dzyaloshinsky-Moriya interaction on the topological surface give rise to Saddle point singularity which leads to electron-like and hole-like Rashba spin split bands in the [Formula: see text] and [Formula: see text] directions, respectively. Supporting evidences of Dzyaloshinsky-Moriya interaction have been obtained as anisotropic magnetoresistance with respect to field direction and first-order type hysteresis in the X-ray diffraction measurements. A giant negative magnetoresistance of 43% in the antiferromagnetic phase and tunable Rashba parameter with temperature makes this material a suitable candidate for application in the antiferromagnetic spintronic devices.

  8. The Interior Structure of Ceres as Revealed by Surface Topography and Gravity

    NASA Astrophysics Data System (ADS)

    Fu, R. R.; Ermakov, A.; Marchi, S.; Castillo, J. C.; Raymond, C. A.; Hager, B. H.; Zuber, M. T.; King, S. D.; De Sanctis, M. C.; Preusker, F.; Park, R. S.; Russell, C. T.; Bland, M. T.

    2016-12-01

    The dwarf planet Ceres, with a mean diameter of 940 km, is the largest object in the asteroid belt. Its low bulk density of 2160 kg m-3, hydrated surface, and ancient surface age suggest that Ceres may be a volatile-rich planetesimal that has survived into the modern solar system. Studying the internal structure of Ceres may therefore offer insights into the interior processes of these planetary building blocks, including their accreted composition and their subsequent thermal and chemical evolution. The NASA Dawn Mission has produced a shape model of Ceres with 130 m spatial resolution. Due to the phenomenon of viscous relaxation, observations of topographic relief may be used to estimate a vertical rheological profile. We conduct viscoelastoplastic modeling of Ceres topography, simulating the evolution of cerean topography between spherical harmonic degrees 4 and 20 (738 to 148 km wavelength, respectively) from 4.3 Ga to the present assuming a range of internal structures. We then compare the outcomes of these simulations to observed topography on Ceres. Our best-fit models suggest that the surface of Ceres is mechanically strong with viscosity of order 1026 Pa s that decays by a factor of 10 per 10-15 km depth. Meanwhile, admittance analysis of Ceres gravity and topography suggests that the bulk density of the crust lies between 1330 and 1430 kg m-3, assuming a simple two-layer structure. A crust made predominantly from water ice is much weaker than the inferred rheology, while a crust consisting mainly of hydrated silicates is too dense. Instead, we favor a crustal composition consisting of >20 vol% hydrated salts, <30 vol% water ice, and <50 vol% phyllosilicates or anhydrous salts such as carbonates, which can simultaneously satisfy both rheological and density constraints. In addition, the presence of water ice, phyllosilicates, and carbonates in this composition is consistent with the surface detection of these phases by the VIR spectrometer. This mineral

  9. 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.

  10. Phenotyping of human melanoma cells reveals a unique composition of receptor targets and a subpopulation co-expressing ErbB4, EPO-R and NGF-R.

    PubMed

    Mirkina, Irina; Hadzijusufovic, Emir; Krepler, Clemens; Mikula, Mario; Mechtcheriakova, Diana; Strommer, Sabine; Stella, Alexander; Jensen-Jarolim, Erika; Höller, Christoph; Wacheck, Volker; Pehamberger, Hubert; Valent, Peter

    2014-01-01

    Malignant melanoma is a life-threatening skin cancer increasingly diagnosed in the western world. In advanced disease the prognosis is grave. Growth and metastasis formation in melanomas are regulated by a network of cytokines, cytokine-receptors, and adhesion molecules. However, little is known about surface antigens and target expression profiles in human melanomas. We examined the cell surface antigen profile of human skin melanoma cells by multicolor flow cytometry, and compared their phenotype with 4 melanoma cell lines (A375, 607B, Mel-Juso, SK-Mel28). Melanoma cells were defined as CD45-/CD31- cells co-expressing one or more melanoma-related antigens (CD63, CD146, CD166). In most patients, melanoma cells exhibited ErbB3/Her3, CD44/Pgp-1, ICAM-1/CD54 and IGF-1-R/CD221, but did not express CD20, ErbB2/Her2, KIT/CD117, AC133/CD133 or MDR-1/CD243. Melanoma cell lines were found to display a similar phenotype. In most patients, a distinct subpopulation of melanoma cells (4-40%) expressed the erythropoietin receptor (EPO-R) and ErbB4 together with PD-1 and NGF-R/CD271. Both the EPO-R+ and EPO-R- subpopulations produced melanoma lesions in NOD/SCID IL-2Rgamma(null) (NSG) mice in first and secondary recipients. Normal skin melanocytes did not express ErbB4 or EPO-R, but expressed a functional KIT receptor (CD117) as well as NGF-R, ErbB3/Her3, IGF-1-R and CD44. In conclusion, melanoma cells display a unique composition of surface target antigens and cytokine receptors. Malignant transformation of melanomas is accompanied by loss of KIT and acquisition of EPO-R and ErbB4, both of which are co-expressed with NGF-R and PD-1 in distinct subfractions of melanoma cells. However, expression of EPO-R/ErbB4/PD-1 is not indicative of a selective melanoma-initiating potential.

  11. Phenotyping of Human Melanoma Cells Reveals a Unique Composition of Receptor Targets and a Subpopulation Co-Expressing ErbB4, EPO-R and NGF-R

    PubMed Central

    Krepler, Clemens; Mikula, Mario; Mechtcheriakova, Diana; Strommer, Sabine; Stella, Alexander; Jensen-Jarolim, Erika; Höller, Christoph; Wacheck, Volker; Pehamberger, Hubert; Valent, Peter

    2014-01-01

    Malignant melanoma is a life-threatening skin cancer increasingly diagnosed in the western world. In advanced disease the prognosis is grave. Growth and metastasis formation in melanomas are regulated by a network of cytokines, cytokine-receptors, and adhesion molecules. However, little is known about surface antigens and target expression profiles in human melanomas. We examined the cell surface antigen profile of human skin melanoma cells by multicolor flow cytometry, and compared their phenotype with 4 melanoma cell lines (A375, 607B, Mel-Juso, SK-Mel28). Melanoma cells were defined as CD45−/CD31− cells co-expressing one or more melanoma-related antigens (CD63, CD146, CD166). In most patients, melanoma cells exhibited ErbB3/Her3, CD44/Pgp-1, ICAM-1/CD54 and IGF-1-R/CD221, but did not express CD20, ErbB2/Her2, KIT/CD117, AC133/CD133 or MDR-1/CD243. Melanoma cell lines were found to display a similar phenotype. In most patients, a distinct subpopulation of melanoma cells (4–40%) expressed the erythropoietin receptor (EPO-R) and ErbB4 together with PD-1 and NGF-R/CD271. Both the EPO-R+ and EPO-R− subpopulations produced melanoma lesions in NOD/SCID IL-2Rgammanull (NSG) mice in first and secondary recipients. Normal skin melanocytes did not express ErbB4 or EPO-R, but expressed a functional KIT receptor (CD117) as well as NGF-R, ErbB3/Her3, IGF-1-R and CD44. In conclusion, melanoma cells display a unique composition of surface target antigens and cytokine receptors. Malignant transformation of melanomas is accompanied by loss of KIT and acquisition of EPO-R and ErbB4, both of which are co-expressed with NGF-R and PD-1 in distinct subfractions of melanoma cells. However, expression of EPO-R/ErbB4/PD-1 is not indicative of a selective melanoma-initiating potential. PMID:24489649

  12. 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.

  13. Structure of the C-terminus of the mRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1

    PubMed Central

    Dossani, Zain Y.; Weirich, Christine S.; Erzberger, Jan P.; Berger, James M.; Weis, Karsten

    2009-01-01

    The DExD/H-box RNA-dependent ATPase Dbp5 plays an essential role in the nuclear export of mRNA. Dbp5 localizes to the nuclear pore complex, where its ATPase activity is stimulated by Gle1 and its coactivator inositol hexakisphosphate. Here, we present the crystal structure of the C-terminal domain of Dbp5, refined to 1.8 Å. The structure reveals a RecA-like fold that contains two defining characteristics not present in other structurally characterized DExD/H-box proteins: a C-terminal α-helix and a loop connecting β5 and α4, both of which are composed of conserved and unique elements in the Dbp5 primary sequence. Using structure-guided mutagenesis, we have identified several charged surface residues that, when mutated, weaken the binding of Gle1 and inhibit the ability of Gle1 to stimulate Dbp5's ATPase activity. In vivo analysis of the same mutations reveals that those mutants displaying the weakest ATPase stimulation in vitro are also unable to support yeast growth. Analysis of the correlation between the in vitro and in vivo data indicates that a threshold level of Dbp5 ATPase activity is required for cellular mRNA export that is not met by the unstimulated enzyme, suggesting a possible mechanism by which Dbp5's activity can be modulated to regulate mRNA export. PMID:19805289

  14. Revealing the fate of cell surface human P-glycoprotein (ABCB1): The Lysosomal Degradation Pathway

    PubMed Central

    Katayama, Kazuhiro; Kapoor, Khyati; Ohnuma, Shinobu; Patel, Atish; Swaim, William; Ambudkar, Indu S.; Ambudkar, Suresh V.

    2015-01-01

    P-glycoprotein (P-gp) transports a variety of chemically dissimilar amphipathic compounds including anticancer drugs. Although mechanisms of P-gp drug transport are widely studied, the pathways involving its internalization are poorly understood. The present study is aimed at elucidating the pathways involved in degradation of cell surface P-gp. The fate of P-gp at the cell surface was determined by biotinylating cell surface proteins followed by flow cytometry and Western blotting. Our data shows that the half-life of endogenously expressed P-gp is 26.7 ± 1.1 h in human colorectal cancer HCT-15 cells. Treatment of cells with Bafilomycin A1 (BafA1) a vacuolar H+ ATPase inhibitor increased the half-life of P-gp at the cell surface to 36.1± 0.5 h. Interestingly, treatment with the proteasomal inhibitors MG132, MG115 or lactacystin alone did not alter the half-life of the protein. When cells were treated with both lysosomal and proteasomal inhibitors (BafA1 and MG132), the half-life was further prolonged to 39-50 h. Functional assays done with rhodamine 123 or calcein-AM, fluorescent substrates of P-gp, indicated that the transport function of P-gp was not affected by either biotinylation or treatment with BafA1 or proteasomal inhibitors. Immunofluorescence studies done with the antibody against lysosomal marker LAMP1 and the P-gp-specific antibody UIC2 in permeabilized cells indicated that intracellular P-gp is primarily localized in the lysosomal compartment. Our results suggest that the lysosomal degradation system could be targeted to increase the sensitivity of P-gp expressing cancer cells towards chemotherapeutic drugs. PMID:26057472

  15. Strong 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

    2017-10-01

    We report the near-surface (<400 m) primary wave velocity (Vp), shear wave velocity (Vs), Vp /Vs ratio, Poisson's ratio and Vs anisotropy of Taiwan by applying seismic coda interferometry to 34 borehole-surface station pairs. We find clear characteristic cos ⁡ 2 θ dependence of Vs in all the determinations, and about half of the amplitudes of anisotropy are larger than 10%, with the largest amplitudes up to 34%. The patterns of anisotropy fall into two categories, OPA (Orogeny-Parallel Anisotropy) and SAA (Stress-Aligned Anisotropy). Both types of anisotropy fit well the local geological fabrics and/or the ambient stress, and show strong correlation with the Poisson's ratios at the borehole sites. With these new findings and reported tomographic results, we infer that the SAA are likely confined to the uppermost portion of the crust, in particular to the fluid-saturated late-Quaternary deposits. 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.

  16. 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

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

    PubMed

    Liang, Mao-Chang; Mahata, Sasadhar

    2015-06-17

    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.

  18. 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.

  19. Surface-based morphometry reveals the neuroanatomical basis of the five-factor model of personality.

    PubMed

    Riccelli, Roberta; Toschi, Nicola; Nigro, Salvatore; Terracciano, Antonio; Passamonti, Luca

    2017-01-24

    The five-factor model (FFM) is a widely used taxonomy of human personality; yet its neuro anatomical basis remains unclear. This is partly because past associations between gray-matter volume and FFM were driven by different surface-based morphometry (SBM) indices (i.e. cortical thickness, surface area, cortical folding or any combination of them). To overcome this limitation, we used Free-Surfer to study how variability in SBM measures was related to the FFM in n = 507 participants from the Human Connectome Project.Neuroticism was associated with thicker cortex and smaller area and folding in prefrontal-temporal regions. Extraversion was linked to thicker pre-cuneus and smaller superior temporal cortex area. Openness was linked to thinner cortex and greater area and folding in prefrontal-parietal regions. Agreeableness was correlated to thinner prefrontal cortex and smaller fusiform gyrus area. Conscientiousness was associated with thicker cortex and smaller area and folding in prefrontal regions. These findings demonstrate that anatomical variability in prefrontal cortices is linked to individual differences in the socio-cognitive dispositions described by the FFM. Cortical thickness and surface area/folding were inversely related each others as a function of different FFM traits (neuroticism, extraversion and consciousness vs openness), which may reflect brain maturational effects that predispose or protect against psychiatric disorders.

  20. 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.

  1. Proteomic Analyses Reveal Common Promiscuous Patterns of Cell Surface Proteins on Human Embryonic Stem Cells and Sperms

    PubMed Central

    Gu, Bin; Zhang, Jiarong; Wu, Ying; Zhang, Xinzong; Tan, Zhou; Lin, Yuanji; Huang, Xiao; Chen, Liangbiao; Yao, Kangshou; Zhang, Ming

    2011-01-01

    Background It has long been proposed that early embryos and reproductive organs exhibit similar gene expression profiles. However, whether this similarity is propagated to the protein level remains largely unknown. We have previously characterised the promiscuous expression pattern of cell surface proteins on mouse embryonic stem (mES) cells. As cell surface proteins also play critical functions in human embryonic stem (hES) cells and germ cells, it is important to reveal whether a promiscuous pattern of cell surface proteins also exists for these cells. Methods and Principal Findings Surface proteins of hES cells and human mature sperms (hSperms) were purified by biotin labelling and subjected to proteomic analyses. More than 1000 transmembrane or secreted cell surface proteins were identified on the two cell types, respectively. Proteins from both cell types covered a large variety of functional categories including signal transduction, adhesion and transporting. Moreover, both cell types promiscuously expressed a wide variety of tissue specific surface proteins, and some surface proteins were heterogeneously expressed. Conclusions/Significance Our findings indicate that the promiscuous expression of functional and tissue specific cell surface proteins may be a common pattern in embryonic stem cells and germ cells. The conservation of gene expression patterns between early embryonic cells and reproductive cells is propagated to the protein level. These results have deep implications for the cell surface signature characterisation of pluripotent stem cells and germ cells and may lead the way to a new area of study, i.e., the functional significance of promiscuous gene expression in pluripotent and germ cells. PMID:21559292

  2. In-situ atomic force microscopy observation revealing gel-like plasticity on a metallic glass surface

    NASA Astrophysics Data System (ADS)

    Lu, Y. M.; Zeng, J. F.; Huang, J. C.; Kuan, S. Y.; Nieh, T. G.; Wang, W. H.; Pan, M. X.; Liu, C. T.; Yang, Y.

    2017-03-01

    It has been decade-long and enduring efforts to decipher the structural mechanism of plasticity in metallic glasses; however, it still remains a challenge to directly reveal the structural change, if any, that precedes; and dominant plastics flow in them. Here, by using the dynamic atomic force microscope as an "imaging" as well as a "forcing" tool, we unfold a real-time sequence of structural evolution occurring on the surface of an Au-Si thin film metallic glass. In sharp contrast to the common notion that plasticity comes along with mechanical softening in bulk metallic glasses, our experimental results directly reveal three types of nano-sized surface regions, which undergo plasticity but exhibit different characters of structural evolution following the local plasticity events, including stochastic structural rearrangement, unusual local relaxation and rejuvenation. As such, yielding on the metallic-glass surface manifests as a dynamic equilibrium between local relaxation and rejuvenation as opposed to shear instability in bulk metallic-glasses. Our finding demonstrates that plasticity on the metallic glass surface of Au-Si metallic glass bears much resemblance to that of the colloidal gels, of which nonlinear rheology rather than shear instability governs the constitutive behavior of plasticity.

  3. Graph-theoretical comparison of protein surfaces reveals potential determinants of cross-reactivity and the molecular mimicry.

    PubMed

    Iakhiaev, Mikhail A; Iakhiaev, Alexei V

    2010-01-01

    Different proteins, even without sequence similarity, still can contain similar surface regions involved in protein-protein interactions with common target. These regions can serve as structural determinants of cross-reactivity and molecular mimicry. Molecular mimicry, defined as the process in which structural properties of one molecule are simulated by the dissimilar molecules, is implicated in several biologically important processes, including autoimmune and allergic reactions, binding of some ligands to common receptor, and interactions in cell signaling. The problem of identification of the determinants of molecular mimicry is not completely solved at this time. We hypothesize that identification of structurally and chemically similar surface regions of two protein molecules capable of binding to the same target will allow us to identify sites involved in cross-reactivity including determinants of the molecular mimicry. We used a graph-theoretical approach in order to determine highly similar surface regions of two proteins with known three-dimensional structures. This approach uses a variation of Maximal Common Subgraph (MCS) isomorphism, where an association graph is constructed based on the surface-exposed residues of the two molecules and the matching regions are found based on the maximum cliques in the association graph. Testing the proposed method on the targets of autoantibody involved in antiphopholipid syndrome (APS)--beta2-GPI, PC, thrombin, factor IX, factor X, and plasmin allowed identifying potential epitopes for antibody that can inhibit coagulation proteases. Application of this method to the Activated Protein C and factor VII Gla-domains revealed surface regions involved in EPCR and plasma membrane binding, consistent with known experimental results. Analysis of major pollen allergen that can cause food allergies through cross-reactivity found known epitopes involved in cross-reactivity and also revealed additional surface regions that can

  4. Localization of mouse isoantigens on teh cell surface as revealed by immunofluorescence

    PubMed Central

    Cerottini, J.-C.; Brunner, K. T.

    1967-01-01

    An immunofluorescent technique is described which permits the localization and the semi-quantitative evaluation of isoantigens. Studies of normal and tumour cells have demonstrated that H-2 isoantigens are located in discrete areas on the cell surface. The thymus of 20–25-day-old mice was found to contain approximately 85 per cent lymphoid cells with a very low isoantigen content. These cells are considered to represent thymus cortical lymphoid cells. Cortisol treatment of mice reduced the relative number of cells with low isoantigen content to 10 per cent. ImagesFIG. 1FIG. 2-4FIG. 5-7 PMID:4168095

  5. Dynamics of HIV-Containing Compartments in Macrophages Reveal Sequestration of Virions and Transient Surface Connections

    PubMed Central

    Gaudin, Raphaël; Berre, Stefano; Cunha de Alencar, Bruna; Decalf, Jérémie; Schindler, Michael; Gobert, François-Xavier; Jouve, Mabel; Benaroch, Philippe

    2013-01-01

    During HIV pathogenesis, infected macrophages behave as “viral reservoirs” that accumulate and retain virions within dedicated internal Virus-Containing Compartments (VCCs). The nature of VCCs remains ill characterized and controversial. Using wild-type HIV-1 and a replication-competent HIV-1 carrying GFP internal to the Gag precursor, we analyzed the biogenesis and evolution of VCCs in primary human macrophages. VCCs appear roughly 14 hours after viral protein synthesis is detected, initially contain few motile viral particles, and then mature to fill up with virions that become packed and immobile. The amount of intracellular Gag, the proportion of dense VCCs, and the density of viral particles in their lumen increased with time post-infection. In contrast, the secretion of virions, their infectivity and their transmission to T cells decreased overtime, suggesting that HIV-infected macrophages tend to pack and retain newly formed virions into dense compartments. A minor proportion of VCCs remains connected to the plasma membrane overtime. Surprisingly, live cell imaging combined with correlative light and electron microscopy revealed that such connections can be transient, highlighting their dynamic nature. Together, our results shed light on the late phases of the HIV-1 cycle and reveal some of its macrophage specific features. PMID:23922713

  6. Complete Fermi Surface and Surface State in WTe2 Revealed by High-Resolution Laser-Based Angle-Resolved Photoemission Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wang, Chenlu; Zhang, Yan; Liu, Guodong; Mao, Zhiqiang; He, Shaolong; Zhao, Lin; Chen, Chuangtian; Xu, Zuyan; Zhou, Xingjiang

    WTe2, an unique transition metal dichalcogenide, attracts considerable attention recently, which shows an extremely large magnetoresistance (MR) with no saturation under very high field. In this talk, we will present our high resolution laser-ARPES study on WTe2. Our distinctive ARPES system is equipped with the VUV laser and the time-of-flight (TOF) electron energy analyzer, being featured by super-high energy resolution, simultaneous data acquisition for two-dimensional momentum space and much reduced nonlinearity effect. With this advanced apparatus, the very high quality of electronic structure data are obtained for WTe2 which gives a full picture of the Fermi surface. Meanwhile, the obtained systematic temperature dependence of its electronic state leads us to a better understanding on the origin of large magnetoresistance in WTe2.

  7. Crystal structure of the complex between Pseudomonas effector AvrPtoB and the tomato Pto kinase reveals both a shared and a unique interface compared with AvrPto-Pto.

    PubMed

    Dong, Jing; Xiao, Fangming; Fan, Fenxia; Gu, Lichuan; Cang, Huaixing; Martin, Gregory B; Chai, Jijie

    2009-06-01

    Resistance to bacterial speck disease in tomato (Solanum lycopersicum) is activated upon recognition by the host Pto kinase of either one of two sequence-unrelated effector proteins, AvrPto or AvrPtoB, from Pseudomonas syringae pv tomato (Pst). Pto induces Pst immunity by acting in concert with the Prf protein. The recently reported structure of the AvrPto-Pto complex revealed that interaction of AvrPto with Pto appears to relieve an inhibitory effect of Pto, allowing Pto to activate Prf. Here, we present the crystal structure of the Pto binding domain of AvrPtoB (residues 121 to 205) at a resolution of 1.9A and of the AvrPtoB(121-205)-Pto complex at a resolution of 3.3 A. AvrPtoB(121-205) exhibits a tertiary fold that is completely different from that of AvrPto, and its conformation remains largely unchanged upon binding to Pto. In common with AvrPto-Pto, the AvrPtoB-Pto complex relies on two interfaces. One of these interfaces is similar in both complexes, although the primary amino acid sequences from the two effector proteins are very different. Amino acid substitutions in Pto at the other interface disrupt the interaction of AvrPtoB-Pto but not that of AvrPto-Pto. Interestingly, substitutions in Pto affecting this unique interface also cause Pto to induce Prf-dependent host cell death independently of either effector protein.

  8. HUBBLE REVEALS HUGE CRATER ON THE SURFACE OF THE ASTEROID VESTA

    NASA Technical Reports Server (NTRS)

    2002-01-01

    [left] A NASA Hubble Space Telescope image of the asteroid Vesta, taken in May 1996 when the asteroid was 110 million miles from Earth. The asymmetry of the asteroid and 'nub' and the south pole is suggestive that it suffered a large impact event. The image was digitally restored to yield an effective scale of six miles per pixel (picture element). [center] A color-encoded elevation map of Vesta clearly shows the giant 285- mile diameter impact basin and 'bull's-eye' central peak. The map was constructed from 78 Wide Field Planetary Camera 2 pictures. Surface topography was estimated by noting irregularities along the limb and at the terminator (day/night boundary) where shadows are enhanced by the low Sun angle. [right] A 3-D computer model of the asteroid Vesta synthesized from Hubble topographic data. The crater's 8-mile high central peak can clearly be seen near the pole. The surface texture on the model is artificial, and is not representative of the true brightness variations on the asteroid. Elevation features have not been exaggerated. Photo Credit: Ben Zellner (Georgia Southern University), Peter Thomas (Cornell University), NASA

  9. In vivo transcriptome of Plasmodium falciparum reveals overexpression of transcripts that encode surface proteins.

    PubMed

    Daily, Johanna P; Le Roch, Karine G; Sarr, Ousmane; Ndiaye, Daouda; Lukens, Amanda; Zhou, Yingyao; Ndir, Omar; Mboup, Soulyemane; Sultan, Ali; Winzeler, Elizabeth A; Wirth, Dyann F

    2005-04-01

    Infections with the human parasite Plasmodium falciparum continue to present a great challenge to global health. Fundamental questions regarding the molecular basis of virulence and immune evasion in P. falciparum have been only partially answered. Because of the parasite's intracellular location and complex life cycle, standard genetic approaches to the study of the pathogenesis of malaria have been limited. The present study presents a novel approach to the identification of the biological processes involved in host-pathogen interactions, one that is based on the analysis of in vivo P. falciparum transcripts. We demonstrate that a sufficient quantity of P. falciparum RNA transcripts can be derived from a small blood sample from infected patients for whole-genome microarray analysis. Overall, excellent correlation was observed between the transcriptomes derived from in vivo samples and in vitro samples with ring-stage P. falciparum 3D7 reference strain. However, gene families that encode surface proteins are overexpressed in vivo. Moreover, this analysis has identified a new family of hypothetical genes that may encode surface variant antigens. Comparative studies of the transcriptomes derived from in vivo samples and in vitro 3D7 samples may identify important strategies used by the pathogen for survival in the human host and highlight, for vaccine development, new candidate antigens that were not previously identified through the use of in vitro cultures.

  10. Diblock copolymer adsorption onto a solid surface as revealed by evanescent wave ellipsometry

    SciTech Connect

    Kim, M.W. ); Russell, T.P. . Almaden Research Center); Moses, T.; Chen, W.; Shen, Y.R. . Center for Advanced Materials Univ. of California, Berkeley, CA . Dept. of Physics)

    1994-12-05

    The interfacial behavior of diblock copolymers play an important role in many practical applications, for example, polymer compatibilization, adhesion, and colloid stabilization. There has been considerable theoretical and experimental effort to understand the adsorption behavior of diblock copolymers from a solution onto a solid surface. Recent neutron reflectivity measurements on solutions of symmetric diblock copolymers of polystyrene and poly(methyl methacrylate), denoted P(S-b-MMA), near a quartz wall have shown that the PMMA segments adsorb preferentially onto the quartz forming a dense layer. However, the segmental concentration of polystyrene (PS) was too low to be observable. Evanescent wave ellipsometry, EWE, on the other hand, allows one to determine the density of molecules adsorbed onto a surface without labeling the segments with deuterium. Here, EWE results on P(S-b-MMA) adsorbed onto a solid substrate are presented as a function of molecular weight. It is shown that the adsorbed amount of copolymer is maximized for a particular molecular weight. This result contradicts theoretical predictions, and a possible origin of this discrepancy is provided.

  11. 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

  12. Light scattered by model phantom bacteria reveals molecular interactions at their surface

    NASA Astrophysics Data System (ADS)

    Ghetta, A.; Prosperi, D.; Mantegazza, F.; Panza, L.; Riva, S.; Bellini, T.

    2005-11-01

    Testing molecular interactions is an ubiquitous need in modern biology and molecular medicine. Here, we present a qualitative and quantitative method rooted in the basic properties of the scattering of light, enabling detailed measurement of ligand-receptor interactions occurring on the surface of colloids. The key factor is the use of receptor-coated nanospheres matched in refractive index with water and therefore optically undetectable ("phantom") when not involved in adhesion processes. At the occurrence of ligand binding at the receptor sites, optically unmatched material adsorbs on the nanoparticle surface, giving rise to an increment in their scattering cross section up to a maximum corresponding to saturated binding sites. The analysis of the scattering growth pattern enables extracting the binding affinity. This label-free method has been assessed through the determination of the binding constant of the antibiotic vancomycin with the tripeptide L-Lys-D-Ala-D-Ala and of the vancomycin dimerization constant. We shed light on the role of chelate effect and molecular hindrance in the activity of this glycopeptide. binding affinity | nanoparticles | vancomycin | ligand-receptor recognition

  13. Deep and shallow sources for the Lusi mud eruption revealed by surface deformation

    NASA Astrophysics Data System (ADS)

    Shirzaei, Manoochehr; Rudolph, Maxwell L.; Manga, Michael

    2015-07-01

    The Lusi mud eruption, in East Java, Indonesia, began in May 2006 and continues to the present. Previous analyses of surface deformation data suggested an exponential decay of the pressure in the mud source but did not constrain the location, geometry, and evolution of the possible source(s) of the erupting mud and fluids. To map the surface deformation, we employ multitemporal interferometric synthetic aperture radar and analyze a well-populated L-band data set acquired by the Advanced Land Observing Satellite (ALOS) between May 2006 and April 2011. We then apply a time-dependent inverse modeling scheme. Volume changes occur in two regions beneath Lusi, at 0.3-2.0 km and 3.5-4.75 km depth. The cumulative volume change within the shallow source is ~2-3 times larger than that of the deep source. The observation and model suggest that a shallow source plays a key role by supplying the erupting mud, but that additional fluids do ascend from depths >4 km on eruptive timescales.

  14. Deep and shallow sources for the Lusi mud eruption revealed by surface deformation

    NASA Astrophysics Data System (ADS)

    Shirzaei, M.; Rudolph, M. L.; Manga, M.

    2015-12-01

    The Lusi mud eruption, near Sidoarjo, East Java, Indonesia, began in May 2006 and continues to the present. Previous analyses of surface deformation data suggested an exponential decay of the pressure in the mud source, but did not constrain the location, geometry and evolution of the possible source(s) of the erupting mud and fluids. To map the surface deformation, we develop and new multitrack multitemporal interferometric processing algorithm and apply it to overlapped zones of three well-populated SAR data sets, including 51 images and acquired by the ALOS L-band satellite between May 2006 and April 2011. To understand the spatiotemporal evolution of the mud and fluid sources, we then apply a time-dependent inverse modeling scheme. Volume changes occur in two regions beneath Lusi, at 0.3-2.0 km and 3.5-4.75 km depth. The cumulative volume change within the shallow source is ~2-3 times larger than that of the deep source. The observation and model suggest that a shallow source plays a key role by supplying the erupting mud, but that additional fluids do ascend from depths >4 km on eruptive timescales.

  15. Coseismic landslides reveal near-surface rock strength in a high-relief tectonically active setting

    USGS Publications Warehouse

    Gallen, Sean F; Clark, Marin K; Godt, Jonathan W.

    2014-01-01

    We present quantitative estimates of near-surface rock strength relevant to landscape evolution and landslide hazard assessment for 15 geologic map units of the Longmen Shan, China. Strength estimates are derived from a novel method that inverts earthquake peak ground acceleration models and coseismic landslide inventories to obtain material proper- ties and landslide thickness. Aggregate rock strength is determined by prescribing a friction angle of 30° and solving for effective cohesion. Effective cohesion ranges are from 70 kPa to 107 kPa for 15 geologic map units, and are approximately an order of magnitude less than typical laboratory measurements, probably because laboratory tests on hand-sized specimens do not incorporate the effects of heterogeneity and fracturing that likely control near-surface strength at the hillslope scale. We find that strength among the geologic map units studied varies by less than a factor of two. However, increased weakening of units with proximity to the range front, where precipitation and active fault density are the greatest, suggests that cli- matic and tectonic factors overwhelm lithologic differences in rock strength in this high-relief tectonically active setting.

  16. Building unique surface structure on aramid fibers through a green layer-by-layer self-assembly technique to develop new high performance fibers with greatly improved surface activity, thermal resistance, mechanical properties and UV resistance

    NASA Astrophysics Data System (ADS)

    Zhou, Lifang; Yuan, Li; Guan, Qingbao; Gu, Aijuan; Liang, Guozheng

    2017-07-01

    Combining green preparation and high performance is becoming the direction of sustainable development of materials. How to simultaneously overcome the two bottlenecks (poor surface activity and UV resistance) of aramid fibers (AFs) while improving thermal and mechanical properties through a green process is still an interesting issue with big challenge. Herein, new AFs (BL-AFs) were prepared by alternately self-assembling SiO2 and MgAlFe layered double hydroxide (LDH) on surfaces of AFs, successively, through a green layer-by-layer (LBL) self-assembly technique without using high temperature and organic solvent. The structures and properties of BL-AFs were systematically studied, which are controllable by adjusting the number of self-assembly cycle. The new fibers with three or more self-assembly cycles have remarkably improved surface activity, thermal resistance, mechanical properties and UV resistance compared with AFs. Typically, with three self-assembly cycles, the initial degradation temperature and char yield of the new fiber (3BL-AF) are as high as 552.9 °C and 81.2%, about 92 °C and 25.2% higher than those of AF, respectively; after 168 h-UV irradiation, the retention of tensile performances of 3BL-AF fiber is as high as 91-95%, about 29-14% higher than that of AF, showing the best overall performances among all modified AFs prepared using a green technique reported so far. The origin behind the attractive performances of BL-AFs is revealed through correlating with structures of original and modified fibers. The excellent comprehensive properties of BL-AFs demonstrate that the green method provided in this study is facile and effective to completely solve the bottlenecks of aramid fibers, and developing higher performance organic fibers.

  17. Sources of mercury to San Francisco Bay surface sediment as revealed by mercury stable isotopes

    USGS Publications Warehouse

    Gehrke, Gretchen E.; Blum, Joel D.; Marvin-DePasquale, Mark

    2011-01-01

    Mercury (Hg) concentrations and isotopic compositions were examined in shallow-water surface sediment (0–2 cm) from San Francisco (SF) Bay to determine the extent to which historic Hg mining contributes to current Hg contamination in SF Bay, and to assess the use of Hg isotopes to trace sources of contamination in estuaries. Inter-tidal and wetland sediment had total Hg (HgT) concentrations ranging from 161 to 1529 ng/g with no simple gradients of spatial variation. In contrast, inter-tidal and wetland sediment displayed a geographic gradient of δ202Hg values, ranging from -0.30% in the southern-most part of SF Bay (draining the New Almaden Hg District) to -0.99% in the northern-most part of SF Bay near the Sacramento–San Joaquin River Delta. Similar to SF Bay inter-tidal sediment, surface sediment from the Alviso Slough channel draining into South SF Bay had a δ202Hg value of -0.29%, while surface sediment from the Cosumnes River and Sacramento–San Joaquin River Delta draining into north SF Bay had lower average δ202Hg values of -0.90% and -0.75%, respectively. This isotopic trend suggests that Hg-contaminated sediment from the New Almaden Hg District mixes with Hg-contaminated sediment from a low δ202Hg source north of SF Bay. Tailings and thermally decomposed ore (calcine) from the New Idria Hg mine in the California Coast Range had average δ202Hg values of -0.37 and +0.03%, respectively, showing that Hg calcination fractionates Hg isotopes resulting in Hg contamination from Hg(II) mine waste products with higher δ202Hg values than metallic Hg(0) produced from Hg mines. Thus, there is evidence for at least two distinct isotopic signals for Hg contamination in SF Bay: Hg associated with calcine waste materials at Hg mines in the Coast Range, such as New Almaden and New Idria; and Hg(0) produced from these mines and used in placer gold mines and/or in other industrial processes in the Sierra Nevada region and SF Bay area.

  18. 10Be surface exposure dating reveals strong active deformation in the central Andean backarc interior

    NASA Astrophysics Data System (ADS)

    García Morabito, Ezequiel; Terrizzano, Carla; Zech, Roland; Willett, Sean; Yamin, Marcela; Haghipour, Negar; Wuethrich, Lorenz; Christl, Marcus; María Cortes, José; Ramos, Victor

    2016-04-01

    Understanding the deformation associated with active thrust wedges is essential to evaluate seismic hazard. How is active faulting distributed throughout the wedge, and how much deformation is taken up by individual structures? We address these questions for our study region, the central Andean backarc of Argentina. We combined a structural and geomorphological approach with surface exposure dating (10Be) of alluvial fans and strath terraces in two key localities at ~32° S: the Cerro Salinas, located in the active orogenic front of the Precordillera, and the Barreal block in the interior of the Andean mountain range. We analysed 22 surface samples and 6 depth profiles. At the thrust front, the oldest terrace (T1) yields an age of 100-130 ka, the intermediate terrace (T2) between 40-95 ka, and the youngest terrace (T3) an age of ~20 ka. In the Andean interior, T1´ dates to 117-146 ka, T2´ to ~70 ka, and T3´ to ~20 ka, all calculations assuming negligible erosion and using the scaling scheme for spallation based on Lal 1991, Stone 2000. Vertical slip rates of fault offsets are 0.3-0.5 mm/yr and of 0.6-1.2 mm/yr at the thrust front and in the Andean interior, respectively. Our results highlight: i) fault activity related to the growth of the Andean orogenic wedge is not only limited to a narrow thrust front zone. Internal structures have been active during the last 150 ka, ii) deformation rates in the Andean interior are comparable or even higher that those estimated and reported along the emerging thrust front, iii) distribution of active faulting seems to account for unsteady state conditions, and iv) seismic hazards may be more relevant in the internal parts of the Andean orogen than assumed so far. References Lal, D., 1991: Cosmic ray labeling of erosion surfaces: In situ nuclide production rates and erosion models. Earth and Planetary Science Letters 104: 424-439. Stone, J.O., 2000: Air pressure and cosmogenic isotope production. Journal of Geophysical

  19. Sources of mercury to San Francisco Bay surface sediment as revealed by mercury stable isotopes

    NASA Astrophysics Data System (ADS)

    Gehrke, Gretchen E.; Blum, Joel D.; Marvin-DiPasquale, Mark

    2011-02-01

    Mercury (Hg) concentrations and isotopic compositions were examined in shallow-water surface sediment (0-2 cm) from San Francisco (SF) Bay to determine the extent to which historic Hg mining contributes to current Hg contamination in SF Bay, and to assess the use of Hg isotopes to trace sources of contamination in estuaries. Inter-tidal and wetland sediment had total Hg (Hg T) concentrations ranging from 161 to 1529 ng/g with no simple gradients of spatial variation. In contrast, inter-tidal and wetland sediment displayed a geographic gradient of δ 202Hg values, ranging from -0.30‰ in the southern-most part of SF Bay (draining the New Almaden Hg District) to -0.99‰ in the northern-most part of SF Bay near the Sacramento-San Joaquin River Delta. Similar to SF Bay inter-tidal sediment, surface sediment from the Alviso Slough channel draining into South SF Bay had a δ 202Hg value of -0.29‰, while surface sediment from the Cosumnes River and Sacramento-San Joaquin River Delta draining into north SF Bay had lower average δ 202Hg values of -0.90‰ and -0.75‰, respectively. This isotopic trend suggests that Hg-contaminated sediment from the New Almaden Hg District mixes with Hg-contaminated sediment from a low δ 202Hg source north of SF Bay. Tailings and thermally decomposed ore (calcine) from the New Idria Hg mine in the California Coast Range had average δ 202Hg values of -0.37 and +0.03‰, respectively, showing that Hg calcination fractionates Hg isotopes resulting in Hg contamination from Hg(II) mine waste products with higher δ 202Hg values than metallic Hg(0) produced from Hg mines. Thus, there is evidence for at least two distinct isotopic signals for Hg contamination in SF Bay: Hg associated with calcine waste materials at Hg mines in the Coast Range, such as New Almaden and New Idria; and Hg(0) produced from these mines and used in placer gold mines and/or in other industrial processes in the Sierra Nevada region and SF Bay area.

  20. Elements of the Chicxulub Impact Structure as Revealed in SRTM and Surface GPS Topographic Data

    NASA Technical Reports Server (NTRS)

    Kinsland, Gary L.; Sanchez, Gary; Kobrick, Michael; Cardador, Manuel Hurtado

    2003-01-01

    Pope et al. [1] utilized the elevations from the Petroleos Mexicanos (PEMEX) gravity data files to show that the main component of the surface expression of the Chicxulub Impact Structure is a roughly semi-circular, lowrelief depression about 90 km in diameter. They also identified other topographic features and the elements of the buried impact, which possibly led to the development of these features. These are summarized in Table 1. Kinsland et al. [2] presented a connection between these topographic anomalies, small gravity anomalies and buried structure of the impact. Very recently we have acquired digital topography data from NASA s Shuttle Radar Topography Mission (SRTM). Our subset covers 6 square degrees from 20deg N 91degW to 22deg N 88degW (corner to corner) with a pixel size of about 90m. This area includes all of the identified portion of the crater on land.

  1. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    SciTech Connect

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

  2. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    DOE PAGES

    Zhang, Meng; Charles, River; Tong, Huimin; ...

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobicmore » environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.« less

  3. Texture in steel plates revealed by laser ultrasonic surface acoustic waves velocity dispersion analysis.

    PubMed

    Yin, Anmin; Wang, Xiaochen; Glorieux, Christ; Yang, Quan; Dong, Feng; He, Fei; Wang, Yanlong; Sermeus, Jan; Van der Donck, Tom; Shu, Xuedao

    2017-02-24

    A photoacoustic, laser ultrasonics based approach in an Impulsive Stimulated Scattering (ISS) implementation was used to investigate the texture in polycrystalline metal plates. The angular dependence of the 'polycrystalline' surface acoustic wave (SAW) velocity measured along regions containing many grains was experimentally determined and compared with simulated results that were based on the angular dependence of the 'single grain' SAW velocity within single grains and the grain orientation distribution. The polycrystalline SAW velocities turn out to vary with texture. The SAW velocities and their angular variations for {110} texture were found to be larger than that the ones for {111} texture or the strong γ fiber texture. The SAW velocities for {001} texture were larger than for {111} texture, but with almost the same angular dependence. The results infer the feasibility to apply angular SAW angular dispersion measurements by laser ultrasonics for on-line texture monitoring.

  4. Elements of the Chicxulub Impact Structure as Revealed in SRTM and Surface GPS Topographic Data

    NASA Technical Reports Server (NTRS)

    Kinsland, Gary L.; Sanchez, Gary; Kobrick, Michael; Cardador, Manuel Hurtado

    2003-01-01

    Pope et al. [1] utilized the elevations from the Petroleos Mexicanos (PEMEX) gravity data files to show that the main component of the surface expression of the Chicxulub Impact Structure is a roughly semi-circular, lowrelief depression about 90 km in diameter. They also identified other topographic features and the elements of the buried impact, which possibly led to the development of these features. These are summarized in Table 1. Kinsland et al. [2] presented a connection between these topographic anomalies, small gravity anomalies and buried structure of the impact. Very recently we have acquired digital topography data from NASA s Shuttle Radar Topography Mission (SRTM). Our subset covers 6 square degrees from 20deg N 91degW to 22deg N 88degW (corner to corner) with a pixel size of about 90m. This area includes all of the identified portion of the crater on land.

  5. Assembly-free metagenomic analysis reveals new metabolic capabilities in surface ocean bacterioplankton.

    PubMed

    Luo, Haiwei; Moran, Mary Ann

    2013-10-01

    Uncovering the metabolic capabilities of microbes is key to understanding global energy flux and nutrient transformations. Since the vast majority of environmental microorganisms are uncultured, metagenomics has become an important tool to genotype the microbial community. This study uses a recently developed computational method to confidently assign metagenomic reads to microbial clades without the requirement of metagenome assembly by comparing the evolutionary pattern of nucleotide sequences at non-synonymous sites between metagenomic and orthologous reference genes. We found evidence for new, ecologically relevant metabolic pathways in several lineages of surface ocean bacterioplankton using the Global Ocean Survey (GOS) metagenomic data, including assimilatory sulfate reduction and alkaline phosphatase capabilities in the alphaproteobacterial SAR11 clade, and proteorhodopsin-like genes in the cyanobacterial genus Prochlorococcus. These findings raise new hypotheses about microbial roles in energy flux and organic matter transformation in the ocean. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  6. Mechanical Properties of Membrane Surface of Cultured Astrocyte Revealed by Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Shiga, Hatsuki; Yamane, Yukako; Ito, Etsuro; Abe, Kazuhiro; Kawabata, Kazushige; Haga, Hisashi

    2000-06-01

    In order to examine the mechanical properties of the membrane surface of astrocytes, we observed living astrocytes by atomic force microscopy (AFM) both in contact mode and force-mapping mode. Ridge-like structures reflecting actin filaments were observed in the topographic images in contact mode, but not in force-mapping mode, using a zero-loading force. When we measured the elasticity of astrocytes, we observed that the cell membrane above the nucleus was soft and the cell membrane above the cytosol was stiff. In particular, the parts reflecting actin filaments were very stiff. This effect of actin filaments on the elasticity of astrocytes was confirmed by the loss of actin filaments after application of actin-polymerization inhibitor.

  7. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

    2015-03-01

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

  8. Interactions of arsenic with calcite surfaces revealed by in situ nanoscale imaging

    NASA Astrophysics Data System (ADS)

    Renard, François; Putnis, Christine V.; Montes-Hernandez, German; Ruiz-Agudo, Encarnacion; Hovelmann, Jörn; Sarret, Géraldine

    2015-06-01

    Arsenic dissolved in water represents a key environmental and health challenge because several million people are under the threat of contamination. In calcareous environments calcite may play an important role in arsenic solubility and transfer in water. Arsenic-calcite interactions remain controversial, especially for As(III) which was proposed to be either incorporated as such, or as As(V) after oxidation. Here, we provide the first time-lapse in situ study of the evolution of the (10-14) calcite cleavage surface morphology during dissolution and growth in the presence of solutions with various amounts of As(III) or As(V) at room temperature and pH range 6-11 using a flow-through cell connected to an atomic force microscope (AFM). Reaction products were then characterized by Raman spectroscopy. In parallel, co-precipitation experiments with either As(III) or As(V) were performed in batch reactors, and the speciation of arsenic in the resulting solids was studied by X-ray absorption spectroscopy (XAS). For As(V), AFM results showed that it interacts strongly with the calcite surface, and XAS results showed that As(V) was mostly incorporated in the calcite structure. For As(III), AFM results showed much less impact on calcite growth and dissolution and less incorporation was observed. This was confirmed by XAS results that indicate that As(III) was partly oxidized into As(V) before being incorporated into calcite and the resulting calcite contained 36% As(III) and 64% As(V). All these experimental results confirm that As(V) has a much stronger interaction with calcite than As(III) and that calcite may represent an important reservoir for arsenic in various geological environments.

  9. Interactions of arsenic with calcite surfaces revealed by in-situ nanoscale imaging

    NASA Astrophysics Data System (ADS)

    Renard, Francois; Putnis, Christine; Montes-Hernandez, German; Ruiz-Agudo, Encarnacion; Hövelmann, Jörn; Sarret, Géraldine

    2015-04-01

    Arsenic dissolved in water represents a key environmental and health challenge because several million people are under the threat of contamination. In calcareous environments calcite may play an important role in arsenic solubility and transfer in water. Arsenic-calcite interactions remain controversial, especially for As(III) which was proposed to be either incorporated as such, or as As(V) after oxidation. Here, we provide the first time-lapse in-situ study of calcite dissolution and growth in the presence of solutions with various amounts of As(III) or As(V). This was performed at room temperature and pH range 6-9 using a flow through cell connected to an atomic force microscope (AFM), to study the evolution of the (10-14) calcite cleavage surface morphology. Reaction products were then characterized by Raman spectroscopy. In parallel, co-precipitation experiments with either As(III) or As(V) were performed in batch reactors, and the speciation of arsenic in the resulting solids was studied by X-ray absorption spectroscopy (XAS). For As(V), AFM results showed that it interacts strongly with the calcite surface, and XAS results showed that As(V) was mostly incorporated in the calcite structure. For As(III), AFM results showed much less impact on calcite growth and dissolution and less incorporation was observed. This was confirmed by XAS results that indicate that As(III) was partly oxidized into As(V) before being incorporated into calcite and the resulting calcite contained 36% As(III) and 64% As(V). All these experimental results confirm that As(V) has a much stronger interaction with calcite than As(III) and that calcite may represent an important reservoir for arsenic in various geological environments.

  10. Autocorrelations at RCLB Station, SE Brazil, Reveal Deep Moho Reflections and Shallow Surface-Wave Reflections

    NASA Astrophysics Data System (ADS)

    Dourado, J. C.; Schimmel, M.; Assumpcao, M.

    2013-05-01

    The RCLB broad band station of UNESP University, located in the Parana Basin, has been operating since 2002. Auto- and cross-correlations between all three components were calculated, using several years of records, to try to find zero-offset reflections from deep interfaces beneath the station, following the technique of (Tibuleac & Seggern, 2012). We used pre-whitening and bit-normalization techniques to remove effects of large events. The auto- and cross-correlograms were band-pass filtered in the range 0.7-1.5 Hz. The Moho interface PmP was identified by a correlation maximum at ~12.5s in the pairs ZZ and ZN . The phase SmS was also recognized by a peak at ~22s in the pair NN . These deep Moho reflections are consistent with the ~40 km Moho depths determined from receiver functions. In addition to the zero-offset Moho reflections, a large phase was obtained at about 40s in the pairs ZZ and ZE and were identified as a Rayleigh-wave. The nature of the Rayleigh-wave is confirmed by elliptical and retrograde particle motion indicating arrival from the West. A probable Love wave was also tentatively identified in the NN autocorrelograms at 26 sec. These surface waves are likely reflections from a shallow structural discontinuity near the Cuesta escarpment in the Paraná Basin, about 40km away. Data from a short-period station, IPNA, 20 km to the West, were also analyzed with auto- and cross-correlations. Signals from Moho reflections were also identified at the expected arrival times. Signals from possible Love (NN auto-correlation) and Rayleigh waves (ZZ) were detected, consistent with the interpretation of a shallow surface-wave reflector near the Cuesta escarpment.

  11. Lead isotopes in marine surface sediments reveal historical use of leaded fuel.

    PubMed

    Larsen, Martin M; Blusztajn, Jerzy S; Andersen, Ole; Dahllöf, Ingela

    2012-11-01

    Analyses of lead (Pb) isotopes have been performed in terrestrial and fresh water environments to estimate historical uses of leaded fuel, but so far this method has not been employed in studies of world-wide marine surface sediments. We analyzed Pb and its isotopes in 23 surface sediments from four continents collected during the Galathea 3 expedition in 2006-2007. To enhance the anthropogenic signal, a partial digestion using nitric acid was performed. The concentrations of Pb, Th, U and Al were determined with an ICP-Quadrupole MS, and Pb-isotope ratios with an ICP-multi-collector MS. The samples could be divided into three groups: Harbor areas in larger cities with concentrations of 150 to 265 mg kg(-1) dry weight, smaller towns with concentrations between 20 and 40 mg kg(-1) dry weight, and remotely located sites with concentrations below 15 mg kg(-1) dry weight. Pb-isotope ratios were compared to literature values for gasoline and local or geological background values, and the contribution of leaded-gasoline to total concentrations was calculated for contaminated sites using both a one-dimensional and a novel two-dimensional (vector) method. The North American sites had Pb-isotope ratios corresponding to the US leaded gasoline, with 24-88% of the Pb from leaded gasoline. Samples from Oceania showed Pb-isotope ratios corresponding to Australian gasoline, with 60% attributed to leaded gasoline in Sydney and 21% in Christchurch. Outside Cape Town, 15 to 46% of Pb in sediments was from leaded gasoline.

  12. Revealing the carbohydrate pattern on a cell surface by super-resolution imaging

    NASA Astrophysics Data System (ADS)

    Chen, Junling; Gao, Jing; Wu, Jiazhen; Zhang, Min; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Tian, Zhiyuan; Wang, Hongda

    2015-02-01

    Carbohydrates are involved in various physiological and pathological activities including cell adhesion, signal transduction and tumor invasion. The distribution of carbohydrates is the molecular basis of their multiple functions, but remains poorly understood. Here, we employed direct stochastic optical reconstruction microscopy (dSTORM) to visualize the pattern of N-acetylglucosamine (N-GlcNAc) on Vero cell membranes at the nanometer level of resolution. We found that N-GlcNAcs exist in irregular clusters on the apical membrane with an average cluster area of about 0.37 μm2. Most of these N-GlcNAc clusters are co-localized with lipid rafts by dual-color dSTORM imaging, suggesting that carbohydrates are closely associated with lipid rafts as the functional domains. Our results demonstrate that super-resolution imaging is capable of characterizing the distribution of carbohydrates on the cellular surface at the molecular level.Carbohydrates are involved in various physiological and pathological activities including cell adhesion, signal transduction and tumor invasion. The distribution of carbohydrates is the molecular basis of their multiple functions, but remains poorly understood. Here, we employed direct stochastic optical reconstruction microscopy (dSTORM) to visualize the pattern of N-acetylglucosamine (N-GlcNAc) on Vero cell membranes at the nanometer level of resolution. We found that N-GlcNAcs exist in irregular clusters on the apical membrane with an average cluster area of about 0.37 μm2. Most of these N-GlcNAc clusters are co-localized with lipid rafts by dual-color dSTORM imaging, suggesting that carbohydrates are closely associated with lipid rafts as the functional domains. Our results demonstrate that super-resolution imaging is capable of characterizing the distribution of carbohydrates on the cellular surface at the molecular level. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05970k

  13. Pronounced Surface Band Bending of Thin-Film Silicon Revealed by Modeling Core Levels Probed with Hard X-rays.

    PubMed

    Wippler, David; Wilks, Regan G; Pieters, Bart E; van Albada, Sacha J; Gerlach, Dominic; Hüpkes, Jürgen; Bär, Marcus; Rau, Uwe

    2016-07-13

    Enhancing the probing depth of photoemission studies by using hard X-rays allows the investigation of buried interfaces of real-world device structures. However, it also requires the consideration of photoelectron-signal attenuation when evaluating surface effects. Here, we employ a computational model incorporating surface band bending and exponential photoelectron-signal attenuation to model depth-dependent spectral changes of Si 1s and Si 2s core level lines. The data were acquired from hydrogenated boron-doped microcrystalline thin-film silicon, which is applied in silicon-based solar cells. The core level spectra, measured by hard X-ray photoelectron spectroscopy using different excitation energies, reveal the presence of a 0.29 nm thick surface oxide layer. In the silicon film a downward surface band bending of eVbb = -0.65 eV over ∼6 nm obtained via inverse modeling explains the observed core level shifts and line broadening. Moreover, the computational model allows the extraction of the "real" Si 1s and Si 2s bulk core level binding energies as 1839.13 and 150.39 eV, and their natural Lorentzian line widths as 496 and 859 meV, respectively. These values significantly differ from those directly extracted from the measured spectra. Because band bending usually occurs at material surfaces we highly recommend the detailed consideration of signal integration over depth for quantitative statements from depth-dependent measurements.

  14. Supra-additive contribution of shape and surface information to individual face discrimination as revealed by fast periodic visual stimulation.

    PubMed

    Dzhelyova, Milena; Rossion, Bruno

    2014-12-24

    Face perception depends on two main sources of information--shape and surface cues. Behavioral studies suggest that both of them contribute roughly equally to discrimination of individual faces, with only a small advantage provided by their combination. However, it is difficult to quantify the respective contribution of each source of information to the visual representation of individual faces with explicit behavioral measures. To address this issue, facial morphs were created that varied in shape only, surface only, or both. Electrocephalogram (EEG) were recorded from 10 participants during visual stimulation at a fast periodic rate, in which the same face was presented four times consecutively and the fifth face (the oddball) varied along one of the morphed dimensions. Individual face discrimination was indexed by the periodic EEG response at the oddball rate (e.g., 5.88 Hz/5 = 1.18 Hz). While shape information was discriminated mainly at right occipitotemporal electrode sites, surface information was coded more bilaterally and provided a larger response overall. Most importantly, shape and surface changes alone were associated with much weaker responses than when both sources of information were combined in the stimulus, revealing a supra-additive effect. These observations suggest that the two kinds of information combine nonlinearly to provide a full individual face representation, face identity being more than the sum of the contribution of shape and surface cues. © 2014 ARVO.

  15. Stream/bounce event perception reveals a temporal limit of motion correspondence based on surface feature over space and time.

    PubMed

    Kawachi, Yousuke; Kawabe, Takahiro; Gyoba, Jiro

    2011-01-01

    We examined how stream/bounce event perception is affected by motion correspondence based on the surface features of moving objects passing behind an occlusion. In the stream/bounce display two identical objects moving across each other in a two-dimensional display can be perceived as either streaming through or bouncing off each other at coincidence. Here, surface features such as colour (Experiments 1 and 2) or luminance (Experiment 3) were switched between the two objects at coincidence. The moment of coincidence was invisible to observers due to an occluder. Additionally, the presentation of the moving objects was manipulated in duration after the feature switch at coincidence. The results revealed that a postcoincidence duration of approximately 200 ms was required for the visual system to stabilize judgments of stream/bounce events by determining motion correspondence between the objects across the occlusion on the basis of the surface feature. The critical duration was similar across motion speeds of objects and types of surface features. Moreover, controls (Experiments 4a-4c) showed that cognitive bias based on feature (colour/luminance) congruency across the occlusion could not fully account for the effects of surface features on the stream/bounce judgments. We discuss the roles of motion correspondence, visual feature processing, and attentive tracking in the stream/bounce judgments.

  16. Stream/bounce event perception reveals a temporal limit of motion correspondence based on surface feature over space and time

    PubMed Central

    Kawachi, Yousuke; Kawabe, Takahiro; Gyoba, Jiro

    2011-01-01

    We examined how stream/bounce event perception is affected by motion correspondence based on the surface features of moving objects passing behind an occlusion. In the stream/bounce display two identical objects moving across each other in a two-dimensional display can be perceived as either streaming through or bouncing off each other at coincidence. Here, surface features such as colour (Experiments 1 and 2) or luminance (Experiment 3) were switched between the two objects at coincidence. The moment of coincidence was invisible to observers due to an occluder. Additionally, the presentation of the moving objects was manipulated in duration after the feature switch at coincidence. The results revealed that a postcoincidence duration of approximately 200 ms was required for the visual system to stabilize judgments of stream/bounce events by determining motion correspondence between the objects across the occlusion on the basis of the surface feature. The critical duration was similar across motion speeds of objects and types of surface features. Moreover, controls (Experiments 4a–4c) showed that cognitive bias based on feature (colour/luminance) congruency across the occlusion could not fully account for the effects of surface features on the stream/bounce judgments. We discuss the roles of motion correspondence, visual feature processing, and attentive tracking in the stream/bounce judgments. PMID:23145236

  17. Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment

    PubMed Central

    Thomas, Torsten; Evans, Flavia F.; Schleheck, David; Mai-Prochnow, Anne; Burke, Catherine; Penesyan, Anahit; Dalisay, Doralyn S.; Stelzer-Braid, Sacha; Saunders, Neil; Johnson, Justin; Ferriera, Steve; Kjelleberg, Staffan; Egan, Suhelen

    2008-01-01

    Background Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions. Methodology/Principal Findings To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions. Conclusions/Significance The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associated community

  18. Revealing the surface and bulk regimes of isothermal graphene growth on Ni with in situ kinetic measurements and modeling

    SciTech Connect

    Puretzky, Alexander A; Merkulov, Igor A; Rouleau, Christopher M; Eres, Gyula; Geohegan, David B

    2014-01-01

    In situ optical diagnostics are used to reveal the isothermal nucleation and growth mechanisms of graphene on Ni across a wide temperature range (560 C < T < 840 C) by chemical vapor deposition from single, sub-second pulses of acetylene. An abrupt, two-orders of magnitude change in growth times (~ 100s to 1s) is revealed at T = 680 C. Below and above this temperature, similar sigmoidal kinetics are measured and attributed to autocatalytic growth reactions but by two different mechanisms, surface assembly and dissolution/precipitation, respectively. These data are used to develop a simple and general kinetic model for graphene growth that includes the nucleation phase and includes the effects of carbon solubility in metals, describes delayed nucleation, and allows the interpretation of the competition between surface and bulk growth modes. The sharp transition in growth kinetics at T = 680 C is explained by a change in defect site density required for nucleation due to a transition in the carbon-induced mobility of the Ni surface. The easily-implemented optical reflectivity diagnostics and the simple kinetic model described here allow a pathway to optimize the growth of graphene on metals with arbitrary carbon solubility.

  19. Non-cellulosic polysaccharides help to reveal the history of thick organic surface layers on calcareous Alpine soils

    NASA Astrophysics Data System (ADS)

    Prietzel, Jörg; Spielvogel, Sandra

    2015-04-01

    We investigated the potential of non-cellulosic polysaccharides (NCP) as biomarkers to identify the plant types that dominate present and past litter input into organic surface covers on calcareous Alpine soils and to reveal historic vegetation changes. At two sites in the Alps, NCP monomers were quantified in different organs of site-dominating plants, the Oa horizon of four Folic Leptosols, and different sections of thick organic surface layers of four Folic Histosols on calcareous bedrock. The dominating plant types at our study sites differ markedly in their NCP composition and (galactose + mannose)/(arabinose + xylose) [GM/AX] ratio (grasses and sedges: 0.2; dicots Fagus and Vaccinium: 0.2-0.6; conifers Abies, Picea, Pinus: 0.7-2.4; mosses: 5). For all except one soil, the NCP signature of the uppermost Oa horizon reflects the present vegetation. For all Histosol O horizons, NCP signatures indicate a dominance of conifer litter throughout their development (up to 1,500 years). Different NCP and GM/AX depth profiles reflect specific patterns of O layer genesis. From those results we conclude that NCP and GM/AX depth profiles in organic surface covers of soils provide important information about dominating litter sources in the past and can be valuable tools to reveal historic vegetation and/ or land use changes.

  20. Amyloid plaque structure and cell surface interactions of β-amyloid fibrils revealed by electron tomography

    PubMed Central

    Han, Shen; Kollmer, Marius; Markx, Daniel; Claus, Stephanie; Walther, Paul; Fändrich, Marcus

    2017-01-01

    The deposition of amyloid fibrils as plaques is a key feature of several neurodegenerative diseases including in particular Alzheimer’s. This disease is characterized, if not provoked, by amyloid aggregates formed from Aβ peptide that deposit inside the brain or are toxic to neuronal cells. We here used scanning transmission electron microscopy (STEM) to determine the fibril network structure and interactions of Aβ fibrils within a cell culture model of Alzheimer’s disease. STEM images taken from the formed Aβ amyloid deposits revealed three main types of fibril network structures, termed amorphous meshwork, fibril bundle and amyloid star. All three were infiltrated by different types of lipid inclusions from small-sized exosome-like structures (50–100 nm diameter) to large-sized extracellular vesicles (up to 300 nm). The fibrils also presented strong interactions with the surrounding cells such that fibril bundles extended into tubular invaginations of the plasma membrane. Amyloid formation in the cell model was previously found to have an intracellular origin and we show here that it functionally destroys the integrity of the intracellular membranes as it leads to lysosomal leakage. These data provide a mechanistic link to explain why intracellular fibril formation is toxic to the cell. PMID:28240273

  1. Amyloid plaque structure and cell surface interactions of β-amyloid fibrils revealed by electron tomography.

    PubMed

    Han, Shen; Kollmer, Marius; Markx, Daniel; Claus, Stephanie; Walther, Paul; Fändrich, Marcus

    2017-02-27

    The deposition of amyloid fibrils as plaques is a key feature of several neurodegenerative diseases including in particular Alzheimer's. This disease is characterized, if not provoked, by amyloid aggregates formed from Aβ peptide that deposit inside the brain or are toxic to neuronal cells. We here used scanning transmission electron microscopy (STEM) to determine the fibril network structure and interactions of Aβ fibrils within a cell culture model of Alzheimer's disease. STEM images taken from the formed Aβ amyloid deposits revealed three main types of fibril network structures, termed amorphous meshwork, fibril bundle and amyloid star. All three were infiltrated by different types of lipid inclusions from small-sized exosome-like structures (50-100 nm diameter) to large-sized extracellular vesicles (up to 300 nm). The fibrils also presented strong interactions with the surrounding cells such that fibril bundles extended into tubular invaginations of the plasma membrane. Amyloid formation in the cell model was previously found to have an intracellular origin and we show here that it functionally destroys the integrity of the intracellular membranes as it leads to lysosomal leakage. These data provide a mechanistic link to explain why intracellular fibril formation is toxic to the cell.

  2. Neutron Reflectometry reveals the interaction between functionalized SPIONs and the surface of lipid bilayers.

    PubMed

    Luchini, Alessandra; Gerelli, Yuri; Fragneto, Giovanna; Nylander, Tommy; Pálsson, Gunnar K; Appavou, Marie-Sousai; Paduano, Luigi

    2017-03-01

    The safe application of nanotechnology devices in biomedicine requires fundamental understanding on how they interact with and affect the different components of biological systems. In this respect, the cellular membrane, the cell envelope, certainly represents an important target or barrier for nanosystems. Here we report on the interaction between functionalized SuperParamagnetic Iron Oxide Nanoparticles (SPIONs), promising contrast agents for Magnetic Resonance Imaging (MRI), and lipid bilayers that mimic the plasma membrane. Neutron Reflectometry, supported by Quartz Crystal Microbalance with Dissipation monitoring (QCM-D) experiments, was used to characterize this interaction by varying both SPION coating and lipid bilayer composition. In particular, the interaction of two different SPIONs, functionalized with a cationic surfactant and a zwitterionic phospholipid, and lipid bilayers, containing different amount of cholesterol, were compared. The obtained results were further validated by Dynamic Light Scattering (DLS) measurements and Cryogenic Transmission Electron Microscopy (Cryo-TEM) images. None of the investigated functionalized SPIONs were found to disrupt the lipid membrane. However, in all case we observed the attachment of the functionalized SPIONs onto the surface of the bilayers, which was affected by the bilayer rigidity, i.e. the cholesterol concentration. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Revealing the nature of trapping sites in nanocrystalline titanium dioxide by selective surface modification.

    SciTech Connect

    Dimitrijevic, N. M.; Saponjic, Z. V.; Bartels, D. M.; Thurnauer, M. C.; Tiede, D. M.; Rajh, T.; Chemistry

    2003-07-31

    Excess electrons in nanocrystalline TiO{sub 2} were studied in bare and dopamine-capped TiO{sub 2} nanoparticles by electron-beam pulse radiolysis. Reaction of hydrated electrons with dopamine-capped TiO{sub 2} nanoparticles was found to be at the diffusion-controlled limit, k = 1 x 10{sup 11} M{sup -1} s{sup -1}, while the reaction with 1-hydroxy-1-methylethyl radicals, (CH{sub 3}){sub 2}{dot C}OH, was 2 orders of magnitude slower, k = 4 x 10{sup 8} M{sup -1} s{sup -1}. The reactions result in injection of electrons into the conduction band of TiO{sub 2} nanoparticles. Optical absorption spectra of injected excess electrons in dopamine-capped nanoparticles display monotonic featureless wavelength dependence up to 1800 nm. In contrast, bare particles have shown two preferential optical transitions with energies in the visible region ({lambda}{sub max} = 670 nm and {lambda}{sub max} = 900 nm). Flat band potential of dopamine-capped TiO{sub 2} nanoparticles was shifted by 100 mV to more negative values. The strong coupling of dopamine to surface Ti atoms was also found to improve the separation of photogenerated charges. This was demonstrated by the enhanced efficiency of photogenerated electrons in reducing silver cations to metallic silver in systems linked via a dopamine bridge, compared to the same systems linked through carboxyl groups.

  4. Probing the phonon confinement in ultrasmall silicon nanocrystals reveals a size-dependent surface energy

    NASA Astrophysics Data System (ADS)

    Crowe, Iain F.; Halsall, Matthew P.; Hulko, Oksana; Knights, Andrew P.; Gwilliam, Russell M.; Wojdak, Maciej; Kenyon, Anthony J.

    2011-04-01

    We validate for the first time the phenomenological phonon confinement model (PCM) of H. Richter, Z. P. Wang, and L. Ley [Solid State Commun. 39, 625 (1981)] for silicon nanostructures on the sub-3 nm length scale. By invoking a PCM that incorporates the measured size distribution, as determined from cross-sectional transmission electron microscopy (X-TEM) images, we are able to accurately replicate the measured Raman line shape, which gives physical meaning to its evolution with high temperature annealing and removes the uncertainty in determining the confining length scale. The ability of our model to explain the presence of a background scattering spectrum implies the existence of a secondary population of extremely small (sub-nm), amorphous silicon nanoclusters which are not visible in the X-TEM images. Furthermore, the inclusion of an additional fitting parameter, which takes into account the observed peak shift, can be explained by a size-dependent interfacial stress that is minimized by the nanocluster/crystal growth. From this we obtain incidental, yet accurate estimates for the silicon surface energy and a Tolman length, δ ≈ 0.15 ± 0.1 nm using the Laplace-Young relation.

  5. Surface Response to Regional Uplift of Madagascar Reveals Short Wavelength Dynamic Topography

    NASA Astrophysics Data System (ADS)

    Stephenson, S.; White, N.

    2016-12-01

    The physiography of Madagascar is characterized by high elevation but low relief topography with 42% of the landscape at an elevation grgeater than 500 m. Eocene marine limestones crop out at an elevation of 400 m, extensive low relief erosion surfaces capped by laterites occur at elevations of up to 2 km, and longitudinal river profiles are disequilibrated. Together, these observations suggest that Madagascar underwent regional uplift in Neogene times. Inverse modeling of drainage networks suggests that regional uplift is diachronous and has occurred on wavelengths of 1000 km. The existence of deeply incised river channels together with low-temperature thermochronologic measurements (i.e. AFT, AHe) implies that erosion occurred in response to regional Neogene uplift. Admittance analysis of long wavelength free-air gravity and topography shows that admittance, Z = 45 ± 5 mGal/km. The history of Neogene volcanism and a lack of significant tectonic shortening both suggest that uplift is dynamically supported. Here we present a suite of U-Th dates of emergent coral reef deposits from northern Madagascar, whose margins are sometimes considered `stable'. Elevation of these coeval coral reefs decreases from 7.2 m at the northern tip of Madagascar to sea level 100 km to the south. The existence of a spatial gradient suggests that differential vertical motions occurred during Late Quaternary times. These results raise significant questions about the reliability both of emergent coral reefs as global sea-level markers and the length-scale of variations in dynamic topography.

  6. Thin-film Electrochemistry of Single Prussian Blue Nanoparticles Revealed by Surface Plasmon Resonance Microscopy.

    PubMed

    Jiang, Dan; Sun, Linlin; Liu, Tao; Wang, Wei

    2017-10-06

    Electrochemical behaviors of Prussian blue (PB) have been intensively studied for decades because it not only serves as a model electro-active nanomaterial in fundamental electrochemistry, but also a promising metal-ion storage electrode material for developing rechargeable batteries. Traditional electrochemical studies are mostly based on bulk materials, leading to an averaged property of billions of PB nanoparticles. In the present work, we employed surface plasmon resonance microscopy (SPRM) to resolve the optical cyclic voltammograms of single PB nanoparticles during electrochemical cycling. It was found that the electrochemical behavior of single PB nanoparticles nicely followed a classical thin-film electrochemistry theory. While kinetic controlled electron transfer was observed at slower scan rates, intra-particle diffusion of K+ ions began to take effect when the scan rate was higher than 60 mV/s. We further found that the electrochemical activity among individual PB nanoparticles was very heterogeneous and such a phenomenon has not been previously observed in the bulk measurements. The present work not only demonstrates the thin-film electrochemical feature of single electro-active nanomaterials for the first time, it also validates the applicability of SPRM technique to investigate a variety of metal ion-storage battery materials, with implications in both fundamental nano-electrochemistry and electro-active materials for sensing and battery applications.

  7. Domain structure of the Acetogenium kivui surface layer revealed by electron crystallography and sequence analysis.

    PubMed Central

    Lupas, A; Engelhardt, H; Peters, J; Santarius, U; Volker, S; Baumeister, W

    1994-01-01

    The three-dimensional structure of the Acetogenium kivui surface layer (S-layer) has been determined to a resolution of 1.7 nm by electron crystallographic techniques. Two independent reconstructions were made from layers negatively stained with uranyl acetate and Na-phosphotungstate. The S-layer has p6 symmetry with a center-to-center spacing of approximately 19 nm. Within the layer, six monomers combine to form a ring-shaped core surrounded by a fenestrated rim and six spokes that point towards the axis of threefold symmetry and provide lateral connectivity to other hexamers in the layer. The structure of the A. kivui S-layer protein is very similar to that of the Bacillus brevis middle wall protein, with which it shares an N-terminal domain of homology. This domain is found in several other extracellular proteins, including the S-layer proteins from Bacillus sphaericus and Thermus thermophilus, Omp alpha from Thermotoga maritima, an alkaline cellulase from Bacillus strain KSM-635, and xylanases from Clostridium thermocellum and Thermoanaerobacter saccharolyticum, and may serve to anchor these proteins to the peptidoglycan. To our knowledge, this is the first example of a domain conserved in several S-layer proteins. Images PMID:8113161

  8. A Homology Model Reveals Novel Structural Features and an Immunodominant Surface Loop/Opsonic Target in the Treponema pallidum BamA Ortholog TP_0326

    PubMed Central

    Luthra, Amit; Anand, Arvind; Hawley, Kelly L.; LeDoyt, Morgan; La Vake, Carson J.; Caimano, Melissa J.; Cruz, Adriana R.; Salazar, Juan C.

    2015-01-01

    ABSTRACT We recently demonstrated that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses characteristic BamA bipartite topology. Herein, we used immunofluorescence analysis (IFA) to show that only the β-barrel domain of TP_0326 contains surface-exposed epitopes in intact T. pallidum. Using the solved structure of Neisseria gonorrhoeae BamA, we generated a homology model of full-length TP_0326. Although the model predicts a typical BamA fold, the β-barrel harbors features not described in other BamAs. Structural modeling predicted that a dome comprised of three large extracellular loops, loop 4 (L4), L6, and L7, covers the barrel's extracellular opening. L4, the dome's major surface-accessible loop, contains mainly charged residues, while L7 is largely neutral and contains a polyserine tract in a two-tiered conformation. L6 projects into the β-barrel but lacks the VRGF/Y motif that anchors L6 within other BamAs. IFA and opsonophagocytosis assay revealed that L4 is surface exposed and an opsonic target. Consistent with B cell epitope predictions, immunoblotting and enzyme-linked immunosorbent assay (ELISA) confirmed that L4 is an immunodominant loop in T. pallidum-infected rabbits and humans with secondary syphilis. Antibody capture experiments using Escherichia coli expressing OM-localized TP_0326 as a T. pallidum surrogate further established the surface accessibility of L4. Lastly, we found that a naturally occurring substitution (Leu593 → Gln593) in the L4 sequences of T. pallidum strains affects antibody binding in sera from syphilitic patients. Ours is the first study to employ a “structure-to-pathogenesis” approach to map the surface topology of a T. pallidum OMP within the context of syphilitic infection. IMPORTANCE Previously, we reported that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses the bipartite topology characteristic of a BamA ortholog

  9. Radiocarbon and uranium isotopes in surface waters reveal enhanced hydrologic connection with permafrost thaw

    NASA Astrophysics Data System (ADS)

    Ewing, S. A.; O'Donnell, J. A.; Koch, J. C.; Paces, J. B.; Aiken, G.; Striegl, R. G.

    2016-12-01

    The residence time of ice in permafrost is an indicator of past climate history, and of the resilience and vulnerability of high-latitude ecosystems to global change. Development of geochemical indicators of ground-ice residence times in permafrost will advance understanding of permafrost formation, preservation, and thaw in response to climate warming and other disturbance. We used uranium activity ratios (234U/238U) and radiocarbon (14C) to evaluate the signal of permafrost thaw at two gaged locations (upstream and downstream) on Beaver Creek, a central Alaskan stream that flows from rocky uplands to terraces and lowlands mantled by thick, ice-rich loess permafrost (yedoma). Uranium activity ratios in surface waters provide a tracer of transit time and source (permafrost thaw water, supra- and sub-permafrost groundwater), but must be interpreted in the context of parent material and hydrology. Previous work has shown that dissolved organic carbon (DOC) from yedoma in the age range of 10-100 ky is highly labile, suggesting ongoing production in permafrost and potential carbon (C) loss upon thaw with increasing permafrost age. Uranium activity ratios were inversely correlated with DOC-14C values in streamwater at the upstream gages throughout the year, and at the downstream gage during summer, indicating aged C that co-occurs with increased nitrate-N in winter baseflow at the upstream site, but not at the downstream site. In the context of observations at a number of sites in central Alaska, these patterns suggest enhanced hydrologic connection of the downstream site in summer that may be facilitated by permafrost thaw and may result in capture of young DOC in the floodplain. In regional streams, mineral substrate dictates hydrologic connection with permafrost thaw, with enhanced mixing of source waters from supra- and sub-permafrost groundwater as thaw progresses.

  10. Ancient rifting zones in eastern North America revealed by the ambient noise surface wave tomography

    NASA Astrophysics Data System (ADS)

    Liang, C.; Langston, C. A.

    2006-12-01

    We use the surface waves extracted from the cross-correlation of ambient noise data to invert for the group velocity structure in eastern North America. Stations of two regional seismic networks (networks deployed to monitor the New Madrid Seismic Zone and the eastern Tennessee seismic zone, respectively), together with the stations of national seismic network, greatly improve the ray coverage compared to earthquake waves. The short period (T=5 sec) group velocity map shows strong correlations with the depth to the Precambrian basement and appears to be positively correlated with the gravity. The long period (T=15 sec) group velocity map shows strong correlations with the regional geology. The most spectacular features are the prominent low velocity anomalies associated with the three arms of the triple junction located at the border of Oklahoma and Texas. The western arm of the triple junction (i.e. the Oklahoma Aulacogen) perpendicularly intersects a linear low velocity belt (LVB) possibly associated with the south portion of the Mid-continent rift. The eastern arm extends along the collision belt of the Ouachita orogeny to meet the south tip of the Appalachian Mountains. The nearly north-south striking LVB in the western Mississippi embayment is associated with the Reel Foot rift. However, the LVB extends further northward to the Great Lakes region and this feature is not present on the gravity anomaly map. One LVB extending from the Great lakes region southeastward to Michigan basin is possibly associated with the east portion of the Mid-continent rift. Those LVBs appear to be correlated with the high gravity anomalies that are associated with the rift belts.

  11. Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef

    PubMed Central

    Matheson, Nicholas J.; Sumner, Jonathan; Wals, Kim; Rapiteanu, Radu; Weekes, Michael P.; Vigan, Raphael; Weinelt, Julia; Schindler, Michael; Antrobus, Robin; Costa, Ana S.H.; Frezza, Christian; Clish, Clary B.; Neil, Stuart J.D.; Lehner, Paul J.

    2015-01-01

    Summary Critical cell surface immunoreceptors downregulated during HIV infection have previously been identified using non-systematic, candidate approaches. To gain a comprehensive, unbiased overview of how HIV infection remodels the T cell surface, we took a distinct, systems-level, quantitative proteomic approach. >100 plasma membrane proteins, many without characterized immune functions, were downregulated during HIV infection. Host factors targeted by the viral accessory proteins Vpu or Nef included the amino acid transporter SNAT1 and the serine carriers SERINC3/5. We focused on SNAT1, a β-TrCP-dependent Vpu substrate. SNAT1 antagonism was acquired by Vpu variants from the lineage of SIVcpz/HIV-1 viruses responsible for pandemic AIDS. We found marked SNAT1 induction in activated primary human CD4+ T cells, and used Consumption and Release (CoRe) metabolomics to identify alanine as an endogenous SNAT1 substrate required for T cell mitogenesis. Downregulation of SNAT1 therefore defines a unique paradigm of HIV interference with immunometabolism. PMID:26439863

  12. Sea surface temperature variability off southern Brazil and Uruguay as revealed from historical data since 1854

    NASA Astrophysics Data System (ADS)

    Zavialov, Peter O.; Wainer, Ilana; Absy, JoãO. M.

    1999-09-01

    About 300,000 quality-controlled local reports from ships of opportunity were complemented with the data extracted from global data records to compile monthly series of sea surface temperature (SST) for the period 1854 to 1994 on a grid 1° × 1° in latitude and longitude. These historical data are used to investigate the variability off the coast of southern Brazil and Uruguay in a broad range of temporal scales from seasonal to secular. With respect to behavior at these scales, three distinct areas can be identified in the study region. The first one, located over the shelf and controlled by winter invasions of subantarctic water along with Rio de la Plata and Patos-Mirim discharges, is characterized by large annual range of SST (7° to over 10°C), energetic mean square variability (from 1.4 to 2.2°C2, after removal of seasonal signal), and an extremely high secular trend toward warming (1.2 to 1.6°C per 100 years), especially in the proximity of the estuaries. The second one, an area of the Brazil Current influence, exhibits smaller annual range (5° to 7°C) and mean square variability (1 to 1.4°C2). The secular trend is from 1° to 1.2°C per 100 years, smaller than observed in the shelf, but still high compared to the global average. The third area, which encompasses the eastern deep ocean part of the region away from the influence of either major currents or coastal discharges, exhibits less energetic variability at all examined scales, as compared to the rest of the region. Everywhere in the region, 50 to 80% of interannual variability is associated with periods smaller than 10 years; however, compared to the rest of the region, the shelf zone is characterized by a relatively large contribution from decadal and interdecadal scales. In austral winter a thermal front forms in the study region, separating warm tropical water associated with the Brazil Current and cold subantarctic water flowing northward on the shelf with an admixture of coastal

  13. Elements of the Chicxulub Impact Structure as revealed in SRTM and surface GPS topographic data

    NASA Astrophysics Data System (ADS)

    Kobrick, M.; Kinsland, G. L.; Sanchez, G.; Cardador, M. H.

    2003-04-01

    Pope et al have utilized elevations from the Petroleos Mexicanos (PEMEX) gravity data files to show that the main component of the surface expression of the Chicxu-lub Impact Structure is a roughly semi-circular, low-relief depression about 90 km in diameter. They also identified other topographic features and the elements of the buried impact which possibly led to the development of these features. Kinsland et al presented a connection between these topographic anomalies, small gravity anomalies and buried structure of the impact. Shaded relief images from recently acquired SRTM elevation data clearly show the circular depression of the crater and the moat/cenote ring. In addition we can readily identify Inner trough 1, Inner trough 2