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Sample records for multiple oligomeric species

  1. Molecular basis of coiled-coil oligomerization-state specificity.

    Science.gov (United States)

    Ciani, Barbara; Bjelic, Saša; Honnappa, Srinivas; Jawhari, Hatim; Jaussi, Rolf; Payapilly, Aishwarya; Jowitt, Thomas; Steinmetz, Michel O; Kammerer, Richard A

    2010-11-16

    Coiled coils are extensively and successfully used nowadays to rationally design multistranded structures for applications, including basic research, biotechnology, nanotechnology, materials science, and medicine. The wide range of applications as well as the important functions these structures play in almost all biological processes highlight the need for a detailed understanding of the factors that control coiled-coil folding and oligomerization. Here, we address the important and unresolved question why the presence of particular oligomerization-state determinants within a coiled coil does frequently not correlate with its topology. We found an unexpected, general link between coiled-coil oligomerization-state specificity and trigger sequences, elements that are indispensable for coiled-coil formation. By using the archetype coiled-coil domain of the yeast transcriptional activator GCN4 as a model system, we show that well-established trimer-specific oligomerization-state determinants switch the peptide's topology from a dimer to a trimer only when inserted into the trigger sequence. We successfully confirmed our results in two other, unrelated coiled-coil dimers, ATF1 and cortexillin-1. We furthermore show that multiple topology determinants can coexist in the same trigger sequence, revealing a delicate balance of the resulting oligomerization state by position-dependent forces. Our experimental results should significantly improve the prediction of the oligomerization state of coiled coils. They therefore should have major implications for the rational design of coiled coils and consequently many applications using these popular oligomerization domains.

  2. Topology and Oligomerization of Mono- and Oligomeric Proteins Regulate Their Half-Lives in the Cell.

    Science.gov (United States)

    Mallik, Saurav; Kundu, Sudip

    2018-06-05

    To find additional structural constraints (besides disordered segments) that regulate protein half-life in the cell, we herein assess the influence of native topology of monomeric and sequestration of oligomeric proteins into multimeric complexes in yeast, human, and mouse. Native topology acts as a molecular marker of globular protein's mechanical resistance and consequently captures their half-life variations on genome scale. Sequestration into multimeric complexes elongates oligomeric protein half-life in the cell, presumably by burying ubiquitinoylation sites and disordered segments required for proteasomal recognition. The latter effect is stronger for proteins associated with multiple complexes and for those binding early during complex self-assembly, including proteins that oligomerize with large proportions of surface buried. After gene duplication, diversification of topology and sequestration into non-identical sets of complexes alter half-lives of paralogous proteins during the course of evolution. Thus, native topology and sequestration into multimeric complexes reflect designing principles of proteins to regulate their half-lives. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. Effects of Glycine, Water, Ammonia, and Ammonium Bicarbonate on the Oligomerization of Methionine

    Science.gov (United States)

    Huang, Rui; Furukawa, Yoshihiro; Otake, Tsubasa; Kakegawa, Takeshi

    2017-06-01

    The abiotic oligomerization of amino acids may have created primordial, protein-like biological catalysts on the early Earth. Previous studies have proposed and evaluated the potential of diagenesis for the amino acid oligomerization, simulating the formation of peptides that include glycine, alanine, and valine, separately. However, whether such conditions can promote the formation of peptides composed of multiple amino acids remains unclear. Furthermore, the chemistry of pore water in sediments should affect the oligomerization and degradation of amino acids and oligomers, but these effects have not been studied extensively. In this study, we investigated the effects of water, ammonia, ammonium bicarbonate, pH, and glycine on the oligomerization and degradation of methionine under high pressure (150 MPa) and high temperature conditions (175 °C) for 96 h. Methionine is more difficult to oligomerize than glycine and methionine dimer was formed in the incubation of dry powder of methionine. Methionine oligomers as long as trimers, as well as methionylglycine and glycylmethionine, were formed under every condition with these additional compounds. Among the compounds tested, the oligomerization reaction rate was accelerated by the presence of water and by an increase in pH. Ammonia also increased the oligomerization rate but consumed methionine by side reactions and resulted in the rapid degradation of methionine and its peptides. Similarly, glycine accelerated the oligomerization rate of methionine and the degradation of methionine, producing water, ammonia, and bicarbonate through its decomposition. With Gly, heterogeneous dimers (methionylglycine and glycylmethionine) were formed in greater amounts than with other additional compounds although smaller amount of these heterogeneous dimers were formed with other additional compounds. These results suggest that accelerated reaction rates induced by water and co-existing reactive compounds promote the oligomerization

  4. Controlling amyloid-beta peptide(1-42) oligomerization and toxicity by fluorinated nanoparticles.

    Science.gov (United States)

    Saraiva, Ana M; Cardoso, Isabel; Pereira, M Carmo; Coelho, Manuel A N; Saraiva, Maria João; Möhwald, Helmuth; Brezesinski, Gerald

    2010-09-03

    The amyloid-beta peptide (Abeta) is a major fibrillar component of neuritic plaques in Alzheimer's disease brains and is related to the pathogenesis of the disease. Soluble oligomers that precede fibril formation have been proposed as the main neurotoxic species that contributes to neurodegeneration and dementia. We hypothesize that oligomerization and cytotoxicity can be repressed by nanoparticles (NPs) that induce conformational changes in Abeta42. We show here that fluorinated and hydrogenated NPs with different abilities to change Abeta42 conformation influence oligomerization as assessed by atomic force microscopy, immunoblot and SDS-PAGE. Fluorinated NPs, which promote an increase in alpha-helical content, exert an antioligomeric effect, whereas hydrogenated analogues do not and lead to aggregation. Cytotoxicity assays confirmed our hypothesis by indicating that the conformational conversion of Abeta42 into an alpha-helical-enriched secondary structure also has antiapoptotic activity, thereby increasing the viability of cells treated with oligomeric species.

  5. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

    Energy Technology Data Exchange (ETDEWEB)

    Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.; Li, Sheng; Tickle, Ian J.; Bricogne, Gérard; Saphire, Erica Ollmann (Scripps); (Globel Phasing); (UCSD)

    2016-11-09

    ABSTRACT

    Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (generaspecies'>Marburgvirusandspecies'>Ebolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV.

    IMPORTANCEMarburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the

  6. Protic ionic liquids based on the dimeric and oligomeric anions: [(AcO)xH(x-1)]-.

    Science.gov (United States)

    Johansson, K M; Izgorodina, E I; Forsyth, M; MacFarlane, D R; Seddon, K R

    2008-05-28

    We describe a fluidity and conductivity study as a function of composition in N-methylpyrrolidine-acetic acid mixtures. The simple 1 : 1 acid-base mixture appears to form an ionic liquid, but its degree of ionicity is quite low and such liquids are better thought of as poorly dissociated mixtures of acid and base. The composition consisting of 3 moles acetic acid and 1 mole N-methylpyrrolidine is shown to form the highest ionicity mixture in this binary due to the presence of oligomeric anionic species [(AcO)(x)H(x-1)](-) stabilised by hydrogen bonds. These oligomeric species, being weaker bases than the acetate anion, shift the proton transfer equilibrium towards formation of ionic species, thus generating a higher degree of ionicity than is present at the 1 : 1 composition. A Walden plot analysis, thermogravimetric behaviour and proton NMR data, as well as ab initio calculations of the oligomeric species, all support this conclusion.

  7. Stability of human interferon-beta 1: oligomeric human interferon-beta 1 is inactive but is reactivated by monomerization.

    Science.gov (United States)

    Utsumi, J; Yamazaki, S; Kawaguchi, K; Kimura, S; Shimizu, H

    1989-10-05

    Human interferon-beta 1 is extremely stable is a low ionic strength solution of pH 2 such as 10 mM HCl at 37 degrees C. However, the presence of 0.15 M NaCl led to a remarkable loss of antiviral activity. The molecular-sieve high-performance liquid chromatography revealed that, whereas completely active human interferon-beta 1 eluted as a 25 kDa species (monomeric form), the inactivated preparation eluted primarily as a 90 kDa species (oligomeric form). The specific activity (units per mg protein) of the oligomeric form was approx. 10% of that of the monomeric form. This observation shows that oligomeric human interferon-beta 1 is apparently in an inactive form. When the oligomeric eluate was resolved by polyacrylamide gel containing sodium dodecyl sulphate (SDS), it appeared to be monomeric under non-reducing conditions. Monomerization of the oligomeric human interferon-beta 1 by treatment with 1% SDS, fully regenerated its antiviral activity. These results suggest that the inactivation of the human interferon-beta 1 preparation was caused by its oligomerization via hydrophobic interactions without the formation of intermolecular disulphide bonds. These oligomers can be dissociated by SDS to restore biological activity.

  8. MxiN Differentially Regulates Monomeric and Oligomeric Species of the Shigella Type Three Secretion System ATPase Spa47.

    Science.gov (United States)

    Case, Heather B; Dickenson, Nicholas E

    2018-04-17

    Shigella rely entirely on the action of a single type three secretion system (T3SS) to support cellular invasion of colonic epithelial cells and to circumvent host immune responses. The ATPase Spa47 resides at the base of the Shigella needle-like type three secretion apparatus (T3SA), supporting protein secretion through the apparatus and providing a likely means for native virulence regulation by Shigella and a much needed target for non-antibiotic therapeutics to treat Shigella infections. Here, we show that MxiN is a differential regulator of Spa47 and that its regulatory impact is determined by the oligomeric state of the Spa47 ATPase, with which it interacts. In vitro and in vivo characterization shows that interaction of MxiN with Spa47 requires the six N-terminal residues of Spa47 that are also necessary for stable Spa47 oligomer formation and activation. This interaction with MxiN negatively influences the activity of Spa47 oligomers while upregulating the ATPase activity of monomeric Spa47. Detailed kinetic analyses of monomeric and oligomeric Spa47 in the presence and absence of MxiN uncover additional mechanistic insights into the regulation of Spa47 by MxiN, suggesting that the MxiN/Spa47 species resulting from interaction with monomeric and oligomeric Spa47 are functionally distinct and that both could be involved in Shigella T3SS regulation. Uncovering regulation of Spa47 by MxiN addresses an important gap in the current understanding of how Shigella controls T3SA activity and provides the first description of differential T3SS ATPase regulation by a native T3SS protein.

  9. Orally administrated cinnamon extract reduces β-amyloid oligomerization and corrects cognitive impairment in Alzheimer's disease animal models.

    Directory of Open Access Journals (Sweden)

    Anat Frydman-Marom

    Full Text Available An increasing body of evidence indicates that accumulation of soluble oligomeric assemblies of β-amyloid polypeptide (Aβ play a key role in Alzheimer's disease (AD pathology. Specifically, 56 kDa oligomeric species were shown to be correlated with impaired cognitive function in AD model mice. Several reports have documented the inhibition of Aβ plaque formation by compounds from natural sources. Yet, evidence for the ability of common edible elements to modulate Aβ oligomerization remains an unmet challenge. Here we identify a natural substance, based on cinnamon extract (CEppt, which markedly inhibits the formation of toxic Aβ oligomers and prevents the toxicity of Aβ on neuronal PC12 cells. When administered to an AD fly model, CEppt rectified their reduced longevity, fully recovered their locomotion defects and totally abolished tetrameric species of Aβ in their brain. Furthermore, oral administration of CEppt to an aggressive AD transgenic mice model led to marked decrease in 56 kDa Aβ oligomers, reduction of plaques and improvement in cognitive behavior. Our results present a novel prophylactic approach for inhibition of toxic oligomericspecies formation in AD through the utilization of a compound that is currently in use in human diet.

  10. A fluorimetric readout reporting the kinetics of nucleotide-induced human ribonucleotide reductase oligomerization.

    Science.gov (United States)

    Fu, Yuan; Lin, Hongyu; Wisitpitthaya, Somsinee; Blessing, William A; Aye, Yimon

    2014-11-24

    Human ribonucleotide reductase (hRNR) is a target of nucleotide chemotherapeutics in clinical use. The nucleotide-induced oligomeric regulation of hRNR subunit α is increasingly being recognized as an innate and drug-relevant mechanism for enzyme activity modulation. In the presence of negative feedback inhibitor dATP and leukemia drug clofarabine nucleotides, hRNR-α assembles into catalytically inert hexameric complexes, whereas nucleotide effectors that govern substrate specificity typically trigger α-dimerization. Currently, both knowledge of and tools to interrogate the oligomeric assembly pathway of RNR in any species in real time are lacking. We therefore developed a fluorimetric assay that reliably reports on oligomeric state changes of α with high sensitivity. The oligomerization-directed fluorescence quenching of hRNR-α, covalently labeled with two fluorophores, allows for direct readout of hRNR dimeric and hexameric states. We applied the newly developed platform to reveal the timescales of α self-assembly, driven by the feedback regulator dATP. This information is currently unavailable, despite the pharmaceutical relevance of hRNR oligomeric regulation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Catalytic oligomerization of terminal alkynes promoted by organo-f-complexes

    International Nuclear Information System (INIS)

    Straub, T.; Haskel, A.; Eisen, M.S.

    1995-01-01

    Organoactinides of the type Cp* 2 AcMe 2 (Cp*=C 5 Me 5 ; Ac=Th, U) are active catalyst precursors for the oligomerization of terminal alkynes HC triple-bond CR (R=alkyl, aryl, SiMe 3 ). The regioselectivity and the extent of oligomerization strongly depend on the alkyne substituent R, whereas the catalytic reactivity is similar for 1 and 2. In the presence of one of these organoactinides, for example, HCCSiMe 3 regioselectively oligomerizes to the head-to-tail dimer 3 (5%) and the trimer 4 (95%). 1 and 2 react with the terminal alkynes, releasing methane, to the corresponding bisacetylide complexes which are active species and in the catalytic reactions. The bisacetylide complex (η 5 -C 5 Me 5 ) 2 U(CCPh) 2 was identified by proton NMR spectroscopy. Subsequent insertion of alkyne molecules in the actinide-carbon σ-bonds leads to the formation of actinide-alkenyl complexes. The turnover limiting step is the release of the organic oligomer from the actinide-organyl complex. A species of the latter has been spectroscopically characterized in the trimerization reaction of HCCSiMe 3 . In this poster, the catalytic reactivity of the actinide alkyls 1 and 2 with various mono-substituted alkynes as well as the spectroscopic characterization of the key organometallic intermediate complexes in the catalytic cycle and a detailed mechanistic discussion are given

  12. Catalyst-controlled oligomerization for the collective synthesis of polypyrroloindoline natural products.

    Science.gov (United States)

    Jamison, Christopher R; Badillo, Joseph J; Lipshultz, Jeffrey M; Comito, Robert J; MacMillan, David W C

    2017-12-01

    In nature, many organisms generate large families of natural product metabolites that have related molecular structures as a means to increase functional diversity and gain an evolutionary advantage against competing systems within the same environment. One pathway commonly employed by living systems to generate these large classes of structurally related families is oligomerization, wherein a series of enzymatically catalysed reactions is employed to generate secondary metabolites by iteratively appending monomers to a growing serial oligomer chain. The polypyrroloindolines are an interesting class of oligomeric natural products that consist of multiple cyclotryptamine subunits. Herein we describe an iterative application of asymmetric copper catalysis towards the synthesis of six distinct oligomeric polypyrroloindoline natural products: hodgkinsine, hodgkinsine B, idiospermuline, quadrigemine H and isopsychotridine B and C. Given the customizable nature of the small-molecule catalysts employed, we demonstrate that this strategy is further amenable to the construction of quadrigemine H-type alkaloids not isolated previously from natural sources.

  13. Biocatalytically Oligomerized Epicatechin with Potent and Specific Anti-proliferative Activity for Human Breast Cancer Cells

    Directory of Open Access Journals (Sweden)

    Ramaswamy Nagarajan

    2008-11-01

    Full Text Available Catechins, naturally occurring flavonoids derived from wine and green tea, are known to exhibit multiple health benefits. Epigallocatechin gallate (EGCG is one of the most widely investigated catechins, but its efficacy in cancer therapy is still inconsistent and limited. The poor stability of EGCG has contributed to the disparity in the reported anti-cancer activity and other beneficial properties. Here we report an innovative enzymatic strategy for the oligomerization of catechins (specifically epicatechin that yields stable, water-soluble oligomerized epicatechins with enhanced and highly specific anti-proliferative activity for human breast cancer cells. This one-pot oxidative oligomerization is carried out in ambient conditions using Horseradish Peroxidase (HRP as a catalyst yielding water-soluble oligo(epicatechins. The oligomerized epicatechins obtained exhibit excellent growth inhibitory effects against human breast cancer cells with greater specificity towards growth-inhibiting cancer cells as opposed to normal cells, achieving a high therapeutic differential. Our studies indicate that water-soluble oligomeric epicatechins surpass EGCG in stability, selectivity and efficacy at lower doses.

  14. Fingolimod phosphate attenuates oligomeric amyloid β-induced neurotoxicity via increased brain-derived neurotrophic factor expression in neurons.

    Directory of Open Access Journals (Sweden)

    Yukiko Doi

    Full Text Available The neurodegenerative processes that underlie Alzheimer's disease are mediated, in part, by soluble oligomeric amyloid β, a neurotoxic protein that inhibits hippocampal long-term potentiation, disrupts synaptic plasticity, and induces the production of reactive oxygen species. Here we show that the sphingosine-1-phosphate (S1P receptor (S1PR agonist fingolimod phosphate (FTY720-P-a new oral drug for multiple sclerosis-protects neurons against oligomeric amyloid β-induced neurotoxicity. We confirmed that primary mouse cortical neurons express all of the S1P receptor subtypes and FTY720-P directly affects the neurons. Treatment with FTY720-P enhanced the expression of brain-derived neurotrophic factor (BDNF in neurons. Moreover, blocking BDNF-TrkB signaling with a BDNF scavenger, TrkB inhibitor, or ERK1/2 inhibitor almost completely ablated these neuroprotective effects. These results suggested that the neuroprotective effects of FTY720-P are mediated by upregulated neuronal BDNF levels. Therefore, FTY720-P may be a promising therapeutic agent for neurodegenerative diseases, such as Alzheimer's disease.

  15. OLIGOMERIZATION AND LIQUEFACTION OF ETHYLENE

    African Journals Online (AJOL)

    oligomerize ethylene gas in a packed bed reactor operated at 100-300°C under apressure of 500psi and ... The gas flow was then switched back to N, gas and temperature controller was simultaneously set to the desired reaction temperature. Once the desired .... be considered non-ideal for ethylene oligomerization.

  16. A Small-Molecule Inhibitor of Bax and Bak Oligomerization Prevents Genotoxic Cell Death and Promotes Neuroprotection.

    Science.gov (United States)

    Niu, Xin; Brahmbhatt, Hetal; Mergenthaler, Philipp; Zhang, Zhi; Sang, Jing; Daude, Michael; Ehlert, Fabian G R; Diederich, Wibke E; Wong, Eve; Zhu, Weijia; Pogmore, Justin; Nandy, Jyoti P; Satyanarayana, Maragani; Jimmidi, Ravi K; Arya, Prabhat; Leber, Brian; Lin, Jialing; Culmsee, Carsten; Yi, Jing; Andrews, David W

    2017-04-20

    Aberrant apoptosis can lead to acute or chronic degenerative diseases. Mitochondrial outer membrane permeabilization (MOMP) triggered by the oligomerization of the Bcl-2 family proteins Bax/Bak is an irreversible step leading to execution of apoptosis. Here, we describe the discovery of small-molecule inhibitors of Bax/Bak oligomerization that prevent MOMP. We demonstrate that these molecules disrupt multiple, but not all, interactions between Bax dimer interfaces thereby interfering with the formation of higher-order oligomers in the MOM, but not recruitment of Bax to the MOM. Small-molecule inhibition of Bax/Bak oligomerization allowed cells to evade apoptotic stimuli and rescued neurons from death after excitotoxicity, demonstrating that oligomerization of Bax is essential for MOMP. Our discovery of small-molecule Bax/Bak inhibitors provides novel tools for the investigation of the mechanisms leading to MOMP and will ultimately facilitate development of compounds inhibiting Bax/Bak in acute and chronic degenerative diseases. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Modelling the interdependence between the stoichiometry of receptor oligomerization and ligand binding for a coexisting dimer/tetramer receptor system.

    Science.gov (United States)

    Rovira, X; Vivó, M; Serra, J; Roche, D; Strange, P G; Giraldo, J

    2009-01-01

    Many G protein-coupled receptors have been shown to exist as oligomers, but the oligomerization state and the effects of this on receptor function are unclear. For some G protein-coupled receptors, in ligand binding assays, different radioligands provide different maximal binding capacities. Here we have developed mathematical models for co-expressed dimeric and tetrameric species of receptors. We have considered models where the dimers and tetramers are in equilibrium and where they do not interconvert and we have also considered the potential influence of the ligands on the degree of oligomerization. By analogy with agonist efficacy, we have considered ligands that promote, inhibit or have no effect on oligomerization. Cell surface receptor expression and the intrinsic capacity of receptors to oligomerize are quantitative parameters of the equations. The models can account for differences in the maximal binding capacities of radioligands in different preparations of receptors and provide a conceptual framework for simulation and data fitting in complex oligomeric receptor situations.

  18. Involvement of C-Terminal Histidines in Soybean PM1 Protein Oligomerization and Cu2+ Binding.

    Science.gov (United States)

    Liu, Guobao; Liu, Ke; Gao, Yang; Zheng, Yizhi

    2017-06-01

    Late embryogenesis abundant (LEA) proteins are widely distributed among plant species, where they contribute to abiotic stress tolerance. LEA proteins can be classified into seven groups according to conserved sequence motifs. The PM1 protein from soybean, which belongs to the Pfam LEA_1 group, has been shown previously to be at least partially natively unfolded, to bind metal ions and potentially to stabilize proteins and membranes. Here, we investigated the role of the PM1 C-terminal domain and in particular the multiple histidine residues in this half of the protein. We constructed recombinant plasmids expressing full-length PM1 and two truncated forms, PM1-N and PM1-C, which represent the N- and C-terminal halves of the protein, respectively. Immunoblotting and cross-linking experiments showed that full-length PM1 forms oligomers and high molecular weight (HMW) complexes in vitro and in vivo, while PM1-C, but not PM1-N, also formed oligomers and HMW complexes in vitro. When the histidine residues in PM1 and PM1-C were chemically modified, oligomerization was abolished, suggesting that histidines play a key role in this process. Furthermore, we demonstrated that high Cu2+ concentrations promote oligomerization and induce PM1 and PM1-C to form HMW complexes. Therefore, we speculate that PM1 proteins not only maintain ion homeostasis in the cytoplasm, but also potentially stabilize and protect other proteins during abiotic stress by forming a large, oligomeric molecular shield around biological targets. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  19. Spa47 is an oligomerization-activated type three secretion system (T3SS) ATPase from Shigella flexneri.

    Science.gov (United States)

    Burgess, Jamie L; Jones, Heather B; Kumar, Prashant; Toth, Ronald T; Middaugh, C Russell; Antony, Edwin; Dickenson, Nicholas E

    2016-05-01

    Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa47 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 with the largest greater than 8 fold more active for ATP hydrolysis than the monomer. An ATPase inactive Spa47 point mutant was then engineered by targeting a conserved Lysine within the predicted Walker A motif of Spa47. Interestingly, the mutant maintained a similar oligomerization pattern as active Spa47, but was unable to restore invasion phenotype when used to complement a spa47 null S. flexneri strain. Together, these results identify Spa47 as a Shigella T3SS ATPase and suggest that its activity is linked to oligomerization, perhaps as a regulatory mechanism as seen in some related pathogens. Additionally, Spa47 catalyzed ATP hydrolysis appears to be essential for host cell invasion, providing a strong platform for additional studies dissecting its role in virulence and providing an attractive target for anti-infective agents. © 2016 The Protein Society.

  20. An Investigation of Chemical Landscapes in Aqueous Electrosprays by Tracking Oligomerization of Isoprene

    KAUST Repository

    Junior, Adair Gallo

    2017-12-01

    Electrospray ionization mass spectrometry (ESIMS) is widely used to characterize neutral and ionic species in solvents. Typically, electrical, thermal, and pneumatic potentials are applied to create electrosprays from which charged ionic species are ejected for downstream analysis by mass spectrometry. Most recently, ESIMS has been exploited to investigate ambient proton transfer reactions at air-water interfaces in real time. We assessed the validity of these experiments via complementary laboratory experiments. Specifically, we characterized the products of two reaction scenarios via ESIMS and proton nuclear magnetic resonance (1H-NMR): (i) emulsions of pH-adjusted water and isoprene (C5H8) that were mechanically agitated, and (ii) electrosprays of pH-adjusted water that were collided with gas-phase isoprene. Our experiments unambiguously demonstrate that, while isoprene does not oligomerize in emulsions, it does undergo protonation and oligomerization in electrosprays, both with and without pH-adjusted water, confirming that C-C bonds form along myriad high-energy pathways during electrospray ionization. We also compared our experimental results with some quantum mechanics simulations of isoprene molecules interacting with hydronium at different hydration levels (gas versus liquid phase). In agreement with our experiments, the kinetic barriers to protonation and oligomerization of isoprene were inaccessible under ambient conditions. Rather, the gas-phase chemistries during electrospray ionization drove the oligomerization of isoprene. Therefore, we consider that ESIMS could induce artifacts in interfacial reactions. These findings warrant a reassessment of previous reports on tracking chemistries under ambient conditions at liquid-vapor interfaces via ESIMS. Further, we took some high-speed images of electrosprays where it was possible to observe the main characteristics of the phenomena, i.e. Taylor cone, charge separation, and Coulomb fission. Finally, we took

  1. Dimerization and oligomerization of the chaperone calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, Charlotte S; Ryder, L Rebekka; Steinø, Anne

    2003-01-01

    protein. Using PAGE, urea gradient gel electrophoresis, capillary electrophoresis and MS, we show that dimerization through the SH group can be induced by lowering the pH to 5-6, heating, or under conditions that favour partial unfolding such as urea concentrations above 2.6 m or SDS concentrations above...... that favour partial unfolding or an intramolecular local conformational change that allows oligomerization, resulting in a heterogeneous mixture of oligomers consisting of up to 10 calreticulin monomers. The oligomeric calreticulin was very stable, but oligomerization was partially reversed by addition of 8 m...

  2. Mechanism of the electrochemical oligomerization of thionaphteneindole: a spectroscopic study

    Science.gov (United States)

    Poggi, Gabriella; Casalbore Miceli, Giuseppe; Beggiato, Giancarlo; Emmi, Salvatore S.

    1997-10-01

    The UV, visible and NIR spectra recorded during electrolysis of TNI in CH 2Cl 2 have been studied as a function of electrolysis time and of the quantity of charge exchanged. Among the oligomeric species that might be responsible for the behaviour observed, particular attention has been devoted to dimers of TNI characterized by different charges, presence of unpaired electrons, and deprotonation of the amino hydrogens. A sample of these species has been described theoretically by means of the PM3 semiempirical hamiltonian and their spectra have been computed giving results in reasonable agreement with the observed transitions.

  3. Crystal Structure of the Oligomeric Form of Lassa Virus Matrix Protein Z.

    Science.gov (United States)

    Hastie, Kathryn M; Zandonatti, Michelle; Liu, Tong; Li, Sheng; Woods, Virgil L; Saphire, Erica Ollmann

    2016-05-01

    The arenavirus matrix protein Z is highly multifunctional and occurs in both monomeric and oligomeric forms. The crystal structure of a dodecamer of Z from Lassa virus, presented here, illustrates a ring-like structure with a highly basic center. Mutagenesis demonstrates that the dimeric interface within the dodecamer and a Lys-Trp-Lys triad at the center of the ring are important for oligomerization. This structure provides an additional template to explore the many functions of Z. The arenavirus Lassa virus causes hundreds of thousands of infections each year, many of which develop into fatal hemorrhagic fever. The arenavirus matrix protein Z is multifunctional, with at least four distinct roles. Z exists in both monomeric and oligomeric forms, each of which likely serves a specific function in the viral life cycle. Here we present the dodecameric form of Lassa virus Z and demonstrate that Z forms a "wreath" with a highly basic center. This structure and that of monomeric Z now provide a pair of critical templates by which the multiple roles of Z in the viral life cycle may be interpreted. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  4. Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides

    International Nuclear Information System (INIS)

    Heintz, Udo; Meinhart, Anton; Winkler, Andreas

    2014-01-01

    Crystal structures of two truncated variants of the transcription factor PpsR from R. sphaeroides are presented that enabled the phasing of a triple PAS domain construct. Together, these structures reveal the importance of α-helical PAS extensions for multi-PAS domain-mediated protein oligomerization and function. Per–ARNT–Sim (PAS) domains are essential modules of many multi-domain signalling proteins that mediate protein interaction and/or sense environmental stimuli. Frequently, multiple PAS domains are present within single polypeptide chains, where their interplay is required for protein function. Although many isolated PAS domain structures have been reported over the last decades, only a few structures of multi-PAS proteins are known. Therefore, the molecular mechanism of multi-PAS domain-mediated protein oligomerization and function is poorly understood. The transcription factor PpsR from Rhodobacter sphaeroides is such a multi-PAS domain protein that, in addition to its three PAS domains, contains a glutamine-rich linker and a C-terminal helix–turn–helix DNA-binding motif. Here, crystal structures of two N-terminally and C-terminally truncated PpsR variants that comprise a single (PpsR Q-PAS1 ) and two (PpsR N-Q-PAS1 ) PAS domains, respectively, are presented and the multi-step strategy required for the phasing of a triple PAS domain construct (PpsR ΔHTH ) is illustrated. While parts of the biologically relevant dimerization interface can already be observed in the two shorter constructs, the PpsR ΔHTH structure reveals how three PAS domains enable the formation of multiple oligomeric states (dimer, tetramer and octamer), highlighting that not only the PAS cores but also their α-helical extensions are essential for protein oligomerization. The results demonstrate that the long helical glutamine-rich linker of PpsR results from a direct fusion of the N-cap of the PAS1 domain with the C-terminal extension of the N-domain that plays an important

  5. Reversible peptide oligomerization over nanoscale gold surfaces

    Directory of Open Access Journals (Sweden)

    Kazushige Yokoyama

    2015-11-01

    Full Text Available A selective oligomeric formation of amyloid beta 1-40 (Ab1-40 monomers over a nanogold colloidal surface was investigated. An unfolded Ab1-40 monomer is considered to construct a dimer or trimer based oligomeric form with its hydrophobic segment placing outward under an acidic condition. Under a basic condition, a conformation of Ab is expected to take a folded monomeric form with its hydrophilic segment folded inward, avoiding the networking with residual colloidal particles. The most probable oligomeric form constructed over a 20 nm gold colloidal surface within a 25 ℃ to 65 ℃ temperature range is a dimer based unit and that over 30 or 40 nm gold colloidal surface below 15 ℃ is concluded to be a trimer based unit. However, selective oligomerization was not successfully reproduced under the rest of the conditions. A dipole-induced dipole interaction must cause a flexible structural change between folded and unfolded forms.

  6. Polymorphism and mesomorphism of oligomeric surfactants: effect of the degree of oligomerization.

    Science.gov (United States)

    Jurašin, D; Pustak, A; Habuš, I; Šmit, I; Filipović-Vinceković, N

    2011-12-06

    A series of cationic oligomeric surfactants (quaternary dodecyldimethylammonium ions with two, three, or four chains connected by an ethylene spacer at the headgroup level, abbreviated as dimer, trimer, and tetramer) were synthesized and characterized. The influence of the degree of oligomerization on their polymorphic and mesomorphic properties was investigated by means of X-ray diffraction, polarizing optical microscopy, thermogravimetry, and differential scanning calorimetry. All compounds display layered arrangements with interdigitated dodecyl chains. The increase in the degree of oligomerization increases the interlayer distance and decreases the ordering in the solid phase; whereas the dimer sample is fully crystalline with well-developed 3D ordering and the trimer and tetramer crystallize as highly ordered crystal smectic phases. The number of thermal phase transitions and sequence of phases are markedly affected by the number of dodecyl chains. Anhydrous samples exhibit polymorphism and thermotropic mesomorphism of the smectic type, with the exception of the tetramer that displays only transitions at higher temperature associated with decomposition and melting. All hydrated compounds form lyotropic mesophases showing reversible phase transitions upon heating and cooling. The sequence of liquid-crystalline phases for the dimer, typical of concentrated ionic surfactant systems, comprises a hexagonal phase at lower temperatures and a smectic phase at higher temperatures. In contrast, the trimer and tetramer reveal textures of the hexagonal phase. © 2011 American Chemical Society

  7. Anesthetic propofol attenuates the isoflurane-induced caspase-3 activation and Aβ oligomerization.

    Directory of Open Access Journals (Sweden)

    Yiying Zhang

    Full Text Available Accumulation and deposition of β-amyloid protein (Aβ are the hallmark features of Alzheimer's disease. The inhalation anesthetic isoflurane has been shown to induce caspase activation and increase Aβ accumulation. In addition, recent studies suggest that isoflurane may directly promote the formation of cytotoxic soluble Aβ oligomers, which are thought to be the key pathological species in AD. In contrast, propofol, the most commonly used intravenous anesthetic, has been reported to have neuroprotective effects. We therefore set out to compare the effects of isoflurane and propofol alone and in combination on caspase-3 activation and Aβ oligomerization in vitro and in vivo. Naïve and stably-transfected H4 human neuroglioma cells that express human amyloid precursor protein, the precursor for Aβ; neonatal mice; and conditioned cell culture media containing secreted human Aβ40 or Aβ42 were treated with isoflurane and/or propofol. Here we show for the first time that propofol can attenuate isoflurane-induced caspase-3 activation in cultured cells and in the brain tissues of neonatal mice. Furthermore, propofol-mediated caspase inhibition occurred when there were elevated levels of Aβ. Finally, isoflurane alone induces Aβ42, but not Aβ40, oligomerization, and propofol can inhibit the isoflurane-mediated oligomerization of Aβ42. These data suggest that propofol may mitigate the caspase-3 activation by attenuating the isoflurane-induced Aβ42 oligomerization. Our findings provide novel insights into the possible mechanisms of isoflurane-induced neurotoxicity that may aid in the development of strategies to minimize potential adverse effects associated with the administration of anesthetics to patients.

  8. Protic Cationic Oligomeric Ionic Liquids of the Urethane Type

    DEFF Research Database (Denmark)

    Shevchenko, V. V.; Stryutsky, A. V.; Klymenko, N. S.

    2014-01-01

    Protic oligomeric cationic ionic liquids of the oligo(ether urethane) type are synthesized via the reaction of an isocyanate prepolymer based on oligo(oxy ethylene)glycol with M = 1000 with hexamethylene-diisocyanate followed by blocking of the terminal isocyanate groups with the use of amine...... derivatives of imidazole, pyridine, and 3-methylpyridine and neutralization of heterocycles with ethanesulfonic acid and p-toluenesulfonic acid. The structures and properties of the synthesized oligomeric ionic liquids substantially depend on the structures of the ionic groups. They are amorphous at room...... temperature, but ethanesulfonate imidazolium and pyridinium oligomeric ionic liquids form a low melting crystalline phase. The proton conductivities of the oligomeric ionic liquids are determined by the type of cation in the temperature range 80-120 degrees C under anhydrous conditions and vary within five...

  9. Different domains are critical for oligomerization compatibility of different connexins

    Science.gov (United States)

    MARTÍNEZ, Agustín D.; MARIPILLÁN, Jaime; ACUÑA, Rodrigo; MINOGUE, Peter J.; BERTHOUD, Viviana M.; BEYER, Eric C.

    2011-01-01

    Oligomerization of connexins is a critical step in gap junction channel formation. Some members of the connexin family can oligomerize with other members and form functional heteromeric hemichannels [e.g. Cx43 (connexin 43) and Cx45], but others are incompatible (e.g. Cx43 and Cx26). To find connexin domains important for oligomerization, we constructed chimaeras between Cx43 and Cx26 and studied their ability to oligomerize with wild-type Cx43, Cx45 or Cx26. HeLa cells co-expressing Cx43, Cx45 or Cx26 and individual chimaeric constructs were analysed for interactions between the chimaeras and the wild-type connexins using cell biological (subcellular localization by immunofluorescence), functional (intercellular diffusion of microinjected Lucifer yellow) and biochemical (sedimentation velocity through sucrose gradients) assays. All of the chimaeras containing the third transmembrane domain of Cx43 interacted with wild-type Cx43 on the basis of co-localization, dominant-negative inhibition of intercellular communication, and altered sedimentation velocity. The same chimaeras also interacted with co-expressed Cx45. In contrast, immunofluorescence and intracellular diffusion of tracer suggested that other domains influenced oligomerization compatibility when chimaeras were co-expressed with Cx26. Taken together, these results suggest that amino acids in the third transmembrane domain are critical for oligomerization with Cx43 and Cx45. However, motifs in different domains may determine oligomerization compatibility in members of different connexin subfamilies. PMID:21348854

  10. Physiological relevance of plant 2-Cys peroxiredoxin overoxidation level and oligomerization status.

    Science.gov (United States)

    Cerveau, Delphine; Ouahrani, Djelloul; Marok, Mohamed Amine; Blanchard, Laurence; Rey, Pascal

    2016-01-01

    Peroxiredoxins are ubiquitous thioredoxin-dependent peroxidases presumed to display, upon environmental constraints, a chaperone function resulting from a redox-dependent conformational switch. In this work, using biochemical and genetic approaches, we aimed to unravel the factors regulating the redox status and the conformation of the plastidial 2-Cys peroxiredoxin (2-Cys PRX) in plants. In Arabidopsis, we show that in optimal growth conditions, the overoxidation level mainly depends on the availability of thioredoxin-related electron donors, but not on sulfiredoxin, the enzyme reducing the 2-Cys PRX overoxidized form. We also observed that upon various physiological temperature, osmotic and light stress conditions, the overoxidation level and oligomerization status of 2-Cys PRX can moderately vary depending on the constraint type. Further, no major change was noticed regarding protein conformation in water-stressed Arabidopsis, barley and potato plants, whereas species-dependent up- and down-variations in overoxidation were observed. In contrast, both 2-Cys PRX overoxidation and oligomerization were strongly induced during a severe oxidative stress generated by methyl viologen. From these data, revealing that the oligomerization status of plant 2-Cys PRX does not exhibit important variation and is not tightly linked to the protein redox status upon physiologically relevant environmental constraints, the possible in planta functions of 2-Cys PRX are discussed. © 2015 John Wiley & Sons Ltd.

  11. An engineered allosteric switch in leucine-zipper oligomerization.

    Science.gov (United States)

    Gonzalez, L; Plecs, J J; Alber, T

    1996-06-01

    Controversy remains about the role of core side-chain packing in specifying protein structure. To investigate the influence of core packing on the oligomeric structure of a coiled coil, we engineered a GCN4 leucine zipper mutant that switches from two to three strands upon binding the hydrophobic ligands cyclohexane and benzene. In solution these ligands increased the apparent thermal stability and the oligomerization order of the mutant leucine zipper. The crystal structure of the peptide-benzene complex shows a single benzene molecule bound at the engineered site in the core of the trimer. These results indicate that coiled coils are well-suited to function as molecular switches and emphasize that core packing is an important determinant of oligomerization specificity.

  12. Oligomerization in health and disease

    CERN Document Server

    Giraldo, Jesus

    2013-01-01

    This special volume of Progress in Molecular Biology and Translational Science focuses on oligomerization in health and disease. Contributions from leading authorities Informs and updates on all the latest developments in the field.

  13. Styrene oligomerization as a molecular probe reaction for zeolite acidity: a UV-Vis spectroscopy and DFT study

    NARCIS (Netherlands)

    Buurmans, I.L.C.; Pidko, E.A.; Groot, de J.M.; Stavitski, E.; Santen, van R.A.; Weckhuysen, B.M.

    2010-01-01

    A series of H-ZSM-5 crystallites with different framework Si/Al ratios was studied by analyzing the kinetics and reaction mechanism of the oligomerization of 4-fluorostyrene as molecular probe reaction for Brønsted acidity. The formation of carbocationic species was followed by UV-Vis spectroscopy.

  14. Simultaneous presence of multiple Campylobacter species in dogs

    NARCIS (Netherlands)

    Koene, M.G.J.; Houwers, D.J.; Dijkstra, J.R.; Duim, B.; Wagenaar, J.A.

    2004-01-01

    The prevalence of coinfection of Campylobacter species in dogs was determined using four isolation methods. In 26% of the positive-testing stools, multiple Campylobacter species were identified. The use of multiple isolation methods as well as the time lapse between sampling and processing are

  15. Multiple mechanisms enable invasive species to suppress native species.

    Science.gov (United States)

    Bennett, Alison E; Thomsen, Meredith; Strauss, Sharon Y

    2011-07-01

    Invasive plants represent a significant threat to ecosystem biodiversity. To decrease the impacts of invasive species, a major scientific undertaking of the last few decades has been aimed at understanding the mechanisms that drive invasive plant success. Most studies and theories have focused on a single mechanism for predicting the success of invasive plants and therefore cannot provide insight as to the relative importance of multiple interactions in predicting invasive species' success. We examine four mechanisms that potentially contribute to the success of invasive velvetgrass Holcus lanatus: direct competition, indirect competition mediated by mammalian herbivores, interference competition via allelopathy, and indirect competition mediated by changes in the soil community. Using a combination of field and greenhouse approaches, we focus on the effects of H. lanatus on a common species in California coastal prairies, Erigeron glaucus, where the invasion is most intense. We found that H. lanatus had the strongest effects on E. glaucus via direct competition, but it also influenced the soil community in ways that feed back to negatively influence E. glaucus and other native species after H. lanatus removal. This approach provided evidence for multiple mechanisms contributing to negative effects of invasive species, and it identified when particular strategies were most likely to be important. These mechanisms can be applied to eradication of H. lanatus and conservation of California coastal prairie systems, and they illustrate the utility of an integrated set of experiments for determining the potential mechanisms of invasive species' success.

  16. Oligomerization interface of RAGE receptor revealed by MS-monitored hydrogen deuterium exchange.

    Directory of Open Access Journals (Sweden)

    Ewa Sitkiewicz

    Full Text Available Activation of the receptor for advanced glycation end products (RAGE leads to a chronic proinflammatory signal, affecting patients with a variety of diseases. Potentially beneficial modification of RAGE activity requires understanding the signal transduction mechanism at the molecular level. The ligand binding domain is structurally uncoupled from the cytoplasmic domain, suggesting receptor oligomerization is a requirement for receptor activation. In this study, we used hydrogen-deuterium exchange and mass spectrometry to map structural differences between the monomeric and oligomeric forms of RAGE. Our results indicated the presence of a region shielded from exchange in the oligomeric form of RAGE and led to the identification of a new oligomerization interface localized at the linker region between domains C1 and C2. Based on this finding, a model of a RAGE dimer and higher oligomeric state was constructed.

  17. Non-transferrin-bound iron (NTBI uptake by T lymphocytes: evidence for the selective acquisition of oligomeric ferric citrate species.

    Directory of Open Access Journals (Sweden)

    Joao Arezes

    Full Text Available Iron is an essential nutrient in several biological processes such as oxygen transport, DNA replication and erythropoiesis. Plasma iron normally circulates bound to transferrin. In iron overload disorders, however, iron concentrations exceed transferrin binding capacity and iron appears complexed with low molecular weight molecules, known as non-transferrin-bound iron (NTBI. NTBI is responsible for the toxicity associated with iron-overload pathologies but the mechanisms leading to NTBI uptake are not fully understood. Here we show for the first time that T lymphocytes are able to take up and accumulate NTBI in a manner that resembles that of hepatocytes. Moreover, we show that both hepatocytes and T lymphocytes take up the oligomeric Fe3Cit3 preferentially to other iron-citrate species, suggesting the existence of a selective NTBI carrier. These results provide a tool for the identification of the still elusive ferric-citrate cellular carrier and may also open a new pathway towards the design of more efficient iron chelators for the treatment of iron overload disorders.

  18. Biophysical characterization of GPCR oligomerization

    DEFF Research Database (Denmark)

    Mathiasen, Signe

    level, and revealed the existence of several dimerization interfaces, each with specific kinetics. Finally we investigated how a property of the membrane solubilizing GPCRs affected oligomerization. We observed a dramatic decrease in oligomer stability with increasing geometrical membrane curvature. We...

  19. Protein dimerization and oligomerization in biology

    National Research Council Canada - National Science Library

    Matthews, Jacqueline M

    2012-01-01

    .... However, protein function is so often linked to both homo- and hetero-oligomerization and many heterologous interactions likely evolved from homologous interaction, so this volume also covers many...

  20. octamethyl-polyhedral oligomeric silsesquioxanes nanocomposites ...

    Indian Academy of Sciences (India)

    In this study, biodegradable poly(p-dioxanone) (PPDO)/octamethyl-polyhedral oligomeric silsesquioxanes (ome-POSS) nanocomposites were fabricated by the simple solution casting method with various ome-POSS loadings. Scanning electron microscopic observations indicate that ome-POSS is well dispersed in the ...

  1. Zn(2+) site engineering at the oligomeric interface of the dopamine transporter

    DEFF Research Database (Denmark)

    Norgaard-Nielsen, Kristine; Norregaard, Lene; Hastrup, Hanne

    2002-01-01

    Increasing evidence suggests that Na(+)/Cl(-)-dependent neurotransmitter transporters exist as homo-oligomeric proteins. However, the functional implication of this oligomerization remains unclear. Here we demonstrate the engineering of a Zn(2+) binding site at the predicted dimeric interface...

  2. Optimal design of compact and connected nature reserves for multiple species.

    Science.gov (United States)

    Wang, Yicheng; Önal, Hayri

    2016-04-01

    When designing a conservation reserve system for multiple species, spatial attributes of the reserves must be taken into account at species level. The existing optimal reserve design literature considers either one spatial attribute or when multiple attributes are considered the analysis is restricted only to one species. We built a linear integer programing model that incorporates compactness and connectivity of the landscape reserved for multiple species. The model identifies multiple reserves that each serve a subset of target species with a specified coverage probability threshold to ensure the species' long-term survival in the reserve, and each target species is covered (protected) with another probability threshold at the reserve system level. We modeled compactness by minimizing the total distance between selected sites and central sites, and we modeled connectivity of a selected site to its designated central site by selecting at least one of its adjacent sites that has a nearer distance to the central site. We considered structural distance and functional distances that incorporated site quality between sites. We tested the model using randomly generated data on 2 species, one ground species that required structural connectivity and the other an avian species that required functional connectivity. We applied the model to 10 bird species listed as endangered by the state of Illinois (U.S.A.). Spatial coherence and selection cost of the reserves differed substantially depending on the weights assigned to these 2 criteria. The model can be used to design a reserve system for multiple species, especially species whose habitats are far apart in which case multiple disjunct but compact and connected reserves are advantageous. The model can be modified to increase or decrease the distance between reserves to reduce or promote population connectivity. © 2015 Society for Conservation Biology.

  3. Genetic noise control via protein oligomerization

    Energy Technology Data Exchange (ETDEWEB)

    Ghim, C; Almaas, E

    2008-06-12

    Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamical role of protein-protein associations. We have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch), integrating quantitative results from previous in vivo and in vitro studies. In particular, we explicitly account for the fast protein binding-unbinding kinetics, RNA polymerases, and the promoter/operator sequences of DNA. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its intrinsic switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced) state from randomly being induced (uninduced). The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise. The stabilization of phenotypically important toggle switches, and nested positive feedback loops in

  4. Cartilage oligomeric matrix protein enhances the vascularization of acellular nerves

    Directory of Open Access Journals (Sweden)

    Wei-ling Cui

    2016-01-01

    Full Text Available Vascularization of acellular nerves has been shown to contribute to nerve bridging. In this study, we used a 10-mm sciatic nerve defect model in rats to determine whether cartilage oligomeric matrix protein enhances the vascularization of injured acellular nerves. The rat nerve defects were treated with acellular nerve grafting (control group alone or acellular nerve grafting combined with intraperitoneal injection of cartilage oligomeric matrix protein (experimental group. As shown through two-dimensional imaging, the vessels began to invade into the acellular nerve graft from both anastomotic ends at day 7 post-operation, and gradually covered the entire graft at day 21. The vascular density, vascular area, and the velocity of revascularization in the experimental group were all higher than those in the control group. These results indicate that cartilage oligomeric matrix protein enhances the vascularization of acellular nerves.

  5. Implication of the oligomeric state of the N-terminal PTX3 domain in cumulus matrix assembly.

    Science.gov (United States)

    Ievoli, Elena; Lindstedt, Ragnar; Inforzato, Antonio; Camaioni, Antonella; Palone, Francesca; Day, Anthony J; Mantovani, Alberto; Salvatori, Giovanni; Salustri, Antonietta

    2011-06-01

    Pentraxin 3 (PTX3) plays a key role in the formation of the hyaluronan-rich matrix of the cumulus oophorus surrounding ovulated eggs that is required for successful fertilization and female fertility. PTX3 is a multimeric protein consisting of eight identical protomers held together by a combination of non-covalent interactions and disulfide bonds. Recent findings suggest that the oligomeric status of PTX3 is important for stabilizing the cumulus matrix. Because the role of PTX3 in the cumulus resides in the unique N-terminal sequence of the protomer, we investigated further this issue by testing the ability of distinct Cys/Ser mutants of recombinant N-terminal region of PTX3 (N(_)PTX3) with different oligomeric arrangement to promote in vitro normal expansion in cumuli from Ptx3-null mice. Here we report that the dimer of the N(_)PTX3 is unable to rescue cumulus matrix organization, and that the tetrameric assembly of the protein is the minimal oligomeric state required for accomplishing this function. We have previously demonstrated that PTX3 binds to HCs of IαI and TSG-6, which are essential for cumulus matrix formation and able to interact with hyaluronan. Interestingly, here we show by solid-phase binding experiments that the dimer of the N(_)PTX3 retains the ability to bind to both IαI and TSG-6, suggesting that the octameric structure of PTX3 provides multiple binding sites for each of these ligands. These findings support the hypothesis that PTX3 contributes to cumulus matrix organization by cross-linking HA polymers through interactions with multiple HCs of IαI and/or TSG-6. The N-terminal PTX3 tetrameric oligomerization was recently reported to be also required for recognition and inhibition of FGF2. Given that this growth factor has been detected in the mammalian preovulatory follicle, we wondered whether FGF2 negatively influences cumulus expansion and PTX3 may also serve in vivo to antagonize its activity. We found that a molar excess of FGF2, above

  6. Transient oligomerization of the SARS-CoV N protein--implication for virus ribonucleoprotein packaging.

    Science.gov (United States)

    Chang, Chung-ke; Chen, Chia-Min Michael; Chiang, Ming-hui; Hsu, Yen-lan; Huang, Tai-huang

    2013-01-01

    The nucleocapsid (N) phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV) packages the viral genome into a helical ribonucleocapsid and plays a fundamental role during viral self-assembly. The N protein consists of two structural domains interspersed between intrinsically disordered regions and dimerizes through the C-terminal structural domain (CTD). A key activity of the protein is the ability to oligomerize during capsid formation by utilizing the dimer as a building block, but the structural and mechanistic bases of this activity are not well understood. By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that CTD acts as a primary transient oligomerization domain in solution. The data is consistent with the helical oligomer packing model of N protein observed in crystal. A systematic study of the oligomerization behavior revealed that altering the intermolecular electrostatic repulsion through changes in solution salt concentration or phosphorylation-mimicking mutations affects oligomerization propensity. We propose a biophysical mechanism where electrostatic repulsion acts as a switch to regulate N protein oligomerization.

  7. Membrane-mediated oligomerization of G protein coupled receptors and its implications for GPCR function

    Directory of Open Access Journals (Sweden)

    Stefan Gahbauer

    2016-10-01

    Full Text Available The dimerization or even oligomerization of G protein coupled receptors (GPCRs causes ongoing, controversial debates about its functional role and the coupled biophysical, biochemical or biomedical implications. A continously growing number of studies hints to a relation between oligomerization and function of GPCRs and strengthens the assumption that receptor assembly plays a key role in the regulation of protein function. Additionally, progress in the structural analysis of GPCR-G protein and GPCR-ligand interactions allows to distinguish between actively functional and non-signalling complexes. Recent findings further suggest that the surrounding membrane, i.e. its lipid composition may modulate the preferred dimerization interface and as a result the abundance of distinct dimeric conformations. In this review, the association of GPCRs and the role of the membrane in oligomerization will be discussed. An overview of the different reported oligomeric interfaces is provided and their capability for signaling discussed. The currently available data is summarized with regard to the formation of GPCR oligomers, their structures and dependency on the membrane microenvironment as well as the coupling of oligomerization to receptor function.

  8. Intraguild predation reduces redundancy of predator species in multiple predator assemblage.

    Science.gov (United States)

    Griffen, Blaine D; Byers, James E

    2006-07-01

    1. Interference between predator species frequently decreases predation rates, lowering the risk of predation for shared prey. However, such interference can also occur between conspecific predators. 2. Therefore, to understand the importance of predator biodiversity and the degree that predator species can be considered functionally interchangeable, we determined the degree of additivity and redundancy of predators in multiple- and single-species combinations. 3. We show that interference between two invasive species of predatory crabs, Carcinus maenas and Hemigrapsus sanguineus, reduced the risk of predation for shared amphipod prey, and had redundant per capita effects in most multiple- and single-species predator combinations. 4. However, when predator combinations with the potential for intraguild predation were examined, predator interference increased and predator redundancy decreased. 5. Our study indicates that trophic structure is important in determining how the effects of predator species combine and demonstrates the utility of determining the redundancy, as well as the additivity, of multiple predator species.

  9. osFP: a web server for predicting the oligomeric states of fluorescent proteins.

    Science.gov (United States)

    Simeon, Saw; Shoombuatong, Watshara; Anuwongcharoen, Nuttapat; Preeyanon, Likit; Prachayasittikul, Virapong; Wikberg, Jarl E S; Nantasenamat, Chanin

    2016-01-01

    Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligomeric states can accelerate the effort of protein engineering efforts of creating monomeric FPs. To the best of our knowledge, this study represents the first computational model for predicting and analyzing FP oligomerization directly from the amino acid sequence. After data curation, an exhaustive data set consisting of 397 non-redundant FP oligomeric states was compiled from the literature. Results from benchmarking of the protein descriptors revealed that the model built with amino acid composition descriptors was the top performing model with accuracy, sensitivity and specificity in excess of 80% and MCC greater than 0.6 for all three data subsets (e.g. training, tenfold cross-validation and external sets). The model provided insights on the important residues governing the oligomerization of FP. To maximize the benefit of the generated predictive model, it was implemented as a web server under the R programming environment. osFP affords a user-friendly interface that can be used to predict the oligomeric state of FP using the protein sequence. The advantage of osFP is that it is platform-independent meaning that it can be accessed via a web browser on any operating system and device. osFP is freely accessible at http://codes.bio/osfp/ while the source code and data set is provided on GitHub at https://github.com/chaninn/osFP/.Graphical Abstract.

  10. Zn(2+) site engineering at the oligomeric interface of the dopamine transporter.

    Science.gov (United States)

    Norgaard-Nielsen, Kristine; Norregaard, Lene; Hastrup, Hanne; Javitch, Jonathan A; Gether, Ulrik

    2002-07-31

    Increasing evidence suggests that Na(+)/Cl(-)-dependent neurotransmitter transporters exist as homo-oligomeric proteins. However, the functional implication of this oligomerization remains unclear. Here we demonstrate the engineering of a Zn(2+) binding site at the predicted dimeric interface of the dopamine transporter (DAT) corresponding to the external end of transmembrane segment 6. Upon binding to this site, which involves a histidine inserted in position 310 (V310H) and the endogenous Cys306 within the same DAT molecule, Zn(2+) potently inhibits [(3)H]dopamine uptake. These data provide indirect evidence that conformational changes critical for the translocation process may occur at the interface between two transporter molecules in the oligomeric structure.

  11. Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding.

    Science.gov (United States)

    Qiu, Wei; Dong, Aiping; Pizarro, Juan C; Botchkarsev, Alexei; Min, Jinrong; Wernimont, Amy K; Hills, Tanya; Hui, Raymond; Artz, Jennifer D

    2012-03-19

    Plasmodium falciparum is the protozoan parasite primarily responsible for more than one million malarial deaths, annually, and is developing resistance to current therapies. Throughout its lifespan, the parasite is subjected to oxidative attack, so Plasmodium antioxidant defences are essential for its survival and are targets for disease control. To further understand the molecular aspects of the Plasmodium redox system, we solved 4 structures of Plasmodium peroxiredoxins (Prx). Our study has confirmed PvTrx-Px1 to be a hydrogen peroxide (H2O2)-sensitive peroxiredoxin. We have identified and characterized the novel toroid octameric oligomer of PyTrx-Px1, which may be attributed to the interplay of several factors including: (1) the orientation of the conserved surface/buried arginine of the NNLA(I/L)GRS-loop; and (2) the C-terminal tail positioning (also associated with the aforementioned conserved loop) which facilitates the intermolecular hydrogen bond between dimers (in an A-C fashion). In addition, a notable feature of the disulfide bonds in some of the Prx crystal structures is discussed. Finally, insight into the latter stages of the peroxiredoxin reaction coordinate is gained. Our structure of PyPrx6 is not only in the sulfinic acid (RSO2H) form, but it is also with glycerol bound in a way (not previously observed) indicative of product binding. The structural characterization of Plasmodium peroxiredoxins provided herein provides insight into their oligomerization and product binding which may facilitate the targeting of these antioxidant defences. Although the structural basis for the octameric oligomerization is further understood, the results yield more questions about the biological implications of the peroxiredoxin oligomerization, as multiple toroid configurations are now known. The crystal structure depicting the product bound active site gives insight into the overoxidation of the active site and allows further characterization of the leaving group

  12. Induced oligomerization targets Golgi proteins for degradation in lysosomes.

    Science.gov (United States)

    Tewari, Ritika; Bachert, Collin; Linstedt, Adam D

    2015-12-01

    Manganese protects cells against forms of Shiga toxin by down-regulating the cycling Golgi protein GPP130. Down-regulation occurs when Mn binding causes GPP130 to oligomerize and traffic to lysosomes. To determine how GPP130 is redirected to lysosomes, we tested the role of GGA1 and clathrin, which mediate sorting in the canonical Golgi-to-lysosome pathway. GPP130 oligomerization was induced using either Mn or a self-interacting version of the FKBP domain. Inhibition of GGA1 or clathrin specifically blocked GPP130 redistribution, suggesting recognition of the aggregated GPP130 by the GGA1/clathrin-sorting complex. Unexpectedly, however, GPP130's cytoplasmic domain was not required, and redistribution also occurred after removal of GPP130 sequences needed for its normal cycling. Therefore, to test whether aggregate recognition might be a general phenomenon rather than one involving a specific GPP130 determinant, we induced homo-oligomerization of two unrelated Golgi-targeted constructs using the FKBP strategy. These were targeted to the cis- and trans-Golgi, respectively, using domains from mannosidase-1 and galactosyltransferase. Significantly, upon oligomerization, each redistributed to peripheral punctae and was degraded. This occurred in the absence of detectable UPR activation. These findings suggest the unexpected presence of quality control in the Golgi that recognizes aggregated Golgi proteins and targets them for degradation in lysosomes. © 2015 Tewari et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  13. Transient oligomerization of the SARS-CoV N protein--implication for virus ribonucleoprotein packaging.

    Directory of Open Access Journals (Sweden)

    Chung-ke Chang

    Full Text Available The nucleocapsid (N phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV packages the viral genome into a helical ribonucleocapsid and plays a fundamental role during viral self-assembly. The N protein consists of two structural domains interspersed between intrinsically disordered regions and dimerizes through the C-terminal structural domain (CTD. A key activity of the protein is the ability to oligomerize during capsid formation by utilizing the dimer as a building block, but the structural and mechanistic bases of this activity are not well understood. By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that CTD acts as a primary transient oligomerization domain in solution. The data is consistent with the helical oligomer packing model of N protein observed in crystal. A systematic study of the oligomerization behavior revealed that altering the intermolecular electrostatic repulsion through changes in solution salt concentration or phosphorylation-mimicking mutations affects oligomerization propensity. We propose a biophysical mechanism where electrostatic repulsion acts as a switch to regulate N protein oligomerization.

  14. Thermal Degradation Mechanism of a Thermostable Polyester Stabilized with an Open-Cage Oligomeric Silsesquioxane

    Directory of Open Access Journals (Sweden)

    Yolanda Bautista

    2017-12-01

    Full Text Available A polyester composite was prepared through the polymerization of an unsaturated ester resin with styrene and an open-cage oligomeric silsesquioxane with methacrylate groups. The effect of the open-cage oligomeric silsesquioxane on the thermal stability of the thermostable polyester was studied using both thermogravimetric analysis and differential thermal analysis. The results showed that the methacryl oligomeric silsesquioxane improved the thermal stability of the polyester. The decomposition mechanism of the polyester/oligomer silsesquioxane composite was proposed by Fourier transform infrared spectroscopy (FTIR analysis of the volatiles.

  15. Oligomerization process

    Science.gov (United States)

    Smith, L.A. Jr.; Hearn, D.; Jones, E.M. Jr.

    1991-03-26

    A liquid phase process is described for oligomerization of C[sub 4] and C[sub 5] isoolefins or the etherification thereof with C[sub 1] to C[sub 6] alcohols wherein the reactants are contacted in a reactor with a fixed bed acid cation exchange resin catalyst at an LHSV of 5 to 20, pressure of 0 to 400 psig and temperature of 120 to 300 F wherein the improvement is the operation of the reactor at a pressure to maintain the reaction mixture at its boiling point whereby at least a portion but less than all of the reaction mixture is vaporized. By operating at the boiling point and allowing a portion of the reaction mixture to vaporize, the exothermic heat of reaction is dissipated by the formation of more boil up and the temperature in the reactor is controlled. 2 figures.

  16. Reactive bay functionalized perylene monoimide-polyhedral oligomeric silsesquioxane organic electronic dye

    Directory of Open Access Journals (Sweden)

    Wangatia Lodrick Makokha

    2015-03-01

    Full Text Available Aggregation-induced quenching is particularly detrimental in perylene diimides, which are characterized by a near-unity fluorescence quantum yield in solution but are far less emissive in the solid state. Previously, perylene diimide has been improved by linking it to the inorganic cage of polyhedral oligomeric silsesquioxanes. As a further study on perylene diimidepolyhedral oligomeric silsesquioxanes, we report on a double functionalized molecular structure, which can be used for substitution at the bay area and as a side group in other materials. Typical solution absorption and emission features of the perylene diimide fragment have been observed in this new reactive perylene diimide-polyhedral oligomeric silsesquioxane. Moreover, reduced stacking during aggregation and spherical particles exhibiting solid fluorescence have been obtained. Organic semiconducting material with enhanced solid state photophysical properties, like solid fluorescence is a subject of great interest owing to its possible high-tech applications in optoelectronic devices.

  17. Methyl methacrylate oligomerically-modified clay and its poly(methyl methacrylate) nanocomposites

    International Nuclear Information System (INIS)

    Zheng Xiaoxia; Jiang, David D.; Wilkie, Charles A.

    2005-01-01

    A methyl methacrylate oligomerically-modified clay was used to prepare poly(methyl methacrylate) clay nanocomposites by melt blending and the effect of the clay loading level on the modified clay and corresponding nanocomposite was studied. These nanocomposites were characterized by X-ray diffraction, transmission electron microscopy, thermogravimetric analysis and cone calorimetry. The results show a mixed intercalated/delaminated morphology with good nanodispersion. The compatibility between the methylacrylate-subsituted clay and poly(methyl methacrylate) (PMMA) are greatly improved compared to other oligomerically-modified clays

  18. Optimal Foraging for Multiple Resources in Several Food Species

    NARCIS (Netherlands)

    Hengeveld, G.M.; Langevelde, van F.; Groen, T.A.; Knegt, de H.J.

    2009-01-01

    The concentrations of resources in forage are not perfectly balanced to the needs of an animal, and food species differ in these concentrations. Under many circumstances, animals should thus forage on multiple food species to attain the maximum and most balanced intake of several resources. In this

  19. Optimal foraging for multiple resources in several food species

    NARCIS (Netherlands)

    Hengeveld, G.M.; van Langevelde, F.; Groen, T.A.; de Knegt, H.J.

    2009-01-01

    The concentrations of resources in forage are not perfectly balanced to the needs of an animal, and food species differ in these concentrations. Under many circumstances, animals should thus forage on multiple food species to attain the maximum and most balanced intake of several resources. In this

  20. Oligomerization of G protein-coupled receptors: computational methods.

    Science.gov (United States)

    Selent, J; Kaczor, A A

    2011-01-01

    Recent research has unveiled the complexity of mechanisms involved in G protein-coupled receptor (GPCR) functioning in which receptor dimerization/oligomerization may play an important role. Although the first high-resolution X-ray structure for a likely functional chemokine receptor dimer has been deposited in the Protein Data Bank, the interactions and mechanisms of dimer formation are not yet fully understood. In this respect, computational methods play a key role for predicting accurate GPCR complexes. This review outlines computational approaches focusing on sequence- and structure-based methodologies as well as discusses their advantages and limitations. Sequence-based approaches that search for possible protein-protein interfaces in GPCR complexes have been applied with success in several studies, but did not yield always consistent results. Structure-based methodologies are a potent complement to sequence-based approaches. For instance, protein-protein docking is a valuable method especially when guided by experimental constraints. Some disadvantages like limited receptor flexibility and non-consideration of the membrane environment have to be taken into account. Molecular dynamics simulation can overcome these drawbacks giving a detailed description of conformational changes in a native-like membrane. Successful prediction of GPCR complexes using computational approaches combined with experimental efforts may help to understand the role of dimeric/oligomeric GPCR complexes for fine-tuning receptor signaling. Moreover, since such GPCR complexes have attracted interest as potential drug target for diverse diseases, unveiling molecular determinants of dimerization/oligomerization can provide important implications for drug discovery.

  1. N-Glycosylation instead of cholesterol mediates oligomerization and apical sorting of GPI-APs in FRT cells.

    Science.gov (United States)

    Imjeti, Naga Salaija; Lebreton, Stéphanie; Paladino, Simona; de la Fuente, Erwin; Gonzalez, Alfonso; Zurzolo, Chiara

    2011-12-01

    Sorting of glycosylphosphatidyl-inositol--anchored proteins (GPI-APs) in polarized epithelial cells is not fully understood. Oligomerization in the Golgi complex has emerged as the crucial event driving apical segregation of GPI-APs in two different kind of epithelial cells, Madin-Darby canine kidney (MDCK) and Fisher rat thyroid (FRT) cells, but whether the mechanism is conserved is unknown. In MDCK cells cholesterol promotes GPI-AP oligomerization, as well as apical sorting of GPI-APs. Here we show that FRT cells lack this cholesterol-driven oligomerization as apical sorting mechanism. In these cells both apical and basolateral GPI-APs display restricted diffusion in the Golgi likely due to a cholesterol-enriched membrane environment. It is striking that N-glycosylation is the critical event for oligomerization and apical sorting of GPI-APs in FRT cells but not in MDCK cells. Our data indicate that at least two mechanisms exist to determine oligomerization in the Golgi leading to apical sorting of GPI-APs. One depends on cholesterol, and the other depends on N-glycosylation and is insensitive to cholesterol addition or depletion.

  2. DNA structure modulates the oligomerization properties of the AAV initiator protein Rep68.

    Directory of Open Access Journals (Sweden)

    Jorge Mansilla-Soto

    2009-07-01

    Full Text Available Rep68 is a multifunctional protein of the adeno-associated virus (AAV, a parvovirus that is mostly known for its promise as a gene therapy vector. In addition to its role as initiator in viral DNA replication, Rep68 is essential for site-specific integration of the AAV genome into human chromosome 19. Rep68 is a member of the superfamily 3 (SF3 helicases, along with the well-studied initiator proteins simian virus 40 large T antigen (SV40-LTag and bovine papillomavirus (BPV E1. Structurally, SF3 helicases share two domains, a DNA origin interaction domain (OID and an AAA(+ motor domain. The AAA(+ motor domain is also a structural feature of cellular initiators and it functions as a platform for initiator oligomerization. Here, we studied Rep68 oligomerization in vitro in the presence of different DNA substrates using a variety of biophysical techniques and cryo-EM. We found that a dsDNA region of the AAV origin promotes the formation of a complex containing five Rep68 subunits. Interestingly, non-specific ssDNA promotes the formation of a double-ring Rep68, a known structure formed by the LTag and E1 initiator proteins. The Rep68 ring symmetry is 8-fold, thus differing from the hexameric rings formed by the other SF3 helicases. However, similiar to LTag and E1, Rep68 rings are oriented head-to-head, suggesting that DNA unwinding by the complex proceeds bidirectionally. This novel Rep68 quaternary structure requires both the DNA binding and AAA(+ domains, indicating cooperativity between these regions during oligomerization in vitro. Our study clearly demonstrates that Rep68 can oligomerize through two distinct oligomerization pathways, which depend on both the DNA structure and cooperativity of Rep68 domains. These findings provide insight into the dynamics and oligomeric adaptability of Rep68 and serve as a step towards understanding the role of this multifunctional protein during AAV DNA replication and site-specific integration.

  3. Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization

    DEFF Research Database (Denmark)

    Teilum, Kaare; Smith, Melanie H; Schulz, Eike

    2009-01-01

    remained enigmatic, however, as is the case in other protein-misfolding diseases. Here, we target the critical conformational change that defines the earliest step toward aggregation. Using nuclear spin relaxation dispersion experiments, we identified a short-lived (0.4 ms) and weakly populated (0.......7%) conformation of metal-depleted SOD1 that triggers aberrant oligomerization. This excited state emanates from the folded ground state and is suppressed by metal binding, but is present in both the disulfide-oxidized and disulfide-reduced forms of the protein. Our results pinpoint a perturbed region......Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease linked to the misfolding of Cu/Zn superoxide dismutase (SOD1). ALS-related defects in SOD1 result in a gain of toxic function that coincides with aberrant oligomerization. The structural events triggering oligomerization have...

  4. Effect Of Oligomeric Enteral Nutrition On Symptoms Of Acute Radiation Enteritis

    International Nuclear Information System (INIS)

    Dubinsky, P.

    2008-01-01

    Radiotherapy of abdominal and pelvic tumours is frequently associated with acute radiation enteritis. Predominant symptoms include diarrhea, watery stools, abdominal pain, nausea and vomiting. There are very few effective interventions available for this condition. Enteral oligomeric nutrition has been used in bowel diseases with functional failure similar to radiation enteritis. The aim of presented work was to observe occurrence of symptoms of radiation enteritis in patients undergoing abdominal or pelvic radiotherapy. Apart from diet and pharmacological therapy, oral oligomeric enteral nutrition (Peptisorb Powder Nutricia) at the dose of 1000 - 2000 ml per day was administered for minimum of 4 days. Planned period of administration was 14 days and longer. Symptoms of radiation enteritis were evaluated at the beginning and in the end of administration. Prevalence of all evaluated symptoms of radiation enteritis was decreased and difference was statistically significant for diarrhea, watery stools, abdominal pain, nausea and vomiting. The use of evaluated oligomeric nutritional support might, in conjunction with pharmacotherapy and diet, alleviate symptoms of acute radiation enteritis and maintain nutritional status of patients. (author)

  5. Concentration-dependent oligomerization of cross-linked complexes between ferredoxin and ferredoxin–NADP+ reductase

    International Nuclear Information System (INIS)

    Kimata-Ariga, Yoko; Kubota-Kawai, Hisako; Lee, Young-Ho; Muraki, Norifumi; Ikegami, Takahisa; Kurisu, Genji; Hase, Toshiharu

    2013-01-01

    Highlights: •Cross-linked complexes of ferredoxin (Fd) and Fd–NADP + reductase form oligomers. •In the crystal structures, Fd- and FNR moieties swap across the molecules. •The complexes exhibit concentration-dependent oligomerization at sub-milimolar order. -- Abstract: Ferredoxin–NADP + reductase (FNR) forms a 1:1 complex with ferredoxin (Fd), and catalyzes the electron transfer between Fd and NADP + . In our previous study, we prepared a series of site-specifically cross-linked complexes of Fd and FNR, which showed diverse electron transfer properties. Here, we show that X-ray crystal structures of the two different Fd–FNR cross-linked complexes form oligomers by swapping Fd and FNR moieties across the molecules; one complex is a dimer from, and the other is a successive multimeric form. In order to verify whether these oligomeric structures are formed only in crystal, we investigated the possibility of the oligomerization of these complexes in solution. The mean values of the particle size of these cross-linked complexes were shown to increase with the rise of protein concentration at sub-milimolar order, whereas the size of dissociable wild-type Fd:FNR complex was unchanged as analyzed by dynamic light scattering measurement. The oligomerization products were detected by SDS–PAGE after chemical cross-linking of these complexes at the sub-milimolar concentrations. The extent and concentration-dependent profile of the oligomerizaion were differentiated between the two cross-linked complexes. These results show that these Fd–FNR cross-linked complexes exhibit concentration-dependent oligomerization, possibly through swapping of Fd and FNR moieties also in solution. These findings lead to the possibility that some native multi-domain proteins may present similar phenomenon in vivo

  6. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny

    2006-01-01

    . aeruginosa were found to be significantly larger than ulcers without the presence of P. aeruginosa (P wound is colonised by multiple bacterial species and that once they are established many of them persist in the wound. Our results suggest that the presence...... of P. aeruginosa in venous leg ulcers can induce ulcer enlargement and/or cause delayed healing....

  7. Role of redox environment on the oligomerization of higher molecular weight adiponectin

    Directory of Open Access Journals (Sweden)

    Nuñez Martha

    2011-05-01

    Full Text Available Abstract Background Adiponectin is an adipocyte-secreted hormone with insulin-sensitizing and anti-inflammatory actions. The assembly of trimeric, hexameric, and higher molecular weight (HMW species of adiponectin is a topic of significant interest because physiological actions of adiponectin are oligomer-specific. In addition, adiponectin assembly is an example of oxidative oligomerization of multi-subunit protein complexes in endoplasmic reticulum (ER. Results We previously reported that trimers assemble into HMW adiponectin via intermediates stabilized by disulfide bonds, and complete oxidation of available cysteines locks adiponectin in hexameric conformation. In this study, we examined the effects of redox environment on the rate of oligomer formation and the distribution of oligomers. Reassembly of adiponectin under oxidizing conditions accelerated disulfide bonding but favored formation of hexamers over the HMW species. Increased ratios of HMW to hexameric adiponectin could be achieved rapidly under oxidizing conditions by promoting disulfide rearrangement. Conclusions Based upon these observations, we propose oxidative assembly of multi-subunit adiponectin complexes in a defined and stable redox environment is favored under oxidizing conditions coupled with high rates of disulfide rearrangement.

  8. Influence of predator density on nonindependent effects of multiple predator species.

    Science.gov (United States)

    Griffen, Blaine D; Williamson, Tucker

    2008-02-01

    Interactions between multiple predator species are frequent in natural communities and can have important implications for shared prey survival. Predator density may be an important component of these interactions between predator species, as the frequency of interactions between species is largely determined by species density. Here we experimentally examine the importance of predator density for interactions between predator species and subsequent impacts on prey. We show that aggressive interactions between the predatory shore crabs Carcinus maenas and Hemigrapsus sanguineus increased with predator density, yet did not increase as fast as negative interactions between conspecifics. At low density, interactions between conspecific and heterospecific predators had similar inhibitory impacts on predator function, whereas conspecific interference was greater than interference from heterospecifics at high predator density. Thus the impact of conspecific interference at high predator density was sufficient in itself that interactions with a second predator species had no additional impact on per capita predation. Spatial and temporal variability in predator density is a ubiquitous characteristic of natural systems that should be considered in studies of multiple predator species.

  9. Cobalt Oxide on N-Doped Carbon for 1-Butene Oligomerization to Produce Linear Octenes

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Dongting [Department; Xu, Zhuoran [Department; Chada, Joseph P. [Department; Carrero, Carlos A. [Department; Rosenfeld, Devon C. [The Dow Chemical Company, 2301 N. Brazosport Boulevard, Freeport, Texas 77541-3257, United States; Rogers, Jessica L. [The Dow Chemical Company, 2301 N. Brazosport Boulevard, Freeport, Texas 77541-3257, United States; Hermans, Ive [Department; Huber, George W. [Department

    2017-10-02

    Cobalt oxide supported on N-doped carbon catalysts were investigated for 1-butene oligomerization. The materials were synthesized by treating activated carbon with nitric acid and subsequently with NH3 at 200, 400, 600, and 800 °C, followed by impregnation with cobalt. The 1-butene oligomerization selectivity increased with ammonia treatment temperature of the carbon support. The oligomerization selectivity of cobalt oxide on N-doped carbon synthesized at 800 °C (800A-CoOx/N-C) is 2.6 times higher than previously reported cobalt oxide on N-doped carbon synthesized with NH4OH (2A-CoOx/N-C). Over 70% of the butene dimers were linear C8 olefins for all catalysts. The oligomerization selectivity increased with 1-butene conversion. The catalysts were characterized by elemental analysis, N2 adsorption, X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), and X-ray photoelectron spectroscopy (XPS). The nitrogen content of the catalysts increases with ammonia treatment temperature as confirmed by elemental analysis. The surface content of pyridinic nitrogen with a binding energy of 398.4 ± 0.1 eV increased with ammonia treatment temperature as evidenced by deconvolution of N 1s XPS spectra.

  10. Endocytic pathways mediating oligomeric Aβ42 neurotoxicity

    Directory of Open Access Journals (Sweden)

    Laxton Kevin

    2010-05-01

    Full Text Available Abstract Background One pathological hallmark of Alzheimer's disease (AD is amyloid plaques, composed primarily of amyloid-β peptide (Aβ. Over-production or diminished clearance of the 42 amino acid form of Aβ (Aβ42 in the brain leads to accumulation of soluble Aβ and plaque formation. Soluble oligomeric Aβ (oAβ has recently emerged to be as a likely proximal cause of AD. Results Here we demonstrate that endocytosis is critical in mediating oAβ42-induced neurotoxicity and intraneuronal accumulation of Aβ. Inhibition of clathrin function either with a pharmacological inhibitor, knock-down of clathrin heavy chain expression, or expression of the dominant-negative mutant of clathrin-assembly protein AP180 did not block oAβ42-induced neurotoxicity or intraneuronal accumulation of Aβ. However, inhibition of dynamin and RhoA by expression of dominant negative mutants reduced neurotoxicity and intraneuronal Aβ accumulation. Pharmacologic inhibition of the dynamin-mediated endocytic pathway by genistein also reduced neurotoxicity. Conclusions These data suggest that dynamin-mediated and RhoA-regulated endocytosis are integral steps for oligomeric Aβ42-induced neurotoxicity and intraneuronal Aβ accumulation.

  11. RIG-I self-oligomerization is either dispensable or very transient for signal transduction.

    Directory of Open Access Journals (Sweden)

    Jade Louber

    Full Text Available Effective host defence against viruses depends on the rapid triggering of innate immunity through the induction of a type I interferon (IFN response. To this end, microbe-associated molecular patterns are detected by dedicated receptors. Among them, the RIG-I-like receptors RIG-I and MDA5 activate IFN gene expression upon sensing viral RNA in the cytoplasm. While MDA5 forms long filaments in vitro upon activation, RIG-I is believed to oligomerize after RNA binding in order to transduce a signal. Here, we show that in vitro binding of synthetic RNA mimicking that of Mononegavirales (Ebola, rabies and measles viruses leader sequences to purified RIG-I does not induce RIG-I oligomerization. Furthermore, in cells devoid of endogenous functional RIG-I-like receptors, after activation of exogenous Flag-RIG-I by a 62-mer-5'ppp-dsRNA or by polyinosinic:polycytidylic acid, a dsRNA analogue, or by measles virus infection, anti-Flag immunoprecipitation and specific elution with Flag peptide indicated a monomeric form of RIG-I. Accordingly, when using the Gaussia Luciferase-Based Protein Complementation Assay (PCA, a more sensitive in cellula assay, no RIG-I oligomerization could be detected upon RNA stimulation. Altogether our data indicate that the need for self-oligomerization of RIG-I for signal transduction is either dispensable or very transient.

  12. Human α4β2 nicotinic acetylcholine receptor as a novel target of oligomeric α-synuclein.

    Directory of Open Access Journals (Sweden)

    Qiang Liu

    Full Text Available Cigarette smoking is associated with a decreased incidence of Parkinson disease (PD through unknown mechanisms. Interestingly, a decrease in the numbers of α4β2 nicotinic acetylcholine receptors (α4β2-nAChRs in PD patients suggests an α4β2-nAChR-mediated cholinergic deficit in PD. Although oligomeric forms of α-synuclein have been recognized to be toxic and involved in the pathogenesis of PD, their direct effects on nAChR-mediated cholinergic signaling remains undefined. Here, we report for the first time that oligomeric α-synuclein selectively inhibits human α4β2-nAChR-mediated currents in a dose-dependent, non-competitive and use-independent manner. We show that pre-loading cells with guanyl-5'-yl thiophosphate fails to prevent this inhibition, suggesting that the α-synuclein-induced inhibition of α4β2-nAChR function is not mediated by nAChR internalization. By using a pharmacological approach and cultures expressing transfected human nAChRs, we have shown a clear effect of oligomeric α-synuclein on α4β2-nAChRs, but not on α4β4- or α7-nAChRs, suggesting nAChR subunit selectivity of oligomeric α-synuclein-induced inhibition. In addition, by combining the size exclusion chromatography and atomic force microscopy (AFM analyses, we find that only large (>4 nm oligomeric α-synuclein aggregates (but not monomeric, small oligomeric or fibrillar α-synuclein aggregates exhibit the inhibitory effect on human α4β2-nAChRs. Collectively, we have provided direct evidence that α4β2-nAChR is a sensitive target to mediate oligomeric α-synuclein-induced modulation of cholinergic signaling, and our data imply that therapeutic strategies targeted toward α4β2-nAChRs may have potential for developing new treatments for PD.

  13. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

    Science.gov (United States)

    Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

    2015-09-15

    There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

  14. Nanomolar oligomerization and selective co-aggregation of α-synuclein pathogenic mutants revealed by single-molecule fluorescence

    Science.gov (United States)

    Sierecki, Emma; Giles, Nichole; Bowden, Quill; Polinkovsky, Mark E.; Steinbeck, Janina; Arrioti, Nicholas; Rahman, Diya; Bhumkar, Akshay; Nicovich, Philip R.; Ross, Ian; Parton, Robert G.; Böcking, Till; Gambin, Yann

    2016-01-01

    Protein aggregation is a hallmark of many neurodegenerative diseases, notably Alzheimer’s and Parkinson’s disease. Parkinson’s disease is characterized by the presence of Lewy bodies, abnormal aggregates mainly composed of α-synuclein. Moreover, cases of familial Parkinson’s disease have been linked to mutations in α-synuclein. In this study, we compared the behavior of wild-type (WT) α-synuclein and five of its pathological mutants (A30P, E46K, H50Q, G51D and A53T). To this end, single-molecule fluorescence detection was coupled to cell-free protein expression to measure precisely the oligomerization of proteins without purification, denaturation or labelling steps. In these conditions, we could detect the formation of oligomeric and pre-fibrillar species at very short time scale and low micromolar concentrations. The pathogenic mutants surprisingly segregated into two classes: one group forming large aggregates and fibrils while the other tending to form mostly oligomers. Strikingly, co-expression experiments reveal that members from the different groups do not generally interact with each other, both at the fibril and monomer levels. Together, this data paints a completely different picture of α-synuclein aggregation, with two possible pathways leading to the development of fibrils. PMID:27892477

  15. Free-energy landscape of protein oligomerization from atomistic simulations

    Science.gov (United States)

    Barducci, Alessandro; Bonomi, Massimiliano; Prakash, Meher K.; Parrinello, Michele

    2013-01-01

    In the realm of protein–protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage. PMID:24248370

  16. Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

    Science.gov (United States)

    Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

    2014-04-01

    Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

  17. N-(1-Pyrenyl Maleimide Induces Bak Oligomerization and Mitochondrial Dysfunction in Jurkat Cells

    Directory of Open Access Journals (Sweden)

    Pei-Rong Huang

    2015-01-01

    Full Text Available N-(1-pyrenyl maleimide (NPM is a fluorescent reagent that is frequently used as a derivatization agent for the detection of thio-containing compounds. NPM has been shown to display a great differential cytotoxicity against hematopoietic cancer cells. In this study, the molecular mechanism by which NPM induces apoptosis was examined. Here, we show that treatment of Jurkat cells with NPM leads to Bak oligomerization, loss of mitochondrial membrane potential (Δψm, and release of cytochrome C from mitochondria to cytosol. Induction of Bak oligomerization appears to play a critical role in NPM-induced apoptosis, as downregulation of Bak by shRNA significantly prevented NPM-induced apoptosis. Inhibition of caspase 8 by Z-IETD-FMK and/or depletion of Bid did not affect NPM-induced oligomerization of Bak. Taken together, these results suggest that NPM-induced apoptosis is mediated through a pathway that is independent of caspase-8 activation.

  18. Oligomerization of optically active N-(4-hydroxyphenylmandelamide in the presence of β-cyclodextrin and the minor role of chirality

    Directory of Open Access Journals (Sweden)

    Helmut Ritter

    2014-10-01

    Full Text Available The oxidative oligomerization of a chiral mandelamide derivative (N-(4-hydroxyphenylmandelamide, 1 was performed in the presence of horseradish peroxidase, laccase and N,N'-bis(salicylideneethylenediamine-iron(II to obtain chiral oligophenols 2. The low enantioselectivity of the enzymatic catalyzed asymmetric enantiomer-differentiating oligomerizations was investigated. In addition, the poor influence of cyclodextrin on the enantioselectivity of enzymatic catalyzed asymmetric enantiomer-differentiating oligomerizations was studied.

  19. 40 CFR 721.3100 - Oligomeric silicic acid ester compound with a hy-droxyl-al-kyla-mine.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Oligomeric silicic acid ester compound with a hy-droxyl-al-kyla-mine. 721.3100 Section 721.3100 Protection of Environment ENVIRONMENTAL... Significant New Uses for Specific Chemical Substances § 721.3100 Oligomeric silicic acid ester compound with a...

  20. Bacterial flagellar capping proteins adopt diverse oligomeric states

    Energy Technology Data Exchange (ETDEWEB)

    Postel, Sandra; Deredge, Daniel; Bonsor, Daniel A.; Yu, Xiong; Diederichs, Kay; Helmsing, Saskia; Vromen, Aviv; Friedler, Assaf; Hust, Michael; Egelman, Edward H.; Beckett, Dorothy; Wintrode, Patrick L.; Sundberg, Eric J. (UV); (Braunschweig); (Maryland-MED); (Konstanz); (Maryland); (Hebrew)

    2016-09-24

    Flagella are crucial for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed, resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD fromPseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. Using this evidence in combination with a multitude of biophysical and functional analyses, we find thatPseudomonasFliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary in protofilament number between bacteria, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies.

  1. Chemical activation of bituminous coal for hampering oligomerization of organic contaminants.

    Science.gov (United States)

    Yan, Liang; Sorial, George A

    2011-12-15

    Activated carbons prepared by KOH activation of bituminous coal were studied for hampering oligomerization of phenolic compounds on its surface. A total of 24 activated carbons with different microporosity and BET surface area were created. The effect of the different variables of the activation process (KOH/bituminous coal ratio, heating temperature, activation time, and flow rate of nitrogen gas) on critical carbon parameters was analyzed. The impact of activated carbon on oligomerization was examined by conducting isotherm experiments at a neutral pH on Carbon(exp) produced with optimal characteristics and granular activated carbon (GAC) F400 for phenol, 2-methylphenol and 2-ethylphenol. These isotherms were collected under anoxic (absence of molecular oxygen) and oxic (presence of molecular oxygen) conditions. The single solute adsorption of phenol, 2-methylphenol and 2-ethylphenol on Carbon(exp) showed no obvious differences between oxic and anoxic environment, which indicated that the Carbon(exp) sample is very effective in hampering the oligomerization of phenolic compounds under oxic conditions. On the other hand, F400, which have lower micropore percentage and BET surface area, significant increases in the adsorptive capacity had been observed when molecular oxygen was present. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. Potential Energy Surfaces and Dynamics of High Energy Species

    Science.gov (United States)

    2009-04-13

    explored include ionic liquids and a range of high-nitrogen content and nitrogen-oxygen content species. Polyhedral oligomeric silisesquioxanes are...Approved for Public Release 13. SUPPLEMENTARY NOTES 14. ABSTRACT Several papers on ionic liquids have been published or submitted as a result of this...in energetic ionic liquids . These are variously substituted triazolium, tertazolium, and pentazolium cations. The heats of formation of all species

  3. Diffusion of multiple species with excluded-volume effects

    KAUST Repository

    Bruna, Maria; Chapman, S. Jonathan

    2012-01-01

    Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results. © 2012 American Institute of Physics.

  4. Conformational detection of p53's oligomeric state by FlAsH Fluorescence

    OpenAIRE

    Webber, Tawnya M.; Allen, Andrew C.; Ma, Wai Kit; Molloy, Rhett G.; Kettelkamp, Charisse N.; Dow, Caitlin A.; Gage, Matthew J.

    2009-01-01

    The p53 tumor suppressor protein is a critical checkpoint in prevention of tumor formation, and the function of p53 is dependent on proper formation of the active tetramer. In vitro studies have shown that p53 binds DNA most efficiently as a tetramer, though inactive p53 is predicted to be monomeric in vivo. We demonstrate that FlAsH binding can be used to distinguish between oligomeric states of p53, providing a potential tool to explore p53 oligomerization in vivo. The FlAsH tetra-cysteine ...

  5. Homologous ELISA for detection of oligomeric human TNF: properties of the assay.

    Science.gov (United States)

    Petyovka, N; Lyach, L; Voitenok, N N

    1995-10-26

    In order to quantify oligomeric human tumor necrosis factor-alpha (TNF), we have developed a sensitive homologous enzyme-linked immunosorbent assay (Hm-ELISA) using the same monoclonal antibody (MoAb) for both solid and liquid phase. Different anti-TNF MoAb have been compared in terms of their efficacy in the Hm-ELISA, affinity, neutralization capacity and epitope specificity. The data suggest, that effectiveness in the Hm-ELISA may represent a novel characteristic of MoAb. Of the MoAbs tested, 5 N was capable of recognizing oligomeric TNF in the Hm-ELISA with a detection limit of 15 pg/ml. Furthermore, using Hm-ELISA against human TNF, interleukin-8 (IL-8) and lymphotoxin, we have demonstrated that these cytokines are oligomeric in physiological solutions, but are converted into monomeric forms in the presence of the non-ionic detergent Tween 20. High salt buffer was employed to abrogate a nonspecific false positive reaction in the Hm-ELISA found in nearly half of the plasma samples obtained from healthy subjects. Finally, a good correlation between the Hm-ELISA and the L929 bioassay was observed for natural and recombinant TNF measured in human plasma.

  6. Cartilage oligomeric matrix protein in patients with juvenile idiopathic arthritis

    DEFF Research Database (Denmark)

    Bjørnhart, Birgitte; Juul, Anders; Nielsen, Susan

    2009-01-01

    Cartilage oligomeric matrix protein (COMP) has been identified as a prognostic marker of progressive joint destruction in rheumatoid arthritis. In this population based study we evaluated associations between plasma concentrations of COMP, disease activity, and growth velocity in patients...

  7. Polybenzoxazine/Polyhedral Oligomeric Silsesquioxane (POSS Nanocomposites

    Directory of Open Access Journals (Sweden)

    Mohamed Gamal Mohamed

    2016-06-01

    Full Text Available The organic/inorganic hybrid materials from polyhedral oligomeric silsesquioxane (POSS, inorganic nanoparticles and polybenzoxazine (PBZ have received much interesting recently due to their excellent thermal and mechanical properties, flame retardance, low dielectric constant, well-defined inorganic framework at nanosized scale level, and higher performance relative to those of non-hybrid PBZs. This review describes the synthesis, dielectric constants, and thermal, rheological, and mechanical properties of covalently bonded mono- and multifunctionalized benzoxazine POSS hybrids, other functionalized benzoxazine POSS derivatives, and non-covalently (hydrogen bonded benzoxazine POSS composites.

  8. Effects of biotic interactions and dispersal on the presence-absence of multiple species

    International Nuclear Information System (INIS)

    Mohd, Mohd Hafiz; Murray, Rua; Plank, Michael J.; Godsoe, William

    2017-01-01

    One of the important issues in ecology is to predict which species will be present (or absent) across a geographical region. Dispersal is thought to have an important influence on the range limits of species, and understanding this problem in a multi-species community with priority effects (i.e. initial abundances determine species presence-absence) is a challenging task because dispersal also interacts with biotic and abiotic factors. Here, we propose a simple multi-species model to investigate the joint effects of biotic interactions and dispersal on species presence-absence. Our results show that dispersal can substantially expand species ranges when biotic and abiotic forces are present; consequently, coexistence of multiple species is possible. The model also exhibits ecologically interesting priority effects, mediated by intense biotic interactions. In the absence of dispersal, competitive exclusion of all but one species occurs. We find that dispersal reduces competitive exclusion effects that occur in no-dispersal case and promotes coexistence of multiple species. These results also show that priority effects are still prevalent in multi-species communities in the presence of dispersal process. We also illustrate the existence of threshold values of competitive strength (i.e. transcritical bifurcations), which results in different species presence-absence in multi-species communities with and without dispersal.

  9. Antibodies against alpha-synuclein reduce oligomerization in living cells.

    Directory of Open Access Journals (Sweden)

    Thomas Näsström

    Full Text Available Recent research implicates soluble aggregated forms of α-synuclein as neurotoxic species with a central role in the pathogenesis of Parkinson's disease and related disorders. The pathway by which α-synuclein aggregates is believed to follow a step-wise pattern, in which dimers and smaller oligomers are initially formed. Here, we used H4 neuroglioma cells expressing α-synuclein fused to hemi:GFP constructs to study the effects of α-synuclein monoclonal antibodies on the early stages of aggregation, as quantified by Bimolecular Fluorescence Complementation assay. Widefield and confocal microscopy revealed that cells treated for 48 h with monoclonal antibodies internalized antibodies to various degrees. C-terminal and oligomer-selective α-synuclein antibodies reduced the extent of α-synuclein dimerization/oligomerization, as indicated by decreased GFP fluorescence signal. Furthermore, ELISA measurements on lysates and conditioned media from antibody treated cells displayed lower α-synuclein levels compared to untreated cells, suggesting increased protein turnover. Taken together, our results propose that extracellular administration of monoclonal antibodies can modify or inhibit early steps in the aggregation process of α-synuclein, thus providing further support for passive immunization against diseases with α-synuclein pathology.

  10. High Content Analysis of Compositional Heterogeneities to Study GPCR Oligomerization

    DEFF Research Database (Denmark)

    Walsh, Samuel McEwen

    In this thesis I demonstrate how the natural compositional heterogeneities of synthetic and living cell model systems can be used to quantitate the mechanics of G-protein coupled receptor (GPCR) oligomerization with Förster resonance energy transfer (FRET). The thesis is structured around three a...

  11. Defining hotspots of characteristic species for multiple taxonomic groups in the Netherlands

    NARCIS (Netherlands)

    Schouten, M.A.; Barendregt, A.; Verweij, P.A.; Kalkman, V.J.; Kleukers, R.J.M.C.; Lenders, H.J.R.; Siebel, H.N.

    2010-01-01

    Biogeographical zonation based on single taxa poses major limitations on planning for nature conservation. This paper identifies biogeographical patterns of multiple taxa in the Netherlands, where no endemics are present at species level, on the basis of characteristic species. We used occurrence

  12. Receptor oligomerization in family B1 of G-protein-coupled receptors

    DEFF Research Database (Denmark)

    Roed, Sarah Norklit; Ørgaard, Anne; Jørgensen, Rasmus

    2012-01-01

    , the glucagon receptor, and the receptors for parathyroid hormone (PTHR1 and PTHR2). The dysregulation of several family B1 receptors is involved in diseases, such as diabetes, chronic inflammation, and osteoporosis which underlines the pathophysiological importance of this GPCR subfamily. In spite of this......, investigation of family B1 receptor oligomerization and especially its pharmacological importance is still at an early stage. Even though GPCR oligomerization is a well-established phenomenon, there is a need for more investigations providing a direct link between these interactions and receptor functionality......The superfamily of the seven transmembrane G-protein-coupled receptors (7TM/GPCRs) is the largest family of membrane-associated receptors. GPCRs are involved in the pathophysiology of numerous human diseases, and they constitute an estimated 30-40% of all drug targets. During the last two decades...

  13. Screening of drugs inhibiting in vitro oligomerization of Cu/Zn-superoxide dismutase with a mutation causing amyotrophic lateral sclerosis

    Directory of Open Access Journals (Sweden)

    Itsuki Anzai

    2016-08-01

    Full Text Available Dominant mutations in Cu/Zn-superoxide dismutase (SOD1 gene have been shown to cause a familial form of amyotrophic lateral sclerosis (SOD1-ALS. A major pathological hallmark of this disease is abnormal accumulation of mutant SOD1 oligomers in the affected spinal motor neurons. While no effective therapeutics for SOD1-ALS is currently available, SOD1 oligomerization will be a good target for developing cures of this disease. Recently, we have reproduced the formation of SOD1 oligomers abnormally cross-linked via disulfide bonds in a test tube. Using our in vitro model of SOD1 oligomerization, therefore, we screened 640 FDA-approved drugs for inhibiting the oligomerization of SOD1 proteins, and three effective classes of chemical compounds were identified. Those hit compounds will provide valuable information on the chemical structures for developing a novel drug candidate suppressing the abnormal oligomerization of mutant SOD1 and possibly curing the disease.

  14. A High Diversity in Chitinolytic and Chitosanolytic Species and Enzymes and Their Oligomeric Products Exist in Soil with a History of Chitin and Chitosan Exposure.

    Science.gov (United States)

    Nampally, Malathi; Rajulu, M B Govinda; Gillet, Dominique; Suryanarayanan, T S; Moerschbacher, Bruno B

    2015-01-01

    Chitin is one of the most abundant biomolecules on earth, and its partially de-N-acetylated counterpart, chitosan, is one of the most promising biotechnological resources due to its diversity in structure and function. Recently, chitin and chitosan modifying enzymes (CCMEs) have gained increasing interest as tools to engineer chitosans with specific functions and reliable performance in biotechnological and biomedical applications. In a search for novel CCME, we isolated chitinolytic and chitosanolytic microorganisms from soils with more than ten-years history of chitin and chitosan exposure and screened them for chitinase and chitosanase isoenzymes as well as for their patterns of oligomeric products by incubating their secretomes with chitosan polymers. Of the 60 bacterial strains isolated, only eight were chitinolytic and/or chitosanolytic, while 20 out of 25 fungal isolates were chitinolytic and/or chitosanolytic. The bacterial isolates produced rather similar patterns of chitinolytic and chitosanolytic enzymes, while the fungal isolates produced a much broader range of different isoenzymes. Furthermore, diverse mixtures of oligosaccharides were formed when chitosan polymers were incubated with the secretomes of select fungal species. Our study indicates that soils with a history of chitin and chitosan exposure are a good source of novel CCME for chitosan bioengineering.

  15. A High Diversity in Chitinolytic and Chitosanolytic Species and Enzymes and Their Oligomeric Products Exist in Soil with a History of Chitin and Chitosan Exposure

    Science.gov (United States)

    Nampally, Malathi; Rajulu, M. B. Govinda; Gillet, Dominique; Suryanarayanan, T. S.; Moerschbacher, Bruno B.

    2015-01-01

    Chitin is one of the most abundant biomolecules on earth, and its partially de-N-acetylated counterpart, chitosan, is one of the most promising biotechnological resources due to its diversity in structure and function. Recently, chitin and chitosan modifying enzymes (CCMEs) have gained increasing interest as tools to engineer chitosans with specific functions and reliable performance in biotechnological and biomedical applications. In a search for novel CCME, we isolated chitinolytic and chitosanolytic microorganisms from soils with more than ten-years history of chitin and chitosan exposure and screened them for chitinase and chitosanase isoenzymes as well as for their patterns of oligomeric products by incubating their secretomes with chitosan polymers. Of the 60 bacterial strains isolated, only eight were chitinolytic and/or chitosanolytic, while 20 out of 25 fungal isolates were chitinolytic and/or chitosanolytic. The bacterial isolates produced rather similar patterns of chitinolytic and chitosanolytic enzymes, while the fungal isolates produced a much broader range of different isoenzymes. Furthermore, diverse mixtures of oligosaccharides were formed when chitosan polymers were incubated with the secretomes of select fungal species. Our study indicates that soils with a history of chitin and chitosan exposure are a good source of novel CCME for chitosan bioengineering. PMID:26273652

  16. Assessing heterogeneity in oligomeric AAA+ machines.

    Science.gov (United States)

    Sysoeva, Tatyana A

    2017-03-01

    ATPases Associated with various cellular Activities (AAA+ ATPases) are molecular motors that use the energy of ATP binding and hydrolysis to remodel their target macromolecules. The majority of these ATPases form ring-shaped hexamers in which the active sites are located at the interfaces between neighboring subunits. Structural changes initiate in an active site and propagate to distant motor parts that interface and reshape the target macromolecules, thereby performing mechanical work. During the functioning cycle, the AAA+ motor transits through multiple distinct states. Ring architecture and placement of the catalytic sites at the intersubunit interfaces allow for a unique level of coordination among subunits of the motor. This in turn results in conformational differences among subunits and overall asymmetry of the motor ring as it functions. To date, a large amount of structural information has been gathered for different AAA+ motors, but even for the most characterized of them only a few structural states are known and the full mechanistic cycle cannot be yet reconstructed. Therefore, the first part of this work will provide a broad overview of what arrangements of AAA+ subunits have been structurally observed focusing on diversity of ATPase oligomeric ensembles and heterogeneity within the ensembles. The second part of this review will concentrate on methods that assess structural and functional heterogeneity among subunits of AAA+ motors, thus bringing us closer to understanding the mechanism of these fascinating molecular motors.

  17. Catalysis of the Oligomerization of O-Phospho-Serine, Aspartic Acid, or Glutamic Acid by Cationic Micelles

    Science.gov (United States)

    Bohler, Christof; Hill, Aubrey R., Jr.; Orgel, Leslie E.

    1996-01-01

    Treatment of relatively concentrated aqueous solutions of 0-phospho-serine (50 mM), aspartic acid (100 mM) or glutamic acid (100 mM) with carbonyldiimidazole leads to the formation of an activated intermediate that oligomerizes efficiently. When the concentration of amino acid is reduced tenfold, few long oligomers can be detected. Positively-charged cetyltrimethyl ammonium bromide micelles concentrate the negatively-charged activated intermediates of the amino acids at their surfaces and catalyze efficient oligomerization even from dilute solutions.

  18. Molecular evidence for high frequency of multiple paternity in a freshwater shrimp species Caridina ensifera.

    Directory of Open Access Journals (Sweden)

    Gen Hua Yue

    2010-09-01

    Full Text Available Molecular genetic analyses of parentage provide insights into mating systems. Although there are 22,000 members in Malacostraca, not much has been known about mating systems in Malacostraca. The freshwater shrimp Caridina ensifera blue, is a new species belonging to Malacostraca which was discovered recently in Sulawesi, Indonesia. Due to its small body size and low fecundity, this species is an ideal species to study the occurrence and frequency of multiple paternity and to understand of how the low fecundity species persist and evolve.In this study, we developed four polymorphic microsatellites from C. ensifera and applied them to investigate the occurrence and frequency of multiple paternity in 20 C. ensifera broods caught from Lake Matano, Sulawesi. By genotyping the mother and all offspring from each brood we discovered multiple paternity in all 20 broods. In most of the 20 broods, fathers contributed skewed numbers of offspring and there was an apparent inverse correlation between reproductive success of sires and their relatedness to mothers.Our results in combination with recent reports on multiple paternity in crayfish, crab and lobster species suggests that multiple paternity is common in Malacostraca. Skewed contribution of fathers to the numbers of offspring and inverse correlation between reproductive success of sires and their relatedness to mothers suggest that sperm competition occurred and/or pre- and postcopulatory female choice happen, which may be important for avoiding the occurrence of inbreeding and optimize genetic variation in offspring and for persistence and evolution of low fecundity species.

  19. Blends of Pheromones, With and Without Host Plant Volatiles, Can Attract Multiple Species of Cerambycid Beetles Simultaneously

    Science.gov (United States)

    L.M. Hanks; J.A. Mongold-Diers; T.H. Atkinson; M.K. Fierke; M.D. Ginzel; E.E. Graham; T.M. Poland; A.B. Richards; M.L. Richardson; J.G. Millar

    2018-01-01

    Pheromone components of cerambycid beetles are often conserved, with a given compound serving as a pheromone component for multiple related species, including species native to different continents. Consequently, a single synthesized compound may attract multiple species to a trap simultaneously. Furthermore, our previous research in east-central Illinois had...

  20. Mapping habitat for multiple species in the Desert Southwest

    Science.gov (United States)

    Inman, Richard D.; Nussear, Kenneth E.; Esque, Todd C.; Vandergast, Amy G.; Hathaway, Stacie A.; Wood, Dustin A.; Barr, Kelly R.; Fisher, Robert N.

    2014-01-01

    Many utility scale renewable energy projects are currently proposed across the Mojave Ecoregion. Agencies that manage biological resources throughout this region need to understand the potential impacts of these renewable energy projects and their associated infrastructure (for example, transmission corridors, substations, access roads, etc.) on species movement, genetic exchange among populations, and species’ abilities to adapt to changing environmental conditions. Understanding these factors will help managers’ select appropriate project sites and possibly mitigate for anticipated effects of management activities. We used species distribution models to map habitat for 15 species across the Mojave Ecoregion to aid regional land-use management planning. Models were developed using a common 1 × 1 kilometer resolution with maximum entropy and generalized additive models. Occurrence data were compiled from multiple sources, including VertNet (http://vertnet.org/), HerpNET (http://www.herpnet.org), and MaNIS (http://manisnet.org), as well as from internal U.S. Geological Survey databases and other biologists. Background data included 20 environmental covariates representing terrain, vegetation, and climate covariates. This report summarizes these environmental covariates and species distribution models used to predict habitat for the 15 species across the Mojave Ecoregion.

  1. Interference with RUNX1/ETO Leukemogenic Function by Cell-Penetrating Peptides Targeting the NHR2 Oligomerization Domain

    Directory of Open Access Journals (Sweden)

    Yvonne Bartel

    2013-01-01

    Full Text Available The leukemia-associated fusion protein RUNX1/ETO is generated by the chromosomal translocation t(8;21 which appears in about 12% of all de novo acute myeloid leukemias (AMLs. Essential for the oncogenic potential of RUNX1/ETO is the oligomerization of the chimeric fusion protein through the nervy homology region 2 (NHR2 within ETO. In previous studies, we have shown that the intracellular expression of peptides containing the NHR2 domain inhibits RUNX1/ETO oligomerization, thereby preventing cell proliferation and inducing differentiation of RUNX1/ETO transformed cells. Here, we show that introduction of a recombinant TAT-NHR2 fusion polypeptide into the RUNX1/ETO growth-dependent myeloid cell line Kasumi-1 results in decreased cell proliferation and increased numbers of apoptotic cells. This effect was highly specific and mediated by binding the TAT-NHR2 peptide to ETO sequences, as TAT-polypeptides containing the oligomerization domain of BCR did not affect cell proliferation or apoptosis in Kasumi-1 cells. Thus, the selective interference with NHR2-mediated oligomerization by peptides represents a challenging but promising strategy for the inhibition of the leukemogenic potential of RUNX1/ETO in t(8;21-positive leukemia.

  2. Where and how to manage: optimal selection of conservation actions for multiple species

    NARCIS (Netherlands)

    Teeffelen, van A.J.A.; Moilanen, A.

    2008-01-01

    Multiple alternative options are frequently available for the protection, maintenance or restoration of conservation areas. The choice of a particular management action can have large effects on the species occurring in the area, because different actions have different effects on different species.

  3. Whole genome phylogenies for multiple Drosophila species

    Directory of Open Access Journals (Sweden)

    Seetharam Arun

    2012-12-01

    Full Text Available Abstract Background Reconstructing the evolutionary history of organisms using traditional phylogenetic methods may suffer from inaccurate sequence alignment. An alternative approach, particularly effective when whole genome sequences are available, is to employ methods that don’t use explicit sequence alignments. We extend a novel phylogenetic method based on Singular Value Decomposition (SVD to reconstruct the phylogeny of 12 sequenced Drosophila species. SVD analysis provides accurate comparisons for a high fraction of sequences within whole genomes without the prior identification of orthologs or homologous sites. With this method all protein sequences are converted to peptide frequency vectors within a matrix that is decomposed to provide simplified vector representations for each protein of the genome in a reduced dimensional space. These vectors are summed together to provide a vector representation for each species, and the angle between these vectors provides distance measures that are used to construct species trees. Results An unfiltered whole genome analysis (193,622 predicted proteins strongly supports the currently accepted phylogeny for 12 Drosophila species at higher dimensions except for the generally accepted but difficult to discern sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. Similar results were obtained when just the melanogaster subgroup was analyzed. Conclusions These results indicate that using our novel phylogenetic method, it is possible to consult and interpret all predicted protein sequences within multiple whole genomes to produce accurate phylogenetic estimations of relatedness between

  4. Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L. Moench and related model species.

    Directory of Open Access Journals (Sweden)

    Adugna Abdi Woldesemayat

    Full Text Available Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations.In this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO, Trait Ontology (TO, Plant Ontology (PO, Growth Ontology (GRO and Environment Ontology (EO were used to semantically integrate drought related information.Target genes linked to Quantitative Trait Loci (QTLs controlling yield and stress tolerance in sorghum (Sorghum bicolor (L. Moench and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%, salt (32%, cold (20%, heat (8% and oxidative stress (25% were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs

  5. A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP.

    Science.gov (United States)

    Serrano, Arnaldo L; Lomont, Justin P; Tu, Ling-Hsien; Raleigh, Daniel P; Zanni, Martin T

    2017-11-22

    Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F 23 G 24 A 25 I 26 L 27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.

  6. Where and how to manage: Optimal selection of conservation actions for multiple species.

    Directory of Open Access Journals (Sweden)

    Astrid van Teeffelen

    2008-01-01

    Full Text Available Multiple alternative options are frequently available for the protection, maintenance or restoration of conservation areas. The choice of a particular management action can have large effects on the species occurring in the area, because different actions have different effects on different species. Together with the fact that conservation funds are limited and particular management actions are costly, it would be desirable to be able to identify where, and what kind of management should be applied to maximize conservation benefits. Currently available site-selection algorithms can identify the optimal set of sites for a reserve network. However, these algorithms have not been designed to answer what kind of action would be most beneficial at these sites when multiple alternative actions are available. We describe an algorithm capable of solving multi-species planning problems with multiple management options per site. The algorithm is based on benefit functions, which translate the effect of a management action on species representation levels into a value, in order to identify the most beneficial option. We test the performance of this algorithm with simulated data for different types of benefit functions and show that the algorithm’s solutions are optimal, or very near globally optimal, partially depending on the type of benefit function used. The good performance of the proposed algorithm suggests that it could be profitably used for large multi-action multi-species conservation planning problems.

  7. Polyhedral Oligomeric Silsesquioxane (POSS)-Containing Polymer Nanocomposites

    Science.gov (United States)

    Ayandele, Ebunoluwa; Sarkar, Biswajit; Alexandridis, Paschalis

    2012-01-01

    Hybrid materials with superior structural and functional properties can be obtained by incorporating nanofillers into polymer matrices. Polyhedral oligomeric silsesquioxane (POSS) nanoparticles have attracted much attention recently due to their nanometer size, the ease of which these particles can be incorporated into polymeric materials and the unique capability to reinforce polymers. We review here the state of POSS-containing polymer nanocomposites. We discuss the influence of the incorporation of POSS into polymer matrices via chemical cross-linking or physical blending on the structure of nanocomposites, as affected by surface functional groups, and the POSS concentration. PMID:28348318

  8. Arc is a flexible modular protein capable of reversible self-oligomerization

    Science.gov (United States)

    Myrum, Craig; Baumann, Anne; Bustad, Helene J.; Flydal, Marte Innselset; Mariaule, Vincent; Alvira, Sara; Cuéllar, Jorge; Haavik, Jan; Soulé, Jonathan; Valpuesta, José Maria; Márquez, José Antonio; Martinez, Aurora; Bramham, Clive R.

    2015-01-01

    The immediate early gene product Arc (activity-regulated cytoskeleton-associated protein) is posited as a master regulator of long-term synaptic plasticity and memory. However, the physicochemical and structural properties of Arc have not been elucidated. In the present study, we expressed and purified recombinant human Arc (hArc) and performed the first biochemical and biophysical analysis of hArc's structure and stability. Limited proteolysis assays and MS analysis indicate that hArc has two major domains on either side of a central more disordered linker region, consistent with in silico structure predictions. hArc's secondary structure was estimated using CD, and stability was analysed by CD-monitored thermal denaturation and differential scanning fluorimetry (DSF). Oligomerization states under different conditions were studied by dynamic light scattering (DLS) and visualized by AFM and EM. Biophysical analyses show that hArc is a modular protein with defined secondary structure and loose tertiary structure. hArc appears to be pyramid-shaped as a monomer and is capable of reversible self-association, forming large soluble oligomers. The N-terminal domain of hArc is highly basic, which may promote interaction with cytoskeletal structures or other polyanionic surfaces, whereas the C-terminal domain is acidic and stabilized by ionic conditions that promote oligomerization. Upon binding of presenilin-1 (PS1) peptide, hArc undergoes a large structural change. A non-synonymous genetic variant of hArc (V231G) showed properties similar to the wild-type (WT) protein. We conclude that hArc is a flexible multi-domain protein that exists in monomeric and oligomeric forms, compatible with a diverse, hub-like role in plasticity-related processes. PMID:25748042

  9. Carbon Domains on MoS2/TiO2 System via Catalytic Acetylene Oligomerization: Synthesis, Structure, and Surface Properties

    Directory of Open Access Journals (Sweden)

    Sara Cravanzola

    2017-11-01

    Full Text Available Carbon domains have been obtained at the surface of a MoS2/TiO2 (Evonik, P25 system via oligomerization and cyclotrimerization reactions involved in the interaction of the photoactive material with acetylene. Firstly, MoS2 nanosheets have been synthesized at the surface of TiO2, via sulfidation of a molybdenum oxide precursor with H2S (bottom-up method. Secondly, the morphology and the structure, the optical and the vibrational properties of the obtained materials, for each step of the synthesis procedure, have been investigated by microscopy and spectroscopy methods. In particular, transmission electron microscopy images provide a simple tool to highlight the effectiveness of the sulfidation process, thus showing 1L, 2L, and stacked MoS2 nanosheets anchored to the surface of TiO2 nanoparticles. Lastly, in-situ FTIR spectroscopy investigation gives insights into the nature of the oligomerized species, showing that the formation of both polyenic and aromatic systems can be taken into account, being their formation promoted by both Ti and Mo catalytic sites. This finding gives an opportunity for the assembly of extended polyenic, polyaromatic, or mixed domains firmly attached at the surface of photoactive materials. The presented approach, somehow different from the carbon adding or doping processes of TiO2, is of potential interest for the advanced green chemistry and energy conversion/transport applications.

  10. Substitution of proline32 by α-methylproline preorganizes β2-microglobulin for oligomerization but not for aggregation into amyloids.

    Science.gov (United States)

    Torbeev, Vladimir; Ebert, Marc-Olivier; Dolenc, Jozica; Hilvert, Donald

    2015-02-25

    Conversion of soluble folded proteins into insoluble amyloids generally proceeds in three distinct mechanistic stages: (1) initial protein misfolding into aggregation-competent conformers, (2) subsequent formation of oligomeric species and, finally, (3) self-assembly into extended amyloid fibrils. In the work reported herein, we interrogated the amyloidogenesis mechanism of human β2-microglobulin (β2m), which is thought to be triggered by a pivotal cis-trans isomerization of a proline residue at position 32 in the polypeptide, with nonstandard amino acids. Using chemical protein synthesis we prepared a β2m analogue in which Pro32 was replaced by the conformationally constrained amino acid α-methylproline (MePro). The strong propensity of MePro to adopt a trans prolyl bond led to enhanced population of a non-native [trans-MePro32]β2m protein conformer, which readily formed oligomers at neutral pH. In the presence of the antibiotic rifamycin SV, which inhibits amyloid growth of wild-type β2m, [MePro32]β2m was nearly quantitatively converted into different spherical oligomeric species. Self-assembly into amyloid fibrils was not observed in the absence of seeding, however, even at low pH (<3), where wild-type β2m spontaneously forms amyloids. Nevertheless, we found that aggregation-preorganized [MePro32]β2m can act in a prion-like fashion, templating misfolded conformations in a natively folded protein. Overall, these results provide detailed insight into the role of cis-trans isomerization of Pro32 and ensuing structural rearrangements that lead to initial β2m misfolding and aggregation. They corroborate the view that conformational protein dynamics enabled by reversible Pro32 cis-trans interconversion rather than simple population of the trans conformer is critical for both nucleation and subsequent growth of β2m amyloid structures.

  11. Oligomerization and polymerization of the filovirus matrix protein VP40

    International Nuclear Information System (INIS)

    Timmins, Joanna; Schoehn, Guy; Kohlhaas, Christine; Klenk, Hans-Dieter; Ruigrok, Rob W.H.; Weissenhorn, Winfried

    2003-01-01

    The matrix protein VP40 from Ebola virus plays an important role in the assembly process of virus particles by interacting with cellular factors, cellular membranes, and the ribonuclearprotein particle complex. Here we show that the N-terminal domain of VP40 folds into a mixture of two different oligomeric states in vitro, namely hexameric and octameric ringlike structures, as detected by gel filtration chromatography, chemical cross-linking, and electron microscopy. Octamer formation depends largely on the interaction with nucleic acids, which in turn confers in vitro SDS resistance. Refolding experiments with a nucleic acid free N-terminal domain preparation reveal a mostly dimeric form of VP40, which is transformed into an SDS resistant octamer upon incubation with E. coli nucleic acids. In addition, we demonstrate that the N-terminal domain of Marburg virus VP40 also folds into ringlike structures, similar to Ebola virus VP40. Interestingly, Marburg virus VP40 rings reveal a high tendency to polymerize into rods composed of stacked rings. These results may suggest distinct roles for different oligomeric forms of VP40 in the filovirus life cycle

  12. Cartilage oligomeric matrix protein specific antibodies are pathogenic

    DEFF Research Database (Denmark)

    Geng, Hui; Nandakumar, Kutty Selva; Pramhed, Anna

    2012-01-01

    -specific monoclonal antibodies (mAbs). METHODS: B cell immunodominant regions on the COMP molecule were measured with a novel enzyme-linked immunosorbent assay using mammalian expressed full-length mouse COMP as well as a panel of recombinant mouse COMP fragments. 18 mAbs specific to COMP were generated......ABSTRACT: INTRODUCTION: Cartilage oligomeric matrix protein (COMP) is a major non-collagenous component of cartilage. Earlier, we developed a new mouse model for rheumatoid arthritis using COMP. This study was undertaken to investigate the epitope specificity and immunopathogenicity of COMP...

  13. Receptor Oligomerization as a Process Modulating Cellular Semiotics

    DEFF Research Database (Denmark)

    Giorgi, Franco; Bruni, Luis Emilio; Maggio, Roberto

    2010-01-01

    be another level of quality control that may help maintaining GPCRs rather stable throughout evolution. We propose here receptor oligomerization to be a basic molecular mechanism controlling GPCRs redundancy in many different cell types, and the plasma membrane as the first hierarchical cell structure...... at which selective categorical sensing may occur. Categorical sensing can be seen as the cellular capacity for identifying and ordering complex patterns of mixed signals out of a contextual matrix, i.e., the recognition of meaningful patterns out of ubiquitous signals. In this context, redundancy...

  14. Genetic components to caste allocation in a multiple-queen ant species

    NARCIS (Netherlands)

    Libbrecht, Romain; Schwander, Tanja; Keller, Laurent

    2011-01-01

    Reproductive division of labor and the coexistence of distinct castes are hallmarks of insect societies. In social insect species with multiple queens per colony, the fitness of nestmate queens directly depends on the process of caste allocation (i.e., the relative investment in queen, sterile

  15. Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study.

    Science.gov (United States)

    Urbanc, B; Betnel, M; Cruz, L; Bitan, G; Teplow, D B

    2010-03-31

    Oligomers of amyloid beta-protein (Abeta) play a central role in the pathology of Alzheimer's disease. Of the two predominant Abeta alloforms, Abeta(1-40) and Abeta(1-42), Abeta(1-42) is more strongly implicated in the disease. We elucidated the structural characteristics of oligomers of Abeta(1-40) and Abeta(1-42) and their Arctic mutants, [E22G]Abeta(1-40) and [E22G]Abeta(1-42). We simulated oligomer formation using discrete molecular dynamics (DMD) with a four-bead protein model, backbone hydrogen bonding, and residue-specific interactions due to effective hydropathy and charge. For all four peptides under study, we derived the characteristic oligomer size distributions that were in agreement with prior experimental findings. Unlike Abeta(1-40), Abeta(1-42) had a high propensity to form paranuclei (pentameric or hexameric) structures that could self-associate into higher-order oligomers. Neither of the Arctic mutants formed higher-order oligomers, but [E22G]Abeta(1-40) formed paranuclei with a similar propensity to that of Abeta(1-42). Whereas the best agreement with the experimental data was obtained when the charged residues were modeled as solely hydrophilic, further assembly from spherical oligomers into elongated protofibrils was induced by nonzero electrostatic interactions among the charged residues. Structural analysis revealed that the C-terminal region played a dominant role in Abeta(1-42) oligomer formation whereas Abeta(1-40) oligomerization was primarily driven by intermolecular interactions among the central hydrophobic regions. The N-terminal region A2-F4 played a prominent role in Abeta(1-40) oligomerization but did not contribute to the oligomerization of Abeta(1-42) or the Arctic mutants. The oligomer structure of both Arctic peptides resembled Abeta(1-42) more than Abeta(1-40), consistent with their potentially more toxic nature.

  16. CARS Spectral Fitting with Multiple Resonant Species using Sparse Libraries

    Science.gov (United States)

    Cutler, Andrew D.; Magnotti, Gaetano

    2010-01-01

    The dual pump CARS technique is often used in the study of turbulent flames. Fast and accurate algorithms are needed for fitting dual-pump CARS spectra for temperature and multiple chemical species. This paper describes the development of such an algorithm. The algorithm employs sparse libraries, whose size grows much more slowly with number of species than a conventional library. The method was demonstrated by fitting synthetic "experimental" spectra containing 4 resonant species (N2, O2, H2 and CO2), both with noise and without it, and by fitting experimental spectra from a H2-air flame produced by a Hencken burner. In both studies, weighted least squares fitting of signal, as opposed to least squares fitting signal or square-root signal, was shown to produce the least random error and minimize bias error in the fitted parameters.

  17. An Intramolecular Salt Bridge in Bacillus thuringiensis Cry4Ba Toxin Is Involved in the Stability of Helix α-3, Which Is Needed for Oligomerization and Insecticidal Activity.

    Science.gov (United States)

    Pacheco, Sabino; Gómez, Isabel; Sánchez, Jorge; García-Gómez, Blanca-Ines; Soberón, Mario; Bravo, Alejandra

    2017-10-15

    Bacillus thuringiensis three-domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Here we identify an intramolecular salt bridge within helix α-3 of Cry4Ba (D111-K115) that is conserved in many members of the family of three-domain Cry toxins. Single point mutations such as D111K or K115D resulted in proteins severely affected in toxicity. These mutants were also altered in oligomerization, and the mutant K115D was more sensitive to protease digestion. The double point mutant with reversed charges, D111K-K115D, recovered both oligomerization and toxicity, suggesting that this salt bridge is highly important for conservation of the structure of helix α-3 and necessary to promote the correct oligomerization of the toxin. IMPORTANCE Domain I has been shown to be involved in oligomerization through helix α-3 in different Cry toxins, and mutations affecting oligomerization also elicit changes in toxicity. The three-dimensional structure of the Cry4Ba toxin reveals an intramolecular salt bridge in helix α-3 of domain I. Mutations that disrupt this salt bridge resulted in changes in Cry4Ba oligomerization and toxicity, while a double point reciprocal mutation that restored the salt bridge resulted in recovery of toxin oligomerization and toxicity. These data highlight the role of oligomer formation as a key step in Cry4Ba toxicity. Copyright © 2017 American Society for Microbiology.

  18. Phylogenetic analysis reveals multiple introductions of Cynodon species in Australia.

    Science.gov (United States)

    Jewell, M; Frère, C H; Harris-Shultz, K; Anderson, W F; Godwin, I D; Lambrides, C J

    2012-11-01

    The distinction between native and introduced flora within isolated land masses presents unique challenges. The geological and colonisation history of Australia, the world's largest island, makes it a valuable system for studying species endemism, introduction, and phylogeny. Using this strategy we investigated Australian cosmopolitan grasses belonging to the genus Cynodon. While it is believed that seven species of Cynodon are present in Australia, no genetic analyses have investigated the origin, diversity and phylogenetic history of Cynodon within Australia. To address this gap, 147 samples (92 from across Australia and 55 representing global distribution) were sequenced for a total of 3336bp of chloroplast DNA spanning six genes. Data showed the presence of at least six putatively introduced Cynodon species (C. transvaalensis, C. incompletus, C. hirsutus, C. radiatus, C. plectostachyus and C. dactylon) in Australia and suggested multiple recent introductions. C. plectostachyus, a species often confused with C. nlemfuensis, was not previously considered to be present in Australia. Most significantly, we identified two common haplotypes that formed a monophyletic clade diverging from previously identified Cynodon species. We hypothesise that these two haplotypes may represent a previously undescribed species of Cynodon. We provide further evidence that two Australian native species, Brachyachne tenella and B. convergens belong in the genus Cynodon and, therefore, argue for the taxonomic revision of the genus Cynodon. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. Oligomerization of a Glucagon-like Peptide 1 Analog: Bridging Experiment and Simulations

    DEFF Research Database (Denmark)

    Frederiksen, Tine Maja; Sønderby, Pernille; Ryberg, Line A.

    2015-01-01

    The glucagon-like peptide 1 (GLP-1) analog, liraglutide, is a GLP-1 agonist and is used in the treatment of type-2 diabetes mellitus and obesity. From a pharmaceutical perspective, it is important to know the oligomerization state of liraglutide with respect to stability. Compared to GLP-1...

  20. The role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase.

    Directory of Open Access Journals (Sweden)

    M Qaiser Fatmi

    Full Text Available The oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. The synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. The present study used molecular dynamics and Brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (TRPS. TRPS uses a set of α/β-dimeric units to catalyze the last two steps of L-tryptophan biosynthesis, and the rate is remarkably slower in the isolated monomers. Our work shows that without their binding partner, the isolated monomers are stable and more rigid. The substrates can form fairly stable interactions with the protein in both forms when the protein reaches the final ligand-bound conformations. Our simulations also revealed that the α/β-dimeric unit stabilizes the substrate-protein conformation in the ligand binding process, which lowers the conformation transition barrier and helps the protein conformations shift from an open/inactive form to a closed/active form. Brownian dynamics simulations with a coarse-grained model illustrate how protein conformations affect substrate channeling. The results highlight the complex roles of protein oligomerization and the fine balance between rigidity and dynamics in protein function.

  1. Influence of oligomeric resins on traction and rolling resistance of silica tire treads

    NARCIS (Netherlands)

    Vleugels, N.; Pille-Wolf, W.; Dierkes, Wilma K.; Noordermeer, Jacobus W.M.

    2016-01-01

    This study concerns the silica-reinforcement of synthetic rubber compounds for passenger tire treads with the objective to gain insight into the beneficial effects of oligomeric resins, derived from natural and synthetic monomers, on the major tire performance factors: rolling resistance and (wet)

  2. Influence of oligomeric resins on traction and rolling resistance of silica tire treads

    NARCIS (Netherlands)

    Vleugels, N.; Pille-Wolf, W.; Dierkes, Wilma K.; Noordermeer, Jacobus W.M.

    2013-01-01

    This study concerns the silica-reinforcement of synthetic rubber compounds for passenger tire treads with the objective to gain insight into the beneficial effects of oligomeric resins, derived from natural and synthetic monomers, on the major tire performance factors: Rolling Resistance and (Wet)

  3. Hydration effect on the electronic transport properties of oligomeric phenylene ethynylene molecular junctions

    International Nuclear Information System (INIS)

    Zong-Liang, Li; Huai-Zhi, Li; Yong, Ma; Guang-Ping, Zhang; Chuan-Kui, Wang

    2010-01-01

    A first-principles computational method based on the hybrid density functional theory is developed to simulate the electronic transport properties of oligomeric phenylene ethynylene molecular junctions with H 2 O molecules accumulated in the vicinity as recently reported by Na et al. [Nanotechnology 18 424001 (2007)]. The numerical results show that the hydrogen bonds between the oxygen atoms of the oligomeric phenylene ethynylene molecule and H 2 O molecules result in the localisation of the molecular orbitals and lead to the lower transition peaks. The H 2 O molecular chains accumulated in the vicinity of the molecular junction can not only change the electronic structure of the molecular junctions, but also open additional electronic transport pathways. The obvious influence of H 2 O molecules on the electronic structure of the molecular junction and its electronic transport properties is thus demonstrated. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  4. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

    Directory of Open Access Journals (Sweden)

    Messeguer Xavier

    2006-10-01

    Full Text Available Abstract Background Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons. Results To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M-GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M-GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 (containing 75 cloned genomes from a set of 15 published enterobacterial genomes in an hour. M-GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations. Conclusion M-GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M-GCAT is freely available for download for academic and non-commercial use at: http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html.

  5. Mechanics of the mannitol transporter from Escherichia coli : substrate-probing and oligomeric structure

    NARCIS (Netherlands)

    Veldhuis, Gertjan

    2006-01-01

    Gertjan Veldhuis bestudeerde de mannitoltransporter van Escherichia coli, EnzymeIImtl (EIImtl), om meer inzicht te krijgen in het bindingsmechanisme en de oligomere toestand van dit membraaneiwit. Hij concludeerde onder andere dat dimeer EIImtl één mannitol bindt, de dimeer zeer stabiel is en dat

  6. The Agrobacterium tumefaciens Transcription Factor BlcR Is Regulated via Oligomerization

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Yi; Fiscus, Valena; Meng, Wuyi; Zheng, Zhida; Zhang, Lian-Hui; Fuqua, Clay; Chen, Lingling (IMCB-Singapore); (Indiana)

    2012-02-08

    The Agrobacterium tumefaciens BlcR is a member of the emerging isocitrate lyase transcription regulators that negatively regulates metabolism of {gamma}-butyrolactone, and its repressing function is relieved by succinate semialdehyde (SSA). Our crystal structure showed that BlcR folded into the DNA- and SSA-binding domains and dimerized via the DNA-binding domains. Mutational analysis identified residues, including Phe{sup 147}, that are important for SSA association; BlcR{sup F147A} existed as tetramer. Two BlcR dimers bound to target DNA and in a cooperative manner, and the distance between the two BlcR-binding sequences in DNA was critical for BlcR-DNA association. Tetrameric BlcR{sup F147A} retained DNA binding activity, and importantly, this activity was not affected by the distance separating the BlcR-binding sequences in DNA. SSA did not dissociate tetrameric BlcR{sup F147A} or BlcR{sup F147A}-DNA. As well as in the SSA-binding site, Phe{sup 147} is located in a structurally flexible loop that may be involved in BlcR oligomerization. We propose that SSA regulates BlcR DNA-binding function via oligomerization.

  7. Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase

    Science.gov (United States)

    Wang, Quan; Serban, Andrew J.; Wachter, Rebekka M.; Moerner, W. E.

    2018-03-01

    Oligomerization plays an important role in the function of many proteins, but a quantitative picture of the oligomer distribution has been difficult to obtain using existing techniques. Here we describe a method that combines sub-stoichiometric labeling and recently developed single-molecule diffusometry to measure the size distribution of oligomers under equilibrium conditions in solution, one molecule at a time. We use this technique to characterize the oligomerization behavior of Nicotiana tabacum (Nt) Rubisco activase (Nt-Rca), a chaperone-like AAA-plus ATPase essential in regulating carbon fixation during photosynthesis. We directly observed monomers, dimers, and a tetramer/hexamer mixture and extracted their fractional abundance as a function of protein concentration. We show that the oligomerization pathway of Nt-Rca is nucleotide dependent: ATPγS binding strongly promotes tetramer/hexamer formation from dimers and results in a preferred tetramer/hexamer population for concentrations in the 1-10 μM range. Furthermore, we directly observed dynamic assembly and disassembly processes of single complexes in real time and from there estimated the rate of subunit exchange to be ˜0.1 s-1 with ATPγS. On the other hand, ADP binding destabilizes Rca complexes by enhancing the rate of subunit exchange by >2 fold. These observations provide a quantitative starting point to elucidate the structure-function relations of Nt-Rca complexes. We envision the method to fill a critical gap in defining and quantifying protein assembly pathways in the small-oligomer regime.

  8. DFT study on the impact of the methylaluminoxane cocatalyst in ethylene oligomerization using a titanium-based catalyst

    KAUST Repository

    Pasha, Farhan Ahmad; Basset, Jean-Marie; Toulhoat, Hervé ; De Bruin, Theodorus J M

    2015-01-01

    A computational study within the framework of density functional theory is presented on the oligomerization of ethylene to yield 1-hexene using [(η5-C5H4CMe2C6H5)]TiCl3/MAO] catalyst. This study explicitly takes into account a methylaluminoxane (MAO) cocatalyst model, where the MAO cluster has become an anionic species after having abstracted one chloride anion, yielding a cationic activated catalyst. Hence, the reaction profile was calculated using the zwitterionic system, and the potential energy surface has been compared to the cationic catalytic system. Modest differences were found between the two free energy profiles. However, we show for the first time that the use of a realistic zwitterionic model is required to obtain a Brønsted-Evans-Polanyi relationship between the energy barriers and reaction energies.

  9. DFT study on the impact of the methylaluminoxane cocatalyst in ethylene oligomerization using a titanium-based catalyst

    KAUST Repository

    Pasha, Farhan Ahmad

    2015-01-26

    A computational study within the framework of density functional theory is presented on the oligomerization of ethylene to yield 1-hexene using [(η5-C5H4CMe2C6H5)]TiCl3/MAO] catalyst. This study explicitly takes into account a methylaluminoxane (MAO) cocatalyst model, where the MAO cluster has become an anionic species after having abstracted one chloride anion, yielding a cationic activated catalyst. Hence, the reaction profile was calculated using the zwitterionic system, and the potential energy surface has been compared to the cationic catalytic system. Modest differences were found between the two free energy profiles. However, we show for the first time that the use of a realistic zwitterionic model is required to obtain a Brønsted-Evans-Polanyi relationship between the energy barriers and reaction energies.

  10. The effects of oligomerization on Saccharomyces cerevisiae Mcm4/6/7 function

    Directory of Open Access Journals (Sweden)

    Davey Megan J

    2010-09-01

    Full Text Available Abstract Background Minichromosome maintenance proteins (Mcm 2, 3, 4, 5, 6 and 7 are related by sequence and form a variety of complexes that unwind DNA, including Mcm4/6/7. A Mcm4/6/7 trimer forms one half of the Mcm2-7 hexameric ring and can be thought of as the catalytic core of Mcm2-7, the replicative helicase in eukaryotic cells. Oligomeric analysis of Mcm4/6/7 suggests that it forms a hexamer containing two Mcm4/6/7 trimers, however, under certain conditions trimeric Mcm4/6/7 has also been observed. The functional significance of the different Mcm4/6/7 oligomeric states has not been assessed. The results of such an assessment would have implications for studies of both Mcm4/6/7 and Mcm2-7. Results Here, we show that Saccharomyces cerevisiae Mcm4/6/7 reconstituted from individual subunits exists in an equilibrium of oligomeric forms in which smaller oligomers predominate in the absence of ATP. In addition, we found that ATP, which is required for Mcm4/6/7 activity, shifts the equilibrium towards larger oligomers, likely hexamers of Mcm4/6/7. ATPγS and to a lesser extent ADP also shift the equilibrium towards hexamers. Study of Mcm4/6/7 complexes containing mutations that interfere with the formation of inter-subunit ATP sites (arginine finger mutants indicates that full activity of Mcm4/6/7 requires all of its ATP sites, which are formed in a hexamer and not a trimer. In keeping with this observation, Mcm4/6/7 binds DNA as a hexamer. Conclusions The minimal functional unit of Mcm4/6/7 is a hexamer. One of the roles of ATP binding by Mcm4/6/7 may be to stabilize formation of hexamers.

  11. Direct Evidence of Intrinsic Blue Fluorescence from Oligomeric Interfaces of Human Serum Albumin.

    Science.gov (United States)

    Bhattacharya, Arpan; Bhowmik, Soumitra; Singh, Amit K; Kodgire, Prashant; Das, Apurba K; Mukherjee, Tushar Kanti

    2017-10-10

    The molecular origin behind the concentration-dependent intrinsic blue fluorescence of human serum albumin (HSA) is not known yet. This unusual blue fluorescence is believed to be a characteristic feature of amyloid-like fibrils of protein/peptide and originates due to the delocalization of peptide bond electrons through the extended hydrogen bond networks of cross-β-sheet structure. Herein, by combining the results of spectroscopy, size exclusion chromatography, native gel electrophoresis, and confocal microscopy, we have shown that the intrinsic blue fluorescence of HSA exclusively originates from oligomeric interfaces devoid of any amyloid-like fibrillar structure. Our study suggests that this low energy fluorescence band is not due to any particular residue/sequence, but rather it is a common feature of self-assembled peptide bonds. The present findings of intrinsic blue fluorescence from oligomeric interfaces pave the way for future applications of this unique visual phenomenon for early stage detection of various protein aggregation related human diseases.

  12. Characterization of oligomerization of a peptide from the ebola virus glycoprotein by small-angle neutron scattering

    International Nuclear Information System (INIS)

    Egorov, V. V.; Gorshkov, A. N.; Murugova, T. N.; Vasin, A. V.; Lebedev, D. V.; Isaev-Ivanov, V. V.; Kiselev, O. I.

    2016-01-01

    Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) studies showed that model peptides QNALVCGLRQ (G33) and QNALVCGLRG (G31) corresponding to region 551–560 of the GP protein of the Sudan Ebola virus are prone to oligomerization in solution. Both peptides can form amyloid-like fibrills. The G33 peptide forms fibrils within one day of incubation, whereas the fibrillogenesis of the G31 peptide is observed only after incubation for several months. The possible role of the observed processes in the pathogenesis and the possibility of applying a combination of the TEM and SANS techniques to search for new compounds that are able to influence the protein oligomerization are discussed

  13. Characterization of oligomerization of a peptide from the ebola virus glycoprotein by small-angle neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Egorov, V. V., E-mail: vlaegur@omrb.pnpi.spb.ru [National Research Center “Kurchatov Institute”, Konstantinov Petersburg Nuclear Physics Institute (Russian Federation); Gorshkov, A. N. [Ministry of Health of the Russian Federation, Research Institute of Influenza (Russian Federation); Murugova, T. N. [Joint Institute for Nuclear Research (Russian Federation); Vasin, A. V. [Ministry of Health of the Russian Federation, Research Institute of Influenza (Russian Federation); Lebedev, D. V.; Isaev-Ivanov, V. V. [National Research Center “Kurchatov Institute”, Konstantinov Petersburg Nuclear Physics Institute (Russian Federation); Kiselev, O. I. [Ministry of Health of the Russian Federation, Research Institute of Influenza (Russian Federation)

    2016-01-15

    Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) studies showed that model peptides QNALVCGLRQ (G33) and QNALVCGLRG (G31) corresponding to region 551–560 of the GP protein of the Sudan Ebola virus are prone to oligomerization in solution. Both peptides can form amyloid-like fibrills. The G33 peptide forms fibrils within one day of incubation, whereas the fibrillogenesis of the G31 peptide is observed only after incubation for several months. The possible role of the observed processes in the pathogenesis and the possibility of applying a combination of the TEM and SANS techniques to search for new compounds that are able to influence the protein oligomerization are discussed.

  14. Characterization of oligomerization of a peptide from the ebola virus glycoprotein by small-angle neutron scattering

    Science.gov (United States)

    Egorov, V. V.; Gorshkov, A. N.; Murugova, T. N.; Vasin, A. V.; Lebedev, D. V.; Isaev-Ivanov, V. V.; Kiselev, O. I.

    2016-01-01

    Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) studies showed that model peptides QNALVCGLRQ (G33) and QNALVCGLRG (G31) corresponding to region 551-560 of the GP protein of the Sudan Ebola virus are prone to oligomerization in solution. Both peptides can form amyloid-like fibrills. The G33 peptide forms fibrils within one day of incubation, whereas the fibrillogenesis of the G31 peptide is observed only after incubation for several months. The possible role of the observed processes in the pathogenesis and the possibility of applying a combination of the TEM and SANS techniques to search for new compounds that are able to influence the protein oligomerization are discussed.

  15. Pro-inflammatory delipidizing cytokines reduce adiponectin secretion from human adipocytes without affecting adiponectin oligomerization

    NARCIS (Netherlands)

    Simons, Peter J.; van den Pangaart, Petra S.; Aerts, Johannes M. F. G.; Boon, Louis

    2007-01-01

    Adiponectin and, especially, its oligomeric complex composition have been suggested to be critical in determining insulin sensitivity. Pro-inflammatory cytokines play an important role in the development of insulin resistance in obesity and associated diseases. Therefore, we investigated the effect

  16. Detection of Amyloid Beta (Aβ) Oligomeric Composition Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS)

    Science.gov (United States)

    Wang, Jasmine S.-H.; Whitehead, Shawn N.; Yeung, Ken K.-C.

    2018-02-01

    The use of MALDI MS as a fast and direct method to detect the Aβ oligomers of different masses is examined in this paper. Experimental results suggest that Aβ oligomers are ionized and detected as singly charged ions, and thus, the resulting mass spectrum directly reports the oligomer size distribution. Validation experiments were performed to verify the MS data against artifacts. Mass spectra collected from modified Aβ peptides with different propensities for aggregation were compared. Generally, the relative intensities of multimers were higher from samples where oligomerization was expected to be more favorable, and vice versa. MALDI MS was also able to detect the differences in oligomeric composition before and after the incubation/oligomerization step. Such differences in sample composition were also independently confirmed with an in vitro Aβ toxicity study on primary rat cortical neurons. An additional validation was accomplished through removal of oligomers from the sample using molecular weight cutoff filters; the resulting MS data correctly reflected the removal at the expected cutoff points. The results collectively validated the ability of MALDI MS to assess the monomeric/multimeric composition of Aβ samples. [Figure not available: see fulltext.

  17. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterization of currently unrecognized taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 573 cox1 sequences from 110 currently recognized species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognized taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g., morphology, life history, ecology) are necessary before any taxonomic changes are formalized.

  18. Purification, crystallization and preliminary crystallographic analysis of Est-Y29: a novel oligomeric β-lactamase

    International Nuclear Information System (INIS)

    Kim, SeungBum; Joo, Sangbum; Yoon, Sangyoung; Kim, Sungsoo; Moon, Jongkook; Ryu, Yeonwoo; Kim, Kyeong Kyu; Kim, T. Doohun

    2009-01-01

    Est-Y29, a novel oligomeric class C β-lactamase from a metagenomic library, was crystallized in space group I4 1 and diffraction data were collected to 1.49 Å resolution. β-Lactam antibiotics such as penicillins and cephalosporins have a four-atom ring as a common element in their structure. The β-lactamases, which catalyze the inactivation of these antibiotics, are of great interest because of their high incidence in pathogenic bacteria. A novel oligomeric class C β-lactamase (Est-Y29) from a metagenomic library was expressed, purified and crystallized. The recombinant protein was expressed in Escherichia coli with an N-terminal 6×His tag and purified to homogeneity. EstY-29 was crystallized and X-ray intensity data were collected to 1.49 Å resolution using synchrotron radiation

  19. Genetic noise control via protein oligomerization

    Directory of Open Access Journals (Sweden)

    Almaas Eivind

    2008-11-01

    Full Text Available Abstract Background Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamic role of protein-protein interactions. Results We have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch, integrating quantitative results from previous in vivo and in vitro studies. In particular, we explicitly account for the fast binding-unbinding kinetics among proteins, RNA polymerases, and the promoter/operator sequences of DNA. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its random switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced state from randomly being induced (uninduced. Conclusion The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise. The stabilization of regulatory circuits

  20. Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil

    Energy Technology Data Exchange (ETDEWEB)

    Ławniczak, Ł., E-mail: lukasz.k.lawniczak@wp.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Syguda, A., E-mail: Anna.Syguda@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Borkowski, A., E-mail: a.borkowski@uw.edu.pl [Faculty of Geology, University of Warsaw, 02-089 Warsaw (Poland); Cyplik, P., E-mail: pcyplik@wp.pl [Department of Biotechnology and Food Microbiology, University of Life Sciences in Poznan, 60-627 Poznan (Poland); Marcinkowska, K., E-mail: k.marcinkowska@iorpib.poznan.pl [Institute of Plant Protection - National Research Institute, Poznan 60-318 (Poland); Wolko, Ł., E-mail: wolko@o2.pl [Department of Biochemistry and Biotechnology, Poznań University of Life Sciences in Poznan, 60-632 Poznan (Poland); Praczyk, T., E-mail: t.praczyk@iorpib.poznan.pl [Institute of Plant Protection - National Research Institute, Poznan 60-318 (Poland); Chrzanowski, Ł., E-mail: Lukasz.Chrzanowski@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Pernak, J., E-mail: Juliusz.Pernak@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland)

    2016-09-01

    The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing {sup 1}H and {sup 13}C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3. - Highlights: • Impact of herbicidal ionic liquids on bacterial community structure was studied. • Oligomeric herbicidal ionic liquids were effective but not readily biodegradable. • Next generation sequencing was used to evaluate shifts in bacterial abundance. • Treatment during field trials resulted in changes at class and species level. • Use of herbicidal ionic liquids affects the structure of autochthonic soil bacteria.

  1. Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil

    International Nuclear Information System (INIS)

    Ławniczak, Ł.; Syguda, A.; Borkowski, A.; Cyplik, P.; Marcinkowska, K.; Wolko, Ł.; Praczyk, T.; Chrzanowski, Ł.; Pernak, J.

    2016-01-01

    The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing "1H and "1"3C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3. - Highlights: • Impact of herbicidal ionic liquids on bacterial community structure was studied. • Oligomeric herbicidal ionic liquids were effective but not readily biodegradable. • Next generation sequencing was used to evaluate shifts in bacterial abundance. • Treatment during field trials resulted in changes at class and species level. • Use of herbicidal ionic liquids affects the structure of autochthonic soil bacteria.

  2. Both Ca2+ and Zn2+ are essential for S100A12 protein oligomerization and function

    Directory of Open Access Journals (Sweden)

    Shekhtman Alexander

    2009-04-01

    Full Text Available Abstract Background Human S100A12 is a member of the S100 family of EF-hand calcium-modulated proteins that are associated with many diseases including cancer, chronic inflammation and neurological disorders. S100A12 is an important factor in host/parasite defenses and in the inflammatory response. Like several other S100 proteins, it binds zinc and copper in addition to calcium. Mechanisms of zinc regulation have been proposed for a number of S100 proteins e.g. S100B, S100A2, S100A7, S100A8/9. The interaction of S100 proteins with their targets is strongly dependent on cellular microenvironment. Results The aim of the study was to explore the factors that influence S100A12 oligomerization and target interaction. A comprehensive series of biochemical and biophysical experiments indicated that changes in the concentration of calcium and zinc led to changes in the oligomeric state of S100A12. Surface plasmon resonance confirmed that the presence of both calcium and zinc is essential for the interaction of S100A12 with one of its extracellular targets, RAGE – the Receptor for Advanced Glycation End products. By using a single-molecule approach we have shown that the presence of zinc in tissue culture medium favors both the oligomerization of exogenous S100A12 protein and its interaction with targets on the cell surface. Conclusion We have shown that oligomerization and target recognition by S100A12 is regulated by both zinc and calcium. Our present work highlighted the potential role of calcium-binding S100 proteins in zinc metabolism and, in particular, the role of S100A12 in the cross talk between zinc and calcium in cell signaling.

  3. Multiple endmember spectral-angle-mapper (SAM) analysis improves discrimination of Savanna tree species

    CSIR Research Space (South Africa)

    Cho, Moses A

    2009-08-01

    Full Text Available of this paper was to evaluate the classification performance of a multiple-endmember spectral angle mapper (SAM) classification approach in discriminating seven common African savanna tree species and to compare the results with the traditional SAM classifier...

  4. Type IX Collagen Gene Mutations Can Result in Multiple Epiphyseal Dysplasia That Is Associated With Osteochondritis Dissecans and a Mild Myopathy

    NARCIS (Netherlands)

    Jackson, Gail C.; Marcus-Soekarman, Dominique; Stolte-Dijkstra, Irene; Verrips, Aad; Taylor, Jacqueline A.; Briggs, Michael D.

    Multiple epiphyseal dysplasia (MED) is a clinically variable and genetically heterogeneous disease that is characterized by mild short stature and early onset osteoarthritis. Autosomal dominant forms are caused by mutations in the genes that encode type IX collagen, cartilage oligomeric matrix

  5. Type IX collagen gene mutations can result in multiple epiphyseal dysplasia that is associated with osteochondritis dissecans and a mild myopathy.

    NARCIS (Netherlands)

    Jackson, G.C.; Marcus-Soekarman, D.; Stolte-Dijkstra, I.; Verrips, A.; Taylor, J.A.; Briggs, M.D.

    2010-01-01

    Multiple epiphyseal dysplasia (MED) is a clinically variable and genetically heterogeneous disease that is characterized by mild short stature and early onset osteoarthritis. Autosomal dominant forms are caused by mutations in the genes that encode type IX collagen, cartilage oligomeric matrix

  6. Fluorescence reporters for Hfq oligomerization and RNA annealing

    Science.gov (United States)

    Panja, Subrata; Woodson, Sarah A.

    2015-01-01

    Fluorescence spectroscopy is a sensitive technique for detecting protein-protein, protein-RNA and RNA-RNA interactions, requiring only nanomolar concentrations of labeled components. Fluorescence anisotropy provides information about the assembly of multi-subunit proteins, while molecular beacons provide a sensitive and quantitative reporter for base pairing between complementary RNAs. Here we present a detailed protocol for labeling Hfq protein with cyanine 3-maleimide and dansyl chloride to study the protein oligomerization and RNA binding by semi-native polyacrylamide gel electrophoresis (PAGE) and fluorescence anisotropy. We also present a detailed protocol for measuring the rate of annealing between a molecular beacon and a target RNA in the presence of Hfq using a stopped-flow spectrometer. PMID:25579597

  7. Electron Microscopy Structural Insights into CPAP Oligomeric Behavior

    DEFF Research Database (Denmark)

    Alvarez-Cabrera, Ana L; Delgado, Sandra; Gil-Carton, David

    2017-01-01

    Centrosomal P4.1-associated protein (CPAP) is a cell cycle regulated protein fundamental for centrosome assembly and centriole elongation. In humans, the region between residues 897-1338 of CPAP mediates interactions with other proteins and includes a homodimerization domain. CPAP mutations cause...... into clearly different regular 3D maps (putatively corresponding to dimers and tetramers) and direct observation of individual images representing other complexes of HsCPAP(897-1338) (i.e., putative flexible monomers and higher-order multimers), we report a dynamic oligomeric behavior of this protein, where...... of different oligomers of CPAP, suggesting further insights to understand how this protein works, contributing to the elucidation of control mechanisms for centriole biogenesis....

  8. Domain architecture and oligomerization properties of the paramyxovirus PIV 5 hemagglutinin-neuraminidase (HN) protein.

    Science.gov (United States)

    Yuan, Ping; Leser, George P; Demeler, Borries; Lamb, Robert A; Jardetzky, Theodore S

    2008-09-01

    The mechanism by which the paramyxovirus hemagglutinin-neuraminidase (HN) protein couples receptor binding to activation of virus entry remains to be fully understood, but the HN stalk is thought to play an important role in the process. We have characterized ectodomain constructs of the parainfluenza virus 5 HN to understand better the underlying architecture and oligomerization properties that may influence HN functions. The PIV 5 neuraminidase (NA) domain is monomeric whereas the ectodomain forms a well-defined tetramer. The HN stalk also forms tetramers and higher order oligomers with high alpha-helical content. Together, the data indicate that the globular NA domains form weak intersubunit interactions at the end of the HN stalk tetramer, while stabilizing the stalk and overall oligomeric state of the ectodomain. Electron microscopy of the HN ectodomain reveals flexible arrangements of the NA and stalk domains, which may be important for understanding how these two HN domains impact virus entry.

  9. Conformational detection of p53's oligomeric state by FlAsH Fluorescence.

    Science.gov (United States)

    Webber, Tawnya M; Allen, Andrew C; Ma, Wai Kit; Molloy, Rhett G; Kettelkamp, Charisse N; Dow, Caitlin A; Gage, Matthew J

    2009-06-19

    The p53 tumor suppressor protein is a critical checkpoint in prevention of tumor formation, and the function of p53 is dependent on proper formation of the active tetramer. In vitro studies have shown that p53 binds DNA most efficiently as a tetramer, though inactive p53 is predicted to be monomeric in vivo. We demonstrate that FlAsH binding can be used to distinguish between oligomeric states of p53, providing a potential tool to explore p53 oligomerization in vivo. The FlAsH tetra-cysteine binding motif has been incorporated along the dimer and tetramer interfaces in the p53 tetramerization domain to create reporters for the dimeric and tetrameric states of p53, though the geometry of the four cysteines is critical for efficient FlAsH binding. Furthermore, we demonstrate that FlAsH binding can be used to monitor tetramer formation in real-time. These results demonstrate the potential for using FlAsH fluorescence to monitor protein-protein interactions in vivo.

  10. RNAi reduces expression and intracellular retention of mutant cartilage oligomeric matrix protein.

    Directory of Open Access Journals (Sweden)

    Karen L Posey

    2010-04-01

    Full Text Available Mutations in cartilage oligomeric matrix protein (COMP, a large extracellular glycoprotein expressed in musculoskeletal tissues, cause two skeletal dysplasias, pseudoachondroplasia and multiple epiphyseal dysplasia. These mutations lead to massive intracellular retention of COMP, chondrocyte death and loss of growth plate chondrocytes that are necessary for linear growth. In contrast, COMP null mice have only minor growth plate abnormalities, normal growth and longevity. This suggests that reducing mutant and wild-type COMP expression in chondrocytes may prevent the toxic cellular phenotype causing the skeletal dysplasias. We tested this hypothesis using RNA interference to reduce steady state levels of COMP mRNA. A panel of shRNAs directed against COMP was tested. One shRNA (3B reduced endogenous and recombinant COMP mRNA dramatically, regardless of expression levels. The activity of the shRNA against COMP mRNA was maintained for up to 10 weeks. We also demonstrate that this treatment reduced ER stress. Moreover, we show that reducing steady state levels of COMP mRNA alleviates intracellular retention of other extracellular matrix proteins associated with the pseudoachondroplasia cellular pathology. These findings are a proof of principle and the foundation for the development of a therapeutic intervention based on reduction of COMP expression.

  11. The cysteines of the extracellular loop are crucial for trafficking of human organic cation transporter 2 to the plasma membrane and are involved in oligomerization.

    Science.gov (United States)

    Brast, Sabine; Grabner, Alexander; Sucic, Sonja; Sitte, Harald H; Hermann, Edwin; Pavenstädt, Hermann; Schlatter, Eberhard; Ciarimboli, Giuliano

    2012-03-01

    Human organic cation transporter 2 (hOCT2) is involved in transport of many endogenous and exogenous organic cations, mainly in kidney and brain cells. Because the quaternary structure of transmembrane proteins plays an essential role for their cellular trafficking and function, we investigated whether hOCT2 forms oligomeric complexes, and if so, which part of the transporter is involved in the oligomerization. A yeast 2-hybrid mating-based split-ubiquitin system (mbSUS), fluorescence resonance energy transfer, Western blot analysis, cross-linking experiments, immunofluorescence, and uptake measurements of the fluorescent organic cation 4-(4-(dimethylamino)styryl)-N-methylpyridinium were applied to human embryonic kidney 293 (HEK293) cells transfected with hOCT2 and partly also to freshly isolated human proximal tubules. The role of cysteines for oligomerization and trafficking of the transporter to the plasma membranes was investigated in cysteine mutants of hOCT2. hOCT2 formed oligomers both in the HEK293 expression system and in native human kidneys. The cysteines of the large extracellular loop are important to enable correct folding, oligomeric assembly, and plasma membrane insertion of hOCT2. Mutation of the first and the last cysteines of the loop at positions 51 and 143 abolished oligomer formation. Thus, the cysteines of the extracellular loop are important for correct trafficking of the transporter to the plasma membrane and for its oligomerization.

  12. Chaperonin of Group I: Oligomeric Spectrum and Biochemical and Biological Implications

    Directory of Open Access Journals (Sweden)

    Silvia Vilasi

    2018-01-01

    Full Text Available Chaperonins play various physiological roles and can also be pathogenic. Elucidation of their structure, e.g., oligomeric status and post-translational modifications (PTM, is necessary to understand their functions and mechanisms of action in health and disease. Group I chaperonins form tetradecamers with two stacked heptameric rings. The tetradecamer is considered the typical functional complex for folding of client polypeptides. However, other forms such as the monomer and oligomers with smaller number of subunits than the classical tetradecamer, also occur in cells. The properties and functions of the monomer and oligomers, and their roles in chaperonin-associated diseases are still incompletely understood. Chaperonin I in eukaryotes occurs in various locations, not just the mitochondrion, which is its canonical place of residence and function. Eukaryotic Chaperonin I, namely Hsp60 (designated HSP60 or HSPD1 in humans has, indeed, been found in the cytosol; the plasma-cell membrane; on the outer surface of cells; in the intercellular space; in biological liquids such as lymph, blood, and cerebrospinal fluid; and in secretions, for instance saliva and urine. Hsp60 has also been found in cell-derived vesicles such as exosomes. The functions of Hsp60 in all these non-canonical locales are still poorly characterized and one of the questions not yet answered is in what form, i.e., monomer or oligomer, is the chaperonin present in these non-canonical locations. In view of the steady increase in interest on chaperonopathies over the last several years, we have studied human HSP60 to determine its role in various diseases, its locations in cells and tissues and migrations in the body, and its post-translational modifications that might have an impact on its location and function. We also carried out experiments to characterize the oligomeric status of extramitochondrial of HSP60 in solution. Here, we provide an overview of our results, focusing on

  13. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.

  14. Understanding the Influence of oligomeric resins on traction and rolling resistance of silica tire treads

    NARCIS (Netherlands)

    Vleugels, N.; Pille-Wolf, W.; Dierkes, Wilma K.; Noordermeer, Jacobus W.M.

    2015-01-01

    This study concerns the silica reinforcement of styrene–butadiene rubber compounds for passenger car tire treads, with the objective of gaining greater insight into the beneficial effects of oligomeric resins. The major tire performance factors predicted are rolling resistance and (wet) skid

  15. Bayesian estimation applied to multiple species

    International Nuclear Information System (INIS)

    Kunz, Martin; Bassett, Bruce A.; Hlozek, Renee A.

    2007-01-01

    Observed data are often contaminated by undiscovered interlopers, leading to biased parameter estimation. Here we present BEAMS (Bayesian estimation applied to multiple species) which significantly improves on the standard maximum likelihood approach in the case where the probability for each data point being ''pure'' is known. We discuss the application of BEAMS to future type-Ia supernovae (SNIa) surveys, such as LSST, which are projected to deliver over a million supernovae light curves without spectra. The multiband light curves for each candidate will provide a probability of being Ia (pure) but the full sample will be significantly contaminated with other types of supernovae and transients. Given a sample of N supernovae with mean probability, , of being Ia, BEAMS delivers parameter constraints equal to N spectroscopically confirmed SNIa. In addition BEAMS can be simultaneously used to tease apart different families of data and to recover properties of the underlying distributions of those families (e.g. the type-Ibc and II distributions). Hence BEAMS provides a unified classification and parameter estimation methodology which may be useful in a diverse range of problems such as photometric redshift estimation or, indeed, any parameter estimation problem where contamination is an issue

  16. Morphology and Phase Transitions in Styrene-Butadiene-Styrene Triblock Copolymer Grafted with Isobutyl Substituted Polyhedral Oligomeric Silsesquioxanes (Postprint)

    National Research Council Canada - National Science Library

    Drazowski, Daniel B; Lee, Andre; Haddad, Timothy S

    2007-01-01

    Two symmetric triblock polystyrene-butadiene-polystyrene (SBS) copolymers with different styrene content were grafted with varying amounts of isobutyl-substituted polyhedral oligomeric silsesquioxane (POSS) molecules...

  17. Morphology and Phase Transitions in Styrene-Butadiene-Styrene Triblock Copolymer Grafted with Isobutyl Substituted Polyhedral Oligomeric Silsesquioxanes (preprint)

    National Research Council Canada - National Science Library

    Drazkowski, Daniel B; Lee, Andre; Haddad, Timothy S

    2006-01-01

    Two symmetric triblock polystyrene-butadiene-polystyrene (SBS) copolymers with different styrene content were grafted with varying amounts of isobutyl-substituted polyhedral oligomeric silsesquioxane (POSS) molecules...

  18. Lepidopteran larva consumption of soybean foliage: basis for developing multiple-species economic thresholds for pest management decisions.

    Science.gov (United States)

    Bueno, Regiane Cristina Oliveira de Freitas; Bueno, Adeney de Freitas; Moscardi, Flávio; Parra, José Roberto Postali; Hoffmann-Campo, Clara Beatriz

    2011-02-01

    Defoliation by Anticarsia gemmatalis (Hübner), Pseudoplusia includens (Walker), Spodoptera eridania (Cramer), S. cosmioides (Walker) and S. frugiperda (JE Smith) (Lepidoptera: Noctuidae) was evaluated in four soybean genotypes. A multiple-species economic threshold (ET), based upon the species' feeding capacity, is proposed with the aim of improving growers' management decisions on when to initiate control measures for the species complex. Consumption by A. gemmatalis, S. cosmioides or S. eridania on different genotypes was similar. The highest consumption of P. includens was 92.7 cm(2) on Codetec 219RR; that of S. frugiperda was 118 cm(2) on Codetec 219RR and 115.1 cm(2) on MSoy 8787RR. The insect injury equivalent for S. cosmoides, calculated on the basis of insect consumption, was double the standard consumption by A. gemmatalis, and statistically different from the other species tested, which were similar to each other. As S. cosmioides always defoliated nearly twice the leaf area of the other species, the injury equivalent would be 2 for this lepidopteran species and 1 for the other species. The recommended multiple-species ET to trigger the beginning of insect control would then be 20 insect equivalents per linear metre. Copyright © 2010 Society of Chemical Industry.

  19. The Pseudo signal peptide of the corticotropin-releasing factor receptor type 2A prevents receptor oligomerization.

    Science.gov (United States)

    Teichmann, Anke; Rutz, Claudia; Kreuchwig, Annika; Krause, Gerd; Wiesner, Burkhard; Schülein, Ralf

    2012-08-03

    N-terminal signal peptides mediate the interaction of native proteins with the translocon complex of the endoplasmic reticulum membrane and are cleaved off during early protein biogenesis. The corticotropin-releasing factor receptor type 2a (CRF(2(a))R) possesses an N-terminal pseudo signal peptide, which represents a so far unique domain within the large protein family of G protein-coupled receptors (GPCRs). In contrast to a conventional signal peptide, the pseudo signal peptide remains uncleaved and consequently forms a hydrophobic extension at the N terminus of the receptor. The functional consequence of the presence of the pseudo signal peptide is not understood. Here, we have analyzed the significance of this domain for receptor dimerization/oligomerization in detail. To this end, we took the CRF(2(a))R and the homologous corticotropin-releasing factor receptor type 1 (CRF(1)R) possessing a conventional cleaved signal peptide and conducted signal peptide exchange experiments. Using single cell and single molecule imaging methods (fluorescence resonance energy transfer and fluorescence cross-correlation spectroscopy, respectively) as well as biochemical experiments, we obtained two novel findings; we could show that (i) the CRF(2(a))R is expressed exclusively as a monomer, and (ii) the presence of the pseudo signal peptide prevents its oligomerization. Thus, we have identified a novel functional domain within the GPCR protein family, which plays a role in receptor oligomerization and which may be useful to study the functional significance of this process in general.

  20. Catalytic Oligomerization of Terminal Alkynes by Lanthanide Carbyls (η5-C5Me5)2LnCH(SiMe3)2 (Ln = Y, La, Ce)

    NARCIS (Netherlands)

    Heeres, H.J.; Teuben, J.H.

    1991-01-01

    Lanthanide and group 3 carbyls Cp*2LnCH(SiMe3)2 (1, Ln = Y; 2, Ln = La; 3, Ln = Ce) are active catalyst precursors for the oligomerization of terminal alkynes HC≡CR (R = alkyl, aryl, SiMe3). The regioselectivity and the extent of oligomerization depend strongly on the lanthanide applied as well as

  1. Ultrafast preparation of a polyhedral oligomeric silsesquioxane-based ionic liquid hybrid monolith via photoinitiated polymerization, and its application to capillary electrochromatography of aromatic compounds.

    Science.gov (United States)

    Zhang, Bingyu; Lei, Xiaoyun; Deng, Lijun; Li, Minsheng; Yao, Sicong; Wu, Xiaoping

    2018-06-06

    An ionic liquid hybrid monolithic capillary column was prepared within 7 min via photoinitiated free-radical polymerization of an ionic liquid monomer (1-butyl-3-vinylimidazolium-bis[(trifluoromethyl)sulfonyl]imide); VBIMNTF 2 ) and a methacryl substituted polyhedral oligomeric silsesquioxane (POSS-MA) acting as a cross-linker. The effects of composition of prepolymerization solution and initiation time on the porous structure and electroosmotic flow (EOF) of monolithic column were investigated. The hybrid monolith was characterized by scanning electron microscopy and FTIR. Owing to the introduction of a rigid nanosized POSS silica core and ionic liquids with multiple interaction sites, the monolithic column has a well-defined 3D skeleton morphology, good mechanical stability, and a stable anodic electroosmotic flow. The hybrid monolithic stationary phase was applied to the capillary electrochromatographic separation of various alkylbenzenes, phenols, anilines and polycyclic aromatic hydrocarbons (PAHs). The column efficiency is highest (98,000 plates/m) in case of alkylbenzenes. Mixed-mode retention mechanisms including hydrophobic interactions, π-π stacking, electrostatic interaction and electrophoretic mobility can be observed. This indicates the potential of this material in terms of efficient separation of analytes of different structural type. Graphical Abstract Preparation of a mixed-mode ionic liquid hybrid monolithic column via photoinitiated polymerization of methacryl substituted polyhedral oligomeric silsesquioxane (POSS-MA) and 1-butyl-3-vinylimidazolium-bis[(trifluoromethyl)sulfonyl]imide (VBIMNTF 2 ) ionic liquid for use in capillary electrochromatography.

  2. Recombination in liquid filled ionisation chambers with multiple charge carrier species: Theoretical and numerical results

    International Nuclear Information System (INIS)

    Aguiar, P.; González-Castaño, D.M.; Gómez, F.; Pardo-Montero, J.

    2014-01-01

    Liquid-filled ionisation chambers (LICs) are used in radiotherapy for dosimetry and quality assurance. Volume recombination can be quite important in LICs for moderate dose rates, causing non-linearities in the dose rate response of these detectors, and needs to be corrected for. This effect is usually described with Greening and Boag models for continuous and pulsed radiation respectively. Such models assume that the charge is carried by two different species, positive and negative ions, each of those species with a given mobility. However, LICs operating in non-ultrapure mode can contain different types of electronegative impurities with different mobilities, thus increasing the number of different charge carriers. If this is the case, Greening and Boag models can be no longer valid and need to be reformulated. In this work we present a theoretical and numerical study of volume recombination in parallel-plate LICs with multiple charge carrier species, extending Boag and Greening models. Results from a recent publication that reported three different mobilities in an isooctane-filled LIC have been used to study the effect of extra carrier species on recombination. We have found that in pulsed beams the inclusion of extra mobilities does not affect volume recombination much, a behaviour that was expected because Boag formula for charge collection efficiency does not depend on the mobilities of the charge carriers if the Debye relationship between mobilities and recombination constant holds. This is not the case in continuous radiation, where the presence of extra charge carrier species significantly affects the amount of volume recombination. - Highlights: • Analytical extension of Greening and Boag theories to multiple charge carriers. • Detailed numerical study of process of volume recombination in LICs. • Recombination in pulsed beams is independent of number and mobilities of carriers. • Multiple charge carriers have a significant effect in continuous

  3. N-way FRET microscopy of multiple protein-protein interactions in live cells.

    Directory of Open Access Journals (Sweden)

    Adam D Hoppe

    Full Text Available Fluorescence Resonance Energy Transfer (FRET microscopy has emerged as a powerful tool to visualize nanoscale protein-protein interactions while capturing their microscale organization and millisecond dynamics. Recently, FRET microscopy was extended to imaging of multiple donor-acceptor pairs, thereby enabling visualization of multiple biochemical events within a single living cell. These methods require numerous equations that must be defined on a case-by-case basis. Here, we present a universal multispectral microscopy method (N-Way FRET to enable quantitative imaging for any number of interacting and non-interacting FRET pairs. This approach redefines linear unmixing to incorporate the excitation and emission couplings created by FRET, which cannot be accounted for in conventional linear unmixing. Experiments on a three-fluorophore system using blue, yellow and red fluorescent proteins validate the method in living cells. In addition, we propose a simple linear algebra scheme for error propagation from input data to estimate the uncertainty in the computed FRET images. We demonstrate the strength of this approach by monitoring the oligomerization of three FP-tagged HIV Gag proteins whose tight association in the viral capsid is readily observed. Replacement of one FP-Gag molecule with a lipid raft-targeted FP allowed direct observation of Gag oligomerization with no association between FP-Gag and raft-targeted FP. The N-Way FRET method provides a new toolbox for capturing multiple molecular processes with high spatial and temporal resolution in living cells.

  4. Low genetic diversity despite multiple introductions of the invasive plant species Impatiens glandulifera in Europe.

    Science.gov (United States)

    Hagenblad, Jenny; Hülskötter, Jennifer; Acharya, Kamal Prasad; Brunet, Jörg; Chabrerie, Olivier; Cousins, Sara A O; Dar, Pervaiz A; Diekmann, Martin; De Frenne, Pieter; Hermy, Martin; Jamoneau, Aurélien; Kolb, Annette; Lemke, Isgard; Plue, Jan; Reshi, Zafar A; Graae, Bente Jessen

    2015-08-20

    Invasive species can be a major threat to native biodiversity and the number of invasive plant species is increasing across the globe. Population genetic studies of invasive species can provide key insights into their invasion history and ensuing evolution, but also for their control. Here we genetically characterise populations of Impatiens glandulifera, an invasive plant in Europe that can have a major impact on native plant communities. We compared populations from the species' native range in Kashmir, India, to those in its invaded range, along a latitudinal gradient in Europe. For comparison, the results from 39 other studies of genetic diversity in invasive species were collated. Our results suggest that I. glandulifera was established in the wild in Europe at least twice, from an area outside of our Kashmir study area. Our results further revealed that the genetic diversity in invasive populations of I. glandulifera is unusually low compared to native populations, in particular when compared to other invasive species. Genetic drift rather than mutation seems to have played a role in differentiating populations in Europe. We find evidence of limitations to local gene flow after introduction to Europe, but somewhat less restrictions in the native range. I. glandulifera populations with significant inbreeding were only found in the species' native range and invasive species in general showed no increase in inbreeding upon leaving their native ranges. In Europe we detect cases of migration between distantly located populations. Human activities therefore seem to, at least partially, have facilitated not only introductions, but also further spread of I. glandulifera across Europe. Although multiple introductions will facilitate the retention of genetic diversity in invasive ranges, widespread invasive species can remain genetically relatively invariant also after multiple introductions. Phenotypic plasticity may therefore be an important component of the

  5. Using AVIRIS data and multiple-masking techniques to map urban forest trees species

    Science.gov (United States)

    Q. Xiao; S.L. Ustin; E.G. McPherson

    2004-01-01

    Tree type and species information are critical parameters for urban forest management, benefit cost analysis and urban planning. However, traditionally, these parameters have been derived based on limited field samples in urban forest management practice. In this study we used high-resolution Airborne Visible Infrared Imaging Spectrometer (AVIRIS) data and multiple-...

  6. Bimolecular Fluorescence Complementation of Alpha-synuclein Demonstrates its Oligomerization with Dopaminergic Phenotype in Mice

    Directory of Open Access Journals (Sweden)

    Waijiao Cai

    2018-03-01

    Full Text Available Alpha-synuclein (αSyn is encoded by the first causal gene identified in Parkinson's disease (PD and is the main component of Lewy bodies, a pathological hallmark of PD. aSyn-based animal models have contributed to our understanding of PD pathophysiology and to the development of therapeutics. Overexpression of human wildtype αSyn by viral vectors in rodents recapitulates the loss of dopaminergic neurons from the substantia nigra, another defining pathological feature of the disease. The development of a rat model exhibiting bimolecular fluorescence complementation (BiFC of αSyn by recombinant adeno-associated virus facilitates detection of the toxic αSyn oligomers species. We report here neurochemical, neuropathological and behavioral characterization of BiFC of αSyn in mice. Overexpression and oligomerization of αSyn through BiFC is detected by conjugated fluorescence. Reduced striatal dopamine and loss of nigral dopaminergic neurons are accompanied neuroinflammation and abnormal motor activities. Our mouse model may provide a valuable tool to study the role of αSyn in PD and to explore therapeutic approaches. Keywords: Parkinson's disease, Alpha-synuclein, Mouse model, Oligomers, Neuroinflammation

  7. The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Chung-ke [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Wu, Tzong-Huah [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan (China); Wu, Chu-Ya [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Graduate Institute of Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Chiang, Ming-hui; Toh, Elsie Khai-Woon [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Hsu, Yin-Chih; Lin, Ku-Feng [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Liao, Yu-heng [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Huang, Tai-huang, E-mail: bmthh@gate.sinica.edu.tw [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Department of Physics, National Taiwan Normal University, Taipei 106, Taiwan (China); Huang, Joseph Jen-Tse, E-mail: jthuang@chem.sinica.edu.tw [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China)

    2012-08-24

    Highlights: Black-Right-Pointing-Pointer The N-terminus of TDP-43 contains an independently folded structural domain (NTD). Black-Right-Pointing-Pointer The structural domains of TDP-43 are arranged in a beads-on-a-string fashion. Black-Right-Pointing-Pointer The NTD promotes TDP-43 oligomerization in a concentration-dependent manner. Black-Right-Pointing-Pointer The NTD may assist nucleic acid-binding activity of TDP-43. -- Abstract: TDP-43 is a DNA/RNA-binding protein associated with different neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-U). Here, the structural and physical properties of the N-terminus on TDP-43 have been carefully characterized through a combination of nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence anisotropy studies. We demonstrate for the first time the importance of the N-terminus in promoting TDP-43 oligomerization and enhancing its DNA-binding affinity. An unidentified structural domain in the N-terminus is also disclosed. Our findings provide insights into the N-terminal domain function of TDP-43.

  8. Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

    Science.gov (United States)

    Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

    2016-11-01

    It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

  9. Oligomerization of optineurin and its oxidative stress- or E50K mutation-driven covalent cross-linking: possible relationship with glaucoma pathology.

    Directory of Open Access Journals (Sweden)

    Jie Gao

    Full Text Available The optineurin gene, OPTN, is one of the causative genes of primary open-angle glaucoma. Although oligomerization of optineurin in cultured cells was previously observed by gel filtration analysis and blue native gel electrophoresis (BNE, little is known about the characteristics of optineurin oligomers. Here, we aimed to analyze the oligomeric state of optineurin and factors affecting oligomerization, such as environmental stimuli or mutations in OPTN. Using BNE or immunoprecipitation followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE, we demonstrated that both endogenous and transfected optineurin exist as oligomers, rather than monomers, in NIH3T3 cells. We also applied an in situ proximity ligation assay to visualize the self-interaction of optineurin in fixed HeLaS3 cells and found that the optineurin oligomers were localized diffusely in the cytoplasm. Optineurin oligomers were usually detected as a single band of a size equal to that of the optineurin monomer upon SDS-PAGE, while an additional protein band of a larger size was observed when cells were treated with H2O2. We showed that larger protein complex is optineurin oligomers by immunoprecipitation and termed it covalent optineurin oligomers. In cells expressing OPTN bearing the most common glaucoma-associated mutation, E50K, covalent oligomers were formed even without H2O2 stimulation. Antioxidants inhibited the formation of E50K-induced covalent oligomers to various degrees. A series of truncated constructs of OPTN was used to reveal that covalent oligomers may be optineurin trimers and that the ubiquitin-binding domain is essential for formation of these trimers. Our results indicated that optineurin trimers may be the basic unit of these oligomers. The oligomeric state can be affected by many factors that induce covalent bonds, such as H2O2 or E50K, as demonstrated here; this provides novel insights into the pathogenicity of E50K. Furthermore

  10. 78 FR 65561 - D-Glucopyranose, oligomeric, decyl octyl glycosides; Exemption from the Requirement of a Tolerance

    Science.gov (United States)

    2013-11-01

    ... metabolize D-glucopyranose, oligomeric, C 10 -C 16 -alkyl glycosides to water-soluble substances... polyoxyethylene polymers and fatty acids; carriers such as clay and diatomaceous earth; thickeners such as... exposure through drinking water and in residential settings, but does not include occupational exposure...

  11. Development, validation and evaluation of an analytical method for the determination of monomeric and oligomeric procyanidins in apple extracts.

    Science.gov (United States)

    Hollands, Wendy J; Voorspoels, Stefan; Jacobs, Griet; Aaby, Kjersti; Meisland, Ane; Garcia-Villalba, Rocio; Tomas-Barberan, Francisco; Piskula, Mariusz K; Mawson, Deborah; Vovk, Irena; Needs, Paul W; Kroon, Paul A

    2017-04-28

    There is a lack of data for individual oligomeric procyanidins in apples and apple extracts. Our aim was to develop, validate and evaluate an analytical method for the separation, identification and quantification of monomeric and oligomeric flavanols in apple extracts. To achieve this, we prepared two types of flavanol extracts from freeze-dried apples; one was an epicatechin-rich extract containing ∼30% (w/w) monomeric (-)-epicatechin which also contained oligomeric procyanidins (Extract A), the second was an oligomeric procyanidin-rich extract depleted of epicatechin (Extract B). The parameters considered for method optimisation were HPLC columns and conditions, sample heating, mass of extract and dilution volumes. The performance characteristics considered for method validation included standard linearity, method sensitivity, precision and trueness. Eight laboratories participated in the method evaluation. Chromatographic separation of the analytes was best achieved utilizing a Hilic column with a binary mobile phase consisting of acidic acetonitrile and acidic aqueous methanol. The final method showed linearity for epicatechin in the range 5-100μg/mL with a correlation co-efficient >0.999. Intra-day and inter-day precision of the analytes ranged from 2 to 6% and 2 to 13% respectively. Up to dp3, trueness of the method was >95% but decreased with increasing dp. Within laboratory precision showed RSD values <5 and 10% for monomers and oligomers, respectively. Between laboratory precision was 4 and 15% (Extract A) and 7 and 30% (Extract B) for monomers and oligomers, respectively. An analytical method for the separation, identification and quantification of procyanidins in an apple extract was developed, validated and assessed. The results of the inter-laboratory evaluation indicate that the method is reliable and reproducible. Copyright © 2017. Published by Elsevier B.V.

  12. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

    Science.gov (United States)

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

  13. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus in China with multiple gene markers.

    Directory of Open Access Journals (Sweden)

    Qing-Yan Dai

    Full Text Available Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI gene and two alternative internal transcribed spacer (ITS genes (ITS1 and ITS2. Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML/Neighbor-joining (NJ, "best close match" (BCM, Minimum distance (MD, and BP-based method (BP, representing commonly used methodology (tree-based and non-tree based in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In

  14. Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers.

    Science.gov (United States)

    Galeano, B K; Ranatunga, W; Gakh, O; Smith, D Y; Thompson, J R; Isaya, G

    2017-06-21

    Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.

  15. Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus

    Directory of Open Access Journals (Sweden)

    Rasoloarison Rodin M

    2009-02-01

    Full Text Available Abstract Background Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus and assess the status of the seven described species, based on phylogenetic and population genetic analysis of mtDNA (cytb + cox2 and three nuclear markers (adora3, fiba and vWF. Results This study identified three distinct evolutionary lineages within the genus Cheirogaleus. Population genetic cluster analyses revealed a further layer of population divergence with six distinct genotypic clusters. Conclusion Based on the general metapopulation lineage concept and multiple concordant data sets, we identify three exclusive groups of dwarf lemur populations that correspond to three of the seven named species: C. major, C. medius and C. crossleyi. These three species were found to be genealogically exclusive in both mtDNA and nDNA loci and are morphologically distinguishable. The molecular and morphometric data indicate that C. adipicaudatus and C. ravus are synonymous with C. medius and C. major, respectively. Cheirogaleus sibreei falls into the C. medius mtDNA clade, but in morphological analyses the membership is not clearly resolved. We do not have sufficient data to assess the status of C. minusculus. Although additional patterns of population differentiation are evident, there are no clear subdivisions that would warrant additional specific status. We propose that ecological and more geographic data should be collected to confirm these results.

  16. Oligomeric adiponectin forms and their complexes in the blood of healthy donors and patients with type 2 diabetes mellitus.

    Science.gov (United States)

    Kogan, Alexander E; Filatov, Vladimir L; Kolosova, Olga V; Katrukha, Ivan A; Mironova, Ekaterina V; Zhuravleva, Natalya S; Nagibin, Oleg A; Kara, Andrei N; Bereznikova, Anastasiya V; Katrukha, Alexey G

    2013-01-01

    Adiponectin (Adn) is a protein that circulates in the blood in several oligomeric forms, namely low-, medium-, and high-molecular-weight forms. Adn may serve as a risk factor for type 2 diabetes mellitus (T2DM). The aims of this work were (1) to produce monoclonal antibodies (MAbs) specific to different Adn oligomeric forms, (2) to design immunoassays suitable for measuring the Adn forms present in human blood, and (3) to investigate the changes in Adn forms that occur in patients with T2DM. Gel filtration, fluoroimmunoassays, and Western blotting were utilized as major techniques in this study. MAbs recognizing various oligomeric forms of Adn were obtained. Complexes between Adn and complement component C1q and between the low molecular weight form of Adn and albumin were described in human blood. A decrease in the total Adn and Adn-albumin complex levels in the blood of patients with T2DM and no difference in the levels of the Adn-C1q complex in comparison with healthy volunteers were demonstrated. An Adn94-Adn63 fluoroimmunoassay was selected as the technique that most accurately measured the mass ratio of Adn oligomers in blood samples, and an Adn214-Adn27 assay that measured the low-molecular-weight form of Adn only.

  17. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    Science.gov (United States)

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Characters with multiple usages- phenotypic variability analysis at Echinacea purpurea (L. Moench species

    Directory of Open Access Journals (Sweden)

    Mihai Radu POP

    2010-11-01

    Full Text Available Merging aesthetics with utility, some medicinal plants can benefit both of a high production and decoration potential. This calls for diversification of improvement directions of the species. Through this article we suggest one of these species, Echinacea purpurea (L. Moench. This is considered to be important at this time, acquisition of new biological forms - varieties in this species, which show multiple attributes utility based on key biological characteristics, agronomic, physiological, biochemical and agrochemical (medicinal, decorative, culinary etc.. To achieve this goal, studies were undertaken, given in this article, which is the starting point for selecting characters representative for our targets.The results presented in this study reveal a pronounced genetic polymorphism showing the selection operation can use the original material for a quantitative and qualitative differentiation of valuable genotypes that could be approved.

  19. In situ oligomerization of 2-(thiophen-3-yl)acetate intercalated into Zn{sub 2}Al layered double hydroxide

    Energy Technology Data Exchange (ETDEWEB)

    Tronto, Jairo, E-mail: jairotronto@ufv.br [Universidade Federal de Viçosa, Instituto de Ciências Exatas e Tecnológicas, Campus de Rio Parsanaíba, Rodovia BR 354 km 310, Cx. Postal 22, CEP, 38.810-000 Rio Paranaíba, MG (Brazil); Pinto, Frederico G.; Costa, Liovando M. da [Universidade Federal de Viçosa, Instituto de Ciências Exatas e Tecnológicas, Campus de Rio Parsanaíba, Rodovia BR 354 km 310, Cx. Postal 22, CEP, 38.810-000 Rio Paranaíba, MG (Brazil); Leroux, Fabrice; Dubois, Marc [Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand (France); CNRS, UMR 6296, ICCF, BP 80026, F-6317 Clermont-Ferrand (France); Valim, João B. [Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Química, Av. dos Bandeirantes 3900, CEP 14.040-901, Ribeirão Preto, SP (Brazil)

    2015-01-15

    A layered double hydroxide (LDH) with cation composition Zn{sub 2}Al was intercalated with 2-(thiophen-3-yl)acetate (3-TA) monomers. To achieve in situ polymerization and/or oligomerization of the intercalated monomers, soft thermal treatments were carried out, and subsequent hybrid LDH materials were analyzed by means of several characterization techniques using powder X-ray diffraction (PXRD), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), {sup 13}C CP–MAS nuclear magnetic resonance (NMR), electron spin resonance (EPR), scanning electron microscopy (SEM), and transmission electron microscopy (TEM), inductively coupled plasma optical emission spectroscopy (ICP–OES), and elemental analysis. PXRD analysis suggested that the intercalated monomers formed a bilayer. Thermal treatment of the hybrid LDH assembly above 120 °C provokes partially the breakdown of the layered structure, generating the phase zincite. EPR results indicated that vicinal monomers (oligomerization) were bound to each other after hydrothermal or thermal treatment, leading to a polaron response characteristic of electron conductivity localized on a restricted number of thiophene-based monomer segments. Localized unpaired electrons exist in the material and interact with the {sup 27}Al nuclei of the LDH layers by superhyperfine coupling. These unpaired electrons also interact with the surface of ZnO (O{sup 2−} vacancies), formed during the thermal treatments. - Graphical abstract: We synthesized a layered double hydroxide (LDH) with cation composition Zn{sub 2}Al, intercalated with 2-(thiophen-3-yl)acetate (3-TA) monomers, by coprecipitation at constant pH. We thermally treated the material, to achieve in situ polymerization and/or oligomerization of the intercalated monomers. - Highlights: • A Zn{sub 2}Al–LDH was intercalated with 2-(thiophen-3-yl)acetate monomers. • To achieve in situ oligomerization of the monomers, thermal treatments were made.

  20. Construction of porous cationic frameworks by crosslinking polyhedral oligomeric silsesquioxane units with N-heterocyclic linkers

    Science.gov (United States)

    Chen, Guojian; Zhou, Yu; Wang, Xiaochen; Li, Jing; Xue, Shuang; Liu, Yangqing; Wang, Qian; Wang, Jun

    2015-06-01

    In fields of materials science and chemistry, ionic-type porous materials attract increasing attention due to significant ion-exchanging capacity for accessing diversified applications. Facing the fact that porous cationic materials with robust and stable frameworks are very rare, novel tactics that can create new type members are highly desired. Here we report the first family of polyhedral oligomeric silsesquioxane (POSS) based porous cationic frameworks (PCIF-n) with enriched poly(ionic liquid)-like cationic structures, tunable mesoporosities, high surface areas (up to 1,025 m2 g-1) and large pore volumes (up to 0.90 cm3 g-1). Our strategy is designing the new rigid POSS unit of octakis(chloromethyl)silsesquioxane and reacting it with the rigid N-heterocyclic cross-linkers (typically 4,4‧-bipyridine) for preparing the desired porous cationic frameworks. The PCIF-n materials possess large surface area, hydrophobic and special anion-exchanging property, and thus are used as the supports for loading guest species PMo10V2O405- the resultant hybrid behaves as an efficient heterogeneous catalyst for aerobic oxidation of benzene and H2O2-mediated oxidation of cyclohexane.

  1. Optimising the application of multiple-capture traps for invasive species management using spatial simulation.

    Science.gov (United States)

    Warburton, Bruce; Gormley, Andrew M

    2015-01-01

    Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production and human health. To manage these species a wide range of tools, including traps, are used. In New Zealand, brushtail possums (Trichosurus vulpecula), stoats (Mustela ermine), and ship rats (Rattus rattus) are invasive and there is an ongoing demand for cost-effective non-toxic methods for controlling these pests. Recently, traps with multiple-capture capability have been developed which, because they do not require regular operator-checking, are purported to be more cost-effective than traditional single-capture traps. However, when pest populations are being maintained at low densities (as is typical of orchestrated pest management programmes) it remains uncertain if it is more cost-effective to use fewer multiple-capture traps or more single-capture traps. To address this uncertainty, we used an individual-based spatially explicit modelling approach to determine the likely maximum animal-captures per trap, given stated pest densities and defined times traps are left between checks. In the simulation, single- or multiple-capture traps were spaced according to best practice pest-control guidelines. For possums with maintenance densities set at the lowest level (i.e. 0.5/ha), 98% of all simulated possums were captured with only a single capacity trap set at each site. When possum density was increased to moderate levels of 3/ha, having a capacity of three captures per trap caught 97% of all simulated possums. Results were similar for stoats, although only two potential captures per site were sufficient to capture 99% of simulated stoats. For rats, which were simulated at their typically higher densities, even a six-capture capacity per trap site only resulted in 80% kill. Depending on target species, prevailing density and extent of immigration, the most cost-effective strategy for pest control in New Zealand might be to deploy several single

  2. Multiple factors contribute to reproductive isolation between two co-existing Habenaria species (Orchidaceae.

    Directory of Open Access Journals (Sweden)

    Wenliu Zhang

    Full Text Available Reproductive isolation is a key feature that forms barriers to gene flow between distinct plants. In orchids, prezygotic reproductive isolation has been considered to be strong, because their associations with highly specific pollinators. In this study, the reproductive ecology and reproductive isolation of two sympatric Habenaria species, H. davidii and H. fordii, was investigated by floral phenology and morphology, hand-pollination experiments and visitor observation in southwest China. The two species were dependent on insects for pollination and completely self-compatible. A number of factors have been identified to limit gene flow between the two species and achieved full reproductive isolation. Ecogeographic isolation was a weak barrier. H. fordii and H. davidii had completely overlapped flowering periods, and floral morphology plays an important role in floral isolation. The two species shared the same hawkmoth pollinator, Cechenena lineosa, but the pollinaria of the two orchids were attached on different body parts of pollinators. Prezygotic isolation was not complete, but the interspecific pollination treatments of each species resulted in no seed sets, indicating that unlike many other orchid species, in which the postzygotic reproductive isolation is very weak or complete absence, the post-zygotic isolation strongly acted in the stage of seed production between two species. The results illustrate the reproductive isolation between two species involves multiple plant life-history stages and a variety of reproductive barriers can contribute to overall isolation.

  3. Age- and brain region-dependent α-synuclein oligomerization is attributed to alterations in intrinsic enzymes regulating α-synuclein phosphorylation in aging monkey brains.

    Science.gov (United States)

    Chen, Min; Yang, Weiwei; Li, Xin; Li, Xuran; Wang, Peng; Yue, Feng; Yang, Hui; Chan, Piu; Yu, Shun

    2016-02-23

    We previously reported that the levels of α-syn oligomers, which play pivotal pathogenic roles in age-related Parkinson's disease (PD) and dementia with Lewy bodies, increase heterogeneously in the aging brain. Here, we show that exogenous α-syn incubated with brain extracts from older cynomolgus monkeys and in Lewy body pathology (LBP)-susceptible brain regions (striatum and hippocampus) forms higher amounts of phosphorylated and oligomeric α-syn than that in extracts from younger monkeys and LBP-insusceptible brain regions (cerebellum and occipital cortex). The increased α-syn phosphorylation and oligomerization in the brain extracts from older monkeys and in LBP-susceptible brain regions were associated with higher levels of polo-like kinase 2 (PLK2), an enzyme promoting α-syn phosphorylation, and lower activity of protein phosphatase 2A (PP2A), an enzyme inhibiting α-syn phosphorylation, in these brain extracts. Further, the extent of the age- and brain-dependent increase in α-syn phosphorylation and oligomerization was reduced by inhibition of PLK2 and activation of PP2A. Inversely, phosphorylated α-syn oligomers reduced the activity of PP2A and showed potent cytotoxicity. In addition, the activity of GCase and the levels of ceramide, a product of GCase shown to activate PP2A, were lower in brain extracts from older monkeys and in LBP-susceptible brain regions. Our results suggest a role for altered intrinsic metabolic enzymes in age- and brain region-dependent α-syn oligomerization in aging brains.

  4. Transport of a multiple ion species plasma in the Pfirsch--Schluter regime

    International Nuclear Information System (INIS)

    Hirshman, S.P.

    1976-10-01

    The classical parallel friction coefficients, which relate the collisional friction forces to the flow of particles and heat along the magnetic field, are calculated for a multiple ion species plasma. In the short mean free path regime, the neoclassical Pfirsch--Schlueter transport coefficients for a toroidally confined multispecies plasma are computed in terms of the classical friction coefficients. The dependence of the neoclassical cross-field transport on the equilibration of the parallel ion temperature profiles is determined

  5. Synthesis and characterization of polyhedral oligomeric titanized silsesquioxane: A new biocompatible cage like molecule for biomedical application

    Energy Technology Data Exchange (ETDEWEB)

    Yahyaei, Hossein [Department of Polymer Engineering and Color Technology, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran (Iran, Islamic Republic of); Mohseni, Mohsen, E-mail: mmohseni@aut.ac.ir [Department of Polymer Engineering and Color Technology, Amirkabir University of Technology, P.O. Box 15875-4413, Tehran (Iran, Islamic Republic of); Ghanbari, Hossein [Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of); Messori, Massimo [Dipartimento di Ingegneria ‘Enzo Ferrari’, Università di Modena e Reggio Emilia, Modena (Italy)

    2016-04-01

    Organic–inorganic hybrid materials have shown improved properties to be used as biocompatible coating in biomedical applications. Polyhedral oligomeric silsesquioxane (POSS) containing coatings are among hybrid materials showing promising properties for these applications. In this work an open cage POSS has been reacted with a titanium alkoxide to end cap the POSS molecule with titanium atom to obtain a so called polyhedral oligomeric metalized silsesquioxane (POMS). The synthesized POMS was characterized by FTIR, RAMAN and UV–visible spectroscopy as well as {sup 29}Si NMR and matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) techniques. Appearance of peaks at 920 cm{sup −1} in FTIR and 491 cm{sup −1} and 1083 cm{sup −1} in Raman spectra confirmed Si–O–Ti linkage formation. It was also demonstrated that POMS was in a monomeric form. To evaluate the biocompatibility of hybrids films, pristine POSS and synthesized POMS were used in synthesis of a polycarbonate urethane polymer. Results revealed that POMS containing hybrid, not only had notable thermal and mechanical stability compared to POSS containing one, as demonstrated by DSC and DMTA analysis, they also showed controlled surface properties in such a manner that hydrophobicity and biocompatibility were both reachable to give rise to improved cell viability in presence of human umbilical vein endothelial cells (HUVEC) and MRC-5 cells. - Highlight: • Polyhedral Oligomeric Metalized Silsesquioxane (POMS) based on titanium was synthesized. • POMS can improve mechanical properties of polyurethane. • POMS increases hydrophobicity of polyurethane. • POMS is a unique nanocage to enhance biocompatibility of polyurethane.

  6. Molecular cloning and functional characterization of duck nucleotide-binding oligomerization domain 1 (NOD1).

    Science.gov (United States)

    Li, Huilin; Jin, Hui; Li, Yaqian; Liu, Dejian; Foda, Mohamed Frahat; Jiang, Yunbo; Luo, Rui

    2017-09-01

    Nucleotide-binding oligomerization domain 1 (NOD1) is an imperative cytoplasmic pattern recognition receptor (PRR) and considered as a key member of the NOD-like receptor (NLR) family which plays a critical role in innate immunity through sensing microbial components derived from bacterial peptidoglycan. In the current study, the full-length of duck NOD1 (duNOD1) cDNA from duck embryo fibroblasts (DEFs) was cloned. Multiple sequence alignment and phylogenetic analysis demonstrated that duNOD1 exhibited a strong evolutionary relationship with chicken and rock pigeon NOD1. Tissue-specific expression analysis showed that duNOD1 was widely distributed in various organs, with the highest expression observed in the liver. Furthermore, duNOD1 overexpression induced NF-κB activation in DEFs and the CARD domain is crucial for duNOD1-mediated NF-κB activation. In addition, silencing the duNOD1 decreased the activity of NF-κB in DEFs stimulated by iE-DAP. Overexpression of duNOD1 significantly increased the expression of TNF-α, IL-6, and RANTES in DEFs. These findings highlight the crucial role of duNOD1 as an intracellular sensor in duck innate immune system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. The role of Vif oligomerization and RNA chaperone activity in HIV-1 replication.

    Science.gov (United States)

    Batisse, Julien; Guerrero, Santiago; Bernacchi, Serena; Sleiman, Dona; Gabus, Caroline; Darlix, Jean-Luc; Marquet, Roland; Tisné, Carine; Paillart, Jean-Christophe

    2012-11-01

    The viral infectivity factor (Vif) is essential for the productive infection and dissemination of HIV-1 in non-permissive cells that involve most natural HIV-1 target cells. Vif counteracts the packaging of two cellular cytidine deaminases named APOBEC3G (A3G) and A3F by diverse mechanisms including the recruitment of an E3 ubiquitin ligase complex and the proteasomal degradation of A3G/A3F, the inhibition of A3G mRNA translation or by a direct competition mechanism. In addition, Vif appears to be an active partner of the late steps of viral replication by participating in virus assembly and Gag processing, thus regulating the final stage of virion formation notably genomic RNA dimerization and by inhibiting the initiation of reverse transcription. Vif is a small pleiotropic protein with multiple domains, and recent studies highlighted the importance of Vif conformation and flexibility in counteracting A3G and in binding RNA. In this review, we will focus on the oligomerization and RNA chaperone properties of Vif and show that the intrinsic disordered nature of some Vif domains could play an important role in virus assembly and replication. Experimental evidence demonstrating the RNA chaperone activity of Vif will be presented. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Regulation of complement by cartilage oligomeric matrix protein allows for a novel molecular diagnostic principle in rheumatoid arthritis

    DEFF Research Database (Denmark)

    Happonen, Kaisa E; Saxne, Tore; Aspberg, Anders

    2010-01-01

    Cartilage oligomeric matrix protein (COMP) is a structural component of cartilage, where it catalyzes collagen fibrillogenesis. Elevated amounts of COMP are found in serum during increased turnover of cartilage associated with active joint disease, such as rheumatoid arthritis (RA) and osteoarthr...

  9. Oligomerization of glycine and alanine catalyzed by iron oxides: implications for prebiotic chemistry.

    Science.gov (United States)

    Shanker, Uma; Bhushan, Brij; Bhattacharjee, G; Kamaluddin

    2012-02-01

    Iron oxide minerals are probable constituents of the sediments present in geothermal regions of the primitive earth. They might have adsorbed different organic monomers (amino acids, nucleotides etc.) and catalyzed polymerization processes leading to the formation of the first living cell. In the present work we tested the catalytic activity of three forms of iron oxides (Goethite, Akaganeite and Hematite) in the intermolecular condensation of each of the amino acids glycine and L-alanine. The effect of zinc oxide and titanium dioxide on the oligomerization has also been studied. Oligomerization studies were performed for 35 days at three different temperatures 50, 90 and 120°C without applying drying/wetting cycling. The products formed were characterized by HPLC and ESI-MS techniques. All three forms of iron oxides catalyzed peptide bond formation (23.2% of gly2 and 10.65% of ala2). The reaction was monitored every 7 days. Formation of peptides was observed to start after 7 days at 50°C. Maximum yield of peptides was found after 35 days at 90°C. Reaction at 120°C favors formation of diketopiperazine derivatives. It is also important to note that after 35 days of reaction, goethite produced dimer and trimer with the highest yield among the oxides tested. We suggest that the activity of goethite could probably be due to its high surface area and surface acidity.

  10. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    International Nuclear Information System (INIS)

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-01-01

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries

  11. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    Energy Technology Data Exchange (ETDEWEB)

    Spill, Fabian, E-mail: fspill@bu.edu [Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Guerrero, Pilar [Department of Mathematics, University College London, Gower Street, London WC1E 6BT (United Kingdom); Alarcon, Tomas [Centre de Recerca Matematica, Campus de Bellaterra, Edifici C, 08193 Bellaterra (Barcelona) (Spain); Departament de Matemàtiques, Universitat Atonòma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Maini, Philip K. [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Byrne, Helen [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Computational Biology Group, Department of Computer Science, University of Oxford, Oxford OX1 3QD (United Kingdom)

    2015-10-15

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries.

  12. Suppression of Stimulated Brillouin Scattering in multiple-ion species inertial confinement fusion Hohlraum Plasmas

    International Nuclear Information System (INIS)

    Neumayer, P

    2007-01-01

    A long-standing problem in the field of laser-plasma interactions is to successfully employ multiple-ion species plasmas to reduce stimulated Brillouin scattering (SBS) in inertial confinement fusion (ICF) hohlraum conditions. Multiple-ion species increase significantly the linear Landau damping for acoustic waves. Consequently, recent hohlraum designs for indirect-drive ignition on the National Ignition Facility investigate wall liner material options so that the liner gain for parametric instabilities will be below threshold for the onset SBS. Although the effect of two-ion species plasmas on Landau damping has been directly observed with Thomson scattering, early experiments on SBS in these plasmas have suffered from competing non-linear effects or laser beam filamentation. In this study, a reduction of SBS scattering to below the percent level has been observed in hohlraums at Omega that emulate the plasma conditions in an indirect drive ICF experiments. These experiments have measured the laser-plasma interaction processes in ignition-relevant high-electron temperature regime demonstrating Landau damping as a controlling process for SBS. The hohlraums have been filled with various fractions of CO 2 and C 3 H 8 varying the ratio of the light (H) to heavy (C and O) ion density from 0 to 2.6. They have been heated by 14.5 kJ of 351-nm light, thus increasing progressively Landau damping by an order of magnitude at constant electron density and temperature. A delayed 351-nm interaction beam, spatially smoothed to produce a 200-(micro)m laser spot at best focus, has propagated along the axis of the hohlraum. The backscattered light, both into the lens and outside, the transmitted light through the hohlraum plasma and the radiation temperature of the hohlraum has been measured. For ignition relevant laser intensities (3-9 10 14 Wcm -2 ), we find that the SBS reflectivity scales as predicted with Landau damping from >30% to <1%. Simultaneously, the hohlraum radiation

  13. Moyamoya disease-associated protein mysterin/RNF213 is a novel AAA+ ATPase, which dynamically changes its oligomeric state

    Science.gov (United States)

    Morito, Daisuke; Nishikawa, Kouki; Hoseki, Jun; Kitamura, Akira; Kotani, Yuri; Kiso, Kazumi; Kinjo, Masataka; Fujiyoshi, Yoshinori; Nagata, Kazuhiro

    2014-03-01

    Moyamoya disease is an idiopathic human cerebrovascular disorder that is characterized by progressive stenosis and abnormal collateral vessels. We recently identified mysterin/RNF213 as its first susceptibility gene, which encodes a 591-kDa protein containing enzymatically active P-loop ATPase and ubiquitin ligase domains and is involved in proper vascular development in zebrafish. Here we demonstrate that mysterin further contains two tandem AAA+ ATPase modules and forms huge ring-shaped oligomeric complex. AAA+ ATPases are known to generally mediate various biophysical and mechanical processes with the characteristic ring-shaped structure. Fluorescence correlation spectroscopy and biochemical evaluation suggested that mysterin dynamically changes its oligomeric forms through ATP/ADP binding and hydrolysis cycles. Thus, the moyamoya disease-associated gene product is a unique protein that functions as ubiquitin ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell.

  14. Moyamoya disease-associated protein mysterin/RNF213 is a novel AAA+ ATPase, which dynamically changes its oligomeric state

    Science.gov (United States)

    Morito, Daisuke; Nishikawa, Kouki; Hoseki, Jun; Kitamura, Akira; Kotani, Yuri; Kiso, Kazumi; Kinjo, Masataka; Fujiyoshi, Yoshinori; Nagata, Kazuhiro

    2014-01-01

    Moyamoya disease is an idiopathic human cerebrovascular disorder that is characterized by progressive stenosis and abnormal collateral vessels. We recently identified mysterin/RNF213 as its first susceptibility gene, which encodes a 591-kDa protein containing enzymatically active P-loop ATPase and ubiquitin ligase domains and is involved in proper vascular development in zebrafish. Here we demonstrate that mysterin further contains two tandem AAA+ ATPase modules and forms huge ring-shaped oligomeric complex. AAA+ ATPases are known to generally mediate various biophysical and mechanical processes with the characteristic ring-shaped structure. Fluorescence correlation spectroscopy and biochemical evaluation suggested that mysterin dynamically changes its oligomeric forms through ATP/ADP binding and hydrolysis cycles. Thus, the moyamoya disease-associated gene product is a unique protein that functions as ubiquitin ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell. PMID:24658080

  15. Multiple species of scuttle flies (Diptera: Phoridae) as contaminants in forensic entomology laboratory insect colony.

    Science.gov (United States)

    Zuha, R M; Jenarthanan, L X Q; Disney, R H L; Omar, B

    2015-09-01

    In forensic entomology, larval rearing usually includes the presence of biological contaminants including scuttle flies (Diptera: Phoridae). Scuttle flies are recognized as forensically important insects and have been reported causing nuisance and contamination in laboratory environments. This paper reports for the first time the finding of multiple scuttle fly species affecting colonies of third instar larvae of the Oriental latrine blowfly, Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae), reared indoors at the Forensic Science Simulation Site, Universiti Kebangsaan Malaysia. Adult scuttle flies were discovered inside a rearing container after the emergence of adult C. megacephala., The scuttle fly species are Megaselia scalaris (Loew), M. spiracularis Schmitz and Puliciphora borinquenensis (Wheeler). Notes on the life history and biology of these species are discussed herein.

  16. Preparation of polyhedral oligomeric silsesquioxane based imprinted monolith.

    Science.gov (United States)

    Li, Fang; Chen, Xiu-Xiu; Huang, Yan-Ping; Liu, Zhao-Sheng

    2015-12-18

    Polyhedral oligomeric silsesquioxane (POSS) was successfully applied, for the first time, to prepare imprinted monolithic column with high porosity and good permeability. The imprinted monolithic column was synthesized with a mixture of PSS-(1-Propylmethacrylate)-heptaisobutyl substituted (MA 0702), naproxon (template), 4-vinylpyridine, and ethylene glycol dimethacrylate, in ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]BF4). The influence of synthesis parameters on the retention factor and imprinting effect, including the amount of MA 0702, the ratio of template to monomer, and the ratio of monomer to crosslinker, was investigated. The greatest imprinting factor on the imprinted monolithic column prepared with MA 0702 was 22, about 10 times higher than that prepared in absence of POSS. The comparisons between MIP monoliths synthesized with POSS and without POSS were made in terms of permeability, column efficiency, surface morphology and pore size distribution. In addition, thermodynamic and Van Deemter analysis were used to evaluate the POSS-based MIP monolith. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Beyond Streptococcus mutans: Dental Caries Onset Linked to Multiple Species by 16S rRNA Community Analysis

    Science.gov (United States)

    Gross, Erin L.; Beall, Clifford J.; Kutsch, Stacey R.; Firestone, Noah D.; Leys, Eugene J.; Griffen, Ann L.

    2012-01-01

    Dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. Dental caries results from a shift within the biofilm community specific to the tooth surface, and acidogenic species are responsible for caries. Streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. Understanding the degree to which multiple acidogenic species provide functional redundancy and resilience to caries-associated communities will be important for developing biologic interventions. In addition, microbial community interactions in health and caries pathogenesis are not well understood. The purpose of this study was to investigate bacterial community profiles associated with the onset of caries in the primary dentition. In a combination cross-sectional and longitudinal design, bacterial community profiles at progressive stages of caries and over time were examined and compared to those of health. 16S rRNA gene sequencing was used for bacterial community analysis. Streptococcus mutans was the dominant species in many, but not all, subjects with caries. Elevated levels of S. salivarius, S. sobrinus, and S. parasanguinis were also associated with caries, especially in subjects with no or low levels of S. mutans, suggesting these species are alternative pathogens, and that multiple species may need to be targeted for interventions. Veillonella, which metabolizes lactate, was associated with caries and was highly correlated with total acid producing species. Among children without previous history of caries, Veillonella, but not S. mutans or other acid-producing species, predicted future caries. Bacterial community diversity was reduced in caries as compared to health, as many species appeared to occur at lower levels or be lost as caries advanced, including the Streptococcus mitis group, Neisseria, and Streptococcus sanguinis. This may have

  18. Synaptic transmission block by presynaptic injection of oligomeric amyloid beta

    Science.gov (United States)

    Moreno, Herman; Yu, Eunah; Pigino, Gustavo; Hernandez, Alejandro I.; Kim, Natalia; Moreira, Jorge E.; Sugimori, Mutsuyuki; Llinás, Rodolfo R.

    2009-01-01

    Early Alzheimer's disease (AD) pathophysiology is characterized by synaptic changes induced by degradation products of amyloid precursor protein (APP). The exact mechanisms of such modulation are unknown. Here, we report that nanomolar concentrations of intraaxonal oligomeric (o)Aβ42, but not oAβ40 or extracellular oAβ42, acutely inhibited synaptic transmission at the squid giant synapse. Further characterization of this phenotype demonstrated that presynaptic calcium currents were unaffected. However, electron microscopy experiments revealed diminished docked synaptic vesicles in oAβ42-microinjected terminals, without affecting clathrin-coated vesicles. The molecular events of this modulation involved casein kinase 2 and the synaptic vesicle rapid endocytosis pathway. These findings open the possibility of a new therapeutic target aimed at ameliorating synaptic dysfunction in AD. PMID:19304802

  19. Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism

    Directory of Open Access Journals (Sweden)

    McLeish Michael J

    2012-01-01

    Full Text Available Abstract Background The interaction between insects and plants takes myriad forms in the generation of spectacular diversity. In this association a species host range is fundamental and often measured using an estimate of phylogenetic concordance between species. Pollinating fig wasps display extreme host species specificity, but the intraspecific variation in empirical accounts of host affiliation has previously been underestimated. In this investigation, lineage delimitation and codiversification tests are used to generate and discuss hypotheses elucidating on pollinating fig wasp associations with Ficus. Results Statistical parsimony and AMOVA revealed deep divergences at the COI locus within several pollinating fig wasp species that persist on the same host Ficus species. Changes in branching patterns estimated using the generalized mixed Yule coalescent test indicated lineage duplication on the same Ficus species. Conversely, Elisabethiella and Alfonsiella fig wasp species are able to reproduce on multiple, but closely related host fig species. Tree reconciliation tests indicate significant codiversification as well as significant incongruence between fig wasp and Ficus phylogenies. Conclusions The findings demonstrate more relaxed pollinating fig wasp host specificity than previously appreciated. Evolutionarily conservative host associations have been tempered by horizontal transfer and lineage duplication among closely related Ficus species. Independent and asynchronistic diversification of pollinating fig wasps is best explained by a combination of both sympatric and allopatric models of speciation. Pollinator host preference constraints permit reproduction on closely related Ficus species, but uncertainty of the frequency and duration of these associations requires better resolution.

  20. N-terminal aliphatic residues dictate the structure, stability, assembly, and small molecule binding of the coiled-coil region of cartilage oligomeric matrix protein.

    Science.gov (United States)

    Gunasekar, Susheel K; Asnani, Mukta; Limbad, Chandani; Haghpanah, Jennifer S; Hom, Wendy; Barra, Hanna; Nanda, Soumya; Lu, Min; Montclare, Jin Kim

    2009-09-15

    The coiled-coil domain of cartilage oligomeric matrix protein (COMPcc) assembles into a homopentamer that naturally recognizes the small molecule 1,25-dihydroxyvitamin D(3) (vit D). To identify the residues critical for the structure, stability, oligomerization, and binding to vit D as well as two other small molecules, all-trans-retinol (ATR) and curcumin (CCM), here we perform an alanine scanning mutagenesis study. Ten residues lining the hydrophobic pocket of COMPcc were mutated into alanine; of the mutated residues, the N-terminal aliphatic residues L37, L44, V47, and L51 are responsible for maintaining the structure and function. Furthermore, two polar residues, T40 and Q54, within the N-terminal region when converted into alanine improve the alpha-helical structure, stability, and self-assembly behavior. Helical stability, oligomerization, and binding appear to be linked in a manner in which mutations that abolish helical structure and assembly bind poorly to vit D, ATR, and CCM. These results provide not only insight into COMPcc and its functional role but also useful guidelines for the design of stable, pentameric coiled-coils capable of selectively storing and delivering various small molecules.

  1. Characterization and ageing study of poly(lactic acid) films plasticized with oligomeric lactic acid

    OpenAIRE

    Burgos, Nuria; Martino, Verónica P.; Jiménez, Alfonso

    2013-01-01

    Poly(lactic acid) (PLA) was melt-blended with a bio-based oligomeric lactic acid (OLA) plasticizer at different concentrations between 15 wt% and 25 wt% in order to enhance PLA ductility and to get a fully biodegradable material with potential application in films manufacturing. OLA was an efficient plasticizer for PLA, as it caused a significant decrease on glass transition temperature (Tg) while improving considerably ductile properties. Only one Tg value was observed in all cases and no ap...

  2. Impact of Vertical Canopy Position on Leaf Spectral Properties and Traits across Multiple Species

    Directory of Open Access Journals (Sweden)

    Tawanda W. Gara

    2018-02-01

    Full Text Available Understanding the vertical pattern of leaf traits across plant canopies provide critical information on plant physiology, ecosystem functioning and structure and vegetation response to climate change. However, the impact of vertical canopy position on leaf spectral properties and subsequently leaf traits across the entire spectrum for multiple species is poorly understood. In this study, we examined the ability of leaf optical properties to track variability in leaf traits across the vertical canopy profile using Partial Least Square Discriminatory Analysis (PLS-DA. Leaf spectral measurements together with leaf traits (nitrogen, carbon, chlorophyll, equivalent water thickness and specific leaf area were studied at three vertical canopy positions along the plant stem: lower, middle and upper. We observed that foliar nitrogen (N, chlorophyll (Cab, carbon (C, and equivalent water thickness (EWT were higher in the upper canopy leaves compared with lower shaded leaves, while specific leaf area (SLA increased from upper to lower canopy leaves. We found that leaf spectral reflectance significantly (P ≤ 0.05 shifted to longer wavelengths in the ‘red edge’ spectrum (685–701 nm in the order of lower > middle > upper for the pooled dataset. We report that spectral bands that are influential in the discrimination of leaf samples into the three groups of canopy position, based on the PLS-DA variable importance projection (VIP score, match with wavelength regions of foliar traits observed to vary across the canopy vertical profile. This observation demonstrated that both leaf traits and leaf reflectance co-vary across the vertical canopy profile in multiple species. We conclude that canopy vertical position has a significant impact on leaf spectral properties of an individual plant’s traits, and this finding holds for multiple species. These findings have important implications on field sampling protocols, upscaling leaf traits to canopy level

  3. Endohedral complexes of Polyhedral Oligomeric Silsesquioxane (POSS) cages with transition metal dihydrides

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xiqiao; Corn, John; Hagelberg, Frank, E-mail: hagelber@etsu.edu

    2013-11-29

    Highlights: • Comparative studies of POSS cages with endohedral metal dihydrides. • Exothermic inclusion was found for the T{sub 10} cage with MH{sub 2}, M = Ti, Ru, Os, Pt. • Within this group of metal atoms, the only exothermic MH{sub 4}@T{sub m} unit is that with M = Os. • Enhanced hydrogen atom density, as compared to free MH{sub 4}, was found in the cage. • No exothermic solutions were identified for MH{sub 6}@T{sub 10}. - Abstract: Polyhedral Oligomeric Silsesquioxane (POSS) cages are investigated in terms of their potential to enclose small metal hydrides, with the objective of defining conditions that maximize the number of encapsulated hydrogen atoms. Systems of the form MH{sub 2n}@T{sub m}, where n = 1–3, m = 8, 10, and M comprises metal atom species of the groups IV, VI, VIII, X, and XII, are studied by methods of ab initio and density functional theory (DFT). The resulting composites are categorized with respect to their structural and energetic features. For MH{sub 2}@T{sub 8}, it is found in all cases considered that including MH{sub 2} into the POSS cage is an endothermic process. For MH{sub 2}@T{sub 10} and M = Ti, Ru, Os, Pt, inclusion of the MH{sub 2} guest into the cage turns out to be exothermic, and also leaves the cage intact. For MH{sub 4}@T{sub m}, this behavior is only observed for one system, OsH{sub 4}@T{sub 10}.

  4. Multifunctional Mesoporous Ionic Gels and Scaffolds Derived from Polyhedral Oligomeric Silsesquioxanes.

    Science.gov (United States)

    Lee, Jin Hong; Lee, Albert S; Lee, Jong-Chan; Hong, Soon Man; Hwang, Seung Sang; Koo, Chong Min

    2017-02-01

    A new methodology for fabrication of inorganic-organic hybrid ionogels and scaffolds is developed through facile cross-linking and solution extraction of a newly developed ionic polyhedral oligomeric silsesquioxane with inorganic core. Through design of various cationic tertiary amines, as well as cross-linkable functional groups on each arm of the inorganic core, high-performance ionogels are fabricated with excellent electrochemical stability and unique ion conduction behavior, giving superior lithium ion battery performance. Moreover, through solvent extraction of the liquid components, hybrid scaffolds with well-defined, interconnected mesopores are utilized as heterogeneous catalysts for the CO 2 -catalyzed cycloaddition of epoxides. Excellent catalytic performance, as well as highly efficient recyclability are observed when compared to other previous literature materials.

  5. Computational Study of the Effect of Confinement within Microporous Structures on the Activity and Selectivity of Metallocene Catalysts for Ethylene Oligomerization

    KAUST Repository

    Toulhoat, Hervé; Lontsi Fomena, Mireille; de Bruin, Theodorus

    2011-01-01

    The effect of confinement within some zeolitic structures on the activity and selectivity of metallocene catalysts for the ethylene oligomerization has been investigated using grand canonical Monte Carlo simulations (GCMC). The following zeolite

  6. Kinetics in Signal Transduction Pathways Involving Promiscuous Oligomerizing Receptors Can Be Determined by Receptor Specificity : Apoptosis Induction by TRAIL

    NARCIS (Netherlands)

    Szegezdi, Eva; van der Sloot, Almer M.; Mahalingam, Devalingam; O'Leary, Lynda; Cool, Robbert H.; Munoz, Ines G.; Montoya, Guillermo; Quax, Wim J.; de Jong, Steven; Samali, Afshin; Serrano, Luis

    Here we show by computer modeling that kinetics and outcome of signal transduction in case of hetero-oligomerizing receptors of a promiscuous ligand largely depend on the relative amounts of its receptors. Promiscuous ligands can trigger the formation of nonproductive receptor complexes, which slows

  7. Hedgehog Buckyball: A High-Symmetry Complete Polyhedral Oligomeric Silsesquioxane (POSS

    Directory of Open Access Journals (Sweden)

    Yu Hu

    2016-08-01

    Full Text Available In this study, we report UV-MALDI-TOF MS evidence of a fullerene-like silsesquioxane, a high-symmetry polyhedral oligomeric silsesquioxane (POSS or SSO formulated as R60-Si60O90 or T60 (T = RSiO1.5. The T60 preparation can be performed using a normal hydrolytic condensation of [(3-methacryloxypropyl]trimethoxysilane (MPMS as an example. Theoretically, four 3sp3 hybrid orbitals (each containing an unpaired electron of a Si atom are generated before the bond formation. Then it bonds to another four atom electrons using the four generated hybrid orbitals which produced a stable configuration. This fullerene-like silsesquioxane should exhibit much more functionality, activity and selectivity and is easier to assemble than the double bonds in a fullerene.

  8. Construction of porous cationic frameworks by crosslinking polyhedral oligomeric silsesquioxane units with N-heterocyclic linkers

    OpenAIRE

    Chen, Guojian; Zhou, Yu; Wang, Xiaochen; Li, Jing; Xue, Shuang; Liu, Yangqing; Wang, Qian; Wang, Jun

    2015-01-01

    In fields of materials science and chemistry, ionic-type porous materials attract increasing attention due to significant ion-exchanging capacity for accessing diversified applications. Facing the fact that porous cationic materials with robust and stable frameworks are very rare, novel tactics that can create new type members are highly desired. Here we report the first family of polyhedral oligomeric silsesquioxane (POSS) based porous cationic frameworks (PCIF-n) with enriched poly(ionic li...

  9. Attempted integration of multiple species of turaco into a mixed-species aviary.

    Science.gov (United States)

    Valuska, Annie J; Leighty, Katherine A; Ferrie, Gina M; Nichols, Valerie D; Tybor, Cheryl L; Plassé, Chelle; Bettinger, Tamara L

    2013-03-01

    Mixed-species exhibits offer a variety of benefits but can be challenging to maintain due to difficulty in managing interspecific interactions. This is particularly true when little has been documented on the behavior of the species being mixed. This was the case when we attempted to house three species of turaco (family: Musophagidae) together with other species in a walk-through aviary. To learn more about the behavior of great blue turacos, violaceous turacos, and white-bellied gray go-away birds, we supplemented opportunistic keeper observations with systematic data collection on their behavior, location, distance from other birds, and visibility to visitors. Keepers reported high levels of aggression among turacos, usually initiated by a go-away bird or a violaceous turaco. Most aggression occurred during feedings or when pairs were defending nest sites. Attempts to reduce aggression by temporarily removing birds to holding areas and reintroducing them days later were ineffective. Systematic data collection revealed increased social behavior, including aggression, during breeding season in the violaceous turacos, as well as greater location fidelity. These behavioral cues may be useful in predicting breeding behavior in the future. Ultimately, we were only able to house three species of turaco together for a short time, and prohibitively high levels of conflict occurred when pairs were breeding. We conclude that mixing these three turaco species is challenging and may not be the most appropriate housing situation for them, particularly during breeding season. However, changes in turaco species composition, sex composition, or exhibit design may result in more compatible mixed-turaco species groups. © 2012 Wiley Periodicals, Inc.

  10. Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species.

    Science.gov (United States)

    Baker, Kate S; Dallman, Timothy J; Field, Nigel; Childs, Tristan; Mitchell, Holly; Day, Martin; Weill, François-Xavier; Lefèvre, Sophie; Tourdjman, Mathieu; Hughes, Gwenda; Jenkins, Claire; Thomson, Nicholas

    2018-04-13

    Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly elucidated. Here, we study parallel epidemic emergences of multiple Shigella species, a priority AMR organism, in men who have sex with men to gain insight into AMR emergence and spread. Using genomic epidemiology, we show that repeated horizontal transfer of a single AMR plasmid among Shigella enhanced existing and facilitated new epidemics. These epidemic patterns contrasted with slighter, slower increases in disease caused by organisms with vertically inherited (chromosomally encoded) AMR. This demonstrates that horizontal transfer of AMR directly affects epidemiological outcomes of globally important AMR pathogens and highlights the need for integration of genomic analyses into all areas of AMR research, surveillance and management.

  11. Immobilization of isolated FI catalyst on polyhedral oligomeric silsesquioxane-functionalized silica for the synthesis of weakly entangled polyethylene.

    Science.gov (United States)

    Li, Wei; Yang, Huaqin; Zhang, Jingjing; Mu, Jingshan; Gong, Dirong; Wang, Xiaodong

    2016-09-25

    Polyhedral oligomeric silsesquioxanes (POSSs) were adsorbed on methylaluminoxane-activated silica for the immobilization of fluorinated bis(phenoxyimine)Ti complexes (FI catalyst). These POSSs have been characterized as horizontal spacers isolating the active sites and hindering the chain overlap in polymerization. The heterogeneous catalyst exhibits considerable activity in the synthesis of weakly entangled polyethylene.

  12. Fusion of the Mycobacterium tuberculosis antigen 85A to an oligomerization domain enhances its immunogenicity in both mice and non-human primates.

    Directory of Open Access Journals (Sweden)

    Alexandra J Spencer

    Full Text Available To prevent important infectious diseases such as tuberculosis, malaria and HIV, vaccines inducing greater T cell responses are required. In this study, we investigated whether fusion of the M. tuberculosis antigen 85A to recently described adjuvant IMX313, a hybrid avian C4bp oligomerization domain, could increase T cell responses in pre-clinical vaccine model species. In mice, the fused antigen 85A showed consistent increases in CD4(+ and CD8(+ T cell responses after DNA and MVA vaccination. In rhesus macaques, higher IFN-γ responses were observed in animals vaccinated with MVA-Ag85A IMX313 after both primary and secondary immunizations. In both animal models, fusion to IMX313 induced a quantitative enhancement in the response without altering its quality: multifunctional cytokines were uniformly increased and differentiation into effector and memory T cell subsets was augmented rather than skewed. An extensive in vivo characterization suggests that IMX313 improves the initiation of immune responses as an increase in antigen 85A specific cells was observed as early as day 3 after vaccination. This report demonstrates that antigen multimerization using IMX313 is a simple and effective cross-species method to improve vaccine immunogenicity with potentially broad applicability.

  13. Synthesis of fuels and feedstocks

    Energy Technology Data Exchange (ETDEWEB)

    Sutton, Andrew D.; Brooks, Ty; Jenkins, Rhodri; Moore, Cameron; Staples, Orion

    2017-10-10

    Disclosed herein are embodiments of a method for making fuels and feedstocks from readily available alcohol starting materials. In some embodiments, the method concerns converting alcohols to carbonyl-containing compounds and then condensing such carbonyl-containing compounds together to form oligomerized species. These oligomerized species can then be reduced using by-products from the conversion of the alcohol. In some embodiments, the method further comprises converting saturated, oligomerized, carbonyl-containing compounds to aliphatic fuels.

  14. Analysis of oligomeric transition of silkworm small heat shock protein sHSP20.8 using high hydrostatic pressure native PAGE

    Science.gov (United States)

    Fujisawa, Tetsuro; Ueda, Toshifumi; Kameyama, Keiichi; Aso, Yoichi; Ishiguro, Ryo

    2013-06-01

    The small heat shock proteins (sHSPs) solubilize thermo-denatured proteins without adenosine triphosphate energy consumption to facilitate protein refolding. sHSP20.8 is one of the silkworm (Bombyx mori) sHSPs having only one cystein in the N-terminal domain: Cys43. We report a simple measurement of oligomeric transition of sHSP20.8 using high hydrostatic pressure native polyacrylamide gel electrophoresis (high hydrostatic pressure (HP) native polyacrylamide gel electrophoresis (PAGE)). At ambient pressure under oxydative condition, the native PAGE of thermal transition of sHSP20.8 oligomer displayed a cooperative association. In contrast, HP native PAGE clearly demonstrated that sHSP20.8 dissociated at 80 MPa and 25°C, and the resultant molecular species gradually reassociated with time under that condition. In addition, the reassociation process was suppressed in the presence of the reductant. These results are consistent with the idea that sHSP20.8 oligomer temporally dissociates at the first thermo-sensing step and reassociates with the oxidation of Cys43.

  15. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

    Science.gov (United States)

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

  16. DC-SIGN neck domain is a pH-sensor controlling oligomerization: SAXS and hydrodynamic studies of extracellular domain.

    Science.gov (United States)

    Tabarani, Georges; Thépaut, Michel; Stroebel, David; Ebel, Christine; Vivès, Corinne; Vachette, Patrice; Durand, Dominique; Fieschi, Franck

    2009-08-07

    DC-SIGN is a C-type lectin receptor of dendritic cells and is involved in the early stages of numerous infectious diseases. DC-SIGN is organized into a tetramer enabling multivalent interaction with pathogens. Once formed, the DC-SIGN-pathogen complex can be internalized into compartments of increasing acidity. We have studied the pH dependence of the oligomerization state and conformation of the entire extracellular domain and neck region. We present evidence for equilibrium between the monomeric and tetrameric states of the extracellular domain, which exhibits a marked dependence with respect to both pH and ionic strength. Using solution x-ray scattering we have obtained a molecular envelope of the extracellular domain in which a model has been built. Our results highlight the central role of the neck domain in the pH-sensitive control of the oligomerization state, in the extended conformation of the protein, and in carbohydrate recognition domain organization and presentation. This work opens new insight into the molecular mechanism of ligand release and points to new avenues to block the first step of this important infection pathway.

  17. Thermo-mechanical characterization of a monochlorophenyl, hepta isobutyl polyhedral oligomeric silsesquioxane/polystyrene composite

    International Nuclear Information System (INIS)

    Blanco, Ignazio; Bottino, Francesco A.; Cicala, Gianluca; Cozzo, Giulia; Latteri, Alberta; Recca, Antonino

    2014-01-01

    The thermal and mechanical properties of a monochlorophenyl, hepta isobutyl Polyhedral Oligomeric Silsesquioxane/Polystyrene (ph,hib-POSS/PS) composite were studied and compared with those of pristine polymer. ph,hib-POSS/PS system was prepared by solubilization and precipitation of Polystyrene (PS) in the presence of POSS. Scanning Electron Microscopy (SEM) was performed to check the distribution of the filler in the polymer matrix. Dynamic Mechanical Analysis (DMA) was carried out to measure viscoelastic properties of solid samples. Degradations were carried out into a thermobalance and the obtained thermogravimetric (TG) and differential thermogravimetric (DTG) curves were discussed and interpreted

  18. An Asymmetric Deuterium Labeling Strategy to Identify Interprotomer and Intraprotomer NOEs in Oligomeric Proteins

    International Nuclear Information System (INIS)

    Jasanoff, Alan

    1998-01-01

    A major difficulty in determining the structure of an oligomeric protein by NMR is the problem of distinguishing inter- from intraprotomer NOEs. In order to address this issue in studies of the 27 kD compact trimeric domain of the MHC class II-associated invariant chain, we compared the 13C NOESY-HSQC spectrum of a uniformly 13C-labeled trimer with the spectrum of the same trimer labeled with 13C in only one protomer, and with deuterium in the other two protomers. The spectrum of the unmixed trimer included both inter- and intraprotomer NOEs while the spectrum of the mixed trimer included only intraprotomer peaks. NOEs clearly absent from the spectrum of the mixed trimer could be confidently assigned to interprotomer interactions. Asymmetrically labeled trimers were isolated by refolding a 13C-labeled shorter form of the protein with a 2H-labeled longer form, chromatographically purifying trimers with only one short chain, and then processing with trypsin to yield only protomers with the desired N- and C-termini. In contrast to earlier studies, in which statistical mixtures of differently labeled protomers were analyzed, our procedure generated only a well-defined 1:2 oligomer, and no other mixed oligomers were present. This increased the maximum possible concentration of NMR-active protomers and thus the sensitivity of the experiments. Related methods should be applicable to many oligomeric proteins, particularly those with slow protomer exchange rates

  19. Prolonged Exposure of Cortical Neurons to Oligomeric Amyloid-β Impairs NMDA Receptor Function Via NADPH Oxidase-Mediated ROS Production: Protective Effect of Green Tea (--Epigallocatechin-3-Gallate

    Directory of Open Access Journals (Sweden)

    Yan He

    2011-01-01

    Full Text Available Excessive production of Aβ (amyloid β-peptide has been shown to play an important role in the pathogenesis of AD (Alzheimer's disease. Although not yet well understood, aggregation of Aβ is known to cause toxicity to neurons. Our recent study demonstrated the ability for oligomeric Aβ to stimulate the production of ROS (reactive oxygen species in neurons through an NMDA (N-methyl-D-aspartate-dependent pathway. However, whether prolonged exposure of neurons to aggregated Aβ is associated with impairment of NMDA receptor function has not been extensively investigated. In the present study, we show that prolonged exposure of primary cortical neurons to Aβ oligomers caused mitochondrial dysfunction, an attenuation of NMDA receptor-mediated Ca2+ influx and inhibition of NMDA-induced AA (arachidonic acid release. Mitochondrial dysfunction and the decrease in NMDA receptor activity due to oligomeric Aβ are associated with an increase in ROS production. Gp91ds-tat, a specific peptide inhibitor of NADPH oxidase, and Mn(III-tetrakis(4-benzoic acid-porphyrin chloride, an ROS scavenger, effectively abrogated Aβ-induced ROS production. Furthermore, Aβ-induced mitochondrial dysfunction, impairment of NMDA Ca2+ influx and ROS production were prevented by pretreatment of neurons with EGCG [(–-epigallocatechin-3-gallate], a major polyphenolic component of green tea. Taken together, these results support a role for NADPH oxidase-mediated ROS production in the cytotoxic effects of Aβ, and demonstrate the therapeutic potential of EGCG and other dietary polyphenols in delaying onset or retarding the progression of AD.

  20. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization

    CSIR Research Space (South Africa)

    Gcebe, N

    2017-04-01

    Full Text Available Journal of Systematic and Evolutionary Microbiology: DOI 10.1099/ijsem.0.001678 Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization Gcebe N Rutten V Gey...

  1. Functional traits drive the contribution of solar radiation to leaf litter decomposition among multiple arid-zone species.

    Science.gov (United States)

    Pan, Xu; Song, Yao-Bin; Liu, Guo-Fang; Hu, Yu-Kun; Ye, Xue-Hua; Cornwell, William K; Prinzing, Andreas; Dong, Ming; Cornelissen, Johannes H C

    2015-08-18

    In arid zones, strong solar radiation has important consequences for ecosystem processes. To better understand carbon and nutrient dynamics, it is important to know the contribution of solar radiation to leaf litter decomposition of different arid-zone species. Here we investigated: (1) whether such contribution varies among plant species at given irradiance regime, (2) whether interspecific variation in such contribution correlates with interspecific variation in the decomposition rate under shade; and (3) whether this correlation can be explained by leaf traits. We conducted a factorial experiment to determine the effects of solar radiation and environmental moisture for the mass loss and the decomposition constant k-values of 13 species litters collected in Northern China. The contribution of solar radiation to leaf litter decomposition varied significantly among species. Solar radiation accelerated decomposition in particular in the species that already decompose quickly under shade. Functional traits, notably specific leaf area, might predict the interspecific variation in that contribution. Our results provide the first empirical evidence for how the effect of solar radiation on decomposition varies among multiple species. Thus, the effect of solar radiation on the carbon flux between biosphere and atmosphere may depend on the species composition of the vegetation.

  2. Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes.

    Science.gov (United States)

    Maugini, Elisa; Tronelli, Daniele; Bossa, Francesco; Pascarella, Stefano

    2009-04-01

    Enzymes from thermophilic and, particularly, from hyperthermophilic organisms are surprisingly stable. Understanding of the molecular origin of protein thermostability and thermoactivity attracted the interest of many scientist both for the perspective comprehension of the principles of protein structure and for the possible biotechnological applications through application of protein engineering. Comparative studies at sequence and structure levels were aimed at detecting significant differences of structural parameters related to protein stability between thermophilic and hyperhermophilic structures and their mesophilic homologs. Comparative studies were useful in the identification of a few recurrent themes which the evolution utilized in different combinations in different protein families. These studies were mostly carried out at the monomer level. However, maintenance of a proper quaternary structure is an essential prerequisite for a functional macromolecule. At the environmental temperatures experienced typically by hyper- and thermophiles, the subunit interactions mediated by the interface must be sufficiently stable. Our analysis was therefore aimed at the identification of the molecular strategies adopted by evolution to enhance interface thermostability of oligomeric enzymes. The variation of several structural properties related to protein stability were tested at the subunit interfaces of thermophilic and hyperthermophilic oligomers. The differences of the interface structural features observed between the hyperthermophilic and thermophilic enzymes were compared with the differences of the same properties calculated from pairwise comparisons of oligomeric mesophilic proteins contained in a reference dataset. The significance of the observed differences of structural properties was measured by a t-test. Ion pairs and hydrogen bonds do not vary significantly while hydrophobic contact area increases specially in hyperthermophilic interfaces. Interface

  3. Synthesis and characterization of an octaimidazolium-based polyhedral oligomeric silsesquioxanes ionic liquid by an ion-exchange reaction.

    Science.gov (United States)

    Tan, Jinglin; Ma, Depeng; Sun, Xingrong; Feng, Shengyu; Zhang, Changqiao

    2013-04-07

    Preparation of POSS-min-DS, an octaimidazolium-based polyhedral oligomeric silsesquioxanes (POSS) room temperature ionic liquid, by an ion-exchange reaction between POSS and sodium dodecyl sulfate was reported. Octaimidazolium-based POSS was synthesized with more than 98% yield within 3 h. POSS-min-DS and octaimidazolium-based POSS were confirmed by (1)H, (13)C, and (29)Si NMR, FT-IR and elemental analysis.

  4. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny

    2006-01-01

    species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus...

  5. Oligomeric protein structure networks: insights into protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

    Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

  6. Sequence-specific electrochemical recognition of multiple species using nanoparticle labels

    International Nuclear Information System (INIS)

    Cai Hong; Shang, Chii; Hsing, I.-Ming

    2004-01-01

    In this work, we report an electrochemical methodology that enables the rapid identification of different DNA sequences on the microfabricated electrodes. Our approach starts with an electropolymerization process on a patterned indium tin oxide (ITO)-coated glass electrode, followed by a selective immobilization of biotin-tagged probes on individually addressable spots via the biotin-streptavidin linkage. An exemplary target mixture containing E. coli and Stachybotrys Chartarum, an airborne pathogen, is then introduced. Recognition of the DNA hybridization event of the immobilized probes with the target pathogen PCR products or synthetic oligonucleotides is achieved by a novel electrochemistry-based technique utilizing the preferential catalytic silver electrodeposition process on the DNA-linked nanogold shells. The ability to selectively immobilize different oligonucleotide probes together with a sensitive electrochemistry-based detection for multiple species, as demonstrated in this study, is an important step forward for the realization of a portable bioanalytical microdevice for the rapid detection of pathogens

  7. Autosomal dominant precocious osteoarthropathy due to a mutation of the cartilage oligomeric matrix protein (COMP) gene: further expansion of the phenotypic variations of COMP defects

    Energy Technology Data Exchange (ETDEWEB)

    Kawaji, Hiroyuki [Department of Orthopaedic Surgery, Sanyudo Hospital, 6-1-219 Chuou, Yonezawa, Yamagata 992-0045 (Japan); Nishimura, Gen [Department of Radiology, Nasu Chuou Hospital, Tochigi (Japan); Watanabe, Sobei; Sasaki, Akira; Sano, Tokuhisa [Department of Orthopaedic Surgery, Tohoku Kohsei-Nenkin Hospital, Miyagi (Japan); Mabuchi, Akihiko; Ikeda, Toshiyuki; Ikegawa, Shiro [Laboratory for Bone and Joint Diseases, SNP Research Center, Tokyo (Japan); Ohashi, Hirofumi [Division of Medical Genetics, Saitama Children' s Medical Center, Saitama (Japan)

    2002-12-01

    We report on a Japanese family of four generations with an autosomal dominant precocious osteoarthropathy. The cardinal clinical manifestations of affected individuals were painful weight-bearing large joints, which started in late childhood or adolescence. The radiological hallmarks included coxa plana, mild epiphyseal dysplasia of the knee, and round talar domes with tibiotalar slant in childhood, which evolved into degenerative joint diseases in adulthood. The disease phenotype was cosegregated with a mutation of the cartilage oligomeric matrix protein (COMP) gene in the family members, who underwent molecular evaluation. COMP mutations have been reported in a mild form of multiple epiphyseal dysplasia (MED), Ribbing type, as well as allied disorders with more severe manifestations, such as MED Fairbank type and pseudoachondroplasia. Unlike previously reported cases with the Ribbing type, the present patients did not have short stature or brachydactyly. This report expands further the phenotypic variations of COMP defects. (orig.)

  8. Polyhedral oligomeric silsequioxane monolayer as a nanoporous interlayer for preparation of low-k dielectric films

    International Nuclear Information System (INIS)

    Liu, Y-L; Liu, C-S; Cho, C-I; Hwu, M-J

    2007-01-01

    Polyhedral oligomeric silsequioxane (POSS) monomer was fixed to a silicon surface by reacting octakis(glycidyldimethylsiloxy)octasilsesquioxane (OG-POSS) with the OH-terminated silicon surface in the presence of tin (II) chloride. The POSS cage layer then served as a nanoporous interlayer to reduce the dielectric constants of polyimide films on silicon surfaces. The chemical structure and surface morphology of OG-POSS modified silicon surfaces were characterized with XPS. With the introduction of a POSS nanopored interlayer, the dielectric constants of polyimide films were reduced

  9. Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species.

    Science.gov (United States)

    Schröder, Markus S; Martinez de San Vicente, Kontxi; Prandini, Tâmara H R; Hammel, Stephen; Higgins, Desmond G; Bagagli, Eduardo; Wolfe, Kenneth H; Butler, Geraldine

    2016-11-01

    Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi.

  10. Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species.

    Directory of Open Access Journals (Sweden)

    Markus S Schröder

    2016-11-01

    Full Text Available Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi.

  11. Protein phosphatase 2a (PP2A binds within the oligomerization domain of striatin and regulates the phosphorylation and activation of the mammalian Ste20-Like kinase Mst3

    Directory of Open Access Journals (Sweden)

    Jones Candace A

    2011-10-01

    residues lying between striatin's calmodulin-binding and WD-domains and recruits the PP2A A/C heterodimer to its coiled-coil/oligomerization domain. Residues outside the previously reported coiled-coil domain of striatin are necessary for its oligomerization. Striatin-associated PP2A is critical for Mst3 dephosphorylation and inactivation. Upon inhibition of PP2A, Mst3 activation appears to involve autophosphorylation of multiple activation loop phosphorylation sites. Mob3 can associate with striatin sequences C-terminal to the Mst3 binding site but also with sequences proximal to striatin-associated PP2A, consistent with a possible role for Mob 3 in the regulation of Mst3 by PP2A.

  12. Welding fumes from stainless steel gas metal arc processes contain multiple manganese chemical species.

    Science.gov (United States)

    Keane, Michael; Stone, Samuel; Chen, Bean

    2010-05-01

    Fumes from a group of gas metal arc welding (GMAW) processes used on stainless steel were generated using three different metal transfer modes and four different shield gases. The objective was to identify and measure manganese (Mn) species in the fumes, and identify processes that are minimal generators of Mn species. The robotic welding system was operated in short-circuit (SC) mode (Ar/CO2 and He/Ar), axial spray (AXS) mode (Ar/O2 and Ar/CO2), and pulsed axial-spray (PAXS) mode (Ar/O2). The fumes were analyzed for Mn by a sequential extraction process followed by inductively coupled plasma-atomic emission spectroscopy (ICP-AES) analysis, and by X-ray diffraction (XRD). Total elemental Mn, iron (Fe), chromium (Cr) and nickel (Ni) were separately measured after aqua regia digestion and ICP-AES analysis. Soluble Mn2+, Fe2+, Fe3+, and Ni2+ in a simple biological buffer (phosphate-buffered saline) were determined at pH 7.2 and 5.0 after 2 h incubation at 37 C by ion chromatography. Results indicate that Mn was present in soluble form, acid-soluble form, and acid-soluble form after reduction by hydroxylamine, which represents soluble Mn0 and Mn2+ compounds, other Mn2+ compounds, and (Mn3+ and Mn4+) compounds, respectively. The dominant fraction was the acid-soluble Mn2+ fraction, but results varied with the process and shield gas. Soluble Mn mass percent in the fume ranged from 0.2 to 0.9%, acid-soluble Mn2+ compounds ranged from 2.6 to 9.3%, and acid plus reducing agent-soluble (Mn3+ and Mn4+) compounds ranged from 0.6 to 5.1%. Total Mn composition ranged from 7 to 15%. XRD results showed fumes had a crystalline content of 90-99% Fe3O4, and showed evidence of multiple Mn oxides, but overlaps and weak signals limited identification. Small amounts of the Mn2+ in the fume (welding process. Mn generation rates for the fractions were tabulated, and the influence of ozone is discussed. The conclusions are that exposures to welding fumes include multiple Mn species, both

  13. Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone.

    Directory of Open Access Journals (Sweden)

    Jason Trigg

    Full Text Available The alpha-helical coiled coil can adopt a variety of topologies, among the most common of which are parallel and antiparallel dimers and trimers. We present Multicoil2, an algorithm that predicts both the location and oligomerization state (two versus three helices of coiled coils in protein sequences. Multicoil2 combines the pairwise correlations of the previous Multicoil method with the flexibility of Hidden Markov Models (HMMs in a Markov Random Field (MRF. The resulting algorithm integrates sequence features, including pairwise interactions, through multinomial logistic regression to devise an optimized scoring function for distinguishing dimer, trimer and non-coiled-coil oligomerization states; this scoring function is used to produce Markov Random Field potentials that incorporate pairwise correlations localized in sequence. Multicoil2 significantly improves both coiled-coil detection and dimer versus trimer state prediction over the original Multicoil algorithm retrained on a newly-constructed database of coiled-coil sequences. The new database, comprised of 2,105 sequences containing 124,088 residues, includes reliable structural annotations based on experimental data in the literature. Notably, the enhanced performance of Multicoil2 is evident when tested in stringent leave-family-out cross-validation on the new database, reflecting expected performance on challenging new prediction targets that have minimal sequence similarity to known coiled-coil families. The Multicoil2 program and training database are available for download from http://multicoil2.csail.mit.edu.

  14. Phosphate and HEPES buffers potently affect the fibrillation and oligomerization mechanism of Alzheimer's Aβ peptide

    International Nuclear Information System (INIS)

    Garvey, Megan; Tepper, Katharina; Haupt, Caroline; Knuepfer, Uwe; Klement, Karolin; Meinhardt, Jessica; Horn, Uwe; Balbach, Jochen; Faendrich, Marcus

    2011-01-01

    Highlights: → Sodium phosphate buffer accelerated Aβ(1-40) nucleation relative to HEPES. → Aβ(1-40) fibrils formed in the two buffers show only minor structural differences. → NMR revealed that Aβ(1-40) histidine residues mediate buffer dependent changes. -- Abstract: The oligomerization of Aβ peptide into amyloid fibrils is a hallmark of Alzheimer's disease. Due to its biological relevance, phosphate is the most commonly used buffer system for studying the formation of Aβ and other amyloid fibrils. Investigation into the characteristics and formation of amyloid fibrils frequently relies upon material formed in vitro, predominantly in phosphate buffers. Herein, we examine the effects on the fibrillation and oligomerization mechanism of Aβ peptide that occur due solely to the influence of phosphate buffer. We reveal that significant differences in amyloid fibrillation are observed due to fibrillation being initiated in phosphate or HEPES buffer (at physiological pH and temperature). Except for the differing buffer ions, all experimental parameters were kept constant. Fibril formation was assessed using fluorescently monitored kinetic studies, microscopy, X-ray fiber diffraction and infrared and nuclear magnetic resonance spectroscopies. Based on this set up, we herein reveal profound effects on the mechanism and speed of Aβ fibrillation. The three histidine residues at positions 6, 13 and 14 of Aβ(1-40) are instrumental in these mechanistic changes. We conclude that buffer plays a more significant role in fibril formation than has been generally acknowledged.

  15. Constitutive homo- and hetero-oligomerization of TbetaRII-B, an alternatively spliced variant of the mouse TGF-beta type II receptor

    DEFF Research Database (Denmark)

    Krishnaveni, Manda S; Hansen, Jakob Lerche; Seeger, Werner

    2006-01-01

    , but the oligomerization pattern and dynamics of TbetaRII splice variants in live cells has not been demonstrated thus far. Using co-immunoprecipitation and bioluminescence resonance energy transfer (BRET), we demonstrate that the mouse TbetaRII receptor splice variant TbetaRII-B is capable of forming ligand...

  16. Extension of the Si:C Stressor Thickness by Using Multiple ClusterCarbon Species

    International Nuclear Information System (INIS)

    Sekar, Karuppanan; Krull, Wade

    2011-01-01

    ClusterCarbon implantation is now well established as an attractive alternative for producing stress in advanced NMOS devices. ClusterCarbon has the advantage over monomer carbon implant in it's self-amorphization feature, eliminating the need for PAI implantation while producing highly substitutional carbon incorporation. To date, the limitation of this approach has been the high energy limit, due to the extraction limit of the available production tools for the preferred carbon species, which has been the C7Hx molecule. It is noted that the C7 species is produced by the breakup of the parent C14H14 molecule in the ion source. It is further noted that the preferred method of producing the Si:C stress layer is a multiple implant sequence with ClusterCarbon implants at various energies and doses designed to produce a carbon profile which is constant in-depth. The stressor thickness limit using C7 is known to be about 40 nm, which is less than the stressor thickness used in the conventional SiGe process for PMOS. In this work, it is shown that utilizing the C5 molecule which is also available from the breakup of C14H14 enables the stressor layer thickness to be extended to at least 60 nm, which is consistent with the conventional SiGe process. It will be shown that one additional C5 implant, performed after a standard C7 multiple implant sequence, can produce the extension of the stressor thickness while maintaining the flat depth profile. A detailed process characterization will be shown for this new process sequence.

  17. Photo-polymerization of photocurable resins containing polyhedral oligomeric silsesquioxane methacrylate

    International Nuclear Information System (INIS)

    Lin, Ho-May; Wu, Shi-Yin; Chang, Feng-Chih; Yen, Ying-Chieh

    2011-01-01

    Photocurable resins, bisphenol A propoxylate glycerolate diacrylate (BPA-PGDA, containing two hydroxyl) and bisphenol A propoxylate diacrylate (BPA-PDA), with fixed photoinitiator (Irgacure 907) concentration and various contents of methacrylisobutyl polyhedral oligomeric silsesquioxane (MI-POSS) were prepared and characterized by FTIR spectroscopy, scanning electron microscope and differential photocalorimetry. The MI-POSS molecules form crystals or aggregated particles in the cured resin matrix. The BPA-PGDA series photocurable resins show higher viscosity and lower photo-polymerization reactivity than the BPA-PDA series resins. The photo-polymerization rate and conversion of BPA-PGDA series are improved with increasing MI-POSS content. On the contrary, the photo-polymerization behavior of BPA-PDA series photocurable resins remains nearly unchanged by the addition of MI-POSS. Hydrogen-bonding interaction between the hydroxyl of BPA-PGDA and the siloxane of MI-POSS tends to attract and concentrate these acrylate double bonds around MI-POSS particles and thus enhances the photo-polymerization rate and conversion.

  18. Exceptionally High Electric Double Layer Capacitances of Oligomeric Ionic Liquids.

    Science.gov (United States)

    Matsumoto, Michio; Shimizu, Sunao; Sotoike, Rina; Watanabe, Masayoshi; Iwasa, Yoshihiro; Itoh, Yoshimitsu; Aida, Takuzo

    2017-11-15

    Electric double layer (EDL) capacitors are promising as next-generation energy accumulators if their capacitances and operation voltages are both high. However, only few electrolytes can simultaneously fulfill these two requisites. Here we report that an oligomeric ionic liquid such as IL4 TFSI with four imidazolium ion units in its structure provides a wide electrochemical window of ∼5.0 V, similar to monomeric ionic liquids. Furthermore, electrochemical impedance measurements using Au working electrodes demonstrated that IL4 TFSI exhibits an exceptionally high EDL capacitance of ∼66 μF/cm 2 , which is ∼6 times as high as those of monomeric ionic liquids so far reported. We also found that an EDL-based field effect transistor (FET) using IL4 TFSI as a gate dielectric material and SrTiO 3 as a channel material displays a very sharp transfer curve with an enhanced carrier accumulation capability of ∼64 μF/cm 2 , as determined by Hall-effect measurements.

  19. Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins.

    Science.gov (United States)

    Romero-Romero, Sergio; Costas, Miguel; Rodríguez-Romero, Adela; Alejandro Fernández-Velasco, D

    2015-08-28

    Temperature is one of the main variables that modulate protein function and stability. Thermodynamic studies of oligomeric proteins, the dominant protein natural form, have been often hampered because irreversible aggregation and/or slow reactions are common. There are no reports on the reversible equilibrium thermal unfolding of proteins composed of (β/α)8 barrel subunits, albeit this "TIM barrel" topology is one of the most abundant and versatile in nature. We studied the eponymous TIM barrel, triosephosphate isomerase (TIM), belonging to five species of different bacterial taxa. All of them were found to be catalytically efficient dimers. The three-dimensional structure of four enzymes was solved at high/medium resolution. Irreversibility and kinetic control were observed in the thermal unfolding of two TIMs, while for the other three the thermal unfolding was found to follow a two-state equilibrium reversible process. Shifts in the global stability curves of these three proteins are related to the organismal temperature range of optimal growth and modulated by variations in maximum stability temperature and in the enthalpy change at that temperature. Reversibility appears to correlate with the low isoelectric point, the absence of a residual structure in the unfolded state, small cavity volume in the native state, low conformational stability and a low melting temperature. Furthermore, the strong coupling between dimer dissociation and monomer unfolding may reduce aggregation and favour reversibility. It is therefore very thought-provoking to find that a common topological ensemble, such as the TIM barrel, can unfold/refold in the Anfinsen way, i.e. without the help of the cellular machinery.

  20. Using empirical models of species colonization under multiple threatening processes to identify complementary threat-mitigation strategies.

    Science.gov (United States)

    Tulloch, Ayesha I T; Mortelliti, Alessio; Kay, Geoffrey M; Florance, Daniel; Lindenmayer, David

    2016-08-01

    Approaches to prioritize conservation actions are gaining popularity. However, limited empirical evidence exists on which species might benefit most from threat mitigation and on what combination of threats, if mitigated simultaneously, would result in the best outcomes for biodiversity. We devised a way to prioritize threat mitigation at a regional scale with empirical evidence based on predicted changes to population dynamics-information that is lacking in most threat-management prioritization frameworks that rely on expert elicitation. We used dynamic occupancy models to investigate the effects of multiple threats (tree cover, grazing, and presence of an hyperaggressive competitor, the Noisy Miner (Manorina melanocephala) on bird-population dynamics in an endangered woodland community in southeastern Australia. The 3 threatening processes had different effects on different species. We used predicted patch-colonization probabilities to estimate the benefit to each species of removing one or more threats. We then determined the complementary set of threat-mitigation strategies that maximized colonization of all species while ensuring that redundant actions with little benefit were avoided. The single action that resulted in the highest colonization was increasing tree cover, which increased patch colonization by 5% and 11% on average across all species and for declining species, respectively. Combining Noisy Miner control with increasing tree cover increased species colonization by 10% and 19% on average for all species and for declining species respectively, and was a higher priority than changing grazing regimes. Guidance for prioritizing threat mitigation is critical in the face of cumulative threatening processes. By incorporating population dynamics in prioritization of threat management, our approach helps ensure funding is not wasted on ineffective management programs that target the wrong threats or species. © 2016 Society for Conservation Biology.

  1. Bias correction in species distribution models: pooling survey and collection data for multiple species.

    Science.gov (United States)

    Fithian, William; Elith, Jane; Hastie, Trevor; Keith, David A

    2015-04-01

    Presence-only records may provide data on the distributions of rare species, but commonly suffer from large, unknown biases due to their typically haphazard collection schemes. Presence-absence or count data collected in systematic, planned surveys are more reliable but typically less abundant.We proposed a probabilistic model to allow for joint analysis of presence-only and survey data to exploit their complementary strengths. Our method pools presence-only and presence-absence data for many species and maximizes a joint likelihood, simultaneously estimating and adjusting for the sampling bias affecting the presence-only data. By assuming that the sampling bias is the same for all species, we can borrow strength across species to efficiently estimate the bias and improve our inference from presence-only data.We evaluate our model's performance on data for 36 eucalypt species in south-eastern Australia. We find that presence-only records exhibit a strong sampling bias towards the coast and towards Sydney, the largest city. Our data-pooling technique substantially improves the out-of-sample predictive performance of our model when the amount of available presence-absence data for a given species is scarceIf we have only presence-only data and no presence-absence data for a given species, but both types of data for several other species that suffer from the same spatial sampling bias, then our method can obtain an unbiased estimate of the first species' geographic range.

  2. Efficient light-emitting devices based on platinum-complexes-anchored polyhedral oligomeric silsesquioxane materials

    KAUST Repository

    Yang, Xiaohui

    2010-08-24

    The synthesis, photophysical, and electrochemical characterization of macromolecules, consisting of an emissive platinum complex and carbazole moieties covalently attached to a polyhedral oligomeric silsesquioxane (POSS) core, is reported. Organic light-emitting devices based on these POSS materials exhibit a peak external quantum efficiency of ca. 8%, which is significantly higher than that of the analogous devices with a physical blend of the platinum complexes and a polymer matrix, and they represent noticeable improvement in the device efficiency of solution-processable phosphorescent excimer devices. Furthermore, the ratio of monomer and excimer/aggregate electroluminescent emission intensity, as well as the device efficiency, increases as the platinum complex moiety presence on the POSS macromolecules decreases. © 2010 American Chemical Society.

  3. Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones

    Directory of Open Access Journals (Sweden)

    Zheng Tong

    2017-05-01

    Full Text Available Rubber elongation factor (REF and small rubber particle protein (SRPP are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF138,175,258 and SRPP117,204,243, were characterized from Hevea brasiliensis Reyan (RY 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE, each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF175 or REF258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.

  4. Oligomeric rare-earth metal cluster complexes with endohedral transition metal atoms

    Energy Technology Data Exchange (ETDEWEB)

    Steinberg, Simon; Zimmermann, Sina; Brühmann, Matthias; Meyer, Eva; Rustige, Christian; Wolberg, Marike; Daub, Kathrin; Bell, Thomas; Meyer, Gerd, E-mail: gerd.meyer@uni-koeln.de

    2014-11-15

    Comproportionation reactions of rare-earth metal trihalides (RX{sub 3}) with the respective rare-earth metals (R) and transition metals (T) led to the formation of 22 oligomeric R cluster halides encapsulating T, in 19 cases for the first time. The structures of these compounds were determined by single-crystal X-ray diffraction and are composed of trimers ((T{sub 3}R{sub 11})X{sub 15}-type, P6{sub 3}/m), tetramers ((T{sub 4}R{sub 16})X{sub 28}(R{sub 4}) (P-43m), (T{sub 4}R{sub 16})X{sub 20} (P4{sub 2}/nnm), (T{sub 4}R{sub 16})X{sub 24}(RX{sub 3}){sub 4} (I4{sub 1}/a) and (T{sub 4}R{sub 16})X{sub 23} (C2/m) types of structure) and pentamers ((Ru{sub 5}La{sub 14}){sub 2}Br{sub 39}, Cc) of (TR{sub r}){sub n} (n=2–5) clusters. These oligomers are further enveloped by inner (X{sup i}) as well as outer (X{sup a}) halido ligands, which possess diverse functionalities and interconnect like oligomers through i–i, i–a and/or a–i bridges. The general features of the crystal structures for these new compounds are discussed and compared to literature entries as well as different structure types with oligomeric T centered R clusters. Dimers and tetramers originating from the aggregation of (TR{sub 6}) octahedra via common edges are more frequent than trimers and pentamers, in which the (TR{sub r}) clusters share common faces. - Graphical abstract: Rare earth-metal cluster complexes with endohedral transition metal atoms (TR{sub 6}) may connect via common edges or faces to form dimers, trimers, tetramers and pentamers of which the tetramers are the most prolific. Packing effects and electron counts play an important role. - Highlights: • Rare-earth metal cluster complexes encapsulate transition metal atoms. • Oligomers are built via connection of octahedral clusters via common edges or faces. • Dimers through pentamers with closed structures are known. • Tetramers including a tetrahedron of endohedral atoms are the most prolific.

  5. Iron-induced oligomerization of human FXN81-210 and bacterial CyaY frataxin and the effect of iron chelators

    DEFF Research Database (Denmark)

    Ahlgren, Eva Christina; Fekry, Mostafa; Wiemann, Mathias

    2017-01-01

    long forms, FXN42-210 and FXN56-210, have been shown to spontaneously form oligomeric particles stabilized by the extended N-terminal sequence. The short variant FXN81-210, on other hand, has only been observed in the monomeric state. However, a highly homologous E. coli frataxin CyaY, which also lacks...

  6. A Distributed Agent Implementation of Multiple Species Flocking Model for Document Partitioning Clustering

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Xiaohui [ORNL; Potok, Thomas E [ORNL

    2006-01-01

    The Flocking model, first proposed by Craig Reynolds, is one of the first bio-inspired computational collective behavior models that has many popular applications, such as animation. Our early research has resulted in a flock clustering algorithm that can achieve better performance than the Kmeans or the Ant clustering algorithms for data clustering. This algorithm generates a clustering of a given set of data through the embedding of the highdimensional data items on a two-dimensional grid for efficient clustering result retrieval and visualization. In this paper, we propose a bio-inspired clustering model, the Multiple Species Flocking clustering model (MSF), and present a distributed multi-agent MSF approach for document clustering.

  7. A comparison of multiple indicator kriging and area-to-point Poisson kriging for mapping patterns of herbivore species abundance in Kruger National Park, South Africa.

    Science.gov (United States)

    Kerry, Ruth; Goovaerts, Pierre; Smit, Izak P J; Ingram, Ben R

    Kruger National Park (KNP), South Africa, provides protected habitats for the unique animals of the African savannah. For the past 40 years, annual aerial surveys of herbivores have been conducted to aid management decisions based on (1) the spatial distribution of species throughout the park and (2) total species populations in a year. The surveys are extremely time consuming and costly. For many years, the whole park was surveyed, but in 1998 a transect survey approach was adopted. This is cheaper and less time consuming but leaves gaps in the data spatially. Also the distance method currently employed by the park only gives estimates of total species populations but not their spatial distribution. We compare the ability of multiple indicator kriging and area-to-point Poisson kriging to accurately map species distribution in the park. A leave-one-out cross-validation approach indicates that multiple indicator kriging makes poor estimates of the number of animals, particularly the few large counts, as the indicator variograms for such high thresholds are pure nugget. Poisson kriging was applied to the prediction of two types of abundance data: spatial density and proportion of a given species. Both Poisson approaches had standardized mean absolute errors (St. MAEs) of animal counts at least an order of magnitude lower than multiple indicator kriging. The spatial density, Poisson approach (1), gave the lowest St. MAEs for the most abundant species and the proportion, Poisson approach (2), did for the least abundant species. Incorporating environmental data into Poisson approach (2) further reduced St. MAEs.

  8. Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API.

    Science.gov (United States)

    Ytow, Nozomi

    2016-01-01

    The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF's ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file.

  9. Mitochondrial genome analyses suggest multiple Trichuris species in humans, baboons, and pigs from different geographical regions

    DEFF Research Database (Denmark)

    Hawash, Mohamed B. F.; Andersen, Lee O.; Gasser, Robin B.

    2015-01-01

    Trichuris from françois' leaf monkey, suggesting multiple whipworm species circulating among non-human primates. The genetic and protein distances between pig Trichuris from Denmark and other regions were roughly 9% and 6%, respectively, while Chinese and Ugandan whipworms were more closely related......) suggesting that they represented different species. Trichuris from the olive baboon in US was genetically related to human Trichuris in China, while the other from the hamadryas baboon in Denmark was nearly identical to human Trichuris from Uganda. Baboon-derived Trichuris was genetically distinct from......BACKGROUND: The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs, respectively. Although whipworms in human and non-human primates historically have been referred to as T. trichiura, recent reports suggest that several Trichuris spp. are found...

  10. Evaluation of a multiple-species approach to monitoring species at the ecoregional scale

    Science.gov (United States)

    Patricia N. Manley; William J. Zielinski; Matthew D. Schlesinger; Sylvia R. Mori

    2004-01-01

    Monitoring is required of land managers and conservation practitioners to assess the success of management actions. "Shortcuts" are sought to reduce monitoring costs, most often consisting of the selection of a small number of species that are closely monitored to represent the status of many associated species and environmental correlates. Assumptions...

  11. Oligomeric forms of the metastasis-related Mts1 (S100A4) protein stimulate neuronal differentiation in cultures of rat hippocampal neurons

    DEFF Research Database (Denmark)

    Novitskaya, V; Grigorian, M; Kriajevska, M

    2000-01-01

    protein family. The oligomeric but not the dimeric form of Mts1 strongly induces differentiation of cultured hippocampal neurons. A mutant with a single Y75F amino acid substitution, which stabilizes the dimeric form of Mts1, is unable to promote neurite extension. Disulfide bonds do not play an essential...

  12. Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth.

    Science.gov (United States)

    Foley, Joseph; Hill, Shannon E; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

    2013-09-28

    Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the

  13. Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

    Science.gov (United States)

    Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

    2013-09-01

    Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the

  14. Genomic resources for multiple species in the Drosophila ananassae species group.

    Science.gov (United States)

    Signor, Sarah; Seher, Thaddeus; Kopp, Artyom

    2013-01-01

    The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa.

  15. Insight into the template effect of vesicles on the laccase-catalyzed oligomerization of N-phenyl-1,4-phenylenediamine from Raman spectroscopy and cyclic voltammetry measurements

    Science.gov (United States)

    Ležaić, Aleksandra Janoševic; Luginbühl, Sandra; Bajuk-Bogdanović, Danica; Pašti, Igor; Kissner, Reinhard; Rakvin, Boris; Walde, Peter; Ćirić-Marjanović, Gordana

    2016-08-01

    We report about the first Raman spectroscopy study of a vesicle-assisted enzyme-catalyzed oligomerization reaction. The aniline dimer N-phenyl-1,4-phenylenediamine (= p-aminodiphenylamine, PADPA) was oxidized and oligomerized with Trametes versicolor laccase and dissolved O2 in the presence of sodium bis(2-ethylhexyl)sulfosuccinate (AOT) vesicles (80-100 nm diameter) as templates. The conversion of PADPA into oligomeric products, poly(PADPA), was monitored during the reaction by in situ Raman spectroscopy. The results obtained are compared with UV/vis/NIR and EPR measurements. All three complementary methods indicate that at least some of the poly(PADPA) products, formed in the presence of AOT vesicles, resemble the conductive emeraldine salt form of polyaniline (PANI-ES). The Raman measurements also show that structural units different from those of “ordinary” PANI-ES are present too. Without vesicles PANI-ES-like products are not obtained. For the first time, the as-prepared stable poly(PADPA)-AOT vesicle suspension was used directly to coat electrodes (without product isolation) for investigating redox activities of poly(PADPA) by cyclic voltammetry (CV). CV showed that poly(PADPA) produced with vesicles is redox active not only at pH 1.1-as expected for PANI-ES-but also at pH 6.0, unlike PANI-ES and poly(PADPA) synthesized without vesicles. This extended pH range of the redox activity of poly(PADPA) is important for applications.

  16. Design of a minimal protein oligomerization domain by a structural approach.

    Science.gov (United States)

    Burkhard, P; Meier, M; Lustig, A

    2000-12-01

    Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system.

  17. Oligomerization of adenosin-5´-O-ylmethylphosphonate, an isopolar AMP analogue: Evaluation of the route to short oligoadenylates

    Czech Academy of Sciences Publication Activity Database

    Pressová, Martina; Buděšínský, Miloš; Kóšiová, Ivana; Kopecký, V. Jr.; Cvačka, Josef; Kašička, Václav; Šimák, Ondřej; Točík, Zdeněk; Rosenberg, Ivan

    2010-01-01

    Roč. 93, č. 3 (2010), s. 277-289 ISSN 0006-3525 R&D Projects: GA MŠk(CZ) LC06077; GA MŠk(CZ) LC06061; GA AV ČR KAN200520801; GA ČR GA203/09/0820; GA ČR GA202/09/0193 Grant - others:EMIL-FW6(XE) 503569 Institutional research plan: CEZ:AV0Z40550506 Keywords : spontaneous oligomerization * oligoadenylates * phosphonate linkage Subject RIV: CC - Organic Chemistry Impact factor: 2.572, year: 2010

  18. In vitro establishment and multiplication of Guettarda clarense, a Cuban endemic species in extinction danger

    Directory of Open Access Journals (Sweden)

    Elisa Quiala

    2005-01-01

    Full Text Available The present work was carried out with the objective of achieving the in vitro establishment and multiplication of Guettarda clarense which is an endemic local of Santa Clara city and it is considered in extinction danger. Seeds of mature fruits collected under field conditions were used. The effect of a concentration of NaOCl (2% during 15, 20 and 25 minutes in the disinfection of the seeds was studied. The seeds were sowed in a culture medium of germination compound by 50% of MS salts. During the multiplication phase of the explants, the effect of three concentrations of 6-BAP (0.2, 0.4 and 0.6 mg. l-1 was studied. The culture medium was compound by the MS salts, 1.0 mg. l-1 of thiamine and 3% of sucrose. The bigger number of seeds free of visible microbial pollutants (50% was obtained when the treatment with 2.0% of NaOCl during 25 minutes was used. The 85% of the seeds germinated in the culture medium compound by the 50% of the MS salts without growth regulators. During the multiplication phase of the explants, the multiplication coefficient and the longitude of the plants were increased in the same proportion as the concentration of 6-BAP was increased. The highest values were obtained (6.1 explants and 6.7 cm respectively in the treatment with 0.6 mg. l-1. Key words: cuabal, in vitro culture, micropropagation, threatened species

  19. VORICONAZOLE TOXICITY IN MULTIPLE PENGUIN SPECIES.

    Science.gov (United States)

    Hyatt, Michael W; Georoff, Timothy A; Nollens, Hendrik H; Wells, Rebecca L; Clauss, Tonya M; Ialeggio, Donna M; Harms, Craig A; Wack, Allison N

    2015-12-01

    Aspergillosis is a common respiratory fungal disease in penguins managed under human care. Triazole antifungal drugs, including itraconazole, are most commonly used for treatment; however, itraconazole treatment failures from drug resistance are becoming more common, requiring newer treatment options. Voriconazole, a newer triazole, is being used more often. Until recently, no voriconazole pharmacokinetic studies had been performed in penguins, leading to empiric dosing based on other avian studies. This has led to increased anecdotal reporting of apparent voriconazole toxicity in penguins. This report describes 18 probable and 6 suspected cases of voriconazole toxicity in six penguin species from nine institutions: 12 African penguins (Spheniscus demersus), 5 Humboldt penguins (Spheniscus humboldti), 3 Magellanic penguins (Spheniscus magellanicus), 2 gentoo penguins (Pygoscelis papua papua), 1 macaroni penguin (Eudyptes chrysolophus), and 1 emperor penguin (Aptenodytes forsteri). Observed clinical signs of toxicity included anorexia, lethargy, weakness, ataxia, paresis, apparent vision changes, seizure-like activity, and generalized seizures. Similar signs of toxicity have also been reported in humans, in whom voriconazole therapeutic plasma concentration for Aspergillus spp. infections is 2-6 μg/ml. Plasma voriconazole concentrations were measured in 18 samples from penguins showing clinical signs suggestive of voriconazole toxicity. The concentrations ranged from 8.12 to 64.17 μg/ml, with penguins having plasma concentrations above 30 μg/ml exhibiting moderate to severe neurologic signs, including ataxia, paresis, and seizures. These concentrations were well above those known to result in central nervous system toxicity, including encephalopathy, in humans. This case series highlights the importance of species-specific dosing of voriconazole in penguins and plasma therapeutic drug monitoring. Further investigation, including pharmacokinetic studies, is

  20. Selective binding and oligomerization of the murine granulocyte colony-stimulating factor receptor by a low molecular weight, nonpeptidyl ligand.

    Science.gov (United States)

    Doyle, Michael L; Tian, Shin-Shay; Miller, Stephen G; Kessler, Linda; Baker, Audrey E; Brigham-Burke, Michael R; Dillon, Susan B; Duffy, Kevin J; Keenan, Richard M; Lehr, Ruth; Rosen, Jon; Schneeweis, Lumelle A; Trill, John; Young, Peter R; Luengo, Juan I; Lamb, Peter

    2003-03-14

    Granulocyte colony-stimulating factor regulates neutrophil production by binding to a specific receptor, the granulocyte colony-stimulating factor receptor, expressed on cells of the granulocytic lineage. Recombinant forms of granulocyte colony-stimulating factor are used clinically to treat neutropenias. As part of an effort to develop granulocyte colony-stimulating factor mimics with the potential for oral bioavailability, we previously identified a nonpeptidyl small molecule (SB-247464) that selectively activates murine granulocyte colony-stimulating factor signal transduction pathways and promotes neutrophil formation in vivo. To elucidate the mechanism of action of SB-247464, a series of cell-based and biochemical assays were performed. The activity of SB-247464 is strictly dependent on the presence of zinc ions. Titration microcalorimetry experiments using a soluble murine granulocyte colony-stimulating factor receptor construct show that SB-247464 binds to the extracellular domain of the receptor in a zinc ion-dependent manner. Analytical ultracentrifugation studies demonstrate that SB-247464 induces self-association of the N-terminal three-domain fragment in a manner that is consistent with dimerization. SB-247464 induces internalization of granulocyte colony-stimulating factor receptor on intact cells, consistent with a mechanism involving receptor oligomerization. These data show that small nonpeptidyl compounds are capable of selectively binding and inducing productive oligomerization of cytokine receptors.

  1. Structural basis for TatA oligomerization: an NMR study of Escherichia coli TatA dimeric structure.

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    Full Text Available Many proteins are transported across lipid membranes by protein translocation systems in living cells. The twin-arginine transport (Tat system identified in bacteria and plant chloroplasts is a unique system that transports proteins across membranes in their fully-folded states. Up to date, the detailed molecular mechanism of this process remains largely unclear. The Escherichia coli Tat system consists of three essential transmembrane proteins: TatA, TatB and TatC. Among them, TatB and TatC form a tight complex and function in substrate recognition. The major component TatA contains a single transmembrane helix followed by an amphipathic helix, and is suggested to form the translocation pore via self-oligomerization. Since the TatA oligomer has to accommodate substrate proteins of various sizes and shapes, the process of its assembly stands essential for understanding the translocation mechanism. A structure model of TatA oligomer was recently proposed based on NMR and EPR observations, revealing contacts between the transmembrane helices from adjacent subunits. Herein we report the construction and stabilization of a dimeric TatA, as well as the structure determination by solution NMR spectroscopy. In addition to more extensive inter-subunit contacts between the transmembrane helices, we were also able to observe interactions between neighbouring amphipathic helices. The side-by-side packing of the amphipathic helices extends the solvent-exposed hydrophilic surface of the protein, which might be favourable for interactions with substrate proteins. The dimeric TatA structure offers more detailed information of TatA oligomeric interface and provides new insights on Tat translocation mechanism.

  2. Core-6 fucose and the oligomerization of the 1918 pandemic influenza viral neuraminidase

    International Nuclear Information System (INIS)

    Wu, Zhengliang L.; Zhou, Hui; Ethen, Cheryl M.; Reinhold, Vernon N.

    2016-01-01

    The 1918 H1N1 influenza virus was responsible for one of the most deadly pandemics in human history. Yet to date, the structure component responsible for its virulence is still a mystery. In order to search for such a component, the neuraminidase (NA) antigen of the virus was expressed, which led to the discovery of an active form (tetramer) and an inactive form (dimer and monomer) of the protein due to different glycosylation. In this report, the N-glycans from both forms were released and characterized by mass spectrometry. It was found that the glycans from the active form had 26% core-6 fucosylated, while the glycans from the inactive form had 82% core-6 fucosylated. Even more surprisingly, the stalk region of the active form was almost completely devoid of core-6-linked fucose. These findings were further supported by the results obtained from in vitro incorporation of azido fucose and "3H-labeled fucose using core-6 fucosyltransferase, FUT8. In addition, the incorporation of fucose did not change the enzymatic activity of the active form, implying that core-6 fucose is not directly involved in the enzymatic activity. It is postulated that core-6 fucose prohibits the oligomerization and subsequent activation of the enzyme. - Graphical abstract: Proposed mechanism for how core-fucose prohibits the tetramerization of the 1918 pandemic viral neuraminidase. Only the cross section of the stalk region with two N-linked glycans are depicted for clarity. (A) Carbohydrate–carbohydrate interaction on non-fucosylated monomer allows tetramerization. (B) Core-fucosylation disrupts the interaction and prevents the tetramerization. - Highlights: • Expressed 1918 pandemic influenza viral neuraminidase has inactive and active forms. • The inactive form contains high level of core-6 fucose, while the active form lacks such modification. • Core fucose could interfere the oligomerization of the neuraminidase and thus its activation. • This discovery may explain why

  3. Core-6 fucose and the oligomerization of the 1918 pandemic influenza viral neuraminidase

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Zhengliang L., E-mail: Leon.wu@bio-techne.com [Bio-Techne Inc., 614 McKinley Place NE, Minneapolis, MN 55413 (United States); Zhou, Hui [Gregg Hall, UNH Glycomics Center, University of New Hampshire (United States); Ethen, Cheryl M. [Bio-Techne Inc., 614 McKinley Place NE, Minneapolis, MN 55413 (United States); Reinhold, Vernon N., E-mail: Vernon.Reinhold@unh.edu [Gregg Hall, UNH Glycomics Center, University of New Hampshire (United States)

    2016-04-29

    The 1918 H1N1 influenza virus was responsible for one of the most deadly pandemics in human history. Yet to date, the structure component responsible for its virulence is still a mystery. In order to search for such a component, the neuraminidase (NA) antigen of the virus was expressed, which led to the discovery of an active form (tetramer) and an inactive form (dimer and monomer) of the protein due to different glycosylation. In this report, the N-glycans from both forms were released and characterized by mass spectrometry. It was found that the glycans from the active form had 26% core-6 fucosylated, while the glycans from the inactive form had 82% core-6 fucosylated. Even more surprisingly, the stalk region of the active form was almost completely devoid of core-6-linked fucose. These findings were further supported by the results obtained from in vitro incorporation of azido fucose and {sup 3}H-labeled fucose using core-6 fucosyltransferase, FUT8. In addition, the incorporation of fucose did not change the enzymatic activity of the active form, implying that core-6 fucose is not directly involved in the enzymatic activity. It is postulated that core-6 fucose prohibits the oligomerization and subsequent activation of the enzyme. - Graphical abstract: Proposed mechanism for how core-fucose prohibits the tetramerization of the 1918 pandemic viral neuraminidase. Only the cross section of the stalk region with two N-linked glycans are depicted for clarity. (A) Carbohydrate–carbohydrate interaction on non-fucosylated monomer allows tetramerization. (B) Core-fucosylation disrupts the interaction and prevents the tetramerization. - Highlights: • Expressed 1918 pandemic influenza viral neuraminidase has inactive and active forms. • The inactive form contains high level of core-6 fucose, while the active form lacks such modification. • Core fucose could interfere the oligomerization of the neuraminidase and thus its activation. • This discovery may explain

  4. A S52P mutation in the 'α-crystallin domain' of Mycobacterium leprae HSP18 reduces its oligomeric size and chaperone function.

    Science.gov (United States)

    Nandi, Sandip K; Rehna, Elengikal A A; Panda, Alok K; Shiburaj, Sugathan; Dharmalingam, Kuppamuthu; Biswas, Ashis

    2013-12-01

    Mycobacterium leprae HSP18 is a small heat shock protein (sHSP). It is a major immunodominant antigen of M. leprae pathogen. Previously, we have reported the existence of two M. leprae HSP18 variants in various leprotic patients. One of the variants has serine at position 52, whereas the other one has proline at the same position. We have also reported that HSP18 having proline at position 52 (HSP18P(52)) is a nonameric protein and exhibits chaperone function. However, the structural and functional characterization of wild-type HSP18 having serine at position 52 (HSP18S(52)) is yet to be explored. Furthermore, the implications of the S52P mutation on the structure and chaperone function of HSP18 are not well understood. Therefore, we cloned and purified these two HSP18 variants. We found that HSP18S(52) is also a molecular chaperone and an oligomeric protein. Intrinsic tryptophan fluorescence and far-UV CD measurements revealed that the S52P mutation altered the tertiary and secondary structure of HSP18. This point mutation also reduced the oligomeric assembly and decreased the surface hydrophobicity of HSP18, as revealed by HPLC and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid binding studies, respectively. Mutant protein was less stable against thermal and chemical denaturation and was more susceptible towards tryptic cleavage than wild-type HSP18. HSP18P(52) had lower chaperone function and was less effective in protecting thermal killing of Escherichia coli than HSP18S(52). Taken together, our data suggest that serine 52 is important for the larger oligomerization and chaperone function of HSP18. Because both variants differ in stability and function, they may have different roles in the survival of M. leprae in infected hosts. © 2013 FEBS.

  5. A New Star-shaped Carbazole Derivative with Polyhedral Oligomeric Silsesquioxane Core: Crystal Structure and Unique Photoluminescence Property.

    Science.gov (United States)

    Xu, Zixuan; Yu, Tianzhi; Zhao, Yuling; Zhang, Hui; Zhao, Guoyun; Li, Jianfeng; Chai, Lanqin

    2016-01-01

    A new inorganic–organic hybrid material based on polyhedral oligomeric silsesquioxane (POSS) capped with carbazolyl substituents, octakis[3-(carbazol-9-yl)propyldimethylsiloxy]-silsesquioxane (POSS-8Cz), was successfully synthesized and characterized. The X-ray crystal structure of POSS-8Cz were described. The photophysical properties of POSS-8Cz were investigated by using UV–vis,photoluminescence spectroscopic analysis. The hybrid material exhibits blue emission in the solution and the solid film.The morphology and thermal stablity properties were measured by X-ray diffraction (XRD) and TG-DTA analysis.

  6. Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

    Science.gov (United States)

    Salzberg, Steven L; Dunning Hotopp, Julie C; Delcher, Arthur L; Pop, Mihai; Smith, Douglas R; Eisen, Michael B; Nelson, William C

    2005-01-01

    The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.

  7. Forward selection for multiple resistance across the non-selective glyphosate, glufosinate and oxyfluorfen herbicides in Lolium weed species.

    Science.gov (United States)

    Fernández, Pablo; Alcántara, Ricardo; Osuna, María D; Vila-Aiub, Martin M; Prado, Rafael De

    2017-05-01

    In the Mediterranean area, Lolium species have evolved resistance to glyphosate after decades of continual use without other alternative chemicals in perennial crops (olive, citrus and vineyards). In recent years, oxyfluorfen alone or mixed with glyphosate and glufosinate has been introduced as a chemical option to control dicot and grass weeds. Dose-response studies confirmed that three glyphosate-resistant Lolium weed species (L. rigidum, L. perenne, L. multiflorum) collected from perennial crops in the Iberian Peninsula have also evolved resistance to glufosinate and oxyfluorfen herbicides, despite their recent introduction. Based on the LD 50 resistance parameter, the resistance factor was similar among Lolium species and ranged from 14- to 21-fold and from ten- to 12-fold for oxyfluorfen and glufosinate respectively. Similarly, about 14-fold resistance to both oxyfluorfen and glufosinate was estimated on average for the three Lolium species when growth reduction (GR 50 ) was assessed. This study identified oxyfluorfen resistance in a grass species for the first time. A major threat to sustainability of perennial crops in the Iberian Peninsula is evident, as multiple resistance to non-selective glyphosate, glufosinate and oxyfluorfen herbicides has evolved in L. rigidum, L. perenne and L. multiflorum weeds. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  8. Genetic diversity and differentiation patterns in Micromeria from the Canary Islands are congruent with multiple colonization dynamics and the establishment of species syngameons.

    Science.gov (United States)

    Curto, M; Puppo, P; Kratschmer, S; Meimberg, H

    2017-08-22

    Especially on islands closer to the mainland, such as the Canary Islands, different lineages that originated by multiple colonization events could have merged by hybridization, which then could have promoted radiation events (Herben et al., J Ecol 93: 572-575, 2005; Saunders and Gibson, J Ecol 93: 649-652, 2005; Caujapé-Castells, Jesters, red queens, boomerangs and surfers: a molecular outlook on the diversity of the Canarian endemic flora, 2011). This is an alternative to the scenario where evolution is mostly driven by drift (Silvertown, J Ecol 92: 168-173, 2004; Silvertown et al., J Ecol 93: 653-657, 2005). In the former case hybridization should be reflected in the genetic structure and diversity patterns of island species. In the present work we investigate Micromeria from the Canary Islands by extensively studying their phylogeographic pattern based on 15 microsatellite loci and 945 samples. These results are interpreted according to the hypotheses outlined above. Genetic structure assessment allowed us to genetically differentiate most Micromeria species and supported their current classification. We found that populations on younger islands were significantly more genetically diverse and less differentiated than those on older islands. Moreover, we found that genetic distance on younger islands was in accordance with an isolation-by-distance pattern, while on the older islands this was not the case. We also found evidence of introgression among species and islands. These results are congruent with a scenario of multiple colonizations during the expansion onto new islands. Hybridization contributes to the grouping of multiple lineages into highly diverse populations. Thus, in our case, islands receive several colonization events from different sources, which are combined into sink populations. This mechanism is in accordance with the surfing syngameon hypothesis. Contrary to the surfing syngameon current form, our results may reflect a slightly different

  9. Hydrolyzable Tannins of Tamaricaceous Plants. 7.1 Structures and Cytotoxic Properties of Oligomeric Ellagitannins from Leaves of Tamarix nilotica and Cultured Tissues of Tamarix tetrandra.

    Science.gov (United States)

    Orabi, Mohamed A A; Taniguchi, Shoko; Sakagami, Hiroshi; Yoshimura, Morio; Amakura, Yoshiaki; Hatano, Tsutomu

    2016-04-22

    Partially unacylated new oligomeric hydrolyzable tannins, nilotinin T2 (1, trimer) and nilotinin Q1 (2, tetramer), together with four known trimers, nilotinin T1 (3) and hirtellins T1-T3 (4-6), and a dimer, tamarixinin B (7), were isolated from the aqueous acetone extracts of leaves of Tamarix nilotica. Among them, the new trimer 1 and the known trimers 4 and 6, in addition to the partially unacylated new trimer nilotinin T3 (8), the known dimers nilotinin D3 (9) and tamarixinin C (10), and the monomer tellimagrandin I (11), were isolated from the cultured shoots of Tamarix tetrandra. The structures of the new hydrolyzable tannins were established by chromatographic analyses and extensive 1D and 2D NMR, HRESI-TOFMS, and ECD spectroscopic experiments. Among the new oligomeric tannins, the particular unacylated position of a glucose core is attributed to a possible biosynthetic route. Isolation of the same oligomeric tannins from cultured shoots of T. tetrandra emphasizes the unique biogenetic ability of the obtained cultures on production of the structurally and biologically characteristic tamaricaceous tannins commonly produced by the intact Tamarix plants. Additionally, tannins obtained in the present study together with gemin D (12) and 1,3-di-O-galloyl-4,6-O-(aS)-hexahydroxydiphenoyl-β-d-glucose (13), from our previous investigation of the leaves of T. nilotica, exhibited variable tumor-specific cytotoxic effects. The ellagitannin trimers 4, 6, and 8 and the dimer 9 exerted predominant tumor-selective cytotoxic effects with high specificity toward human promyelocytic leukemia cells.

  10. Oligomeric recombinant H5 HA1 vaccine produced in bacteria protects ferrets from homologous and heterologous wild-type H5N1 influenza challenge and controls viral loads better than subunit H5N1 vaccine by eliciting high-affinity antibodies.

    Science.gov (United States)

    Verma, Swati; Dimitrova, Milena; Munjal, Ashok; Fontana, Juan; Crevar, Corey J; Carter, Donald M; Ross, Ted M; Khurana, Surender; Golding, Hana

    2012-11-01

    Recombinant hemagglutinin from influenza viruses with pandemic potential can be produced rapidly in various cell substrates. In this study, we compared the functionality and immunogenicity of bacterially produced oligomeric or monomeric HA1 proteins from H5N1 (A/Vietnam/1203/04) with those of the egg-based licensed subunit H5N1 (SU-H5N1) vaccine in ferrets challenged with homologous or heterologous H5N1 highly pathogenic influenza strains. Ferrets were vaccinated twice with the oligomeric or monomeric rHA1 or with SU-H5N1 (Sanofi Pasteur) emulsified with Titermax adjuvant and were challenged with wild-type homologous (A/Vietnam/1203/04; clade 1) or heterologous (A/Whooperswan/Mongolia/244/2005; clade 2.2) virus. Only the oligomeric rHA1 (not the monomeric rHA1) immunogen and the SU-H5N1 vaccine provided protection against the lethality and morbidity of homologous and heterologous highly pathogenic H5N1. Oligomeric rHA1 generated more cross-neutralizing antibodies and higher levels of serum antibody binding to HA1, with stronger avidity and a better IgG/IgM ratio, than monomeric HA1 and SU-H5N1 vaccines, as determined by surface plasmon resonance (SPR). Importantly, viral loads after heterologous H5N1 challenge were more efficiently controlled in ferrets vaccinated with the oligomeric rHA1 immunogen than in SU-H5N1-vaccinated ferrets. The reduction of viral loads in the nasal washes correlated strongly with higher-avidity antibodies to oligomeric rHA1 derived from H5N1 clade 1 and clade 2.2 viruses, as measured by SPR. This is the first study to show the role of antibody avidity for the HA1 globular head domain in reduction of viral loads in the upper respiratory tract, which could significantly reduce viral transmission.

  11. Diverse oligomeric states of CEACAM IgV domains.

    Science.gov (United States)

    Bonsor, Daniel A; Günther, Sebastian; Beadenkopf, Robert; Beckett, Dorothy; Sundberg, Eric J

    2015-11-03

    Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) comprise a large family of cell surface adhesion molecules that bind to themselves and other family members to carry out numerous cellular functions, including proliferation, signaling, differentiation, tumor suppression, and survival. They also play diverse and significant roles in immunity and infection. The formation of CEACAM oligomers is caused predominantly by interactions between their N-terminal IgV domains. Although X-ray crystal structures of CEACAM IgV domain homodimers have been described, how CEACAMs form heterodimers or remain monomers is poorly understood. To address this key aspect of CEACAM function, we determined the crystal structures of IgV domains that form a homodimeric CEACAM6 complex, monomeric CEACAM8, and a heterodimeric CEACAM6-CEACAM8 complex. To confirm and quantify these interactions in solution, we used analytical ultracentrifugation to measure the dimerization constants of CEACAM homodimers and isothermal titration calorimetry to determine the thermodynamic parameters and binding affinities of CEACAM heterodimers. We found the CEACAM6-CEACAM8 heterodimeric state to be substantially favored energetically relative to the CEACAM6 homodimer. Our data provide a molecular basis for the adoption of the diverse oligomeric states known to exist for CEACAMs and suggest ways in which CEACAM6 and CEACAM8 regulate the biological functions of one another, as well as of additional CEACAMs with which they interact, both in cis and in trans.

  12. Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

    Directory of Open Access Journals (Sweden)

    Jörger Katharina M

    2012-12-01

    Full Text Available Abstract Background Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic and the success rate has never been explored on mesopsammic Mollusca. Results We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH. In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC, statistical parsimony, Bayesian Species Delineation (BPP and Automatic Barcode Gap Discovery (ABGD. The secondary species hypothesis (SSH is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’, resulting in the discovery of a radiation of (at least 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions. Conclusions Our study confirms extensive, morphologically

  13. Protective Effects of Testosterone on Presynaptic Terminals against Oligomeric β-Amyloid Peptide in Primary Culture of Hippocampal Neurons

    Directory of Open Access Journals (Sweden)

    Chi-Fai Lau

    2014-01-01

    Full Text Available Increasing lines of evidence support that testosterone may have neuroprotective effects. While observational studies reported an association between higher bioavailable testosterone or brain testosterone levels and reduced risk of Alzheimer’s disease (AD, there is limited understanding of the underlying neuroprotective mechanisms. Previous studies demonstrated that testosterone could alleviate neurotoxicity induced by β-amyloid (Aβ, but these findings mainly focused on neuronal apoptosis. Since synaptic dysfunction and degeneration are early events during the pathogenesis of AD, we aim to investigate the effects of testosterone on oligomeric Aβ-induced synaptic changes. Our data suggested that exposure of primary cultured hippocampal neurons to oligomeric Aβ could reduce the length of neurites and decrease the expression of presynaptic proteins including synaptophysin, synaptotagmin, and synapsin-1. Aβ also disrupted synaptic vesicle recycling and protein folding machinery. Testosterone preserved the integrity of neurites and the expression of presynaptic proteins. It also attenuated Aβ-induced impairment of synaptic exocytosis. By using letrozole as an aromatase antagonist, we further demonstrated that the effects of testosterone on exocytosis were unlikely to be mediated through the estrogen receptor pathway. Furthermore, we showed that testosterone could attenuate Aβ-induced reduction of HSP70, which suggests a novel mechanism that links testosterone and its protective function on Aβ-induced synaptic damage. Taken together, our data provide further evidence on the beneficial effects of testosterone, which may be useful for future drug development for AD.

  14. Formation of semisolid, oligomerized aqueous SOA: lab simulations of cloud processing.

    Science.gov (United States)

    Hawkins, Lelia N; Baril, Molly J; Sedehi, Nahzaneen; Galloway, Melissa M; De Haan, David O; Schill, Gregory P; Tolbert, Margaret A

    2014-02-18

    Glyoxal, methylglyoxal, glycolaldehyde, and hydroxyacetone form N-containing and oligomeric compounds during simulated cloud processing with small amines. Using a novel hygroscopicity tandem differential mobility analysis (HTDMA) system that allows varied humidification times, the hygroscopic growth (HG) of each of the resulting products of simulated cloud processing was measured. Continuous water uptake (gradual deliquescence) was observed beginning at ∼ 40% RH for all aldehyde-methylamine products. Particles containing ionic reaction products of either glyoxal or glycine were most hygroscopic, with HG between 1.16 and 1.20 at 80% RH. Longer humidification times (up to 20 min) produced an increase in growth factors for glyoxal-methylamine (19% by vol) and methylglyoxal-methylamine (8% by vol) aerosol, indicating that unusually long equilibration times can be required for HTDMA measurements of such particles. Glyoxal- and methylglyoxal-methylamine aerosol particles shattered in Raman microscopy impact-flow experiments, revealing that the particles were semisolid. Similar experiments on glycolaldehyde- and hydroxyacetone-methylamine aerosol found that the aerosol particles were liquid when dried for glyoxal > glycolaldehyde = hydroxyacetone, likely caused by the speed of oligomer formation in each system.

  15. Brain propagation of transduced α-synuclein involves non-fibrillar protein species and is enhanced in α-synuclein null mice.

    Science.gov (United States)

    Helwig, Michael; Klinkenberg, Michael; Rusconi, Raffaella; Musgrove, Ruth E; Majbour, Nour K; El-Agnaf, Omar M A; Ulusoy, Ayse; Di Monte, Donato A

    2016-03-01

    Aggregation and neuron-to-neuron transmission are attributes of α-synuclein relevant to its pathogenetic role in human synucleinopathies such as Parkinson's disease. Intraparenchymal injections of fibrillar α-synuclein trigger widespread propagation of amyloidogenic protein species via mechanisms that require expression of endogenous α-synuclein and, possibly, its structural corruption by misfolded conformers acting as pathological seeds. Here we describe another paradigm of long-distance brain diffusion of α-synuclein that involves inter-neuronal transfer of monomeric and/or oligomeric species and is independent of recruitment of the endogenous protein. Targeted expression of human α-synuclein was induced in the mouse medulla oblongata through an injection of viral vectors into the vagus nerve. Enhanced levels of intra-neuronal α-synuclein were sufficient to initiate its caudo-rostral diffusion that likely involved at least one synaptic transfer and progressively reached specific brain regions such as the locus coeruleus, dorsal raphae and amygdala in the pons, midbrain and forebrain. Transfer of human α-synuclein was compared in two separate lines of α-synuclein-deficient mice versus their respective wild-type controls and, interestingly, lack of endogenous α-synuclein expression did not counteract diffusion but actually resulted in a more pronounced and advanced propagation of exogenous α-synuclein. Self-interaction of adjacent molecules of human α-synuclein was detected in both wild-type and mutant mice. In the former, interaction of human α-synuclein with mouse α-synuclein was also observed and might have contributed to differences in protein transmission. In wild-type and α-synuclein-deficient mice, accumulation of human α-synuclein within recipient axons in the pons, midbrain and forebrain caused morphological evidence of neuritic pathology. Tissue sections from the medulla oblongata and pons were stained with different antibodies recognizing

  16. Assembly of the intrinsic factor domains and oligomerization of the protein in the presence of cobalamin

    DEFF Research Database (Denmark)

    Fedosov, Sergey N; Fedosova, Natalya U; Berglund, Lars

    2004-01-01

    oligomerized. A mixture of two fragments IF(30) + IF(20) and Cbl produced a firm complex, IF(30+20).Cbl, which could not associate to dimers. In contrast to IF(30+20).Cbl, the saturated full-length monomers IF(50).Cbl dimerized with K(d) approximately 1 microM. We suggest a two-domain organization of the full......-length protein, where two distant units, IF(30) and IF(20), can be assembled only by Cbl. They are connected by a protease-sensitive link, whose native structure is likely to be important for dimerization. However, linkage between two domains is not compulsory for Cbl binding. Advantages of the two...

  17. Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain

    International Nuclear Information System (INIS)

    Meinke, Gretchen; Phelan, Paul; Fradet-Turcotte, Amélie; Archambault, Jacques; Bullock, Peter A.

    2011-01-01

    With the aim of forming the ‘lock-washer’ conformation of the origin-binding domain of SV40 large T antigen in solution, using structure-based analysis an intermolecular disulfide bridge was engineered into the origin-binding domain to generate higher order oligomers in solution. The 1.7 Å resolution structure shows that the mutant forms a spiral in the crystal and has the de novo disulfide bond at the protein interface, although structural rearrangements at the interface are observed relative to the wild type. The modular multifunctional protein large T antigen (T-ag) from simian virus 40 orchestrates many of the events needed for replication of the viral double-stranded DNA genome. This protein assembles into single and double hexamers on specific DNA sequences located at the origin of replication. This complicated process begins when the origin-binding domain of large T antigen (T-ag ODB) binds the GAGGC sequences in the central region (site II) of the viral origin of replication. While many of the functions of purified T-ag OBD can be studied in isolation, it is primarily monomeric in solution and cannot assemble into hexamers. To overcome this limitation, the possibility of engineering intermolecular disulfide bonds in the origin-binding domain which could oligomerize in solution was investigated. A recent crystal structure of the wild-type T-ag OBD showed that this domain forms a left-handed spiral in the crystal with six subunits per turn. Therefore, we analyzed the protein interface of this structure and identified two residues that could potentially support an intermolecular disulfide bond if changed to cysteines. SDS–PAGE analysis established that the mutant T-ag OBD formed higher oligomeric products in a redox-dependent manner. In addition, the 1.7 Å resolution crystal structure of the engineered disulfide-linked T-ag OBD is reported, which establishes that oligomerization took place in the expected manner

  18. High prevalence of co-infection with multiple Torque teno sus virus species in Italian pig herds.

    Directory of Open Access Journals (Sweden)

    Sylvain Blois

    Full Text Available Torque teno viruses (TTVs are a large group of vertebrate-infecting small viruses with circular single-stranded DNA, classified in the Anelloviridae family. In swine, two genetically distinct species, Torque teno sus virus 1a (TTSuV1a and 1b (TTSuV1b are currently grouped into the genus Iotatorquevirus. More recently, a novel Torque teno sus virus species, named Torque teno sus virus k2b (TTSuVk2b, has been included with Torque teno sus virus k2a (TTSuVk2a into the genus Kappatorquevirus. In the present study, TTSuV1 (TTSuV1a and TTSuV1b, TTSuVk2a and TTSuVk2b prevalence was evaluated in 721 serum samples of healthy pigs from Sardinian farms, insular Italy. This is the largest study to date on the presence of TTSuV in healthy pigs in Italy. The global prevalence of infection was 83.2% (600/721, being 62.3% (449/721, 60.6% (437/721, and 11.5% (83/721 the prevalence of TTSuV1, TTSuVk2a and TTSuVk2b, respectively. The rate of co-infection with two and/or three species was also calculated, and data show that co-infections were significantly more frequent than infections with single species, and that TTSuV1+TTSuVk2a double infection was the prevalent combination (35.4%. Quantitative results obtained using species-specific real time-qPCR evidenced the highest mean levels of viremia in the TTSuV1 subgroup, and the lowest in the TTSuVk2b subgroup. Interestingly, multiple infections with distinct TTSuV species seemed to significantly affect the DNA load and specifically, data highlighted that double infection with TTSuVk2a increased the viral titers of TTSuV1, likewise the co-infection with TTSuVk2b increased the titers of TTSuVk2a.

  19. High prevalence of co-infection with multiple Torque teno sus virus species in Italian pig herds.

    Science.gov (United States)

    Blois, Sylvain; Mallus, Francesca; Liciardi, Manuele; Pilo, Cristian; Camboni, Tania; Macera, Lisa; Maggi, Fabrizio; Manzin, Aldo

    2014-01-01

    Torque teno viruses (TTVs) are a large group of vertebrate-infecting small viruses with circular single-stranded DNA, classified in the Anelloviridae family. In swine, two genetically distinct species, Torque teno sus virus 1a (TTSuV1a) and 1b (TTSuV1b) are currently grouped into the genus Iotatorquevirus. More recently, a novel Torque teno sus virus species, named Torque teno sus virus k2b (TTSuVk2b), has been included with Torque teno sus virus k2a (TTSuVk2a) into the genus Kappatorquevirus. In the present study, TTSuV1 (TTSuV1a and TTSuV1b), TTSuVk2a and TTSuVk2b prevalence was evaluated in 721 serum samples of healthy pigs from Sardinian farms, insular Italy. This is the largest study to date on the presence of TTSuV in healthy pigs in Italy. The global prevalence of infection was 83.2% (600/721), being 62.3% (449/721), 60.6% (437/721), and 11.5% (83/721) the prevalence of TTSuV1, TTSuVk2a and TTSuVk2b, respectively. The rate of co-infection with two and/or three species was also calculated, and data show that co-infections were significantly more frequent than infections with single species, and that TTSuV1+TTSuVk2a double infection was the prevalent combination (35.4%). Quantitative results obtained using species-specific real time-qPCR evidenced the highest mean levels of viremia in the TTSuV1 subgroup, and the lowest in the TTSuVk2b subgroup. Interestingly, multiple infections with distinct TTSuV species seemed to significantly affect the DNA load and specifically, data highlighted that double infection with TTSuVk2a increased the viral titers of TTSuV1, likewise the co-infection with TTSuVk2b increased the titers of TTSuVk2a.

  20. Changes in the oligomerization potential of the division inhibitor UgtP co-ordinate Bacillus subtilis cell size with nutrient availability.

    Science.gov (United States)

    Chien, An-Chun; Zareh, Shannon Kian Gharabiklou; Wang, Yan Mei; Levin, Petra Anne

    2012-11-01

    How cells co-ordinate size with growth and development is a major, unresolved question in cell biology. In previous work we identified the glucosyltransferase UgtP as a division inhibitor responsible for increasing the size of Bacillus subtilis cells under nutrient-rich conditions. In nutrient-rich medium, UgtP is distributed more or less uniformly throughout the cytoplasm and concentrated at the cell poles and/or the cytokinetic ring. Under these conditions, UgtP interacts directly with FtsZ to inhibit division and increase cell size. Conversely, under nutrient-poor conditions, UgtP is sequestered away from FtsZ in punctate foci, and division proceeds unimpeded resulting in a reduction in average cell size. Here we report that nutrient-dependent changes in UgtP's oligomerization potential serve as a molecular rheostat to precisely co-ordinate B. subtilis cell size with nutrient availability. Our data indicate UgtP interacts with itself and the essential cell division protein FtsZ in a high-affinity manner influenced in part by UDP glucose, an intracellular proxy for nutrient availability. These findings support a model in which UDP-glc-dependent changes in UgtP's oligomerization potential shift the equilibrium between UgtP•UgtP and UgtP•FtsZ, fine-tuning the amount of FtsZ available for assembly into the cytokinetic ring and with it cell size. © 2012 Blackwell Publishing Ltd.

  1. Assessment of Escherichia coli selenophosphate synthetase oligomeric states by analytical ultracentrifugation and small angle X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Silva, I.R.; Faim, F.M.; Oliveira Neto, M.; Thiemann, O.H. [Universidade de Sao Paulo (USP-SC), Sao Carlos, SP (Brazil); Borges, J.C. [Universidade de Sao Paulo (IQSC/USP), Sao Carlos, SP (Brazil). Inst. de Quimica

    2012-07-01

    Full text: Selenium is an essential micronutrient for many organisms and is present in selenium-containing proteins as selenocysteine (Sec) and RNAs as selenouridine. Specific selenium incorporation into selenoproteins and RNAs requires the generation of a biologically active selenium donor compound, selenophosphate, which is produced from the activation of selenide with adenosine 5-triphosphate (ATP) in a reaction catalyzed by Selenophosphate Synthetase (SELD). Therefore, SELD is a key enzyme of the selenium pathway in the cell. The Escherichia coli SELD open reading frame was cloned into pET28a (Novagen) expression vector and the recombinant protein was over expressed in Escherichia coli BL21(DE3) strain. In order to purify the protein, we used metal-chelate affinity chromatography followed by a gel filtration step. Analytical Ultracentrifugation (AUC) and Small Angle X-ray Scattering (SAXS) were employed to study the oligomeric states of the soluble protein. The results of AUC revealed dimer-tetramer and tetramer-octamer equilibrium at low concentrations of protein, with dissociation constants of 70 2 and 560 40 M, respectively. Moreover, the SAXS results pointed the oligomeric state of the protein at higher concentrations as predominantly dimeric and the p(r) and the SAXS envelope revealed the SELD as elongated. We also performed initial crystallization trials with protein samples at 7 mg/ml in 96-well sitting-drop crystallization plates at room temperature using a crystallization robot. Needle crystals appeared after some days. X-ray diffraction for these crystals were tested in the MX2 beamline at the Brazilian Synchrotron Laboratory (LNLS Campinas). We are now working to improve these crystals in order to obtain suitable crystals for structure determination. (author)

  2. IntraGolgi distribution of the Conserved Oligomeric Golgi (COG) complex

    International Nuclear Information System (INIS)

    Vasile, Eliza; Oka, Toshihiko; Ericsson, Maria; Nakamura, Nobuhiro; Krieger, Monty

    2006-01-01

    The Conserved Oligomeric Golgi (COG) complex is an eight-subunit (Cog1-8) peripheral Golgi protein involved in membrane trafficking and glycoconjugate synthesis. COG appears to participate in retrograde vesicular transport and is required to maintain normal Golgi structure and function. COG mutations interfere with normal transport, distribution, and/or stability of Golgi proteins associated with glycoconjugate synthesis and trafficking, and lead to failure of spermatogenesis in Drosophila melanogaster, misdirected migration of gonadal distal tip cells in Caenorhabditis elegans, and type II congenital disorders of glycosylation in humans. The mechanism by which COG influences Golgi structure and function is unclear. Immunogold electron microscopy was used to visualize the intraGolgi distribution of a functional, hemagglutinin epitope-labeled COG subunit, Cog1-HA, that complements the Cog1-deficiency in Cog1-null Chinese hamster ovary cells. COG was found to be localized primarily on or in close proximity to the tips and rims of the Golgi's cisternae and their associated vesicles and on vesicles and vesiculo-tubular structures seen on both the cis and trans-Golgi Network faces of the cisternal stacks, in some cases on COPI containing vesicles. These findings support the proposal that COG is directly involved in controlling vesicular retrograde transport of Golgi resident proteins throughout the Golgi apparatus

  3. Diversified Native Species Restoration for Recovery of Multiple Ecosystem Services in a Highly Disturbed Tropical Dry Forest Landscape of Southwestern Nicaragua

    Science.gov (United States)

    Williams-Guillen, K.; Otterstrom, S.; Perla, C.

    2015-12-01

    Tropical dry forests have been reduced to a fraction of their original extent in the Neotropics due to conversion to agriculture and cattle pasture. While TDF can recover via natural regeneration, resulting forests are dominated by wind-dispersed pioneer species of limited value for frugivorous wildlife. Additionally, passive restoration can be perceived as "abandonment" resulting in neighbors casually invading property to rear livestock and extract timber. In 2007, the NGO Paso Pacífico initiated restoration in a highly degraded tropical dry forest landscape of southwestern Nicaragua; funded by an ex-ante carbon purchase, the project was designed to integrate multiple native tree species known to provide resources used by local wildlife. We restored roughly 400 hectares spanning a rainfall gradient from dry to transitional moist forest, using reforestation (planting 70 species of tree seedlings in degraded pastures on a 4x4 m grid, leaving occurring saplings) and assisted regeneration (clearing vines and competing vegetation from saplings in natural regeneration and strategically managing canopy cover). In just over seven years, mean carbon increased nearly threefold, from to 21.5±5.0 to 57.9±9.6 SE tonnes/ha. Current carbon stocks match those of 20-year-old forests in the area, accumulated in less than a decade. Stem density per 15-m radius plot decreased from 16.3±2.3 to 12.5±0.9 SE, while species richness increased from 3.9±0.4 to 18.4±1.4 SE. Alpha richness of woody stems across plots increased from 36 to 94 species, and over 20 tree species established as a result of natural dispersal and recruitment. We have observed sensitive species such as spider monkeys and parrots foraging in restoration areas. Managed reforestation is a highly effective method for rapidly restoring the functionality of multiple ecosystem services in degraded TDF, particularly when social and political realities force restoration to coexist with human productive activities

  4. Effects of Bentonite on p-Methoxybenzyl Acetate: A Theoretical Model for Oligomerization via an Electrophilic-Substitution Mechanism

    Directory of Open Access Journals (Sweden)

    Manuel Salmón

    2011-02-01

    Full Text Available Tonsil Actisil FF, a commercial bentonitic clay, promotes the formation of a series of electrophilic-aromatic-substitution products from para-methoxybenzyl acetate in carbon disulfide. The molecules obtained correspond to linear isomeric dimers, trimers, tetramers and a pentamer, according to their spectroscopic data. A clear indication of the title mechanistic pathway for the oligomerization growth was obtained from the analysis of a set of computational-chemistry calculations using the density-functional-theory level B3LYP/6-311++G(d,p. The corresponding conclusions were based on the computed dipole moments, the HOMO/LUMO distributions, and a natural-populations analysis of the studied molecules.

  5. The long N-terminus of the human monocarboxylate transporter 8 is a target of ubiquitin-dependent proteasomal degradation which regulates protein expression and oligomerization capacity.

    Science.gov (United States)

    Zwanziger, Denise; Schmidt, Mathias; Fischer, Jana; Kleinau, Gunnar; Braun, Doreen; Schweizer, Ulrich; Moeller, Lars Christian; Biebermann, Heike; Fuehrer, Dagmar

    2016-10-15

    Monocarboxylate transporter 8 (MCT8) equilibrates thyroid hormones between the extra- and the intracellular sides. MCT8 exists either with a short or a long N-terminus, but potential functional differences between both variants are yet not known. We, therefore, generated MCT8 constructs which are different in N-terminal length: MCT8(1-613), MCT8(25-613), MCT8(49-613) and MCT8(75-613). The M75G substitution prevents translation of MCT8(75-613) and ensures expression of full-length MCT8 protein. The K56G substitution was made to prevent ubiquitinylation. Cell-surface expression, localization and proteasomal degradation were investigated using C-terminally GFP-tagged MCT8 constructs (HEK293 and MDCK1 cells) and oligomerization capacity was determined using N-terminally HA- and C-terminally FLAG-tagged MCT8 constructs (COS7 cells). MCT8(1-613)-GFP showed a lower protein expression than the shorter MCT8(75-613)-GFP protein. The proteasome inhibitor lactacystin increased MCT8(1-613)-GFP protein amount, suggesting proteasomal degradation of MCT8 with the long N-terminus. Ubiquitin conjugation of MCT8(1-613)-GFP was found by immuno-precipitation. A diminished ubiquitin conjugation caused by K56G substitution resulted in increased MCT8(1-613)-GFP protein expression. Sandwich ELISA was performed to investigate if the bands at higher molecular weight observed in Western blot analysis are due to MCT8 oligomerization, which was indeed shown. Our data imply a role of the long N-terminus of MCT8 as target of ubiquitin-dependent proteasomal degradation affecting MCT8 amount and subsequently oligomerization capacity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Transparent cellulose/polyhedral oligomeric silsesquioxane nanocomposites with enhanced UV-shielding properties.

    Science.gov (United States)

    Feng, Ye; Zhang, Jinming; He, Jiasong; Zhang, Jun

    2016-08-20

    The solubility of eight types of polyhedral oligomeric silsesquioxane (POSS) derivatives in an ionic liquid 1-allyl-3-methylimidazolium chloride (AmimCl) and the dispersion of POSS in cellulose matrix were examined. Only a special POSS containing both aminophenyl and nitrophenyl groups (POSS-AN, NH2:NO2=2:6) was selected to prepare nanocomposites, because of its good solubility in AmimCl and high stability during the preparation process. POSS-AN nanoparticles were uniformly dispersed in a cellulose matrix with a size of 30-40nm, and so the resultant cellulose/POSS-AN nanocomposite films were transparent. The mechanical properties of the films achieved a maximum tensile strength of 190MPa after addition of 2wt% POSS-AN. Interestingly, all of the cellulose/POSS-AN films exhibited high UV-absorbing capability. For the 15wt% cellulose/POSS-AN film, the transmittance of UVA (315-400nm) and UVB (280-315nm) was only 9.1% and nearly 0, respectively. The UV aging and shielding experiments showed that the transparent cellulose/POSS-AN nanocomposite films possessed anti-UV aging and UV shielding properties. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. In-situ photocrosslinkable nanohybrid elastomer based on polybutadiene/polyhedral oligomeric silsesquioxane

    Energy Technology Data Exchange (ETDEWEB)

    Mirmohammadi, Seyed Amin, E-mail: mirmohammadi.sa@gmail.com [Department of Polymerization Engineering, Iran Polymer and Petrochemical Institute (IPPI), P. O. Box: 14965/115, Tehran (Iran, Islamic Republic of); Nekoomanesh-Haghighi, Mehdi, E-mail: m.nekoomanesh@ippi.ac.ir [Department of Polymerization Engineering, Iran Polymer and Petrochemical Institute (IPPI), P. O. Box: 14965/115, Tehran (Iran, Islamic Republic of); Mohammadian Gezaz, Somayyeh [Department of Chemical Engineering, Payame Noor University (PNU), P. O. Box: 19395-3697, Tehran (Iran, Islamic Republic of); Bahri-Laleh, Naeimeh [Department of Polymerization Engineering, Iran Polymer and Petrochemical Institute (IPPI), P. O. Box: 14965/115, Tehran (Iran, Islamic Republic of); Atai, Mohammad [Department of Polymer Science, Iran Polymer and Petrochemical Institute (IPPI), P. O. Box: 14965/115, Tehran (Iran, Islamic Republic of)

    2016-11-01

    Hydroxyl functionalized nano-sized POSS or ethyleneglycol as diol monomers was incorporated to hydroxyl-terminated polybutadiene (HTPBD) chain in the presence of fumaryl chloride as extender. Blue light photocrosslinking system based on camphorquinone (photoinitiator) and dimethylaminoethyl methacrylate (accelerator) was applied to cure these two synthesized fumarate based macromers. Self-crosslinkability of unsaturated macromers and also crosslinking in presence of a reactive diluent were investigated in absence and presence of 1,4-butanediol dimethacrylate, respectively. Finally, photocured samples were characterized by XRD, SEM, equilibrium swelling study, TGA, DMTA, AFM and cell culture. The results showed that incorporation of POSS nanoparticle into the polymer matrix with a perfect distribution and dispersion can enhance thermal stability, mechanical and biocompatibility properties which can prove a good potential of this in-situ photocrosslinkable nanohybrid in medical applications. - Highlights: • Polyhedral oligomeric silsesquioxane was incorporated to HTPBD by fumaryl chloride as extender. • A reactive diluent was used to improve photocrosslinking process of the unsaturated nanohybrid elastomers. • Nanohybrids showed enhanced properties such as thermal stability, mechanical and biocompatibility. • Improved properties were obtained for photocured samples in presence of reactive diluent.

  8. Eicosanoyl-5-hydroxytryptamide (EHT prevents Alzheimer's disease-related cognitive and electrophysiological impairments in mice exposed to elevated concentrations of oligomeric beta-amyloid.

    Directory of Open Access Journals (Sweden)

    Kesava Asam

    Full Text Available Soluble forms of oligomeric beta-amyloid (Aβ are thought to play a central role in Alzheimer's disease (AD. Transgenic manipulation of methylation of the serine/threonine protein phosphatase, PP2A, was recently shown to alter the sensitivity of mice to AD-related impairments resulting from acute exposure to elevated levels of Aβ. In addition, eicosanoyl-5-hydroxytryptamide (EHT, a naturally occurring component from coffee beans that modulates PP2A methylation, was shown to confer therapeutic benefits in rodent models of AD and Parkinson's disease. Here, we tested the hypothesis that EHT protects animals from the pathological effects of exposure to elevated levels of soluble oligomeric Aβ. We treated mice with EHT-containing food at two different doses and assessed the sensitivity of these animals to Aβ-induced behavioral and electrophysiological impairments. We found that EHT administration protected animals from Aβ-induced cognitive impairments in both a radial-arm water maze and contextual fear conditioning task. We also found that both chronic and acute EHT administration prevented Aβ-induced impairments in long-term potentiation. These data add to the accumulating evidence suggesting that interventions with pharmacological agents, such as EHT, that target PP2A activity may be therapeutically beneficial for AD and other neurological conditions.

  9. Cyclic GMP-AMP synthase is activated by double-stranded DNA-induced oligomerization.

    Science.gov (United States)

    Li, Xin; Shu, Chang; Yi, Guanghui; Chaton, Catherine T; Shelton, Catherine L; Diao, Jiasheng; Zuo, Xiaobing; Kao, C Cheng; Herr, Andrew B; Li, Pingwei

    2013-12-12

    Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor mediating innate antimicrobial immunity. It catalyzes the synthesis of a noncanonical cyclic dinucleotide, 2',5' cGAMP, that binds to STING and mediates the activation of TBK1 and IRF-3. Activated IRF-3 translocates to the nucleus and initiates the transcription of the IFN-β gene. The structure of mouse cGAS bound to an 18 bp dsDNA revealed that cGAS interacts with dsDNA through two binding sites, forming a 2:2 complex. Enzyme assays and IFN-β reporter assays of cGAS mutants demonstrated that interactions at both DNA binding sites are essential for cGAS activation. Mutagenesis and DNA binding studies showed that the two sites bind dsDNA cooperatively and that site B plays a critical role in DNA binding. The structure of mouse cGAS bound to dsDNA and 2',5' cGAMP provided insight into the catalytic mechanism of cGAS. These results demonstrated that cGAS is activated by dsDNA-induced oligomerization. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

    Science.gov (United States)

    Beauparlant, Marc A; Drouin, Guy

    2014-02-01

    Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

  11. Species turnover drives β-diversity patterns across multiple spatial scales of plant-galling interactions in mountaintop grasslands.

    Science.gov (United States)

    Coelho, Marcel Serra; Carneiro, Marco Antônio Alves; Branco, Cristina Alves; Borges, Rafael Augusto Xavier; Fernandes, Geraldo Wilson

    2018-01-01

    This study describes differences in species richness and composition of the assemblages of galling insects and their host plants at different spatial scales. Sampling was conducted along altitudinal gradients composed of campos rupestres and campos de altitude of two mountain complexes in southeastern Brazil: Espinhaço Range and Mantiqueira Range. The following hypotheses were tested: i) local and regional richness of host plants and galling insects are positively correlated; ii) beta diversity is the most important component of regional diversity of host plants and galling insects; and iii) Turnover is the main mechanism driving beta diversity of both host plants and galling insects. Local richness of galling insects and host plants increased with increasing regional richness of species, suggesting a pattern of unsaturated communities. The additive partition of regional richness (γ) into local and beta components shows that local richnesses (α) of species of galling insects and host plants are low relative to regional richness; the beta (β) component incorporates most of the regional richness. The multi-scale analysis of additive partitioning showed similar patterns for galling insects and host plants with the local component (α) incorporated a small part of regional richness. Beta diversity of galling insects and host plants were mainly the result of turnover, with little contribution from nesting. Although the species composition of galling insects and host plant species varied among sample sites, mountains and even mountain ranges, local richness remained relatively low. In this way, the addition of local habitats with different landscapes substantially affects regional richness. Each mountain contributes fundamentally to the composition of regional diversity of galling insects and host plants, and so the design of future conservation strategies should incorporate multiple scales.

  12. Simultaneous separation and identification of oligomeric procyanidins and anthocyanin-derived pigments in raw red wine by HPLC-UV-ESI-MSn.

    Science.gov (United States)

    Pati, S; Losito, I; Gambacorta, G; La Notte, E; Palmisano, F; Zambonin, P G

    2006-07-01

    Samples of raw red wine (Primitivo di Manduria, Apulia, Southern Italy) were analysed without any pre-treatment (except 1:2 dilution with water) using HPLC with detection based on UV absorbance and Electrospray Ionisation Sequential Mass Spectrometry (ESI-MSn, with n = 1-3) in a series configuration. In particular, absorbance at 520 nm was monitored for UV detection in order to identify pigments responsible for wine colour. On the other hand, two subsequent stages of MS detection based on positive ions were adopted. The first consisted of an explorative MS acquisition, aimed at the individuation of the m/z ratios for positively charged compounds; the second was based on fragmentation of the detected ions within an ion trap analyser, followed by MS/MS and, if required, MS3 acquisitions. The synergy between UV detection and MSn analysis led to the identification of 41 pigments, which can be classified into five groups: grape anthocyanins, pyranoanthocyanins, vinyl-linked anthocyanin-flavanol pigments, ethyl-bridged anthocyanin-flavanol pigments and flavanol-anthocyanin compounds. Many isomeric and oligomeric structures were found within each group. A further class of compounds, not absorbing in the visible spectrum, could be also characterised by ESI-MSn and corresponded to B-type procyanidins, i.e. proanthocyanidins arising from C4-->C8/C4-->C6 couplings between catechin or epicatechin units. In particular, oligomeric structures (from dimers to pentamers), often present with several isomers, were identified and their fragmentation patterns clarified.

  13. Ring species as demonstrations of the continuum of species formation

    DEFF Research Database (Denmark)

    Pereira, Ricardo José Do Nascimento; Wake, David B.

    2015-01-01

    In the mid-20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of 'circular overlaps' or 'ring species' as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier......? What conditions favour their formation? Modelling studies have attempted to address these knowledge gaps by estimating the biological parameters that result in stable ring species (Martins et al. 2013), and determining the necessary topographic parameters of the barriers encircled (Monahan et al. 2012......). However, any generalization is undermined by a major limitation: only a handful of ring species are known to exist in nature. In addition, many of them have been broken into multiple species presumed to be evolving independently, usually obscuring the evolutionary dynamics that generate diversity. A paper...

  14. Multiple epiphyseal dysplasia: radiographic abnormalities correlated with genotype

    Energy Technology Data Exchange (ETDEWEB)

    Unger, S.L. [Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Los Angeles, CA (United States); Briggs, M.D.; Holden, P. [Wellcome Trust Centre for Cell-Matrix Research, University of Manchester (United Kingdom); Zabel, B. [Children' s Hospital, Univ. of Mainz (Germany); Ala-Kokko, L.; Paassilta, P.; Lohiniva, J. [Dept. of Medical Biochemistry, Univ. of Oulu (Finland); Rimoin, D.L. [Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Los Angeles, CA (United States); Department of Pediatrics, UCLA School of Medicine, Los Angeles, CA (United States); Lachman, R.S. [Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Los Angeles, CA (United States); Department of Pediatrics, UCLA School of Medicine, Los Angeles, CA (United States); Department of Radiology, UCLA School of Medicine, Los Angeles, CA (United States); Cohn, D.H. [Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Los Angeles, CA (United States); Department of Human Genetics, UCLA School of Medicine, Los Angeles, CA (United States)

    2001-01-01

    Multiple epiphyseal dysplasia (MED) is an osteochondrodysplasia characterized clinically by mild short stature and early-onset degenerative joint disease and radiographically by epiphyseal hypoplasia/dysplasia. MED is genetically heterogeneous, with autosomal dominant cases resulting from mutations in at least three genes: the cartilage oligomeric matrix protein (COMP) gene (EDM1) and the COL9A2 (EDM2) and COL9A3 (EDM3) genes of type IX procollagen. We present here a comparison of the radiographic phenotypes of MED patients with type IX collagen gene mutations and those with COMP gene mutations. We reviewed radiographs from two patients with MED produced by COMP mutations, two families with COL9A2 mutations, and one family with a mutation in COL9A3. The data demonstrated that the patients with type IX collagen defects had more severe joint involvement at the knees and relative hip sparing, while the patients with COMP mutations had significant involvement at the capital femoral epiphyses and irregular acetabuli. This pattern of joint involvement was consistent regardless of overall degree of severity of the phenotype. (orig.)

  15. Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae.

    Directory of Open Access Journals (Sweden)

    Justin C Bagley

    Full Text Available Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the

  16. Multiple glacial refugia of the low-dispersal ground beetle Carabus irregularis: molecular data support predictions of species distribution models.

    Directory of Open Access Journals (Sweden)

    Katharina Homburg

    Full Text Available Classical glacial refugia such as the southern European peninsulas were important for species survival during glacial periods and acted as sources of post-glacial colonisation processes. Only recently, some studies have provided evidence for glacial refugia north of the southern European peninsulas. In the present study, we combined species distribution models (SDMs with phylogeographic analyses (using mitochondrial DNA = mtDNA to investigate if the cold-adapted, stenotopic and flightless ground beetle species, Carabus irregularis, survived the Last Glacial Maximum (LGM in classical and/or other refugia. SDMs (for both a western European and for a Carpathian subgroup were calculated with MAXENT on the basis of 645 species records to predict current and past distribution patterns. Two mtDNA loci (CO1 and ND5, concatenated sequence length: 1785 bp were analyzed from 91 C. irregularis specimens to reconstruct the phylogeography of Central and eastern European populations and to estimate divergence times of the given lineages. Strong intra-specific genetic differentiation (inter-clade ΦST values ranged from 0.92 to 0.99 implied long-term isolation of major clades and subsclades. The high divergence between the nominate subspecies and the Carpathian subspecies C. i. montandoni points to two independent species rather than subspecies (K-2P distance 0.042 ± 0.004; supposed divergence of the maternal lineages dated back 1.6 to 2.5 million years BP differing not only morphologically but also genetically and ecologically from each other. The SDMs also inferred classical as well as other refugia for C. irregularis, especially north of the Alps, in southeastern Europe and in the Carpathians. The coincidences between the results of both methods confirm the assumption of multiple glacial refugia for the studied species and the usefulness of combining methodological approaches for the understanding of the history of low-dispersal insect species.

  17. Reactive Oxygen Species along with Reactive Nitrogen Species (ROS/RNS) as the Main Cause of Multiple Sclerosis

    OpenAIRE

    Somayeh Zaminpira; Sorush Niknamian

    2017-01-01

    Multiple Sclerosis is a condition of demyelination of the nerve cells in the brain and spinal cord. It is possible that multiple factors are involved in causing multiple sclerosis, including DNA defects in nuclear and mitochondrial genomes, viral infection, hypoxia, oxidative stress, lack of sunlight, and increased macrophages and lymphocytes in the brain. This meta-analysis has gone through many researches and reviews to find the similarities and differences in the cause of this disease. The...

  18. Sedimentation Velocity Analysis of Large Oligomeric Chromatin Complexes Using Interference Detection.

    Science.gov (United States)

    Rogge, Ryan A; Hansen, Jeffrey C

    2015-01-01

    Sedimentation velocity experiments measure the transport of molecules in solution under centrifugal force. Here, we describe a method for monitoring the sedimentation of very large biological molecular assemblies using the interference optical systems of the analytical ultracentrifuge. The mass, partial-specific volume, and shape of macromolecules in solution affect their sedimentation rates as reflected in the sedimentation coefficient. The sedimentation coefficient is obtained by measuring the solute concentration as a function of radial distance during centrifugation. Monitoring the concentration can be accomplished using interference optics, absorbance optics, or the fluorescence detection system, each with inherent advantages. The interference optical system captures data much faster than these other optical systems, allowing for sedimentation velocity analysis of extremely large macromolecular complexes that sediment rapidly at very low rotor speeds. Supramolecular oligomeric complexes produced by self-association of 12-mer chromatin fibers are used to illustrate the advantages of the interference optics. Using interference optics, we show that chromatin fibers self-associate at physiological divalent salt concentrations to form structures that sediment between 10,000 and 350,000S. The method for characterizing chromatin oligomers described in this chapter will be generally useful for characterization of any biological structures that are too large to be studied by the absorbance optical system. © 2015 Elsevier Inc. All rights reserved.

  19. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A.; Lane, Charles R.; Thon, Michael R.; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production. PMID:26086351

  20. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

    Directory of Open Access Journals (Sweden)

    Riccardo Baroncelli

    Full Text Available Fragaria × ananassa (common name: strawberry is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l. is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

  1. Cartilage oligomeric matrix protein in patients with juvenile idiopathic arthritis: relation to growth and disease activity

    DEFF Research Database (Denmark)

    Bjørnhart, Birgitte; Juul, Anders; Nielsen, Susan

    2009-01-01

    OBJECTIVE: Cartilage oligomeric matrix protein (COMP) has been identified as a prognostic marker of progressive joint destruction in rheumatoid arthritis. In this population based study we evaluated associations between plasma concentrations of COMP, disease activity, and growth velocity...... in patients with recent-onset juvenile idiopathic arthritis (JIA). COMP levels in JIA and healthy children were compared with those in healthy adults. Plasma levels of insulin-like growth factor I (IGF-1), which has been associated with COMP expression and growth velocity, were studied in parallel. METHODS......: 87 patients with JIA entered the study, including oligoarticular JIA (n = 34), enthesitis-related arthritis (n = 8), polyarticular rheumatoid factor (RF)-positive JIA (n = 2), polyarticular RF-negative JIA (n = 27), systemic JIA (n = 6), and undifferentiated JIA (n = 10). Plasma levels of COMP were...

  2. Invasive species information networks: Collaboration at multiple scales for prevention, early detection, and rapid response to invasive alien species

    Science.gov (United States)

    Simpson, Annie; Jarnevich, Catherine S.; Madsen, John; Westbrooks, Randy G.; Fournier, Christine; Mehrhoff, Les; Browne, Michael; Graham, Jim; Sellers, Elizabeth A.

    2009-01-01

    Accurate analysis of present distributions and effective modeling of future distributions of invasive alien species (IAS) are both highly dependent on the availability and accessibility of occurrence data and natural history information about the species. Invasive alien species monitoring and detection networks (such as the Invasive Plant Atlas of New England and the Invasive Plant Atlas of the MidSouth) generate occurrence data at local and regional levels within the United States, which are shared through the US National Institute of Invasive Species Science. The Inter-American Biodiversity Information Network's Invasives Information Network (I3N), facilitates cooperation on sharing invasive species occurrence data throughout the Western Hemisphere. The I3N and other national and regional networks expose their data globally via the Global Invasive Species Information Network (GISIN). International and interdisciplinary cooperation on data sharing strengthens cooperation on strategies and responses to invasions. However, limitations to effective collaboration among invasive species networks leading to successful early detection and rapid response to invasive species include: lack of interoperability; data accessibility; funding; and technical expertise. This paper proposes various solutions to these obstacles at different geographic levels and briefly describes success stories from the invasive species information networks mentioned above. Using biological informatics to facilitate global information sharing is especially critical in invasive species science, as research has shown that one of the best indicators of the invasiveness of a species is whether it has been invasive elsewhere. Data must also be shared across disciplines because natural history information (e.g. diet, predators, habitat requirements, etc.) about a species in its native range is vital for effective prevention, detection, and rapid response to an invasion. Finally, it has been our

  3. MAK33 antibody light chain amyloid fibrils are similar to oligomeric precursors.

    Directory of Open Access Journals (Sweden)

    Manuel Hora

    Full Text Available Little structural information is available so far on amyloid fibrils consisting of immunoglobulin light chains. It is not understood which features of the primary sequence of the protein result in fibril formation. We report here MAS solid-state NMR studies to identify the structured core of κ-type variable domain light chain fibrils. The core contains residues of the CDR2 and the β-strands D, E, F and G of the native immunoglobulin fold. The assigned core region of the fibril is distinct in comparison to the core identified in a previous solid-state NMR study on AL-09 by Piehl at. al, suggesting that VL fibrils can adopt different topologies. In addition, we investigated a soluble oligomeric intermediate state, previously termed the alternatively folded state (AFS, using NMR and FTIR spectroscopy. The NMR oligomer spectra display a high degree of similarity when compared to the fibril spectra, indicating a high structural similarity of the two aggregation states. Based on comparison to the native state NMR chemical shifts, we suggest that fibril formation via domain-swapping seems unlikely. Moreover, we used our results to test the quality of different amyloid prediction algorithms.

  4. Dielectric properties of polyhedral oligomeric silsesquioxane (POSS)-based nanocomposites at 77k

    International Nuclear Information System (INIS)

    Pan, Ming-Jen; Gorzkowski, Edward; McAllister, Kelly

    2011-01-01

    The goal of this study is to develop dielectric nanocomposites for high energy density applications at liquid nitrogen temperature by utilizing a unique nano-material polyhedral oligomeric silsesquioxanes (POSS). A POSS molecule is consisted of a silica cage core with 8 silicon and 12 oxygen atoms and organic functional groups attached to the corners of the cage. In this study, we utilize POSS for the fabrication of nanocomposites both as a silica nanoparticle filler to enhance the breakdown strength and as a surfactant for effective dispersion of high permittivity ceramic nanoparticles in a polymer matrix. The matrix materials selected for the study are polyvinylidene fluoride (PVDF) and poly(methyl methacrylate) (PMMA). The ceramic nanoparticles are barium strontium titanate (BST 50/50) and strontium titanate. The dielectric properties of the solution-cast nanocomposites films were correlated to the composition and processing conditions. We determined that the addition of POSS did not provide enhanced dielectric performance in PVDF- and PMMA-based materials at either room temperature or 77K. In addition, we found that the dielectric breakdown strength of PMMA is lower at 77K than at room temperature, contradicting literature data.

  5. Polyhedral oligomeric silsesquioxane (POSS)–poly(ethylene glycol) (PEG) hybrids as injectable biomaterials

    International Nuclear Information System (INIS)

    Engstrand, Johanna; López, Alejandro; Engqvist, Håkan; Persson, Cecilia

    2012-01-01

    One of the major issues with the currently available injectable biomaterials for hard tissue replacement is the mismatch between their mechanical properties and those of the surrounding bone. Hybrid bone cements that combine the benefits of tough polymeric and bioactive ceramic materials could become a good alternative. In this work, polyhedral oligomeric silsesquioxane (POSS) was copolymerized with poly(ethylene glycol) (PEG) to form injectable in situ cross-linkable hybrid cements. The hybrids were characterized in terms of their mechanical, rheological, handling and in vitro bioactive properties. The results indicated that hybridization improves the mechanical and bioactive properties of POSS and PEG. The Young moduli of the hybrids were lower than those of commercial cements and more similar to those of cancellous bone. Furthermore, the strength of the hybrids was similar to that of commercial cements. Calcium deficient hydroxyapatite grew on the surface of the hybrids after 28 days in PBS, indicating bioactivity. The study showed that PEG–POSS-based hybrid materials are a promising alternative to commercial bone cements. (paper)

  6. Mutations increasing exposure of a receptor binding site epitope in the soluble and oligomeric forms of the caprine arthritis-encephalitis lentivirus envelope glycoprotein

    International Nuclear Information System (INIS)

    Hoetzel, Isidro; Cheevers, William P.

    2005-01-01

    The caprine arthritis-encephalitis (CAEV) and ovine maedi-visna (MVV) viruses are resistant to antibody neutralization, a feature shared with all other lentiviruses. Whether the CAEV gp135 receptor binding site(s) (RBS) in the functional surface envelope glycoprotein (Env) is protected from antibody binding, allowing the virus to resist neutralization, is not known. Two CAEV gp135 regions were identified by extrapolating a gp135 structural model that could affect binding of antibodies to the RBS: the V1 region and a short sequence analogous in position to the human immunodeficiency virus type 1 gp120 loop B postulated to be located between two major domains of CAEV gp135. Mutation of isoleucine-166 to alanine in the putative loop B of gp135 increased the affinity of soluble gp135 for the CAEV receptor(s) and goat monoclonal antibody (Mab) F7-299 which recognizes an epitope overlapping the gp135 RBS. The I166A mutation also stabilized or exposed the F7-299 epitope in anionic detergent buffers, indicating that the I166A mutation induces conformational changes and stabilizes the RBS of soluble gp135 and enhances Mab F7-299 binding. In contrast, the affinity of a V1 deletion mutant of gp135 for the receptor and Mab F7-299 and its structural stability did not differ from that of the wild-type gp135. However, both the I166A mutation and the V1 deletion of gp135 increased cell-to-cell fusion activity and binding of Mab F7-299 to the oligomeric Env. Therefore, the CAEV gp135 RBS is protected from antibody binding by mechanisms both dependent and independent of Env oligomerization which are disrupted by the V1 deletion and the I166A mutation, respectively. In addition, we found a correlation between side-chain β-branching at amino acid position 166 and binding of Mab F7-299 to oligomeric Env and cell-to-cell fusion, suggesting local secondary structure constraints in the region around isoleucine-166 as one determinant of gp135 RBS exposure and antibody binding

  7. Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α-synuclein assemblies by mass spectrometry.

    Science.gov (United States)

    Shrivastava, Amulya Nidhi; Redeker, Virginie; Fritz, Nicolas; Pieri, Laura; Almeida, Leandro G; Spolidoro, Maria; Liebmann, Thomas; Bousset, Luc; Renner, Marianne; Léna, Clément; Aperia, Anita; Melki, Ronald; Triller, Antoine

    2016-06-01

    α-Synuclein (α-syn) is the principal component of Lewy bodies, the pathophysiological hallmark of individuals affected by Parkinson disease (PD). This neuropathologic form of α-syn contributes to PD progression and propagation of α-syn assemblies between neurons. The data we present here support the proteomic analysis used to identify neuronal proteins that specifically interact with extracellularly applied oligomeric or fibrillar α-syn assemblies (conditions 1 and 2, respectively) (doi: 10.15252/embj.201591397[1]). α-syn assemblies and their cellular partner proteins were pulled down from neuronal cell lysed shortly after exposure to exogenous α-syn assemblies and the associated proteins were identified by mass spectrometry using a shotgun proteomic-based approach. We also performed experiments on pure cultures of astrocytes to identify astrocyte-specific proteins interacting with oligomeric or fibrillar α-syn (conditions 3 and 4, respectively). For each condition, proteins interacting selectively with α-syn assemblies were identified by comparison to proteins pulled-down from untreated cells used as controls. The mass spectrometry data, the database search and the peak lists have been deposited to the ProteomeXchange Consortium database via the PRIDE partner repository with the dataset identifiers PRIDE: PXD002256 to PRIDE: PXD002263 and doi: 10.6019/PXD002256 to 10.6019/PXD002263.

  8. Multiple ion species fluid modeling of sprite halos and the role of electron detachment from O- in their dynamics

    Science.gov (United States)

    Liu, N.

    2011-12-01

    Sprite halos are brief descending glows appearing at the lower ionosphere boundary, which follow impulsive cloud-to-ground lightning discharges [e.g., Barrington-Leigh et al., JGR, 106, 1741, 2001, Wescott et al., JGR, 106, 10467, 2001; Pasko, JGR, 115, A00E35, 2010]. They last for a few milliseconds, with horizontal extension of tens of kilometers and vertical thickness of several kilometers. According to global survey of the occurrence of transient luminous events by the ISUAL instruments on the FORMOSAT-2 satellite, on average sprite halos occur once every minute on Earth [Chen et al., JGR, 113, A08306, 2008]. It has been established that sprite halos are caused by electron heating, and molecule excitation and ionization in the lower ionosphere due to lightning quasi-electrostatic field [e.g., Pasko et al., JGR, 102, 4529, 1997; Barrington-Leigh et al., 2001; Pasko, 2010]. Past modeling work on sprite halos was conducted using either a two dimensional (2D) model of at most three charged species or a zero dimensional model of multiple ion species. In this talk, we report a modeling study of sprite halos using a recently developed 2D fluid model of multiple charged species. The model charged species include the ion species set used in [Lehtinen and Inan, GRL, 34, L08804, 2007] to study the dynamics of ionization perturbations produced by gigantic jets in the middle and upper atmosphere. In addition, another charged species, O-, is added to this set, because electron detachment of O- can proceed very fast under moderate electric field [Rayment and Moruzzi, Int. J. Mass Spectrom., 26, 321, 1978], requiring a separate treatment from the other light negative ions. The modeling results of a sprite halo driven by positive cloud-to-ground lightning indicate that the halo can descend to lower altitude with much higher electron density behind its front when the O- detachment process is included. Electron density ahead of the halo front is not significantly reduced from the

  9. Flow cytometry evidence of human granulocytes interaction with polyhedral oligomeric silsesquioxanes: effect of nanoparticle charge

    International Nuclear Information System (INIS)

    Renò, Filippo; Rizzi, Manuela; Pittarella, Pamela; Carniato, Fabio; Olivero, Francesco; Marchese, Leonardo

    2013-01-01

    Nanoparticles (NPs) entering the human body are immediately confronted with the innate part of human immune system. In particular, monocyte and neutrophil granulocytes readily clear particles by phagocytosis, even if in the case of NPs the uptake mechanism may be classified as macropinocytosis. Among engineered nanoparticles, in the last years, siliceous materials have emerged as promising materials for several applications ranging from catalysis to biomedical. The polyhedral oligomeric silsesquioxanes (POSS) are nanodimensional, easily synthesizable molecular compounds and POSS-based systems are promising carriers for biological molecules. In this work, the ability of human granulocytes to uptake positively and negatively charged POSS was measured using a simple flow cytometry analysis based on cell size modifications. The data obtained showed that after a 30 min exposure only positive NPs were uptaken by human granulocyte using both macropinocytosis and clathrin-mediated mechanisms as demonstrated by uptake inhibition mediated by amiloride and chlorpromazine. (paper)

  10. Multiple-level defect species evaluation from average carrier decay

    Science.gov (United States)

    Debuf, Didier

    2003-10-01

    An expression for the average decay is determined by solving the the carrier continuity equations, which include terms for multiple defect recombination. This expression is the decay measured by techniques such as the contactless photoconductance decay method, which determines the average or volume integrated decay. Implicit in the above is the requirement for good surface passivation such that only bulk properties are observed. A proposed experimental configuration is given to achieve the intended goal of an assessment of the type of defect in an n-type Czochralski-grown silicon semiconductor with an unusually high relative lifetime. The high lifetime is explained in terms of a ground excited state multiple-level defect system. Also, minority carrier trapping is investigated.

  11. Phylogeography in Nassarius mud snails: Complex patterns in congeneric species.

    Directory of Open Access Journals (Sweden)

    Chuanliang Pu

    Full Text Available One major goal for phylogeographical studies is to elucidate respective roles of multiple evolutionary and ecological forces that shape the current distribution patterns. In marine and coastal ecosystems, it has been generated a common realization that species with enormous population size and pelagic larval stages can disperse across broad geographical scales, leading to weak or even no phylogeographical structure across large geographical scales. However, the violation of such realization has been frequently reported, and it remains largely unexplored on mechanisms responsible for various phylogeographical patterns observed in different species at varied geographical scales. Here, we used a species-rich genus Nassarius to assess and compare phylogeographical patterns in congeneric species, and discuss causes and consequences underlying varied phylogeographical patterns. Interestingly, we observed complex phylogeographical patterns both within single species and across multiple species, and multiple analyses showed varied levels of genetic heterogeneity among sites within and across species. Available evidence suggests that related species with similar biological characteristics may not be necessary to result in consistent phylogeographical patterns. Multiple factors, including larval ecology, interactions between dispersal and natural selection, and human activity-mediated dispersal, can partially explain the complex patterns observed in this study. Deep investigations should be performed on these factors, particularly their respective roles in determining evolutionary/ecological processes to form phylogeographical patterns in species with high dispersal capacities in marine and coastal ecosystems.

  12. Characterizing lentic freshwater fish assemblages using multiple sampling methods

    Science.gov (United States)

    Fischer, Jesse R.; Quist, Michael C.

    2014-01-01

    Characterizing fish assemblages in lentic ecosystems is difficult, and multiple sampling methods are almost always necessary to gain reliable estimates of indices such as species richness. However, most research focused on lentic fish sampling methodology has targeted recreationally important species, and little to no information is available regarding the influence of multiple methods and timing (i.e., temporal variation) on characterizing entire fish assemblages. Therefore, six lakes and impoundments (48–1,557 ha surface area) were sampled seasonally with seven gear types to evaluate the combined influence of sampling methods and timing on the number of species and individuals sampled. Probabilities of detection for species indicated strong selectivities and seasonal trends that provide guidance on optimal seasons to use gears when targeting multiple species. The evaluation of species richness and number of individuals sampled using multiple gear combinations demonstrated that appreciable benefits over relatively few gears (e.g., to four) used in optimal seasons were not present. Specifically, over 90 % of the species encountered with all gear types and season combinations (N = 19) from six lakes and reservoirs were sampled with nighttime boat electrofishing in the fall and benthic trawling, modified-fyke, and mini-fyke netting during the summer. Our results indicated that the characterization of lentic fish assemblages was highly influenced by the selection of sampling gears and seasons, but did not appear to be influenced by waterbody type (i.e., natural lake, impoundment). The standardization of data collected with multiple methods and seasons to account for bias is imperative to monitoring of lentic ecosystems and will provide researchers with increased reliability in their interpretations and decisions made using information on lentic fish assemblages.

  13. Determinants of species richness patterns in the Netherlands across multiple taxonomic groups

    NARCIS (Netherlands)

    Schouten, M.A.; Verweij, P.A.; Barendrecht, A.; Kleukers, R.

    2009-01-01

    We examined the species richness patterns of five different species groups (mosses, reptiles and amphibians, grasshoppers and crickets, dragonflies, and hoverflies) in the Netherlands (41,500 km2) using sampling units of 5 × 5 km. We compared the spatial patterns of species richness of the five

  14. Cartilage oligomeric matrix protein deficiency promotes early onset and the chronic development of collagen-induced arthritis

    DEFF Research Database (Denmark)

    Geng, Hui; Carlsen, Stefan; Nandakumar, Kutty

    2008-01-01

    ABSTRACT: INTRODUCTION: Cartilage oligomeric matrix protein (COMP) is a homopentameric protein in cartilage. The development of arthritis, like collagen-induced arthritis (CIA), involves cartilage as a target tissue. We have investigated the development of CIA in COMP-deficient mice. METHODS: COMP......-deficient mice in the 129/Sv background were backcrossed for 10 generations against B10.Q mice, which are susceptible to chronic CIA. COMP-deficient and wild-type mice were tested for onset, incidence, and severity of arthritis in both the collagen and collagen antibody-induced arthritis models. Serum anti......-collagen II and anti-COMP antibodies as well as serum COMP levels in arthritic and wild-type mice were measured by enzyme-linked immunosorbent assay. RESULTS: COMP-deficient mice showed a significant early onset and increase in the severity of CIA in the chronic phase, whereas collagen II-antibody titers were...

  15. Priority setting for invasive species management: risk assessment of Ponto-Caspian invasive species into Great Britain.

    Science.gov (United States)

    Gallardo, Belinda; Aldridge, David C

    2013-03-01

    Invasive species drive important ecological and economic losses across wide geographies, with some regions supporting especially large numbers of nonnative species and consequently suffering relatively high impacts. For this reason, integrated risk assessments able to screen a suite of multiple invaders over large geographic areas are needed for prioritizing the allocation of limited resources. A total of 16 Ponto-Caspian aquatic species (10 gammarids, one isopod, two mysids, and three fishes) have been short-listed as recent or potential future invaders of British waters, whose introduction and spread is of high concern. In this study, we use multiple modeling techniques to assess their risk of establishment and spread into Great Britain. Climate suitability maps for these 16 species differed depending on the eastern and western distribution of species in continental Europe, which was related to their respective migration corridor: southern (Danube-Rhine rivers), and northern (Don and Volga rivers and Baltic lakes). Species whose suitability was high across large parts of Great Britain included four gammarids (Cheliorophium robustum, Dikerogammarus bispinosus, D. villosus, and Echinogammarus trichiatus) and a mysid (Hemimysis anomala). A climatic "heat map" combining the results of all 16 species together pointed to the southeast of England as the area most vulnerable to multiple invasions, particularly the Thames, Anglian, Severn, and Humber river basin districts. Regression models further suggested that alkalinity concentration > 120 mg/L in southeast England may favor the establishment of Ponto-Caspian invaders. The production of integrated risk maps for future invaders provides a means for the scientifically informed prioritization of resources toward particular species and geographic regions. Such tools have great utility in helping environmental managers focus efforts on the most effective prevention, management, and monitoring programs.

  16. Contaminant Effects on California Bay–Delta Species and Human Health

    Directory of Open Access Journals (Sweden)

    Stephanie Fong

    2016-12-01

    Full Text Available doi: https://doi.org/10.15447/sfews.2016v14iss4art5Many contaminants in the California Bay–Delta (Bay–Delta exceed regulatory standards, affect aquatic species, and potentially affect human health. Recent studies provide multiple lines of evidence that contaminants affect species of concern in the Bay–Delta (e.g., the decline of several important fish species referred to as the “Pelagic Organism Decline” or POD. Contaminants occur as dynamic complex mixtures and exert effects at multiple levels of biological organization. Multiple chemicals impair processes at cellular and physiological levels (measured as growth, development, and behavior abnormalities, and when viability and reproductive output are affected, populations are affected. As an important example, the population decline of the endangered Delta Smelt (Hypomesus transpacificus is significantly associated with multiple stressors, including insecticide use. New analyses presented in this paper show significant correlations between pyrethroid use and declining abundance of POD fish species. Water sampled from the Bay–Delta causes multiple deleterious effects in fish, and Delta Smelt collected from the Bay–Delta exhibit contaminant effects. Fish prey items are also affected by contaminants; this may have an indirect effect on their populations. Co-occurrence with thermal changes or disease can exacerbate contaminant effects. Contaminants also pose threats to human health via consumption of fish and shellfish, drinking water, and contact recreation, in particular, mercury, cyanobacteria toxins, disinfection byproducts, pathogens, pesticides, and pharmaceuticals and personal care products. The role of contaminants in the decline of Bay–Delta species is difficult to accurately assess in a complex, dynamic system. However, tools and approaches are available to evaluate contaminant effects on Bay–Delta species, and separate the effects of multiple stressors. Integrated

  17. Assembled cross-species perchlorate dose-response data

    Data.gov (United States)

    U.S. Environmental Protection Agency — This data set contains dose-response data for perchlorate exposure in multiple species. These data were assembled from peer-reviewed studies. Species included in...

  18. Species limits and relationships within Otidea inferred from multiple gene phylogenies

    NARCIS (Netherlands)

    Hansen, K.; Olariaga, I.

    2015-01-01

    The genus Otidea is one of the more conspicuous members of the Pyronemataceae, with high species diversity in hemiboreal and boreal forests. The genus is morphologically coherent and in previous higher-level multi-gene analyses it formed a highly supported monophyletic group. Species delimitation

  19. Predictions for an invaded world: A strategy to predict the distribution of native and non-indigenous species at multiple scales

    Science.gov (United States)

    Reusser, D.A.; Lee, H.

    2008-01-01

    Habitat models can be used to predict the distributions of marine and estuarine non-indigenous species (NIS) over several spatial scales. At an estuary scale, our goal is to predict the estuaries most likely to be invaded, but at a habitat scale, the goal is to predict the specific locations within an estuary that are most vulnerable to invasion. As an initial step in evaluating several habitat models, model performance for a suite of benthic species with reasonably well-known distributions on the Pacific coast of the US needs to be compared. We discuss the utility of non-parametric multiplicative regression (NPMR) for predicting habitat- and estuary-scale distributions of native and NIS. NPMR incorporates interactions among variables, allows qualitative and categorical variables, and utilizes data on absence as well as presence. Preliminary results indicate that NPMR generally performs well at both spatial scales and that distributions of NIS are predicted as well as those of native species. For most species, latitude was the single best predictor, although similar model performance could be obtained at both spatial scales with combinations of other habitat variables. Errors of commission were more frequent at a habitat scale, with omission and commission errors approximately equal at an estuary scale. ?? 2008 International Council for the Exploration of the Sea. Published by Oxford Journals. All rights reserved.

  20. Inside-out signaling promotes dynamic changes in the carcinoembryonic antigen-related cellular adhesion molecule 1 (CEACAM1) oligomeric state to control its cell adhesion properties.

    Science.gov (United States)

    Patel, Prerna C; Lee, Hannah S W; Ming, Aaron Y K; Rath, Arianna; Deber, Charles M; Yip, Christopher M; Rocheleau, Jonathan V; Gray-Owen, Scott D

    2013-10-11

    Cell-cell contacts are fundamental to multicellular organisms and are subject to exquisite levels of control. The carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) can engage in both cis-homophilic (parallel) oligomerization and trans-homophilic (anti-parallel) binding. In this study, we establish that the CEACAM1 transmembrane domain has a propensity to form cis-dimers via the transmembrane-embedded (432)GXXXG(436) motif and that this basal state is overcome when activated calmodulin binds to the CEACAM1 cytoplasmic domain. Although mutation of the (432)GXXXG(436) motif reduced CEACAM1 oligomerization, it did not affect surface localization of the receptor or influence CEACAM1-dependent cellular invasion by the pathogenic Neisseria. The mutation did, however, have a striking effect on CEACAM1-dependent cellular aggregation, increasing both the kinetics of cell-cell association and the size of cellular aggregates formed. CEACAM1 association with tyrosine kinase c-Src and tyrosine phosphatases SHP-1 and SHP-2 was not affected by the (432)GXXXG(436) mutation, consistent with their association with the monomeric form of wild type CEACAM1. Collectively, our results establish that a dynamic oligomer-to-monomer shift in surface-expressed CEACAM1 facilitates trans-homophilic binding and downstream effector signaling.

  1. Projecting future expansion of invasive species: comparing and improving methodologies for species distribution modeling.

    Science.gov (United States)

    Mainali, Kumar P; Warren, Dan L; Dhileepan, Kunjithapatham; McConnachie, Andrew; Strathie, Lorraine; Hassan, Gul; Karki, Debendra; Shrestha, Bharat B; Parmesan, Camille

    2015-12-01

    Modeling the distributions of species, especially of invasive species in non-native ranges, involves multiple challenges. Here, we developed some novel approaches to species distribution modeling aimed at reducing the influences of such challenges and improving the realism of projections. We estimated species-environment relationships for Parthenium hysterophorus L. (Asteraceae) with four modeling methods run with multiple scenarios of (i) sources of occurrences and geographically isolated background ranges for absences, (ii) approaches to drawing background (absence) points, and (iii) alternate sets of predictor variables. We further tested various quantitative metrics of model evaluation against biological insight. Model projections were very sensitive to the choice of training dataset. Model accuracy was much improved using a global dataset for model training, rather than restricting data input to the species' native range. AUC score was a poor metric for model evaluation and, if used alone, was not a useful criterion for assessing model performance. Projections away from the sampled space (i.e., into areas of potential future invasion) were very different depending on the modeling methods used, raising questions about the reliability of ensemble projections. Generalized linear models gave very unrealistic projections far away from the training region. Models that efficiently fit the dominant pattern, but exclude highly local patterns in the dataset and capture interactions as they appear in data (e.g., boosted regression trees), improved generalization of the models. Biological knowledge of the species and its distribution was important in refining choices about the best set of projections. A post hoc test conducted on a new Parthenium dataset from Nepal validated excellent predictive performance of our 'best' model. We showed that vast stretches of currently uninvaded geographic areas on multiple continents harbor highly suitable habitats for parthenium

  2. Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins.

    Science.gov (United States)

    Kamariah, Neelagandan; Eisenhaber, Birgit; Eisenhaber, Frank; Grüber, Gerhard

    2018-04-01

    Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (C P ) located in a conserved sequence Pxxx(T/S)xxC P motif known as C P -loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the C P -loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the C P -loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the C P -loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the C P -loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the C P -loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted C P -loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the C P -loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. Hydroxychloroquine induces inhibition of collagen type II and oligomeric matrix protein COMP expression in chondrocytes

    Directory of Open Access Journals (Sweden)

    Tao Li

    2016-06-01

    Full Text Available The aim of this study was to investigate the effect of hydroxychloroquine on the level of collagen type II and oligomeric matrix protein COMP expression in chondrocytes of knee osteoarthritis. The rate of growth in cartilage cells was analyzed using MTT assay whereas the Col-2 and COMP expression levels were detected by RT-PCR and Western blotting analyses. For the determination of MMP-13 expression, ELISA test was used. The results revealed no significant change in the rate of cartilage cell proliferation in hydroxychloroquine-treated compared to untreated cells. Hydroxychloro-quine treatment exhibited concentration- and time-dependent effect on the inhibition of collagen type II and COMP expression in chondrocytes. However, its treatment caused a significant enhancement in the expression levels of MMP-13 compared to the untreated cells. Therefore, hydroxychloro-quine promotes expression of MMP-13 and reduces collagen type II and COMP expression levels in chondrocytes without any significant change in the growth of cells.

  4. Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization.

    Science.gov (United States)

    Gong, Xin; Qian, Hongwu; Shao, Wei; Li, Jingxian; Wu, Jianping; Liu, Jun-Jie; Li, Wenqi; Wang, Hong-Wei; Espenshade, Peter; Yan, Nieng

    2016-11-01

    Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.

  5. Biological interactions and cooperative management of multiple species.

    Science.gov (United States)

    Jiang, Jinwei; Min, Yong; Chang, Jie; Ge, Ying

    2017-01-01

    Coordinated decision making and actions have become the primary solution for the overexploitation of interacting resources within ecosystems. However, the success of coordinated management is highly sensitive to biological, economic, and social conditions. Here, using a game theoretic framework and a 2-species model that considers various biological relationships (competition, predation, and mutualism), we compute cooperative (or joint) and non-cooperative (or separate) management equilibrium outcomes of the model and investigate the effects of the type and strength of the relationships. We find that cooperation does not always show superiority to non-cooperation in all biological interactions: (1) if and only if resources are involved in high-intensity predation relationships, cooperation can achieve a win-win scenario for ecosystem services and resource diversity; (2) for competitive resources, cooperation realizes higher ecosystem services by sacrificing resource diversity; and (3) for mutual resources, cooperation has no obvious advantage for either ecosystem services or resource evenness but can slightly improve resource abundance. Furthermore, by using a fishery model of the North California Current Marine Ecosystem with 63 species and seven fleets, we demonstrate that the theoretical results can be reproduced in real ecosystems. Therefore, effective ecosystem management should consider the interconnection between stakeholders' social relationship and resources' biological relationships.

  6. Two competing species in super-diffusive dynamical regimes

    Science.gov (United States)

    La Cognata, A.; Valenti, D.; Spagnolo, B.; Dubkov, A. A.

    2010-09-01

    The dynamics of two competing species within the framework of the generalized Lotka-Volterra equations, in the presence of multiplicative α-stable Lévy noise sources and a random time dependent interaction parameter, is studied. The species dynamics is characterized by two different dynamical regimes, exclusion of one species and coexistence of both, depending on the values of the interaction parameter, which obeys a Langevin equation with a periodically fluctuating bistable potential and an additive α-stable Lévy noise. The stochastic resonance phenomenon is analyzed for noise sources asymmetrically distributed. Finally, the effects of statistical dependence between multiplicative noise and additive noise on the dynamics of the two species are studied.

  7. Multiwalled carbon nanotubes@octavinyl polyhedral oligomeric silsesquioxanes nanocomposite preparation via cross-linking reaction in acidic media

    Energy Technology Data Exchange (ETDEWEB)

    Somasekharan, Lakshmipriya; Thomas, Sabu [Mahatma Gandhi University, International and Interuniversity Centre for Nanoscience and Nanotechnology (India); Comoy, Corinne [Université de Lorraine, SRSMC, UMR 7565 (France); Sivasankarapillai, Anilkumar [NSS Hindu College (India); Kalarikkal, Nandakumar [Mahatma Gandhi University, International and Interuniversity Centre for Nanoscience and Nanotechnology (India); Lamouroux, Emmanuel, E-mail: Emmanuel.Lamouroux@univ-lorraine.fr [Université de Lorraine, SRSMC, UMR 7565 (France)

    2016-11-15

    Multiwalled carbon nanotubes have unique properties allowing their use in a wide range of applications—from microelectronics to biomedical and polymer fields. Nevertheless, a crucial aspect for their use resides in the ease of handling them during the process. Here, we report a facile route to prepare multiwalled carbon nanotubes@octavinyl polyhedral oligomeric silsesquioxanes (MWCNT@POSS) nanocomposite. The method involves the formation of a covalent bond between carboxylated MWCNTs and OV-POSS using acid-catalyzed electrophilic addition reaction. The resulting nanocomposite have been characterized by Fourier transform infrared spectroscopy (FTIR), powder X-Ray diffraction (PXRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and thermogravimetric analysis (TGA). The results confirmed that the formation of MWCNT@POSS nanocomposite did not deteriorate MWCNT structure or morphology. Here, we used a 1:1 ratio of carboxylated MWCNTs and OV-POSS and the POSS content in the nanocomposite was 39.5 wt%.

  8. Characterisation of purified parvalbumin from five fish species and nucleotide sequencing of this major allergen from Pacific pilchard, Sardinops sagax.

    Science.gov (United States)

    Beale, Janine E; Jeebhay, Mohamed F; Lopata, Andreas L

    2009-09-01

    IgE-mediated allergic reaction to seafood is a common cause of food allergy including anaphylactic reactions. Parvalbumin, the major fish allergen, has been shown to display IgE cross-reactivity among fish species consumed predominantly in Europe and the Far East. However, cross-reactivity studies of parvalbumin from fish species widely consumed in the Southern hemisphere are limited as is data relating to immunological and molecular characterisation. In this study, antigenic cross-reactivity and the presence of oligomers and isomers of parvalbumin from five highly consumed fish species in Southern Africa were assessed by immunoblotting using purified parvalbumin and crude fish extracts. Pilchard (Sardinops sagax) parvalbumin was found to display the strongest IgE reactivity among 10 fish-allergic consumers. The cDNA sequence of the beta-form of pilchard parvalbumin was determined and designated Sar sa 1.0101 (accession number FM177701 EMBL/GenBank/DDBJ databases). Oligomeric forms of parvalbumin were observed in all fish species using a monoclonal anti-parvalbumin antibody and subject's sera. Isoforms varied between approximately 10-13 kDa. A highly cross-reactive allergenic isoform of parvalbumin was identified and sequenced, providing a successful primary step towards the generation of a recombinant form that could be used for diagnostic and potential therapeutic use in allergic individuals.

  9. Liquid chromatographic/electrospray ionization quadrupole/time of flight tandem mass spectrometric study of polyphenolic composition of different Vaccinium berry species and their comparative evaluation.

    Science.gov (United States)

    Ancillotti, Claudia; Ciofi, Lorenzo; Rossini, Daniele; Chiuminatto, Ugo; Stahl-Zeng, Jianru; Orlandini, Serena; Furlanetto, Sandra; Del Bubba, Massimo

    2017-02-01

    Ultra-high-performance liquid chromatography coupled with high-resolution quadrupole-time of flight mass spectrometry with both negative and positive ionization was used for comprehensively investigating the phenolic and polyphenolic compounds in berries from three spontaneous or cultivated Vaccinium species (i.e., Vaccinium myrtillus, Vaccinium uliginosum subsp. gaultherioides, and Vaccinium corymbosum). More than 200 analytes, among phenolic and polyphenolic compounds belonging to the classes of anthocyanins, monomeric and oligomeric flavonols, flavanols, dihydrochalcones, phenolic acids, together with other polyphenolic compounds of mixed structural characteristics, were identified. Some of the polyphenols herein investigated, such as anthocyanidin glucuronides and malvidin-feruloyl-hexosides in V. myrtillus, or anthocyanindin aldopentosides and coumaroyl-hexosides in V. uliginosum subsp. gaultherioides and a large number of proanthocyanidins with high molecular weight in all species, were described for the first time in these berries. Principal component analysis applied on original LC-TOF data, acquired in survey scan mode, successfully discriminated the three Vaccinium berry species investigated, on the basis of their polyphenolic composition, underlying one more time the fundamental role of mass spectrometry for food characterization.

  10. Structure-properties relationships of polyhedral oligomeric silsesquioxane (POSS filled PS nanocomposites

    Directory of Open Access Journals (Sweden)

    J. J. Schwab

    2012-07-01

    Full Text Available The polyhedral oligomeric silsesquioxane (POSS additivated polystyrene (PS based nanocomposites were prepared by melt processing and the structure-properties relationships of the POSS-PS systems were compared to those of the neat PS. In order to investigate the effect of these structural parameters on the final properties of the polymer nanocomposites, five different kinds of POSS samples were used, in particular, POSS with different inorganic cage and with different organic pendent groups. The rheological investigation suggests clearly that the POSS acts as a plasticizer and that the processability of the PS was positively modified. The affinity between the POSS samples and the PS matrix was estimated by the calculated theoretical solubility parameters, considering the Hoy’s method and by morphology analysis. Minor difference between the solubility parameter of POSS and the matrix means better compatibility and no aggregation tendency. Furthermore, the POSS loading leads to a decrease of the rigidity, of the glass transition temperature and of the damping factor of the nanocomposite systems. The loading of different POSS molecules with open cage leads to a more pronounced effect on all the investigated properties that the loading of the POSS molecules with closed cage. Moreover, the melt properties are significantly influenced by the type of inorganic framework, by the type of the pendent organic groups and by the interaction between the POSS organic groups and the host matrix, while, the solid state properties appears to be influenced more by the kind of cage.

  11. Effects of industrial processing on the immunogenicity of commonly ingested fish species.

    Science.gov (United States)

    Sletten, Gaynour; Van Do, Thien; Lindvik, Helene; Egaas, Eliann; Florvaag, Erik

    2010-01-01

    Food-processing techniques may induce changes in fish protein immunogenicity. Allergens from >100 fish species have been identified, but little is known on the effects of processing on fish protein immunogenicity. IgE binding of sera of patients allergic to fresh and processed (smoked, salted/sugar-cured, canned, lye-treated and fermented) cod, haddock, salmon, trout, tuna, mackerel and herring and of hydrolysates based on salmon and whiting was investigated using immunoblot and inhibition ELISA. Parvalbumin oligomers were identified using monoclonal and polyclonal antibodies. IgE binding was seen in most sera at 12-14 kDa (parvalbumin), and at 17-60 kDa for all fish except tuna. Changes in IgE binding appeared to reflect altered parvalbumin monomers and oligomers. Smoked haddock, salmon and mackerel had increased IgE binding and novel bands at 30 kDa. Chemically processed cod, salmon, trout and pickled herring had reduced or abolished IgE binding. The serum of 1 subject, however, had increased IgE binding to these products and also inhibition of binding by both fish hydrolysates to their constituent fish species. Process-induced changes in fish protein immunogenicity were more dependent on process rather than species, although individual responses varied. Changes in the allergenicity of a product may depend on the net effect of processing on parvalbumin oligomerization patterns, which may also vary in different species. Chemical processes generally caused loss in IgE-binding activity, though sensitization may occur to modified or degraded rather than intact peptides as shown by increased binding by chemically processed fish and hydrolysates in 1 subject. The clinical significance of these findings remains to be established.

  12. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau.

    Science.gov (United States)

    Wang, Bin; Xie, Feng; Li, Jiannan; Wang, Gang; Li, Cheng; Jiang, Jianping

    2017-01-01

    The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

  13. Understanding tantalum-catalyzed ethylene trimerization: When things go wrong

    KAUST Repository

    Chen, Yin

    2013-06-07

    Ethylene oligomerization to linear low-molecular-mass α-olefins is an open industrial challenge. Ta-based catalysts are promising systems, but the unclear understanding of their behavior prevents systematic advances in the field. We demonstrate here that a well-defined (î -SiO)3Ta III species is able to promote ethylene oligo-/polymerization without any cocatalyst, confirming that the active species in Ta systems corresponds to a TaIII species. DFT calculations on a series of Ta systems ranging from ethylene trimerization to ethylene polymerization catalysts highlight the key factors controlling their experimental behavior. Comparison of these Ta systems allows one to set general rules for the rational development of new ethylene Ta oligomerization catalysts. © 2013 American Chemical Society.

  14. Targeting multiple pathogenic mechanisms with polyphenols for the treatment of Alzheimer’s disease: Experimental approach and therapeutic implications

    Directory of Open Access Journals (Sweden)

    Jun eWang

    2014-03-01

    Full Text Available Alzheimer’s disease (AD is the most prevalent neurodegenerative disease of aging and currently has no cure. Its onset and progression are influenced by multiple factors. There is growing consensus that successful treatment will rely on simultaneously targeting multiple pathological features of AD. Polyphenol compounds have many proven health benefits. In this study, we tested the hypothesis that combining three polyphenolic preparations (grape seed extract, resveratrol and Concord grape juice extract, with different polyphenolic compositions and partially redundant bioactivities, may simultaneously and synergistically mitigate amyloid-β (Aβ mediated neuropathology and cognitive impairments in a mouse model of AD. We found that administration of the polyphenols in combination did not alter the profile of bioactive polyphenol metabolites in the brain. We also found that combination treatment resulted in better protection against cognitive impairments compared to individual treatments, in J20 AD mice. Electrophysiological examination showed that acute treatment with select brain penetrating polyphenol metabolites, derived from these polyphenols, improved oligomeric Aβ (oAβ-induced long term potentiation (LTP deficits in hippocampal slices. Moreover, we found greatly reduced total amyloid content in the brain following combination treatment. Our studies provided experimental evidence that application of polyphenols targeting multiple disease-mechanisms may yield a greater likelihood of therapeutic efficacy.

  15. Effects of different dispersal patterns on the presence-absence of multiple species

    Science.gov (United States)

    Mohd, Mohd Hafiz; Murray, Rua; Plank, Michael J.; Godsoe, William

    2018-03-01

    Predicting which species will be present (or absent) across a geographical region remains one of the key problems in ecology. Numerous studies have suggested several ecological factors that can determine species presence-absence: environmental factors (i.e. abiotic environments), interactions among species (i.e. biotic interactions) and dispersal process. While various ecological factors have been considered, less attention has been given to the problem of understanding how different dispersal patterns, in interaction with other factors, shape community assembly in the presence of priority effects (i.e. where relative initial abundances determine the long-term presence-absence of each species). By employing both local and non-local dispersal models, we investigate the consequences of different dispersal patterns on the occurrence of priority effects and coexistence in multi-species communities. In the case of non-local, but short-range dispersal, we observe agreement with the predictions of local models for weak and medium dispersal strength, but disagreement for relatively strong dispersal levels. Our analysis shows the existence of a threshold value in dispersal strength (i.e. saddle-node bifurcation) above which priority effects disappear. These results also reveal a co-dimension 2 point, corresponding to a degenerate transcritical bifurcation: at this point, the transcritical bifurcation changes from subcritical to supercritical with corresponding creation of a saddle-node bifurcation curve. We observe further contrasting effects of non-local dispersal as dispersal distance changes: while very long-range dispersal can lead to species extinctions, intermediate-range dispersal can permit more outcomes with multi-species coexistence than short-range dispersal (or purely local dispersal). Overall, our results show that priority effects are more pronounced in the non-local dispersal models than in the local dispersal models. Taken together, our findings highlight

  16. Small molecule CP-31398 induces reactive oxygen species-dependent apoptosis in human multiple myeloma.

    Science.gov (United States)

    Arihara, Yohei; Takada, Kohichi; Kamihara, Yusuke; Hayasaka, Naotaka; Nakamura, Hajime; Murase, Kazuyuki; Ikeda, Hiroshi; Iyama, Satoshi; Sato, Tsutomu; Miyanishi, Koji; Kobune, Masayoshi; Kato, Junji

    2017-09-12

    Reactive oxygen species (ROS) are normal byproducts of a wide variety of cellular processes. ROS have dual functional roles in cancer cell pathophysiology. At low to moderate levels, ROS act as signaling transducers to activate cell proliferation, migration, invasion, and angiogenesis. In contrast, high levels of ROS induce cell death. In multiple myeloma (MM), ROS overproduction is the trigger for apoptosis induced by several anticancer compounds, including proteasome inhibitors. However, no drugs for which oxidative stress is the main mechanism of action are currently used for treatment of MM in clinical situations. In this study, we demonstrate that the p53-activating small molecule CP-31398 (CP) effectively inhibits the growth of MM cell lines and primary MM isolates from patients. CP also suppresses the growth of MM xenografts in mice. Mechanistically, CP was found to induce intrinsic apoptosis in MM cells via increasing ROS production. Interestingly, CP-induced apoptosis occurs regardless of the p53 status, suggesting that CP has additional mechanisms of action. Our findings thus indicate that CP could be an attractive candidate for treatment of MM patients harboring p53 abnormalities; this satisfies an unmet clinical need, as such individuals currently have a poor prognosis.

  17. Central-marginal population dynamics in species invasions

    Directory of Open Access Journals (Sweden)

    Qinfeng eGuo

    2014-06-01

    Full Text Available The species’ range limits and associated central-marginal (C-M; i.e., from species range center to margin population dynamics continue to draw increasing attention because of their importance for current emerging issues such as biotic invasions and epidemic diseases under global change. Previous studies have mainly focused on species borders and C-M process in natural settings for native species. More recently, growing efforts are devoted to examine the C-M patterns and process for invasive species partly due to their relatively short history, highly dynamic populations, and management implications. Here I examine recent findings and information gaps related to (1 the C-M population dynamics linked to species invasions, and (2 the possible effects of climate change and land use on the C-M patterns and processes. Unlike most native species that are relatively stable (some even having contracting populations or ranges, many invasive species are still spreading fast and form new distribution or abundance centers. Because of the strong nonlinearity of population demographic or vital rates (i.e. birth, death, immigration and emigration across the C-M gradients and the increased complexity of species ranges due to habitat fragmentation, multiple introductions, range-wide C-M comparisons and simulation involving multiple vital rates are needed in the future.

  18. MED, COMP, multilayered and NEIN: an overview of multiple epiphyseal dysplasia

    Energy Technology Data Exchange (ETDEWEB)

    Lachman, Ralph S. [International Skeletal Dysplasia Registry, UCLA School of Medicine, Radiological Services, Department of Pediatrics, Los Angeles, CA (United States); International Skeletal Dysplasia Registry, Los Angeles, CA (United States); Krakow, Deborah; Cohn, Daniel H.; Rimoin, David L. [International Skeletal Dysplasia Registry, UCLA School of Medicine, Radiological Services, Department of Pediatrics, Los Angeles, CA (United States)

    2005-02-01

    This overview covers the group of disorders that presents radiographically as multiple epiphyseal dysplasia (MED). The disorders include ''classic MED'' (Ribbing and Fairbank types): MED that is caused by mutations in the cartilage oligomeric matrix protein (COMP), type IX collagen, and matrilin 3 genes (MATN3); and MED with multilayered patella, brachydactyly, and clubbed feet resultant from mutations in gene defect diastrophic dysplasia (DTDST). The recently identified gene/molecular abnormalities in these disorders have made more exact identification possible in many cases, although clinical testing is not always available. However, there are specific radiographic findings that allow the accurate diagnosis to be made, thus potentially guiding which molecular defect(s) should be investigated. The modes of inheritance of these distinct MED conditions are not identical. When a specific diagnosis is made, proper genetic counseling as well as prognostication, management issues and complications can be delineated to the patient and family. This review will include the mechanics of diagnostic and molecular triage for these disorders. (orig.)

  19. Structural Analysis of Polyhedral Oligomeric Silsesquioxane Coated SiC Nanoparticles and Their Applications in Thermoset Polymers

    International Nuclear Information System (INIS)

    Reza-E-Rabby, M.; Jeelani, Sh.; Rangari, V. K.

    2015-01-01

    The SiC nanoparticles (NPs) were sonochemically coated with Octa Isobutyl (OI) polyhedral oligomeric silsesquioxane (POSS) to create a compatible interface between particle and thermoset polymer. X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD) techniques were used to analyze the structure of OI-POSS coated SiC nanoparticles. These results revealed the formation of a covalent bonding between SiC and OI-POSS. The transmission electron microscopy (TEM) analysis of OI-POSS coated SiC nanoparticles has also shown the indication of attachment between these two nanoparticles. The OI-POSS coated SiC nanoparticles were further reinforced into a thermoset resin system in order to evaluate mechanical and thermal properties of nano composites. The flexural strength, modulus, and glass transition temperature were found to be enhanced while SiC and OI-POSS coated SiC were infused into epoxy system compared to those properties of neat epoxy resin

  20. Structural Analysis of Polyhedral Oligomeric Silsesquioxane Coated SiC Nanoparticles and Their Applications in Thermoset Polymers

    Directory of Open Access Journals (Sweden)

    Md. Reza-E-Rabby

    2015-01-01

    Full Text Available The SiC nanoparticles (NPs were sonochemically coated with OctaIsobutyl (OI polyhedral oligomeric silsesquioxane (POSS to create a compatible interface between particle and thermoset polymer. X-ray photoelectron spectroscopy (XPS, Fourier transform infrared spectroscopy (FTIR, and X-ray diffraction (XRD techniques were used to analyze the structure of OI-POSS coated SiC nanoparticles. These results revealed the formation of a covalent bonding between SiC and OI-POSS. The transmission electron microscopy (TEM analysis of OI-POSS coated SiC nanoparticles has also shown the indication of attachment between these two nanoparticles. The OI-POSS coated SiC nanoparticles were further reinforced into a thermoset resin system in order to evaluate mechanical and thermal properties of nanocomposites. The flexural strength, modulus, and glass transition temperature were found to be enhanced while SiC and OI-POSS coated SiC were infused into epoxy system compared to those properties of neat epoxy resin.

  1. Interplay of histidine residues of the Alzheimer’s disease Aβ peptide governs its Zn-induced oligomerization

    Science.gov (United States)

    Istrate, Andrey N.; Kozin, Sergey A.; Zhokhov, Sergey S.; Mantsyzov, Alexey B.; Kechko, Olga I.; Pastore, Annalisa; Makarov, Alexander A.; Polshakov, Vladimir I.

    2016-02-01

    Conformational changes of Aβ peptide result in its transformation from native monomeric state to the toxic soluble dimers, oligomers and insoluble aggregates that are hallmarks of Alzheimer’s disease (AD). Interactions of zinc ions with Aβ are mediated by the N-terminal Aβ1-16 domain and appear to play a key role in AD progression. There is a range of results indicating that these interactions trigger the Aβ plaque formation. We have determined structure and functional characteristics of the metal binding domains derived from several Aβ variants and found that their zinc-induced oligomerization is governed by conformational changes in the minimal zinc binding site 6HDSGYEVHH14. The residue H6 and segment 11EVHH14, which are part of this site are crucial for formation of the two zinc-mediated interaction interfaces in Aβ. These structural determinants can be considered as promising targets for rational design of the AD-modifying drugs aimed at blocking pathological Aβ aggregation.

  2. Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α-synuclein assemblies by mass spectrometry

    Directory of Open Access Journals (Sweden)

    Amulya Nidhi Shrivastava

    2016-06-01

    Full Text Available α-Synuclein (α-syn is the principal component of Lewy bodies, the pathophysiological hallmark of individuals affected by Parkinson disease (PD. This neuropathologic form of α-syn contributes to PD progression and propagation of α-syn assemblies between neurons. The data we present here support the proteomic analysis used to identify neuronal proteins that specifically interact with extracellularly applied oligomeric or fibrillar α-syn assemblies (conditions 1 and 2, respectively (doi: 10.15252/embj.201591397 [1]. α-syn assemblies and their cellular partner proteins were pulled down from neuronal cell lysed shortly after exposure to exogenous α-syn assemblies and the associated proteins were identified by mass spectrometry using a shotgun proteomic-based approach. We also performed experiments on pure cultures of astrocytes to identify astrocyte-specific proteins interacting with oligomeric or fibrillar α-syn (conditions 3 and 4, respectively. For each condition, proteins interacting selectively with α-syn assemblies were identified by comparison to proteins pulled-down from untreated cells used as controls. The mass spectrometry data, the database search and the peak lists have been deposited to the ProteomeXchange Consortium database via the PRIDE partner repository with the dataset identifiers PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002256 to PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002263 and doi: 10.6019/http://www.ebi.ac.uk/pride/archive/projects/PXD002256 to 10.6019/http://www.ebi.ac.uk/pride/archive/projects/PXD002263.

  3. Complex patterns of speciation in cosmopolitan "rock posy" lichens--discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota).

    Science.gov (United States)

    Leavitt, Steven D; Fankhauser, Johnathon D; Leavitt, Dean H; Porter, Lyndon D; Johnson, Leigh A; St Clair, Larry L

    2011-06-01

    A growing body of evidence indicates that in some cases morphology-based species circumscription of lichenized fungi misrepresents the number of existing species. The cosmopolitan "rock posy" lichen (Rhizoplaca melanophthalma) species-complex includes a number of morphologically distinct species that are both geographically and ecologically widespread, providing a model system to evaluate speciation in lichen-forming ascomycetes. In this study, we assembled multiple lines of evidence from nuclear DNA sequence data, morphology, and biochemistry for species delimitation in the R. melanophthalma species-complex. We identify a total of ten candidate species in this study, four of which were previously recognized as distinct taxa and six previously unrecognized lineages found within what has been thus far considered a single species. Candidate species are supported using inferences from multiple empirical operational criteria. Multiple instances of sympatry support the view that these lineages merit recognition as distinct taxa. Generally, we found little corroboration between morphological and chemical characters, and previously unidentified lineages were morphologically polymorphic. However, secondary metabolite data supported one cryptic saxicolous lineage, characterized by orsellinic-derived gyrophoric and lecanoric acids, which we consider to be taxonomically significant. Our study of the R. melanophthalma species-complex indicates that the genus Rhizoplaca, as presently circumscribed, is more diverse in western North American than originally perceived, and we present our analyses as a working example of species delimitation in morphologically cryptic and recently diverged lichenized fungi. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. San Diego Multiple Species Conservation Program (MSCP) Rare Plant Monitoring Review and Revision

    Science.gov (United States)

    McEachern, Kathryn; Pavlik, Bruce M.; Rebman, Jon; Sutter, Rob

    2007-01-01

    Introduction The San Diego Multiple Species Conservation Program (MSCP) was developed for the conservation of plants and animals in the south part of San Diego County, under the California Natural Community Conservation Planning Act of 1991 (California Department of Fish and Game) and the Federal Endangered Species Act of 1973, as amended (16 U.S. Code 1531-1544.) The Program is on the leading edge of conservation, as it seeks to both guide development and conserve at-risk species with the oversight of both State and Federal agencies. Lands were identified for inclusion in the MSCP based on their value as habitat for at-risk plants or plant communities (Natural Community Conservation Planning, 2005). Since its inception in the mid-1990s the Program has protected over 100,000 acres, involving 15 jurisdictions and the U.S. Fish and Wildlife Service (USFWS) and California Department of Fish and Game (CDFG) in the conservation of 87 taxa. Surveys for covered species have been conducted, and management and monitoring have been implemented at some high priority sites. Each jurisdiction or agency manages and monitors their conservation areas independently, while collaborating regionally for long-term protection. The San Diego MSCP is on the forefront of conservation, in one of the most rapidly growing urban areas of the country. The planning effort that developed the MSCP was state-of-the-art, using expert knowledge, spatial habitat modeling, and principles of preserve design to identify and prioritize areas for protection. Land acquisition and protection are ahead of schedule for most jurisdictions. Surveys have verified the locations of many rare plant populations known from earlier collections, and they provide general information on population size and health useful for further conservation planning. Management plans have been written or are in development for most MSCP parcels under jurisdictional control. Several agencies are developing databases for implementation

  5. Multiple paternity and hybridization in two smooth-hound sharks.

    Science.gov (United States)

    Marino, Ilaria A M; Riginella, Emilio; Gristina, Michele; Rasotto, Maria B; Zane, Lorenzo; Mazzoldi, Carlotta

    2015-08-10

    Multiple paternity appears to be a common trait of elasmobranch mating systems, with its occurrence likely driven by convenience, due to females seeking to minimize the stress of male harassment. Here we use molecular markers to analyse the frequency of multiple paternity in two related viviparous sharks, Mustelus mustelus and Mustelus punctulatus. We first applied molecular methods to assign pregnant females, embryos and additional reference adults (N = 792) to one of the two species. Paternity analysis was performed using a total of 9 polymorphic microsatellites on 19 females and 204 embryos of M. mustelus, and on 13 females and 303 embryos of M. punctulatus. Multiple paternity occurs in both species, with 47% of M. mustelus and 54% of M. punctulatus litters sired by at least two fathers. Female fecundity is not influenced by multiple mating and in 56% of polyandrous litters paternity is skewed, with one male siring most of the pups. Genetic analyses also revealed hybridization between the two species, with a M. punctulatus female bearing pups sired by a M. mustelus male. The frequency of polyandrous litters in these species is consistent with aspects of their reproductive biology, such as synchronous ovulation and possible occurrence of breeding aggregations.

  6. A Physiologically Based Pharmacokinetic (PB/PK) Model for Multiple Exposure Routes of Soman in Multiple Species

    National Research Council Canada - National Science Library

    Sweeney, Richard E; Langenberg, Jan P; Maxwell, Donald M

    2006-01-01

    ...) levels of soman challenge in three species (rat, guinea pig, marmoset). Allometric formulae were used to compute the compartment volumes, blood flow rates, tidal volume and respiratory rate based upon total animal weight...

  7. Reversible unfolding of infectious prion assemblies reveals the existence of an oligomeric elementary brick.

    Directory of Open Access Journals (Sweden)

    Angélique Igel-Egalon

    2017-09-01

    Full Text Available Mammalian prions, the pathogens that cause transmissible spongiform encephalopathies, propagate by self-perpetuating the structural information stored in the abnormally folded, aggregated conformer (PrPSc of the host-encoded prion protein (PrPC. To date, no structural model related to prion assembly organization satisfactorily describes how strain-specified structural information is encoded and by which mechanism this information is transferred to PrPC. To achieve progress on this issue, we correlated the PrPSc quaternary structural transition from three distinct prion strains during unfolding and refolding with their templating activity. We reveal the existence of a mesoscopic organization in PrPSc through the packing of a highly stable oligomeric elementary subunit (suPrP, in which the strain structural determinant (SSD is encoded. Once kinetically trapped, this elementary subunit reversibly loses all replicative information. We demonstrate that acquisition of the templating interface and infectivity requires structural rearrangement of suPrP, in concert with its condensation. The existence of such an elementary brick scales down the SSD support to a small oligomer and provide a basis of reflexion for prion templating process and propagation.

  8. The Importance of Providing Multiple-Channel Sections in Dredging Activities to Improve Fish Habitat Environments

    Directory of Open Access Journals (Sweden)

    Hung-Pin Chiu

    2016-01-01

    Full Text Available After Typhoon Morakot, dredging engineering was conducted while taking the safety of humans and structures into consideration, but partial stream reaches were formed in the multiple-channel sections in Cishan Stream because of anthropogenic and natural influences. This study mainly explores the distribution of each fish species in both the multiple- and single-channel sections in the Cishan Stream. Parts of the environments did not exhibit significant differences according to a one-way ANOVA comparing the multiple- and single-channel sections, but certain areas of the multiple-channel sections had more diverse habitats. Each fish species was widely distributed by non-metric multidimensional scaling in the multiple-channel sections as compared to those in the single-channel sections. In addition, according to the principal component analysis, each fish species has a preferred environment, and all of them have a wide choice of habitat environments in the multiple-channel sections. Finally, the existence of multiple-channel sections could significantly affect the existence of the fish species under consideration in this study. However, no environmental factors were found to have an influence on fish species in the single-channel sections, with the exception of Rhinogobius nantaiensis. The results show that providing multiple-channel sections in dredging activities could improve fish habitat environments.

  9. Molecular assessment of Podarcis sicula populations in Britain, Greece and Turkey reinforces a multiple-origin invasion pattern in this species

    Directory of Open Access Journals (Sweden)

    Iolanda Silva-Rocha

    2014-12-01

    Full Text Available Biological invasions are a challenge to conservation and constitute a threat to biodiversity worldwide. The Italian wall lizard Podarcis sicula has been widely introduced, and seems capable of adapting to most of the regions where it is established and to impact on native biota. Here we construct a phylogenetic framework to assess the origin of the introduced populations in the United Kingdom, Greece and Turkey comparing cytochrome-b gene sequences of lizards from five locations to published sequences from the native range and other non-native locations. The results support an origin from central Italy for the United Kingdom population, from the Adriatic region for the Greek population and from Calabria for the population from Turkey. These results emphasise the multiple-source pattern of introduction of this species identified in previous studies. The improvement in the knowledge of the origin and pathways by which invaders arrive in new areas, as well as the monitoring of their populations, are crucial for successful strategies to deal with exotic species.

  10. Efficient species-level monitoring at the landscape scale

    Science.gov (United States)

    Barry R. Noon; Larissa L. Bailey; Thomas D. Sisk; Kevin S. McKelvey

    2012-01-01

    Monitoring the population trends of multiple animal species at a landscape scale is prohibitively expensive. However, advances in survey design, statistical methods, and the ability to estimate species presence on the basis of detection­nondetection data have greatly increased the feasibility of species-level monitoring. For example, recent advances in monitoring make...

  11. Genetic assessment of ornamental fish species from North East India.

    Science.gov (United States)

    Dhar, Bishal; Ghosh, Sankar Kumar

    2015-01-25

    Ornamental fishes are traded with multiple names from various parts around the world, including North East India. Most are collected from the wild, due to lack of species-specific culture or breeding, and therefore, such unmanaged collection of the wild and endemic species could lead to severe threats to biodiversity. Despite many regulatory policies, trade of threatened species, including the IUCN listed species have been largely uncontrolled, due to species identification problems arising from the utilization of multiple trade names. So, the development of species-specific DNA marker is indispensable where DNA Barcoding is proved to be helpful in species identification. Here, we investigated, through DNA Barcoding and morphological assessment, the identification of 128 ornamental fish specimens exported from NE India from different exporters. The generated sequences were subjected to similarity match in BOLD-IDS as well as BLASTN, and analysed using MEGA5.2 for species identification through Neighbour-Joining (NJ) clustering, and K2P distance based approach. The analysis revealed straightforward identification of 84 specimens into 35 species, while 44 specimens were difficult to distinguish based on CO1 barcode alone. However, these cases were resolved through morphology, NJ and distanced based method and found to be belonging to 16 species. Among the 51 identified species, 14 species represented multiple trade names; 17 species belonged to threatened category. Species-level identification through DNA Barcoding along with traditional morphotaxonomy reflects its efficacy in regulating ornamental fish trade and therefore, appeals for their conservation in nature. The use of trade names rather than the zoological name created the passage for trafficking of the threatened species and demands immediate attention for sustaining wildlife conservation. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Relating biomarkers to whole-organism effects using species sensitivity distributions : A pilot study for marine species exposed to oil

    NARCIS (Netherlands)

    Smit, M.G.D.; Bechmann, R.K.; Hendriks, A.J.; Skadsheim, A.; Larsen, B.K.; Baussant, T.; Bamber, S.; Sannei, S.

    2009-01-01

    Biomarkers are widely used to measure environmental impacts on marine species. For many biomarkers, it is not clear how the signal levels relate to effects on the whole organism. This paper shows how species sensitivity distributions (SSDs) can be applied to evaluate multiple biomarker responses in

  13. Differential recognition of the multiple banded antigen isoforms across Ureaplasma parvum and Ureaplasma urealyticum species by monoclonal antibodies.

    Science.gov (United States)

    Aboklaish, Ali F; Ahmed, Shatha; McAllister, Douglas; Cassell, Gail; Zheng, Xiaotian T; Spiller, Owen B

    2016-08-01

    Two separate species of Ureaplasma have been identified that infect humans: Ureaplasma parvum and Ureaplasma urealyticum. Most notably, these bacteria lack a cell wall and are the leading infectious organism associated with infection-related induction of preterm birth. Fourteen separate representative prototype bacterial strains, called serovars, are largely differentiated by the sequence of repeating units in the C-terminus of the major surface protein: multiple-banded antigen (MBA). Monoclonal antibodies that recognise single or small groups of serovars have been previously reported, but these reagents remain sequestered in individual research laboratories. Here we characterise a panel of commercially available monoclonal antibodies raised against the MBA and describe the first monoclonal antibody that cross-reacts by immunoblot with all serovars of U. parvum and U. urealyticum species. We also describe a recombinant MBA expressed by Escherichia coli which facilitated further characterisation by immunoblot and demonstrate immunohistochemistry of paraffin-embedded antigens. Immunoblot reactivity was validated against well characterised previously published monoclonal antibodies and individual commercial antibodies were found to recognise all U. parvum strains, only serovars 3 and 14 or only serovars 1 and 6, or all strains belonging to U. parvum and U. urealyticum. MBA mass was highly variable between strains, consistent with variation in the number of C-terminal repeats between strains. Antibody characterisation will enable future investigations to correlate severity of pathogenicity to MBA isoform number or mass, in addition to development of antibody-based diagnostics that will detect infection by all Ureaplasma species or alternately be able to differentiate between U. parvum, U. urealyticum or mixed infections. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Single Site Silica Supported Tetramethyl Niobium by the SOMC Strategy: Synthesis, Characterization and Structure-Activity Relationship in Ethylene Oligomerization Reaction

    KAUST Repository

    Hamieh, Ali Imad Ali

    2017-06-06

    Silica supported Tetramethyl niobium complex [(≡SiO)NbMe4] 2 has been isolated by surface alkylation of [(≡SiO-)NbCl3Me] 1 with dimethyl zinc in pentane. 1 can be easily synthesized by grafting of NbCl3Me2 on to the surface of partially dehydroxylated silica by the SOMC strategy. Precise structural analysis was carried out by the FTIR, advance solid state NMR, elemental analysis and mass balance techniques (gas quantification after treating 2 with degassed water) . Complex 1 was found to be active in the ethylene oligomerization to produce up to C30, whereas to our surprise complex 2 selectively dimerizes ethylene into 1-butene in the absence of a co-catalyst at the same conversion levels.

  15. Two intestinal specific nuclear factors binding to the lactase-phlorizin hydrolase and sucrase-isomaltase promoters are functionally related oligomeric molecules

    DEFF Research Database (Denmark)

    Troelsen, J T; Mitchelmore, C; Sjöström, H

    1994-01-01

    Lactase-phlorizin hydrolase (LPH) and sucrase-isomaltase (SI) are enterocyte-specific gene products. The identification of regulatory cis-elements in the promoter of these two genes has enabled us to carry out comparative studies of the corresponding intestinal-specific nuclear factors (NF-LPH1...... and SIF1-BP). Electrophoretic mobility shift assays demonstrated that the two nuclear factors compete for binding on the same cis-elements. The molecular size of the DNA binding polypeptide is estimated to be approximately 50 kDa for both factors. In the native form the factors are found as 250 k......Da oligomeric complexes. Based on these results NF-LPH1 and SIF1-BP are suggested to be either identical or closely related molecules....

  16. Single Site Silica Supported Tetramethyl Niobium by the SOMC Strategy: Synthesis, Characterization and Structure-Activity Relationship in Ethylene Oligomerization Reaction

    KAUST Repository

    Hamieh, Ali Imad Ali; Dey, Raju; Nekoueishahraki, Bijan; Samantaray, Manoja; Chen, Yin; Abou-Hamad, Edy; Basset, Jean-Marie

    2017-01-01

    Silica supported Tetramethyl niobium complex [(≡SiO)NbMe4] 2 has been isolated by surface alkylation of [(≡SiO-)NbCl3Me] 1 with dimethyl zinc in pentane. 1 can be easily synthesized by grafting of NbCl3Me2 on to the surface of partially dehydroxylated silica by the SOMC strategy. Precise structural analysis was carried out by the FTIR, advance solid state NMR, elemental analysis and mass balance techniques (gas quantification after treating 2 with degassed water) . Complex 1 was found to be active in the ethylene oligomerization to produce up to C30, whereas to our surprise complex 2 selectively dimerizes ethylene into 1-butene in the absence of a co-catalyst at the same conversion levels.

  17. Alternaria section Alternaria: Species, formae speciales or pathotypes'

    NARCIS (Netherlands)

    Woudenberg, J.H.C.; Seidl, M.F.; Groenewald, J.Z.; de Vries, M .; Stielow, B.; Thomma, B.P.H.J.; Crous, P.W.

    2015-01-01

    The cosmopolitan fungal genus Alternaria consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternaria sect. Alternaria contains most of the small-spored Alternaria species with concatenated

  18. Alternaria section Alternaria: Species, formae speciales or pathotypes?

    NARCIS (Netherlands)

    Woudenberg, J.H.C.; Seidl, M.F.; Groenewald, J.Z.; Vries, de M.; Stielow, J.B.; Thomma, B.; Crous, P.W.

    2015-01-01

    The cosmopolitan fungal genus Alternaria consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternaria sect. Alternaria contains most of the small-spored Alternaria species with concatenated

  19. As multiple fish species in large marine ecosystems are harvested ...

    African Journals Online (AJOL)

    CMPTMAC10

    and of other top predators such as marine mammals. This concern ... whereas single-species fishing theory implies that fishing leads to surplus by removing larger, older, less-productive ...... pools (the “cod is not a tuna” problem, Longhurst.

  20. Multicore Magnetic Nanoparticles Coated with Oligomeric Micelles: Characterization and Potential for the Extraction of Contaminants over a Wide Polarity Range.

    Science.gov (United States)

    Naous, Mohamed; García-Gómez, Diego; López-Jiménez, Francisco José; Bouanani, Farida; Lunar, María Loreto; Rubio, Soledad

    2017-01-17

    Oligomeric micelles from sodium undecylenate (oSUD) were chemisorbed to magnetic iron oxide nanoparticles (MNPs) through a single-step synthetic route involving the simultaneous nanoparticle formation and functionalization in an aqueous medium. The resulting spherical nanoparticles (MNPs-oSUD) consisted of a concatenation of iron oxide cores, with an average size of 7.7 nm, bound by oSUD micelles (particle average diameter of ca. 200 nm). Micellar coverage was ∼50% of the MNP-oSUD (by weight) and offered multiple retention mechanisms (e.g., dispersion, hydrogen bonding, polar, and ionic) for solute solubilization while keeping it intact during analyte elution. The high density of micelles and variety of interactions provided by this sorbent rendered it highly efficient for the extraction of aromatic amines in a wide polarity range (log K ow values from -0.80 to 4.05) from textiles, urine, and wastewater. Extraction took 5 min, no cleanup or evaporation of the extracts was needed and the method, based on LC-MS/MS quantitation, proved matrix-independent. Recoveries for 17 aromatic amines in samples were in the range of 93%-123% while those with negative log K ow values were in the range of 69%-87%. Detection limits for aromatic amines in textiles (0.007-2 mg kg -1 ) were well below the limits legislated by the European Union (EU) (30 mg kg -1 ) and those in urine and wastewater (0.004-1.5 μg L -1 ) were at the level usually found in real-world applications. All the analyzed samples were positive in aromatic amines. The easy synthesis and excellent extraction properties of MNPs-oSUD anticipate their high potential not only for multiresidue analysis but also in other fields such as water remediation.

  1. Nucleotide-Binding Oligomerization Domain-1 and -2 Play No Role in Controlling Brucella abortus Infection in Mice

    Directory of Open Access Journals (Sweden)

    Fernanda S. Oliveira

    2012-01-01

    Full Text Available Nucleotide-binding oligomerization domain proteins (NODs are modular cytoplasmic proteins implicated in the recognition of peptidoglycan-derived molecules. Further, several in vivo studies have demonstrated a role for Nod1 and Nod2 in host defense against bacterial pathogens. Here, we demonstrated that macrophages from NOD1-, NOD2-, and Rip2-deficient mice produced lower levels of TNF-α following infection with live Brucella abortus compared to wild-type mice. Similar reduction on cytokine synthesis was not observed for IL-12 and IL-6. However, NOD1, NOD2, and Rip2 knockout mice were no more susceptible to infection with virulent B. abortus than wild-type mice. Additionally, spleen cells from NOD1-, NOD2-, and Rip2-deficient mice showed unaltered production of IFN-γ compared to C57BL/6 mice. Taken together, this study demonstrates that NOD1, NOD2 and Rip2 are dispensable for the control of B. abortus during in vivo infection.

  2. Preparation of polyhedral oligomeric silsesquioxane based hybrid monoliths by ring-opening polymerization for capillary LC and CEC.

    Science.gov (United States)

    Lin, Hui; Zhang, Zhenbin; Dong, Jing; Liu, Zhongshan; Ou, Junjie; Zou, Hanfa

    2013-09-01

    A new organic-inorganic hybrid monolith was prepared by the ring-opening polymerization of octaglycidyldimethylsilyl polyhedral oligomeric silsesquioxane (POSS) with 1,4-butanediamine (BDA) using 1-propanol, 1,4-butanediol, and PEG 10,000 as a porogenic system. Benefiting from the moderate phase separation process, the resulting poly(POSS-co-BDA) hybrid monolith possessed a uniform microstructure and exhibited excellent performance in chromatographic applications. Neutral, acidic, and basic compounds were successfully separated on the hybrid monolith in capillary LC (cLC), and high column efficiencies were achieved in all of the separations. In addition, as the amino groups could generate a strong EOF, the hybrid monolith was also applied in CEC for the separation of neutral and polar compounds, and a satisfactory performance was obtained. These results demonstrate that the poly(POSS-co-BDA) hybrid monolith is a good separation media in chromatographic separations of various types of compounds by both cLC and CEC. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Functional significance of the oligomeric structure of the Na,K-pump from radiation inactivation and ligand binding

    International Nuclear Information System (INIS)

    Norby, J.G.; Jensen, J.

    1991-01-01

    The present article is concerned with the oligomeric structure and function of the Na,K-pump (Na,K-ATPase). The questions we have addressed, using radiation inactivation and target size analysis as well as ligand binding, are whether the minimal structural unit and the functional unit have more than one molecule of the catalytic subunit, alpha. The authors first discuss the fundamentals of the radiation inactivation method and emphasize the necessity for rigorous internal standardization with enzymes of known molecular mass. They then demonstrate that the radiation inactivation of Na,K-ATPase is a stepwise process which leads to intermediary fragments of the alpha-subunit with partial catalytic activity. From the target size analysis it is most likely that the membrane-bound Na,K-ATPase is structurally organized as a diprotomer containing two alpha-subunits. Determination of ADP- and ouabain-binding site stoichiometry favors a theory with one substrate site per (alpha beta) 2. 47 references

  4. Multiple Phytophthora species associated with a single riparian ecosystem in South Africa.

    Science.gov (United States)

    Nagel, Jan H; Slippers, Bernard; Wingfield, Michael J; Gryzenhout, Marieka

    2015-01-01

    The diversity of Phytophthora spp. in rivers and riparian ecosystems has received considerable international attention, although little such research has been conducted in South Africa. This study determined the diversity of Phytophthora spp. within a single river in Gauteng province of South Africa. Samples were collected over 1 y including biweekly river baiting with Rhododendron indicum leaves. Phytophthora isolates were identified with phylogenetic analyses of sequences for the internal transcribed spacer (ITS) region of the ribosomal DNA and the mitochondrial cytochrome oxidase c subunit I (coxI) gene. Eight Phytophthora spp. were identified, including a new taxon, P. taxon Sisulu-river, and two hybrid species from Cooke's ITS clade 6. Of these, species from Clade 6 were the most abundant, including P. chlamydospora and P. lacustris. Species residing in Clade 2 also were encountered, including P. multivora, P. plurivora and P. citrophthora. The detection of eight species in this investigation of Phytophthora diversity in a single riparian river ecosystem in northern South Africa adds to the known diversity of this genus in South Africa and globally. © 2015 by The Mycological Society of America.

  5. Semiparametric bivariate zero-inflated Poisson models with application to studies of abundance for multiple species

    Science.gov (United States)

    Arab, Ali; Holan, Scott H.; Wikle, Christopher K.; Wildhaber, Mark L.

    2012-01-01

    Ecological studies involving counts of abundance, presence–absence or occupancy rates often produce data having a substantial proportion of zeros. Furthermore, these types of processes are typically multivariate and only adequately described by complex nonlinear relationships involving externally measured covariates. Ignoring these aspects of the data and implementing standard approaches can lead to models that fail to provide adequate scientific understanding of the underlying ecological processes, possibly resulting in a loss of inferential power. One method of dealing with data having excess zeros is to consider the class of univariate zero-inflated generalized linear models. However, this class of models fails to address the multivariate and nonlinear aspects associated with the data usually encountered in practice. Therefore, we propose a semiparametric bivariate zero-inflated Poisson model that takes into account both of these data attributes. The general modeling framework is hierarchical Bayes and is suitable for a broad range of applications. We demonstrate the effectiveness of our model through a motivating example on modeling catch per unit area for multiple species using data from the Missouri River Benthic Fishes Study, implemented by the United States Geological Survey.

  6. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.

    Science.gov (United States)

    Chen, Wen; Djama, Zeinab Robleh; Coffey, Michael D; Martin, Frank N; Bilodeau, Guillaume J; Radmer, Lorien; Denton, Geoff; Lévesque, C André

    2013-01-01

    Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

  7. Comparative microbial modules resource: generation and visualization of multi-species biclusters.

    Science.gov (United States)

    Kacmarczyk, Thadeous; Waltman, Peter; Bate, Ashley; Eichenberger, Patrick; Bonneau, Richard

    2011-12-01

    The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures - results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation. © 2011 Kacmarczyk et al.

  8. Comparative microbial modules resource: generation and visualization of multi-species biclusters.

    Directory of Open Access Journals (Sweden)

    Thadeous Kacmarczyk

    2011-12-01

    Full Text Available The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html. The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures - results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation.

  9. Coatings of molecularly imprinted polymers based on polyhedral oligomeric silsesquioxane for open tubular capillary electrochromatography.

    Science.gov (United States)

    Zhao, Qing-Li; Zhou, Jin; Zhang, Li-Shun; Huang, Yan-Ping; Liu, Zhao-Sheng

    2016-05-15

    Polyhedral oligomeric silsesquioxane (POSS) was successfully applied, for the first time, to prepare imprinted monolithic coating for capillary electrochromatography. The imprinted monolithic coating was synthesized with a mixture of PSS-(1-Propylmethacrylate)-heptaisobutyl substituted (MA 0702), S-amlodipine (template), methacrylic acid (functional monomer), and 2-methacrylamidopropyl methacrylate (crosslinker), in a porogenic mixture of toluene-isooctane. The influence of synthesis parameters on the imprinting effect and separation performance, including the amount of MA 0702, the ratio of template to monomer, and the ratio of monomer to crosslinker, was investigated. The greatest resolution for enantiomers separation on the imprinted monolithic column prepared with MA 0702 was up to 22.3, about 2 times higher than that prepared in absence of the POSS. Column efficiency on the POSS-based MIP coatings was beyond 30,000 plate m(-1). The comparisons between MIP coating synthesized with the POSS and without the POSS were made in terms of selectivity, column efficiency, and resolution. POSS-based MIP capillaries with naproxen or zopiclone was also prepared and separation of enantiomers can be achieved. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Morphological evolution in dewetting polystyrene/polyhedral oligomeric silsesquioxane thin film bilayers.

    Science.gov (United States)

    Paul, Rituparna; Karabiyik, Ufuk; Swift, Michael C; Hottle, John R; Esker, Alan R

    2008-05-06

    Morphological evolution in dewetting thin film bilayers of polystyrene (PS) and a polyhedral oligomeric silsesquioxane (POSS), trisilanolphenyl-POSS (TPP), was studied as a function of annealing temperature and annealing time. The results demonstrate unique dewetting morphologies in PS/TPP bilayers at elevated temperatures that are significantly different from those typically observed in dewetting polymer/polymer bilayers. During temperature ramp studies by optical microscopy (OM) in the reflection mode, PS/TPP bilayers form cracks with a weak optical contrast at approximately 130 degrees C. The crack formation is attributed to tensile stresses within the upper TPP layer. The weak optical contrast of the cracks observed in the bilayers for annealing temperatures below approximately 160 degrees C is consistent with the cracking and dewetting of only the upper TPP layer from the underlying PS layer. The optical contrast of the morphological features is significantly enhanced at annealing temperatures of >160 degrees C. This observation suggests dewetting of both the upper TPP and the lower PS layers that results in the exposure of the silicon substrate. Upon annealing the PS/TPP bilayers at 200 degrees C in a temperature jump experiment, the upper TPP layer undergoes instantaneous cracking as observed by OM. These cracks in the upper TPP layer serve as nucleation sites for rapid dewetting and aggregation of the TPP layer, as revealed by OM and atomic force microscopy (AFM). X-ray photoelectron spectroscopy (XPS) results indicated that dewetting of the lower PS layer ensued for annealing times >5 min and progressed up to 90 min. For annealing times >90 min, OM, AFM, and XPS results revealed complete dewetting of both the layers with the formation of TPP encapsulated PS droplets.

  11. Time-domain multiple-quantum NMR

    International Nuclear Information System (INIS)

    Weitekamp, D.P.

    1982-11-01

    The development of time-domain multiple-quantum nuclear magnetic resonance is reviewed through mid 1982 and some prospects for future development are indicated. Particular attention is given to the problem of obtaining resolved, interpretable, many-quantum spectra for anisotropic magnetically isolated systems of coupled spins. New results are presented on a number of topics including the optimization of multiple-quantum-line intensities, analysis of noise in two-dimensional spectroscopy, and the use of order-selective excitation for cross polarization between nuclear-spin species

  12. No Inbreeding depression for low temperature developmental acclimation across multiple drosophila species

    DEFF Research Database (Denmark)

    Kristensen, Torsten Nygård; Loeschcke, Volker; Bilde, Trine

    2011-01-01

    stressful temperatures, but whether adaptation to thermal stress through plastic responses also is affected by inbreeding is so far not clear. In this study, we test inherent cold resistance and the ability to respond plastically to temperature changes through developmental cold acclimation in inbred...... the ability to respond adaptively to temperature acclimation, and (3) tropical species with low basal resistance show stronger adaptive plastic responses to developmental acclimation compared to widespread species...

  13. Method for aquatic multiple species toxicant testing: acute toxicity of 10 chemicals to 5 vertebrates and 2 invertebrates. [Pimephales promelas; Carassius auratus; Ictalurus punctatus; Lepomis macrochirus; Salmo gairdneri; Orconectes immunis; Aplexa hypnorum

    Energy Technology Data Exchange (ETDEWEB)

    Phipps, G.L.; Holcombe, G.W.

    1985-01-01

    A method was developed to simultaneously ascertain 96 h LC/sub 50/ values for seven freshwater species in a single flow through test with measured concentrations. It allows interspecific comparisons, easy determination of the most sensitive species, and cuts cost of labor, materials and chemical analysis for measured concentration tests. Species tested included fathead minnows Pimephales promelas, goldfish Carassius auratus, channel catfish Ictalurus punctatus, bluegill Lepomis macrochirus, rainbow trout Salmo gairdneri, crayfish Orconectes immunis and snails Aplexa hypnorum. Compounds tested were pentachlorophenol, 2-chloroethanol, 2,4-pentanedione, hexachloroethane, ..cap alpha..-bromo-2',5'-dimethoxyacetophenone, benzaldehyde, 1,3-dichloro-4,6-dinitro-benzene, dursban, sevin and cadmium chloride. The LC/sub 50/ values from these multiple species tests compared favourably with those determined using single species tests at this laboratory, usually within 20%.

  14. Cross-species infection trials reveal cryptic parasite varieties and a putative polymorphism shared among host species.

    Science.gov (United States)

    Luijckx, Pepijn; Duneau, David; Andras, Jason P; Ebert, Dieter

    2014-02-01

    A parasite's host range can have important consequences for ecological and evolutionary processes but can be difficult to infer. Successful infection depends on the outcome of multiple steps and only some steps of the infection process may be critical in determining a parasites host range. To test this hypothesis, we investigated the host range of the bacterium Pasteuria ramosa, a Daphnia parasite, and determined the parasites success in different stages of the infection process. Multiple genotypes of Daphnia pulex, Daphnia longispina and Daphnia magna were tested with four Pasteuria genotypes using infection trials and an assay that determines the ability of the parasite to attach to the hosts esophagus. We find that attachment is not specific to host species but is specific to host genotype. This may suggest that alleles on the locus controlling attachment are shared among different host species that diverged 100 million year. However, in our trials, Pasteuria was never able to reproduce in nonnative host species, suggesting that Pasteuria infecting different host species are different varieties, each with a narrow host range. Our approach highlights the explanatory power of dissecting the steps of the infection process and resolves potentially conflicting reports on parasite host ranges. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  15. Federated or cached searches: providing expected performance from multiple invasive species databases

    Science.gov (United States)

    Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

    2011-01-01

    Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

  16. Localization of A11-reactive oligomeric species in prion diseases

    DEFF Research Database (Denmark)

    Aidt, Frederik H; Hasholt, Lis F; Christiansen, Michael

    2013-01-01

    To investigate in prion diseases the in-situ localization of prion protein oligomers sharing a common epitope with amyloid oligomers involved in a range of neurodegenerative diseases.......To investigate in prion diseases the in-situ localization of prion protein oligomers sharing a common epitope with amyloid oligomers involved in a range of neurodegenerative diseases....

  17. Genetic complexity and multiple infections with more Parvovirus species in naturally infected cats

    Directory of Open Access Journals (Sweden)

    Battilani Mara

    2011-03-01

    Full Text Available Abstract Parvoviruses of carnivores include three closely related autonomous parvoviruses: canine parvovirus (CPV, feline panleukopenia virus (FPV and mink enteritis virus (MEV. These viruses cause a variety of serious diseases, especially in young patients, since they have a remarkable predilection for replication in rapidly dividing cells. FPV is not the only parvovirus species which infects cats; in addition to MEV, the new variants of canine parvovirus, CPV-2a, 2b and 2c have also penetrated the feline host-range, and they are able to infect and replicate in cats, causing diseases indistinguishable from feline panleukopenia. Furthermore, as cats are susceptible to both CPV-2 and FPV viruses, superinfection and co-infection with multiple parvovirus strains may occur, potentially facilitating recombination and high genetic heterogeneity. In the light of the importance of cats as a potential source of genetic diversity for parvoviruses and, since feline panleukopenia virus has re-emerged as a major cause of mortality in felines, the present study has explored the molecular characteristics of parvovirus strains circulating in cat populations. The most significant findings reported in this study were (a the detection of mixed infection FPV/CPV with the presence of one parvovirus variant which is a true intermediate between FPV/CPV and (b the quasispecies cloud size of one CPV sample variant 2c. In conclusion, this study provides new important results about the evolutionary dynamics of CPV infections in cats, showing that CPV has presumably started a new process of readaptation in feline hosts.

  18. Multi-species biofilm of Candida albicans and non-Candida albicans Candida species on acrylic substrate

    Directory of Open Access Journals (Sweden)

    Apurva K Pathak

    2012-02-01

    Full Text Available OBJECTIVE: In polymicrobial biofilms bacteria extensively interact with Candida species, but the interaction among the different species of the Candida is yet to be completely evaluated. In the present study, the difference in biofilm formation ability of clinical isolates of four species of Candida in both single-species and multi-species combinations on the surface of dental acrylic resin strips was evaluated. MATERIAL AND METHODS: The species of Candida, isolated from multiple species oral candidiasis of the neutropenic patients, were used for the experiment. Organisms were cultured on Sabouraud dextrose broth with 8% glucose (SDB. Biofilm production on the acrylic resins strips was determined by crystal violet assay. Student's t-test and ANOVA were used to compare in vitro biofilm formation for the individual species of Candida and its different multi-species combinations. RESULTS: In the present study, differences between the mean values of the biofilm-forming ability of individual species (C. glabrata>C. krusei>C. tropicalis>C. albicans and in its multi-species' combinations (the highest for C. albicans with C. glabrata and the lowest for all the four species combination were reported. CONCLUSIONS: The findings of this study showed that biofilm-forming ability was found greater for non-Candida albicans Candida species (NCAC than for C. albicans species with intra-species variation. Presence of C. albicans in multi-species biofilms increased, whereas; C. tropicalis decreased the biofilm production with all other NCAC species.

  19. Ward identities and consistency relations for the large scale structure with multiple species

    International Nuclear Information System (INIS)

    Peloso, Marco; Pietroni, Massimo

    2014-01-01

    We present fully nonlinear consistency relations for the squeezed bispectrum of Large Scale Structure. These relations hold when the matter component of the Universe is composed of one or more species, and generalize those obtained in [1,2] in the single species case. The multi-species relations apply to the standard dark matter + baryons scenario, as well as to the case in which some of the fields are auxiliary quantities describing a particular population, such as dark matter halos or a specific galaxy class. If a large scale velocity bias exists between the different populations new terms appear in the consistency relations with respect to the single species case. As an illustration, we discuss two physical cases in which such a velocity bias can exist: (1) a new long range scalar force in the dark matter sector (resulting in a violation of the equivalence principle in the dark matter-baryon system), and (2) the distribution of dark matter halos relative to that of the underlying dark matter field

  20. Computational Study of the Effect of Confinement within Microporous Structures on the Activity and Selectivity of Metallocene Catalysts for Ethylene Oligomerization

    KAUST Repository

    Toulhoat, Hervé

    2011-03-02

    The effect of confinement within some zeolitic structures on the activity and selectivity of metallocene catalysts for the ethylene oligomerization has been investigated using grand canonical Monte Carlo simulations (GCMC). The following zeolite (host) frameworks displaying different pore sizes, have been studied as solid hosts: mazzite (MAZ), AIPO-8 (AET), UTD-1F (DON), faujasite (FAU), and VPI-5 (VFI). Intermediates and transition states involved in the ethylene trimerization reaction catalyzed by a Ti-based catalyst [(η5-C5H4CMe2C6H 5)TiCl3/MAO] have been used as sorbates (guests). We have demonstrated linear correlations with slope aH,j between the adsorption enthalpy and the molecular volume Vm of the sorbates, each holding for a given microporous host below a host-specific threshold V mmax,j. Beyond this maximal molecular volume, the adsorption vanishes due to steric exclusion. aH,j increases, and Vmmax,j decreases with decreasing host pore size, in line with the confinement concept. We moreover showed that, in the limit of vanishing loading (Henry regime), the enthalpies and entropies of adsorption in a given host are linearly correlated. We have defined a host-specific confinement compensation temperature a j, which refers to a temperature where the stabilizing adsorption enthalpic interactions are canceled out against the loss in entropy. However, calculated aj are much larger than the operating temperatures. With a setup microkinetic model, we predict that the activity and selectivity of the confined Ti-catalyst in ethylene oligomerization can be significantly altered with respect to homogeneous phase conditions, since the adsorption free energies of transition states and intermediates also become functions of aH,j and Vm. We have applied this theory to predict the optimum host pore size to get maximum α-octene production, instead of α-hexene, which is primarily produced in the homogeneous phase. We also predict a significantly increased activity for

  1. Biological species in the viral world.

    Science.gov (United States)

    Bobay, Louis-Marie; Ochman, Howard

    2018-06-05

    Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.

  2. Preliminary assessment of the ecological risks to wide-ranging wildlife species on the Oak Ridge Reservation

    Energy Technology Data Exchange (ETDEWEB)

    Sample, B.E.; Baron, L.A.; Jackson, B.L.

    1995-08-01

    Historically, ecological risk assessment at CERCLA sites [such as the Oak Ridge Reservation (ORR)], has focused on species that may be definitively associated with a contaminated area or source operable unit. Consequently the species that are generally considered are those with home ranges small enough such that multiple individuals or a distinct population can be expected to reside within the boundaries of the contaminated site. This approach is adequate for sites with single, discrete areas of contamination that only provide habitat for species with limited requirements. This approach is not adequate however for large sites with multiple, spatially separated contaminated areas that provide habitat for wide-ranging wildlife species. Because wide-ranging wildlife species may travel between and use multiple contaminated sites they may be exposed to and be at risk from contaminants from multiple locations. Use of a particular contaminated site by wide-ranging species will be dependent upon the amount of suitable habitat available at that site. Therefore to adequately evaluate risks to wide-ranging species at the ORR-wide scale, the use of multiple contaminated sites must be weighted by the amount of suitable habitat on OUs. This reservation-wide ecological risk assessment is intended to identify which endpoints are significantly at risk; which contaminants are responsible for this risk; and which OUs significantly contribute to risk.

  3. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

    DEFF Research Database (Denmark)

    Friis-Nielsen, Jens; Kjartansdóttir, Kristín Rós; Mollerup, Sarah

    2016-01-01

    have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32...

  4. Hybrid approaches for multiple-species stochastic reaction-diffusion models

    Science.gov (United States)

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-10-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  5. Hybrid approaches for multiple-species stochastic reaction-diffusion models.

    KAUST Repository

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K; Byrne, Helen

    2015-01-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  6. Hybrid approaches for multiple-species stochastic reaction-diffusion models.

    KAUST Repository

    Spill, Fabian

    2015-10-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  7. The reverse effects of random perturbation on discrete systems for single and multiple population models

    International Nuclear Information System (INIS)

    Kang, Li; Tang, Sanyi

    2016-01-01

    Highlights: • The discrete single species and multiple species models with random perturbation are proposed. • The complex dynamics and interesting bifurcation behavior have been investigated. • The reverse effects of random perturbation on discrete systems have been discussed and revealed. • The main results can be applied for pest control and resources management. - Abstract: The natural species are likely to present several interesting and complex phenomena under random perturbations, which have been confirmed by simple mathematical models. The important questions are: how the random perturbations influence the dynamics of the discrete population models with multiple steady states or multiple species interactions? and is there any different effects for single species and multiple species models with random perturbation? To address those interesting questions, we have proposed the discrete single species model with two stable equilibria and the host-parasitoid model with Holling type functional response functions to address how the random perturbation affects the dynamics. The main results indicate that the random perturbation does not change the number of blurred orbits of the single species model with two stable steady states compared with results for the classical Ricker model with same random perturbation, but it can strength the stability. However, extensive numerical investigations depict that the random perturbation does not influence the complexities of the host-parasitoid models compared with the results for the models without perturbation, while it does increase the period of periodic orbits doubly. All those confirm that the random perturbation has a reverse effect on the dynamics of the discrete single and multiple population models, which could be applied in reality including pest control and resources management.

  8. Multifaceted, cross-generational costs of hybridization in sibling Drosophila species.

    Directory of Open Access Journals (Sweden)

    Erin M Myers

    Full Text Available Maladaptive hybridization, as determined by the pattern and intensity of selection against hybrid individuals, is an important factor contributing to the evolution of prezygotic reproductive isolation. To identify the consequences of hybridization between Drosophila pseudoobscura and D. persimilis, we estimated multiple fitness components for F1 hybrids and backcross progeny and used these to compare the relative fitness of parental species and their hybrids across two generations. We document many sources of intrinsic (developmental and extrinsic (ecological selection that dramatically increase the fitness costs of hybridization beyond the well-documented F1 male sterility in this model system. Our results indicate that the cost of hybridization accrues over multiple generations and reinforcement in this system is driven by selection against hybridization above and beyond the cost of hybrid male sterility; we estimate a fitness loss of >95% relative to the parental species across two generations of hybridization. Our findings demonstrate the importance of estimating hybridization costs using multiple fitness measures from multiple generations in an ecologically relevant context; so doing can reveal intense postzygotic selection against hybridization and thus, an enhanced role for reinforcement in the evolution of populations and diversification of species.

  9. Multifaceted, cross-generational costs of hybridization in sibling Drosophila species.

    Science.gov (United States)

    Myers, Erin M; Harwell, Tiffany I; Yale, Elizabeth L; Lamb, Abigail M; Frankino, W Anthony

    2013-01-01

    Maladaptive hybridization, as determined by the pattern and intensity of selection against hybrid individuals, is an important factor contributing to the evolution of prezygotic reproductive isolation. To identify the consequences of hybridization between Drosophila pseudoobscura and D. persimilis, we estimated multiple fitness components for F1 hybrids and backcross progeny and used these to compare the relative fitness of parental species and their hybrids across two generations. We document many sources of intrinsic (developmental) and extrinsic (ecological) selection that dramatically increase the fitness costs of hybridization beyond the well-documented F1 male sterility in this model system. Our results indicate that the cost of hybridization accrues over multiple generations and reinforcement in this system is driven by selection against hybridization above and beyond the cost of hybrid male sterility; we estimate a fitness loss of >95% relative to the parental species across two generations of hybridization. Our findings demonstrate the importance of estimating hybridization costs using multiple fitness measures from multiple generations in an ecologically relevant context; so doing can reveal intense postzygotic selection against hybridization and thus, an enhanced role for reinforcement in the evolution of populations and diversification of species.

  10. Micropropagation and cytogenetic assessment of Zingiber species of Northeast India.

    Science.gov (United States)

    Das, Archana; Kesari, Vigya; Rangan, Latha

    2013-12-01

    An improved micropropagation protocol was developed for Zingiber moran and Z. zerumbet, two wild species of the genus Zingiber, found in Northeast India. The effects of growth regulators, sugar concentrations, and nutrients were tested on the rate of shoot initiation and multiplication. An increase in proliferation and multiplication occurred in modified Murashige and Skoog (MS) medium supplemented with benzyladenine and kinetin. About 2 % sucrose and 0.7 % agar were found to be the optimum for shoot multiplication and regeneration. Naphthalene acetic acid at 0.5 mg/L produced the best rooting response for both the species. Regenerated plantlets were acclimatized successfully and cytogenetic stability was confirmed by RAPD profiling and ploidy checks.

  11. Redox-Stratified Bacterial Communities in Sediments Associated with Multiple Lucinid Bivalve Species: Implications for Symbiosis in Changing Coastal Habitats

    Science.gov (United States)

    Paterson, A. T.; Fortier, C. M.; Long, B.; Kokesh, B. S.; Lim, S. J.; Campbell, B. J.; Anderson, L. C.; Engel, A. S.

    2017-12-01

    Lucinids, chemosymbiotic marine bivalves, occupy strong redox gradient habitats, including the rhizosphere of coastal seagrass beds and mangrove forests in subtropical to tropical ecosystems. Lucinids and their sulfide-oxidizing gammaproteobacterial endosymbionts, which are acquired from the environment, provide a critical ecosystem service by removing toxic reduced sulfur compounds from the surrounding environment, and lucinids may be an important food source to economically valuable fisheries. The habitats of Phacoides pectinatus, Stewartia floridana, Codakia orbicularis, Ctena orbiculata, and Lucina pensylvanica lucinids in Florida and San Salvador in The Bahamas were evaluated in comprehensive malacological, microbiological, and geochemical surveys. Vegetation cover included different seagrass species or calcareous green macroalgae. All sites were variably affected by anthropogenic activities, as evidenced by visible prop scars in seagrass beds, grain size distributions atypical of low energy environments (i.e., artificial fill or dredge material from nearby channels), and high levels of pyrogenic hydrocarbon compounds in sediment indicative of urbanization impact. Where present, lucinid population densities frequently exceeded 2000 individuals per cubic meter, and were typically more abundant underlying seagrass compared to unvegetated, bare sand. Dissolved oxygen and sulfide levels varied from where lucinids were recovered. The sediment bacterial communities from classified 16S rRNA gene sequences indicated that the diversity of putative anaerobic groups increased with sediment depth, but putative aerobes, including of Gammaproteobacteria related to the lucinid endosymbionts, decreased with depth. Where multiple seagrass species co-occurred, retrieved bacterial community compositions correlated to overlying seagrass species, but diversity differed from bare sand patches, including among putative free-living endosymbiont groups. As such, continued sea

  12. Cryptosporidium rubeyi n. sp. (Apicomplexa: Cryptosporidiidae in multiple Spermophilus ground squirrel species

    Directory of Open Access Journals (Sweden)

    Xunde Li

    2015-12-01

    Full Text Available Previously we reported the unique Cryptosporidium sp. “c” genotype (e.g., Sbey03c, Sbey05c, Sbld05c, Sltl05c from three species of Spermophilus ground squirrel (Spermophilus beecheyi, Spermophilus beldingi, Spermophilus lateralis located throughout California, USA. This follow-up work characterizes the morphology and animal infectivity of this novel genotype as the final step in proposing it as a new species of Cryptosporidium. Analysis of sequences of 18S rRNA, actin, and HSP70 genes of additional Cryptosporidium isolates from recently sampled California ground squirrels (S. beecheyi confirms the presence of the unique Sbey-c genotype in S. beecheyi. Phylogenetic and BLAST analysis indicates that the c-genotype in Spermophilus ground squirrels is distinct from Cryptosporidium species/genotypes from other host species currently available in GenBank. We propose to name this c-genotype found in Spermophilus ground squirrels as Cryptosporidium rubeyi n. sp. The mean size of C. rubeyi n. sp. oocysts is 4.67 (4.4–5.0 μm × 4.34 (4.0–5.0 μm, with a length/width index of 1.08 (n = 220. Oocysts of C. rubeyi n. sp. are not infectious to neonatal BALB/c mice and Holstein calves. GenBank accession numbers for C. rubeyi n. sp. are DQ295012, AY462233, and KM010224 for the 18S rRNA gene, KM010227 for the actin gene, and KM010229 for the HSP70 gene.

  13. Prevalence of Multiple Antibiotics Resistant (MAR) Pseudomonas Species in the Final Effluents of Three Municipal Wastewater Treatment Facilities in South Africa

    Science.gov (United States)

    Odjadjare, Emmanuel E.; Igbinosa, Etinosa O.; Mordi, Raphael; Igere, Bright; Igeleke, Clara L.; Okoh, Anthony I.

    2012-01-01

    The final effluents of three (Alice, Dimbaza, and East London) wastewater treatment plants (WWTPs) were evaluated to determine their physicochemical quality and prevalence of multiple antibiotics resistant (MAR) Pseudomonas species, between August 2007 and July 2008. The annual mean total Pseudomonas count (TPC) was 1.20 × 104 (cfu/100 mL), 1.08 × 104 (cfu/100 mL), and 2.66 × 104 (cfu/100 mL), for the Alice, Dimbaza, and East London WWTPs respectively. The effluents were generally compliant with recommended limits for pH, temperature, TDS, DO, nitrite and nitrate; but fell short of target standards for turbidity, COD, and phosphate. The tested isolates were highly sensitive to gentamicin (100%), ofloxacin (100%), clindamycin (90%), erythromycin (90%) and nitrofurantoin (80%); whereas high resistance was observed against the penicillins (90–100%), rifampin (90%), sulphamethoxazole (90%) and the cephems (70%). MAR index ranged between 0.26 and 0.58. The study demonstrated that MAR Pseudomonas species were quite prevalent in the final effluents of WWTPs in South Africa; and this can lead to serious health risk for communities that depend on the effluent-receiving waters for sundry purposes. PMID:22829792

  14. Linking Resilience of Aquatic Species to Watershed Condition

    Science.gov (United States)

    Flitcroft, R. L.

    2017-12-01

    Watershed condition means different things to different people. From the perspective of aquatic ecology, watershed condition may be interpreted to mean the capacity of a watershed to support life history diversity of native species. Diversity in expression of life history is thought to confer resilience allowing portions of the broader population to survive stressful conditions. Different species have different life history strategies, many of which were developed through adaptation to regional or local environmental conditions and natural disturbance regimes. By reviewing adaptation strategies for species of interest at regional scales, characteristics of watersheds that confer resilience may be determined. Such assessments must be completed at multiple levels of spatial organization (i.e. sub-watershed, watershed, region) allowing assessments to be inferred across broad spatial extents. In a project on the Wenatchee River watershed, we guided models of wildfire effects on bull trout and spring Chinook from a meta-population perspective to determine risks to survival at local and population scales over multiple extents of spatial organization. In other work in the Oregon Coast Range, we found that historic landslides continue to exert habitat-forming pressure at local scales, leading to patchiness in distribution of habitats for different life stages of coho salmon. Further, climate change work in Oregon estuaries identified different vulnerabilities in terms of juvenile rearing habitat depending on the species of interest and the intensity of future changes in climate. All of these studies point to the importance of considering physical conditions in watersheds at multiple spatial extents from the perspective of native aquatic species in order to understand risks to long-term survival. The broader implications of watershed condition, from this perspective, is the determination of physical attributes that confer resilience to native biota. This may require

  15. Multiple phenological responses to climate change among 42 plant species in Xi'an, China.

    Science.gov (United States)

    Dai, Junhu; Wang, Huanjiong; Ge, Quansheng

    2013-09-01

    Phenological data of 42 woody plants in a temperate deciduous forest from the Chinese Phenological Observation Network (CPON) and the corresponding meteorological data from 1963 to 2011 in Xi'an, Shaanxi Province, China were collected and analyzed. The first leaf date (FLD), leaf coloring date (LCD) and first flower date (FFD) are revealed as strong biological signals of climatic change. The FLD, LCD and FFD of most species are sensitive to average temperature during a certain period before phenophase onset. Regional precipitation also has a significant impact on phenophases of about half of the species investigated. Affected by climate change, the FLD and FFD of these species have advanced by 5.54 days and 10.20 days on average during 2003-2011 compared with the period 1963-1996, respectively. Meanwhile, the LCD has delayed by 10.59 days, and growing season length has extended 16.13 days. Diverse responses of phenology commonly exist among different species and functional groups during the study period. Especially for FFD, the deviations between the above two periods ranged from -20.68 to -2.79 days; biotic pollination species showed a significantly greater advance than abiotic pollination species. These results were conducive to the understanding of possible changes in both the structure of plant communities and interspecific relationships in the context of climate change.

  16. Pleiotropic benefit of monomeric and oligomeric flavanols on vascular health--a randomized controlled clinical pilot study.

    Science.gov (United States)

    Weseler, Antje R; Ruijters, Erik J B; Drittij-Reijnders, Marie-José; Reesink, Koen D; Haenen, Guido R M M; Bast, Aalt

    2011-01-01

    Cardiovascular diseases are expanding to a major social-economic burden in the Western World and undermine man's deep desire for healthy ageing. Epidemiological studies suggest that flavanol-rich foods (e.g. grapes, wine, chocolate) sustain cardiovascular health. For an evidenced-based application, however, sound clinical data on their efficacy are strongly demanded. In a double-blind, randomized, placebo-controlled intervention study we supplemented 28 male smokers with 200 mg per day of monomeric and oligomeric flavanols (MOF) from grape seeds. At baseline, after 4 and 8 weeks we measured macro- and microvascular function and a cluster of systemic biomarkers for major pathological processes occurring in the vasculature: disturbances in lipid metabolism and cellular redox balance, and activation of inflammatory cells and platelets. In the MOF group serum total cholesterol and LDL decreased significantly (P ≤ 0.05) by 5% (n = 11) and 7% (n = 9), respectively in volunteers with elevated baseline levels. Additionally, after 8 weeks the ratio of glutathione to glutathione disulphide in erythrocytes rose from baseline by 22% (n = 15, Pbenefit of an 8 weeks supplementation with 200 mg/d MOF in humans. ClinicalTrials.gov NCT00742287.

  17. Crystal structure of the Haemophilus influenzae Hap adhesin reveals an intercellular oligomerization mechanism for bacterial aggregation

    Science.gov (United States)

    Meng, Guoyu; Spahich, Nicole; Kenjale, Roma; Waksman, Gabriel; St Geme, Joseph W

    2011-01-01

    Bacterial biofilms are complex microbial communities that are common in nature and are being recognized increasingly as an important determinant of bacterial virulence. However, the structural determinants of bacterial aggregation and eventual biofilm formation have been poorly defined. In Gram-negative bacteria, a major subgroup of extracellular proteins called self-associating autotransporters (SAATs) can mediate cell–cell adhesion and facilitate biofilm formation. In this study, we used the Haemophilus influenzae Hap autotransporter as a prototype SAAT to understand how bacteria associate with each other. The crystal structure of the H. influenzae HapS passenger domain (harbouring the SAAT domain) was determined to 2.2 Å by X-ray crystallography, revealing an unprecedented intercellular oligomerization mechanism for cell–cell interaction. The C-terminal SAAT domain folds into a triangular-prism-like structure that can mediate Hap–Hap dimerization and higher degrees of multimerization through its F1–F2 edge and F2 face. The intercellular multimerization can give rise to massive buried surfaces that are required for overcoming the repulsive force between cells, leading to bacterial cell–cell interaction and formation of complex microcolonies. PMID:21841773

  18. Self-association of the Lentivirus protein, Nef

    Directory of Open Access Journals (Sweden)

    Garcia J Victor

    2010-09-01

    Full Text Available Abstract Background The HIV-1 pathogenic factor, Nef, is a multifunctional protein present in the cytosol and on membranes of infected cells. It has been proposed that a spatial and temporal regulation of the conformation of Nef sequentially matches Nef's multiple functions to the process of virion production. Further, it has been suggested that dimerization is required for multiple Nef activities. A dimerization interface has been proposed based on intermolecular contacts between Nefs within hexagonal Nef/FynSH3 crystals. The proposed dimerization interface consists of the hydrophobic B-helix and flanking salt bridges between R105 and D123. Here, we test whether Nef self-association is mediated by this interface and address the overall significance of oligomerization. Results By co-immunoprecipitation assays, we demonstrated that HIV-1Nef exists as monomers and oligomers with about half of the Nef protomers oligomerized. Nef oligomers were found to be present in the cytosol and on membranes. Removal of the myristate did not enhance the oligomerization of soluble Nef. Also, SIVNef oligomerizes despite lacking a dimerization interface functionally homologous to that proposed for HIV-1Nef. Moreover, HIV-1Nef and SIVNef form hetero-oligomers demonstrating the existence of homologous oligomerization interfaces that are distinct from that previously proposed (R105-D123. Intracellular cross-linking by formaldehyde confirmed that SF2Nef dimers are present in intact cells, but surprisingly self-association was dependent on R105, but not D123. SIVMAC239Nef can be cross-linked at its only cysteine, C55, and SF2Nef is also cross-linked, but at C206 instead of C55, suggesting that Nefs exhibit multiple dimeric structures. ClusPro dimerization analysis of HIV-1Nef homodimers and HIV-1Nef/SIVNef heterodimers identified a new potential dimerization interface, including a dibasic motif at R105-R106 and a six amino acid hydrophobic surface. Conclusions We have

  19. Single Site Mutations in the Hetero-oligomeric Mrp Antiporter from Alkaliphilic Bacillus pseudofirmus OF4 That Affect Na+/H+ Antiport Activity, Sodium Exclusion, Individual Mrp Protein Levels, or Mrp Complex Formation*

    OpenAIRE

    Morino, Masato; Natsui, Shinsuke; Ono, Tomohiro; Swartz, Talia H.; Krulwich, Terry A.; Ito, Masahiro

    2010-01-01

    Mrp systems are widely distributed and structurally complex cation/proton antiporters. Antiport activity requires hetero-oligomeric complexes of all six or seven hydrophobic Mrp proteins (MrpA–MrpG). Here, a panel of site-directed mutants in conserved or proposed motif residues was made in the Mrp Na+(Li+)/H+ antiporter from an alkaliphilic Bacillus. The mutant operons were expressed in antiporter-deficient Escherichia coli KNabc and assessed for antiport properties, support of sodium resista...

  20. Crustacean zooplankton species richness in Chilean lakes and ponds (23°-51°S

    Directory of Open Access Journals (Sweden)

    Patricio De los Ríos-Escalante

    2013-07-01

    Full Text Available Chilean inland-water ecosystems are characterized by their low species-level biodiversity. This study analyses available data on surface area, maximum depth, conductivity, chlorophyll-α concentration, and zooplankton crustacean species number in lakes and ponds between 23° and 51°S. The study uses multiple regression analysis to identify the potential factors affecting the species number. The partial correlation analysis indicated a direct significant correlation between chlorophyll-α concentration and species number, whereas the multiple regression analysis indicated a direct significant response of species number to latitude and chlorophyll-α concentration. These results agree with findings from comparable ecosystems in Argentina and New Zealand.

  1. Deriving field-based species sensitivity distributions (f-SSDs) from stacked species distribution models (S-SDMs).

    Science.gov (United States)

    Schipper, Aafke M; Posthuma, Leo; de Zwart, Dick; Huijbregts, Mark A J

    2014-12-16

    Quantitative relationships between species richness and single environmental factors, also called species sensitivity distributions (SSDs), are helpful to understand and predict biodiversity patterns, identify environmental management options and set environmental quality standards. However, species richness is typically dependent on a variety of environmental factors, implying that it is not straightforward to quantify SSDs from field monitoring data. Here, we present a novel and flexible approach to solve this, based on the method of stacked species distribution modeling. First, a species distribution model (SDM) is established for each species, describing its probability of occurrence in relation to multiple environmental factors. Next, the predictions of the SDMs are stacked along the gradient of each environmental factor with the remaining environmental factors at fixed levels. By varying those fixed levels, our approach can be used to investigate how field-based SSDs for a given environmental factor change in relation to changing confounding influences, including for example optimal, typical, or extreme environmental conditions. This provides an asset in the evaluation of potential management measures to reach good ecological status.

  2. Global Existence Analysis of Cross-Diffusion Population Systems for Multiple Species

    Science.gov (United States)

    Chen, Xiuqing; Daus, Esther S.; Jüngel, Ansgar

    2018-02-01

    The existence of global-in-time weak solutions to reaction-cross-diffusion systems for an arbitrary number of competing population species is proved. The equations can be derived from an on-lattice random-walk model with general transition rates. In the case of linear transition rates, it extends the two-species population model of Shigesada, Kawasaki, and Teramoto. The equations are considered in a bounded domain with homogeneous Neumann boundary conditions. The existence proof is based on a refined entropy method and a new approximation scheme. Global existence follows under a detailed balance or weak cross-diffusion condition. The detailed balance condition is related to the symmetry of the mobility matrix, which mirrors Onsager's principle in thermodynamics. Under detailed balance (and without reaction) the entropy is nonincreasing in time, but counter-examples show that the entropy may increase initially if detailed balance does not hold.

  3. Live cell imaging unveils multiple domain requirements for in vivo dimerization of the glucocorticoid receptor

    DEFF Research Database (Denmark)

    Presman, Diego M; Ogara, M Florencia; Stortz, Martín

    2014-01-01

    Glucocorticoids are essential for life, but are also implicated in disease pathogenesis and may produce unwanted effects when given in high doses. Glucocorticoid receptor (GR) transcriptional activity and clinical outcome have been linked to its oligomerization state. Although a point mutation wi...

  4. Partitioning sources of variation in vertebrate species richness

    Science.gov (United States)

    Boone, R.B.; Krohn, W.B.

    2000-01-01

    Aim: To explore biogeographic patterns of terrestrial vertebrates in Maine, USA using techniques that would describe local and spatial correlations with the environment. Location: Maine, USA. Methods: We delineated the ranges within Maine (86,156 km2) of 275 species using literature and expert review. Ranges were combined into species richness maps, and compared to geomorphology, climate, and woody plant distributions. Methods were adapted that compared richness of all vertebrate classes to each environmental correlate, rather than assessing a single explanatory theory. We partitioned variation in species richness into components using tree and multiple linear regression. Methods were used that allowed for useful comparisons between tree and linear regression results. For both methods we partitioned variation into broad-scale (spatially autocorrelated) and fine-scale (spatially uncorrelated) explained and unexplained components. By partitioning variance, and using both tree and linear regression in analyses, we explored the degree of variation in species richness for each vertebrate group that Could be explained by the relative contribution of each environmental variable. Results: In tree regression, climate variation explained richness better (92% of mean deviance explained for all species) than woody plant variation (87%) and geomorphology (86%). Reptiles were highly correlated with environmental variation (93%), followed by mammals, amphibians, and birds (each with 84-82% deviance explained). In multiple linear regression, climate was most closely associated with total vertebrate richness (78%), followed by woody plants (67%) and geomorphology (56%). Again, reptiles were closely correlated with the environment (95%), followed by mammals (73%), amphibians (63%) and birds (57%). Main conclusions: Comparing variation explained using tree and multiple linear regression quantified the importance of nonlinear relationships and local interactions between species

  5. Production of sophorolipids biosurfactants by multiple species of the Starmerella (Candida) bombicola yeast clade

    Science.gov (United States)

    Sophorolipid production was tested for 26 strains representing 19 species of the Starmerella yeast clade, including S. bombicola and Candida apicola, which were previously reported to produce sophorolipids. Five of the 19 species tested showed significant production of sophorolipids: S. bombicola, ...

  6. One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

    Science.gov (United States)

    Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

    2014-12-01

    G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

  7. Heterogeneity in Red Wine Polyphenolic Contents Differentially Influences Alzheimer's Disease-type Neuropathology and Cognitive Deterioration

    Science.gov (United States)

    Ho, Lap; Chen, Ling Hong; Wang, Jun; Zhao, Wei; Talcott, Stephen T.; Ono, Kenjiro; Teplow, David; Humala, Nelson; Cheng, Alice; Percival, Susan S.; Ferruzzi, Mario; Janle, Elsa; Dickstein, Dara L.; Pasinetti, Giulio Maria

    2009-01-01

    We recently found that moderate consumption of two unrelated red wines generate from different grape species, a Cabernet Sauvignon and a muscadine wine that are characterized by distinct component composition of polyphenolic compounds, significantly attenuated the development of Alzheimer's disease (AD)-type brain pathology and memory deterioration in a transgenic AD mouse model. Interestingly, our evidence suggests that the two red wines attenuated AD phenotypes through independent mechanisms. In particular, we previously found that treatment with Cabernet Sauvignon reduced the generation of AD-type amyloid-β (Aβ) peptides. In contrast, evidence from our present study suggests that muscadine treatment attenuates Aβ neuropathology and Aβ-related cognitive deterioration in Tg2576 mice by interfering with the oligomerization of Aβ molecules to soluble high-molecular-weight Aβ oligomer species that are responsible for initiating a cascade of cellular events resulting in cognitive decline. Collectively, our observations suggest that distinct polyphenolic compounds from red wines may be bioavailable at the organism level and beneficially modulate AD phenotypes through multiple Aβ-related mechanisms. Results from these studies suggest the possibility of developing a “combination” of dietary polyphenolic compounds for AD prevention and/or therapy by modulating multiple Aβ-related mechanisms. PMID:19158422

  8. Metals and organotins in multiple bivalve species in a one-off global survey

    DEFF Research Database (Denmark)

    Larsen, Martin Mørk; Strand, Jakob; Christensen, Jan H.

    2011-01-01

    contamination levels on a global scale. Metal concentrations in nine bivalve species were normalised to the Mytilidae family using conversion factors based on cosampled species and literature bioconcentration factors. The lowest metal and tributyltin concentrations were below background assessment...... were low, but not always lower than expected impacted areas. The most contaminated areas were harbours, where especially Copenhagen, St Croix and Sydney, can be considered hotspots of tributyltin as well as a number of metals....

  9. EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA); Scientific Opinion on the substantiation of health claims related to oligomeric procyanidins (OPCs) from grape (Vitis vinifera L.) seeds and improvement of visual adaptation to the dark (ID 680) pursuant to Article 13(1) of Regulation

    DEFF Research Database (Denmark)

    Tetens, Inge

    claims in relation to oligomeric procyanidins (OPCs) from grape (Vitis vinifera L.) seeds and improvement of visual adaptation to the dark. The scientific substantiation is based on the information provided by the Member States in the consolidated list of Article 13 health claims and references that EFSA...... has received from Member States or directly from stakeholders. The food constituent that is the subject of the health claim is oligomeric procyanidins (OPCs) from grape (Vitis vinifera L.) seeds. The Panel considers that OPCs from grape (Vitis vinifera L.) seeds are sufficiently characterised....... The claimed effect is “ocular system: OPCs play an important role in the structure and physiological functions of cornea, OPCs protect the cornea and improve visual adaptation to low luminances”. The target population is assumed to be the general population. In the context of the proposed wordings...

  10. Taking a multiple intelligences (MI) perspective.

    Science.gov (United States)

    Gardner, Howard

    2017-01-01

    The theory of multiple intelligences (MI) seeks to describe and encompass the range of human cognitive capacities. In challenging the concept of general intelligence, we can apply an MI perspective that may provide a more useful approach to cognitive differences within and across species.

  11. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  12. CSA: An efficient algorithm to improve circular DNA multiple alignment

    Directory of Open Access Journals (Sweden)

    Pereira Luísa

    2009-07-01

    Full Text Available Abstract Background The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools. Results In this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes. To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView. Conclusion The results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment

  13. High-Performance Oligomeric Catholytes for Effective Macromolecular Separation in Nonaqueous Redox Flow Batteries.

    Science.gov (United States)

    Hendriks, Koen H; Robinson, Sophia G; Braten, Miles N; Sevov, Christo S; Helms, Brett A; Sigman, Matthew S; Minteer, Shelley D; Sanford, Melanie S

    2018-02-28

    Nonaqueous redox flow batteries (NRFBs) represent an attractive technology for energy storage from intermittent renewable sources. In these batteries, electrical energy is stored in and extracted from electrolyte solutions of redox-active molecules (termed catholytes and anolytes) that are passed through an electrochemical flow cell. To avoid battery self-discharge, the anolyte and catholyte solutions must be separated by a membrane in the flow cell. This membrane prevents crossover of the redox active molecules, while simultaneously allowing facile transport of charge-balancing ions. A key unmet challenge for the field is the design of redox-active molecule/membrane pairs that enable effective electrolyte separation while maintaining optimal battery properties. Herein, we demonstrate the development of oligomeric catholytes based on tris(dialkylamino)cyclopropenium (CP) salts that are specifically tailored for pairing with size-exclusion membranes composed of polymers of intrinsic microporosity (PIMs). Systematic studies were conducted to evaluate the impact of oligomer size/structure on properties that are crucial for flow battery performance, including cycling stability, charge capacity, solubility, electron transfer kinetics, and crossover rates. These studies have led to the identification of a CP-derived tetramer in which these properties are all comparable, or significantly improved, relative to the monomeric counterpart. Finally, a proof-of-concept flow battery is demonstrated by pairing this tetrameric catholyte with a PIM membrane. After 6 days of cycling, no crossover is detected, demonstrating the promise of this approach. These studies provide a template for the future design of other redox-active oligomers for this application.

  14. Removal of multiple metallic species from a sludge by electromigration

    Energy Technology Data Exchange (ETDEWEB)

    Ricart, M.T.; Cameselle, C. [Dept. of Chemical Engineering., Univ. of Vigo (Spain); Lema, J.M. [Dept. of Chemical Engineering., Univ. of Vigo (Spain)]|[Dept. of Chemical Engineering, Univ. of Santiago de Compostela (Spain)

    2001-07-01

    This study deals with the treatment of sludge from a wastewater treatment plant contaminated several metallic species. Electromigration laboratory experiments were conducted in an electrokinetic cell with or without cathode solution pH control. A large pH influence has been observed over metals removal. The neutralisation of basic environment at cathode deals with a increasing in current intensity and power consumption, but also in a large removal of Fe, Ca, Mg, Na, Mn, Sr, Zn and Cu from sludge sample. (orig.)

  15. Analysis of monomeric and oligomeric organophosphorus flame retardants in fish muscle tissues using liquid chromatography–electrospray ionization tandem mass spectrometry: Application to Nile tilapia (Oreochromis niloticus) from an e-waste processing area in northern Vietnam

    OpenAIRE

    Matsukami, Hidenori; Suzuki, Go; Tue, Nguyen Minh; Tuyen, Le Huu; Viet, Pham Hung; Takahashi, Shin; Tanabe, Shinsuke; Takigami, Hidetaka

    2016-01-01

    Using electrospray ionization tandem mass spectrometry combined with liquid chromatography (LC), a novel analytical method was developed to quantify eight monomeric organophosphorus flame retardants (m-PFRs) and three oligomeric organophosphorus flame retardants (o-PFRs) in fish muscle samples. The optimization and validation experiments indicate that the developed method can determine accurately the concentrations of analytes in fish muscle samples. The recoveries of analytes in fish muscle ...

  16. Ion Channel Conformation and Oligomerization Assessment by Site-Directed Spin Labeling and Pulsed-EPR.

    Science.gov (United States)

    Pliotas, Christos

    2017-01-01

    Mechanosensitive (MS) ion channels are multimeric integral membrane proteins that respond to increased lipid bilayer tension by opening their nonselective pores to release solutes and relieve increased cytoplasmic pressure. These systems undergo major conformational changes during gating and the elucidation of their mechanism requires a deep understanding of the interplay between lipids and proteins. Lipids are responsible for transmitting lateral tension to MS channels and therefore play a key role in obtaining a molecular-detail model for mechanosensation. Site-directed spin labeling combined with electron paramagnetic resonance (EPR) spectroscopy is a powerful spectroscopic tool in the study of proteins. The main bottleneck for its use relates to challenges associated with successful isolation of the protein of interest, introduction of paramagnetic labels on desired sites, and access to specialized instrumentation and expertise. The design of sophisticated experiments, which combine a variety of existing EPR methodologies to address a diversity of specific questions, require knowledge of the limitations and strengths, characteristic of each particular EPR method. This chapter is using the MS ion channels as paradigms and focuses on the application of different EPR techniques to ion channels, in order to investigate oligomerization, conformation, and the effect of lipids on their regulation. The methodology we followed, from the initial strategic selection of mutants and sample preparation, including protein purification, spin labeling, reconstitution into lipid mimics to the complete set-up of the pulsed-EPR experiments, is described in detail. © 2017 Elsevier Inc. All rights reserved.

  17. Frequent cross-species transmission of parvoviruses among diverse carnivore hosts

    Science.gov (United States)

    Allison, Andrew B.; Kohler, Dennis J.; Fox, Karen A.; Brown, Justin D.; Gerhold, Richard W.; Shearn-Bochsler, Valerie I.; Dubovi, Edward J.; Parrish, Colin R.; Holmes, Edward C.

    2013-01-01

    Although parvoviruses are commonly described in domestic carnivores, little is known about their biodiversity in nondomestic species. A phylogenetic analysis of VP2 gene sequences from puma, coyote, gray wolf, bobcat, raccoon, and striped skunk revealed two major groups related to either feline panleukopenia virus (“FPV-like”) or canine parvovirus (“CPV-like”). Cross-species transmission was commonplace, with multiple introductions into each host species but, with the exception of raccoons, relatively little evidence for onward transmission in nondomestic species.

  18. DNA barcode detects high genetic structure within neotropical bird species.

    Directory of Open Access Journals (Sweden)

    Erika Sendra Tavares

    Full Text Available BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520 of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21 or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20. Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent

  19. Induction of apoptosis in human multiple myeloma cell lines by ebselen via enhancing the endogenous reactive oxygen species production.

    Science.gov (United States)

    Zhang, Liang; Zhou, Liwei; Du, Jia; Li, Mengxia; Qian, Chengyuan; Cheng, Yi; Peng, Yang; Xie, Jiayin; Wang, Dong

    2014-01-01

    Ebselen a selenoorganic compound showing glutathione peroxidase like activity is an anti-inflammatory and antioxidative agent. Its cytoprotective activity has been investigated in recent years. However, experimental evidence also shows that ebselen causes cell death in several cancer cell types whose mechanism has not yet been elucidated. In this study, we examined the effect of ebselen on multiple myeloma (MM) cell lines in vitro. The results showed that ebselen significantly enhanced the production of reactive oxygen species (ROS) accompanied by cell viability decrease and apoptosis rate increase. Further studies revealed that ebselen can induce Bax redistribution from the cytosol to mitochondria leading to mitochondrial membrane potential ΔΨm changes and cytochrome C release from the mitochondria to cytosol. Furtherly, we found that exogenous addition of N-acetyl cysteine (NAC) completely diminished the cell damage induced by ebselen. This result suggests that relatively high concentration of ebselen can induce MM cells apoptosis in culture by enhancing the production of endogenous ROS and triggering mitochondria mediated apoptotic pathway.

  20. Optimization of oligomeric enzyme activity in ionic liquids using Rhodotorula glutinis yeast phenylalanine ammonia lyase.

    Science.gov (United States)

    Barron, Christiaan C; Sponagle, Brandon J D; Arivalagan, Pugazhendhi; D'Cunha, Godwin B

    2017-01-01

    Phenylalanine ammonia lyase (E.C.4.3.1.24, PAL) activity of Rhodotorula glutinis yeast has been demonstrated in four commonly used ionic liquids. PAL forward reaction was carried out in 1-butyl-3-methylimidazolium methyl sulfate ([BMIM][MeSO 4 ]), 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF 4 ]), 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF 6 ]) and 1-butyl-3-methylimidazolium lactate ([BMIM][lactate]). Our experiments have revealed that PAL is catalytically active in ionic liquids and the enzyme activity in ([BMIM][PF 6 ]) is comparable to that obtained in aqueous buffer medium. Different conditions were optimized for maximal PAL forward activity including time of incubation (30.0min) L -phenylalanine substrate concentration (30.0mM), nature of buffer (50.0mM Tris-HCl), pH (9.0), temperature (37°C), and speed of agitation (100 rev min -1 ). Under these optimized conditions, about 83% conversion of substrate to product was obtained for the PAL forward reaction that was determined using UV spectroscopy at 290nm. PAL reverse reaction in ([BMIM][PF 6 ]) was determined spectrophotometrically at 520nm; and about 59% substrate conversion was obtained. This data provides further knowledge in enzyme biocatalysis in non-aqueous media, and may be of importance when studying the function of other oligomeric/multimeric proteins and enzymes in ionic liquids. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Hexokinase 2 from Saccharomyces cerevisiae: regulation of oligomeric structure by in vivo phosphorylation at serine-14.

    Science.gov (United States)

    Behlke, J; Heidrich, K; Naumann, M; Müller, E C; Otto, A; Reuter, R; Kriegel, T

    1998-08-25

    Homodimeric hexokinase 2 from Saccharomyces cerevisiae is known to have two sites of phosphorylation: for serine-14 the modification in vivo increases with glucose exhaustion [Kriegel et al. (1994) Biochemistry 33, 148-152], while for serine-157 it occurs in vitro with ATP in the presence of nonphosphorylateable five-carbon analogues of glucose [Heidrich et al. (1997) Biochemistry 36, 1960-1964]. We show now by site-directed mutagenesis and sedimentation analysis that serine-14 phosphorylation affects the oligomeric state of hexokinase, its substitution by glutamate causing complete dissociation; glutamate exchange for serine-157 does not. Phosphorylation of wild-type hexokinase at serine-14 likewise causes dissociation in vitro. In view of the higher glucose affinity of monomeric hexokinase and the high hexokinase concentration in yeast [Womack, F., and Colowick, S. P. (1978) Arch. Biochem. Biophys. 191, 742-747; Mayes, E. L., Hoggett, J. G., and Kellett, G. L. (1983) Eur. J. Biochem. 133, 127-134], we speculate that the in vivo phosphorylation at serine-14 as transiently occurring in glucose derepression might provide a mechanism to improve glucose utilization from low level and/or that nuclear localization of the monomer might be involved in the signal transduction whereby glucose causes catabolite repression.

  2. Glycerol-Induced Aggregation of the Oligomeric L-Asparaginase II from E. coli Monitored with ATR-FTIR

    Directory of Open Access Journals (Sweden)

    Koba Adeishvili

    2001-06-01

    Full Text Available Abstract: In this paper attenuated total reflectance Fourier transform infrared spectroscopy has been employed for the study of the structural composition of aggregates of the oligomeric L-asparaginase II from E.coli formed in the presence of glycerol after the induction of refolding of the protein. Apart from the perfect coincidence of the secondary structure composition of EcA2 as determined by FTIR and crystallography [1], it has also been shown that secondary structure of protein in asparaginase deposits is similar to that of the native conformation: 20.7% extended, 22.3% disordered, 31.4% helix and 25.6% turn/bend/β sheet. Certain structural similarities in the range of experimental error was observed for all three protein deposits presented in this paper, indicating a common structural basis for the composition of this types of aggregates. It is concluded that in the constitution of such precipitates, a partially folded (molten globule like state(s is involved, and its stabilisation is a key factor leading to the aggregation. The results presented in this paper might serve to be a good explanation and an excellent basis for the fundamental theory of protein (oligomers precipitation by osmotic substances.

  3. Unusual Emission of Polystyrene-Based Alternating Copolymers Incorporating Aminobutyl Maleimide Fluorophore-Containing Polyhedral Oligomeric Silsesquioxane Nanoparticles

    Directory of Open Access Journals (Sweden)

    Mohamed Gamal Mohamed

    2017-03-01

    Full Text Available In this study, we synthesized an unusual 2-aminobutyl maleimide isobutyl polyhedral oligomeric silsesquioxane (MIPOSS-NHBu monomer lacking conventional fluorescent groups. We then prepared poly(styrene-alt-2-aminobutyl maleimide isobutyl POSS [poly(S-alt-MIPOSS-NHBu] and poly(4-acetoxystyrene-alt-2-aminobutyl maleimide isobutyl POSS [poly(AS-alt-MIPOSS-NHBu] copolymers through facile free radical copolymerizations using azobisisobutyronitrile as the initiator and tetrahydrofuran as the solvent. A poly(4-hydroxystyrene-alt-2-aminobutyl maleimide isobutyl POSS [poly(HS-alt-MIPOSS-NHBu] copolymer was prepared through acetoxyl hydrazinolysis of poly(AS-alt-MIPOSS-NHBu. We employed 1H, 13C, and 29Si nuclear magnetic resonance spectroscopy; Fourier transform infrared spectroscopy; differential scanning calorimetry; and photoluminescence spectroscopy to investigate the structures and the thermal and optical properties of the monomers and novel POSS-containing alternating copolymers. Intramolecular hydrogen bonding between the amino and dihydrofuran-2,5-dione group and clustering of the locked C=O groups from the POSS nanoparticles in the MIPOSS-NHBu units restricted the intramolecular motion of the polymer chain, causing it to exhibit strong light emission. As a result, the MIPOSS-NHBu monomer and the poly(AS-alt-MIPOSS-NHBu copolymer both have potential applicability in the detection of metal ions with good selectivity.

  4. MURI Center for Materials Chemistry in the Space Environment

    Science.gov (United States)

    2006-11-30

    ionic species in relevant reaction environments, surface photochemistry expertise, synchrotron-based measurement and irradiation, synthesis of structural...and Ne+ ions with dodecanethiolate and semifluorinated dodecanethiolate self-assembled monolayers (SAM), polyhedral oligomeric silsesquioxane (POSS...POSS/Kapton models as gas phase species, and with alkane thiol self assembled monolayers on gold surfaces, and with liquid squalane. We have also

  5. Ribosomal DNA in diploid and polyploid Setaria (Poaceae) species: number and distribution

    OpenAIRE

    Nani, Thaís Furtado; Cenzi, Gisele; Pereira, Daniele Lais; Davide, Lisete Chamma; Techio, Vania Helena

    2015-01-01

    Abstract Setaria Beauvois, 1812 is a genus of economically important forage species, including Setaria italica (Linnaeus, 1753) Beauvois, 1812 and Setaria viridis (Linnaeus, 1753) Beauvois, 1812, closely related species and considered as model systems for studies of C4 plants. However, complications and uncertainties related to taxonomy of other species of the genus are frequent due to the existence of numerous synonyms for the same species or multiple species with the same name, and overlapp...

  6. Engineering a plant community to deliver multiple ecosystem services.

    Science.gov (United States)

    Storkey, Jonathan; Döring, Thomas; Baddeley, John; Collins, Rosemary; Roderick, Stephen; Jones, Hannah; Watson, Christine

    2015-06-01

    The sustainable delivery of multiple ecosystem services requires the management of functionally diverse biological communities. In an agricultural context, an emphasis on food production has often led to a loss of biodiversity to the detriment of other ecosystem services such as the maintenance of soil health and pest regulation. In scenarios where multiple species can be grown together, it may be possible to better balance environmental and agronomic services through the targeted selection of companion species. We used the case study of legume-based cover crops to engineer a plant community that delivered the optimal balance of six ecosystem services: early productivity, regrowth following mowing, weed suppression, support of invertebrates, soil fertility building (measured as yield of following crop), and conservation of nutrients in the soil. An experimental species pool of 12 cultivated legume species was screened for a range of functional traits and ecosystem services at five sites across a geographical gradient in the United Kingdom. All possible species combinations were then analyzed, using a process-based model of plant competition, to identify the community that delivered the best balance of services at each site. In our system, low to intermediate levels of species richness (one to four species) that exploited functional contrasts in growth habit and phenology were identified as being optimal. The optimal solution was determined largely by the number of species and functional diversity represented by the starting species pool, emphasizing the importance of the initial selection of species for the screening experiments. The approach of using relationships between functional traits and ecosystem services to design multifunctional biological communities has the potential to inform the design of agricultural systems that better balance agronomic and environmental services and meet the current objective of European agricultural policy to maintain viable food

  7. Tetrameric structure of the flagellar cap protein FliD from Serratia marcescens.

    Science.gov (United States)

    Cho, So Yeon; Song, Wan Seok; Hong, Ho Jeong; Lee, Geun-Shik; Kang, Seung Goo; Ko, Hyun-Jeong; Kim, Pyeung-Hyeun; Yoon, Sung-Il

    2017-07-15

    Bacterial motility is provided by the flagellum. FliD is located at the distal end of the flagellum and plays a key role in the insertion of each flagellin protein at the growing tip of the flagellar filament. Because FliD functions as an oligomer, the determination of the oligomeric state of FliD is critical to understanding the molecular mechanism of FliD-mediated flagellar growth. FliD has been shown to adopt a pentameric or a hexameric structure depending on the bacterial species. Here, we report another distinct oligomeric form of FliD based on structural and biochemical studies. The crystal structures of the D2 and D3 domains of Serratia marcescens FliD (smFliD) were determined in two crystal forms and together revealed that smFliD assembles into a tetrameric architecture that resembles a four-pointed star plate. smFliD tetramerization was also confirmed in solution by cross-linking experiments. Although smFliD oligomerizes in a head-to-tail orientation using a common primary binding interface between the D2 and D3' domains (the prime denotes the second subunit in the oligomer) similarly to other FliD orthologs, the smFliD tetramer diverges to present a unique secondary D2-D2' binding interface. Our structure-based comparative analysis of FliD suggests that bacteria have developed diverse species-specific oligomeric forms of FliD that range from tetramers to hexamers for flagellar growth. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Consumer preference for seeds and seedlings of rare species impacts tree diversity at multiple scales.

    Science.gov (United States)

    Young, Hillary S; McCauley, Douglas J; Guevara, Roger; Dirzo, Rodolfo

    2013-07-01

    Positive density-dependent seed and seedling predation, where herbivores selectively eat seeds or seedlings of common species, is thought to play a major role in creating and maintaining plant community diversity. However, many herbivores and seed predators are known to exhibit preferences for rare foods, which could lead to negative density-dependent predation. In this study, we first demonstrate the occurrence of increased predation of locally rare tree species by a widespread group of insular seed and seedling predators, land crabs. We then build computer simulations based on these empirical data to examine the effects of such predation on diversity patterns. Simulations show that herbivore preferences for locally rare species are likely to drive scale-dependent effects on plant community diversity: at small scales these foraging patterns decrease plant community diversity via the selective consumption of rare plant species, while at the landscape level they should increase diversity, at least for short periods, by promoting clustered local dominance of a variety of species. Finally, we compared observed patterns of plant diversity at the site to those obtained via computer simulations, and found that diversity patterns generated under simulations were highly consistent with observed diversity patterns. We posit that preference for rare species by herbivores may be prevalent in low- or moderate-diversity systems, and that these effects may help explain diversity patterns across different spatial scales in such ecosystems.

  9. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].

  10. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  11. Delineation of Culicoides species by morphology and barcode exemplified by three new species of the subgenus Culicoides (Diptera: Ceratopogonidae) from Scandinavia

    DEFF Research Database (Denmark)

    Nielsen, Søren Achim; Kristensen, Michael

    2015-01-01

    new species initially separated by DNA barcoding with mitochondrial COI can be distinguished by morphological characters. In this context a key to Scandinavian subgenus Culicoides using wing and maxillary palp characters is presented. The key is including the three new species Culicoides boyi...... is considered, as well as the evolutionary relationships between species within this genus remains problematic. In recent years molecular barcoding has assisted substantially in the identification of biting midges in the multiple entomological survey projects which were initiated in many European countries...... following the bluetongue outbreak in 2006–2009. These studies revealed potentially new species and “species-complexes” with large genetic and morphological variability. Here we use molecular barcoding, together with morphological analysis, to study subgenus Culicoides Latreille from Scandinavia with focus...

  12. Multidrug-resistant Nocardia pseudobrasiliensis presenting as multiple muscle abscesses.

    Science.gov (United States)

    Veerappan Kandasamy, Vimalkumar; Nagabandi, Arun; Horowitz, Edward A; Vivekanandan, Renuga

    2015-05-06

    A 79-year-old Caucasian man presented with multiple leg abscesses due to Nocardia pseudobrasiliensis. He was on chronic steroid therapy for myasthenia gravis. We present the difficulties in diagnosis and treatment of this rare organism. N. pseudobrasiliensis is a new emerging species that was previously thought to belong to the N. brasiliensis species. The distinction between the two species is extremely important given the different antibiotic susceptibility pattern and association of N. pseudobrasiliensis with more invasive and disseminated disease. 2015 BMJ Publishing Group Ltd.

  13. Functional labeling of insulin receptor subunits in live cells. Alpha 2 beta 2 species is the major autophosphorylated form

    International Nuclear Information System (INIS)

    Le Marchand-Brustel, Y.; Ballotti, R.; Gremeaux, T.; Tanti, J.F.; Brandenburg, D.; Van Obberghen, E.

    1989-01-01

    Both receptor subunits were functionally labeled in order to provide methods allowing, in live cells and in broken cell systems, concomitant evaluation of the insulin receptor dual function, hormone binding, and kinase activity. In cell-free systems, insulin receptors were labeled on their alpha-subunit with 125I-photoreactive insulin, and on their beta-subunit by autophosphorylation. Thereafter, phosphorylated receptors were separated from the complete set of receptors by means of anti-phosphotyrosine antibodies. Using this approach, a subpopulation of receptors was found which had bound insulin, but which were not phosphorylated. Under nonreducing conditions, receptors appeared in three oligomeric species identified as alpha 2 beta 2, alpha 2 beta, and alpha 2. Mainly the alpha 2 beta 2 receptor species was found to be phosphorylated while insulin was bound to alpha 2 beta 2, alpha 2 beta, and alpha 2 forms. In live cells, biosynthetic labeling of insulin receptors was used. Receptors were first labeled with [35S]methionine. Subsequently, the addition of insulin led to receptor autophosphorylation by virtue of the endogenous ATP pool. The total amount of [35S]methionine-labeled receptors was precipitated with antireceptor antibodies, whereas with anti-phosphotyrosine antibodies, only the phosphorylated receptors were isolated. Using this approach we made the two following key findings: (1) Both receptor species, alpha 2 beta 2 and alpha 2 beta, are present in live cells and in comparable amounts. This indicates that the alpha 2 beta form is not a degradation product of the alpha 2 beta 2 form artificially generated during receptor preparation. (2) The alpha 2 beta 2 species is the prevalently autophosphorylated form

  14. Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure

    Energy Technology Data Exchange (ETDEWEB)

    Korasick, David A. [Department of Biochemistry, University of Missouri, Columbia MO USA; Singh, Harkewal [Department of Chemistry, University of Missouri, Columbia MO USA; Pemberton, Travis A. [Department of Chemistry, University of Missouri, Columbia MO USA; Luo, Min [Department of Chemistry, University of Missouri, Columbia MO USA; Dhatwalia, Richa [Department of Chemistry, University of Missouri, Columbia MO USA; Tanner, John J. [Department of Biochemistry, University of Missouri, Columbia MO USA; Department of Chemistry, University of Missouri, Columbia MO USA

    2017-08-01

    Many enzymes form homooligomers, yet the functional significance of self-association is seldom obvious. Herein, we examine the connection between oligomerization and catalytic function for proline utilization A (PutA) enzymes. PutAs are bifunctional enzymes that catalyze both reactions of proline catabolism. Type A PutAs are the smallest members of the family, possessing a minimal domain architecture consisting of N-terminal proline dehydrogenase and C-terminal l-glutamate-γ-semialdehyde dehydrogenase modules. Type A PutAs form domain-swapped dimers, and in one case (Bradyrhizobium japonicum PutA), two of the dimers assemble into a ring-shaped tetramer. Whereas the dimer has a clear role in substrate channeling, the functional significance of the tetramer is unknown. To address this question, we performed structural studies of four-type A PutAs from two clades of the PutA tree. The crystal structure of Bdellovibrio bacteriovorus PutA covalently inactivated by N-propargylglycine revealed a fold and substrate-channeling tunnel similar to other PutAs. Small-angle X-ray scattering (SAXS) and analytical ultracentrifugation indicated that Bdellovibrio PutA is dimeric in solution, in contrast to the prediction from crystal packing of a stable tetrameric assembly. SAXS studies of two other type A PutAs from separate clades also suggested that the dimer predominates in solution. To assess whether the tetramer of B. japonicum PutA is necessary for catalytic function, a hot spot disruption mutant that cleanly produces dimeric protein was generated. The dimeric variant exhibited kinetic parameters similar to the wild-type enzyme. These results implicate the domain-swapped dimer as the core structural and functional unit of type A PutAs.

  15. Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia.

    Science.gov (United States)

    Esselstyn, Jacob A; Maharadatunkamsi; Achmadi, Anang S; Siler, Cameron D; Evans, Ben J

    2013-10-01

    In theory, competition among species in a shared habitat results in niche separation. In the case of small recondite mammals such as shrews, little is known about their autecologies, leaving open questions regarding the degree to which closely related species co-occur and how or whether ecological niches are partitioned. The extent to which species are able to coexist may depend on the degree to which they exploit different features of their habitat, which may in turn influence our ability to recognize them as species. We explored these issues in a biodiversity hotspot, by surveying shrew (genus Crocidura) diversity on the Indonesian island of Java. We sequenced portions of nine unlinked genes in 100-117 specimens of Javan shrews and incorporated homologous data from most known Crocidura species from other parts of island South-East Asia. Current taxonomy recognizes four Crocidura species on Java, including two endemics. However, our phylogenetic, population genetic and species delimitation analyses identify five species on the island, and all are endemic to Java. While the individual ranges of these species may not overlap in their entirety, we found up to four species living syntopically and all five species co-occurring on one mountain. Differences in species' body size, use of above ground-level habitats by one species and habitat partitioning along ecological gradients may have facilitated species diversification and coexistence. © 2013 John Wiley & Sons Ltd.

  16. Novel multiplex PCR reveals multiple trypanosomatid species infecting North American bumble bees (Hymenoptera: Apidae: Bombus).

    Science.gov (United States)

    Tripodi, Amber D; Szalanski, Allen L; Strange, James P

    2018-03-01

    Crithidia bombi and Crithidia expoeki (Trypanosomatidae) are common parasites of bumble bees (Bombus spp.). Crithidia bombi was described in the 1980s, and C. expoeki was recently discovered using molecular tools. Both species have cosmopolitan distributions among their bumble bee hosts, but there have been few bumble bee studies that have identified infections to species since the original description of C. expoeki in 2010. Morphological identification of species is difficult due to variability within each stage of their complex lifecycles, although they can be easily differentiated through DNA sequencing. However, DNA sequencing can be expensive, particularly with many samples to diagnose. In order to reliably and inexpensively distinguish Crithidia species for a large-scale survey, we developed a multiplex PCR protocol using species-specific primers with a universal trypanosomatid primer set to detect unexpected relatives. We applied this method to 356 trypanosomatid-positive bumble bees from North America as a first-look at the distribution and host range of each parasite in the region. Crithidia bombi was more common (90.2%) than C. expoeki (21.3%), with most C. expoeki-positive samples existing as co-infections with C. bombi (13.8%). This two-step detection method also revealed that 2.2% samples were positive for trypanosmatids that were neither C. bombi nor C. expoeki. Sequencing revealed that two individuals were positive for C. mellificae, one for Lotmaria passim, and three for two unclassified trypanosomatids. This two-step method is effective in diagnosing known bumble bee infecting Crithidia species, and allowing for the discovery of unknown potential symbionts. Published by Elsevier Inc.

  17. Swimming with multiple propulsors: measurement and comparison of swimming gaits in three species of neotropical cichlids.

    Science.gov (United States)

    Feilich, Kara L

    2017-11-15

    Comparative studies of fish swimming have been limited by the lack of quantitative definitions of fish gaits. Traditionally, steady swimming gaits have been defined categorically by the fin or region of the body that is used as the main propulsor and named after major fish clades (e.g. carangiform, anguilliform, balistiform, labriform). This method of categorization is limited by the lack of explicit measurements, the inability to incorporate contributions of multiple propulsors and the inability to compare gaits across different categories. I propose an alternative framework for the definition and comparison of fish gaits based on the propulsive contribution of each structure (body and/or fin) being used as a propulsor relative to locomotor output, and demonstrate the effectiveness of this framework by comparing three species of neotropical cichlids with different body shapes. This approach is modular with respect to the number of propulsors considered, flexible with respect to the definition of the propulsive inputs and the locomotor output of interest, and designed explicitly to handle combinations of propulsors. Using this approach, gait can be defined as a trajectory through propulsive space, and gait transitions can be defined as discontinuities in the gait trajectory. By measuring and defining gait in this way, patterns of clustering corresponding to existing categorical definitions of gait may emerge, and gaits can be rigorously compared across categories. © 2017. Published by The Company of Biologists Ltd.

  18. Multiple prismatic calcium phosphate layers in the jaws of present-day sharks (Chondrichthyes; Selachii).

    Science.gov (United States)

    Dingerkus, G; Séret, B; Guilbert, E

    1991-01-15

    Jaws of large individuals, over 2 m in total length, of the shark species Carcharodon carcharias (great white shark) and Isurus oxyrinchus (mako shark) of the family Lamnidae, and Galeocerdo cuvieri (tiger shark) and Carcharhinus leucas (bull shark) of the family Carcharhinidae were found to have multiple, up to five, layers of prismatic calcium phosphate surrounding the cartilages. Smaller individuals of these species and other known species of living chondrichthyans have only one layer of prismatic calcium phosphate surrounding the cartilages, as also do most species of fossil chondrichthyans. Two exceptions are the fossil shark genera Xenacanthus and Tamiobatis. Where it is found in living forms, this multiple layered calcification does not appear to be phylogenetic, as it appears to be lacking in other lamnid and carcharhinid genera and species. Rather it appears to be functional, only appearing in larger individuals and species of these two groups, and hence may be necessary to strengthen the jaw cartilages of such individuals for biting.

  19. The Hyalella (Crustacea: Amphipoda) species cloud of the ancient Lake Titicaca originated from multiple colonizations.

    Science.gov (United States)

    Adamowicz, Sarah J; Marinone, María Cristina; Menu-Marque, Silvina; Martin, Jeffrey W; Allen, Daniel C; Pyle, Michelle N; De Los Ríos, Patricio; Sobel, Crystal N; Ibañez, Carla; Pinto, Julio; Witt, Jonathan D S

    2018-08-01

    Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalella (Crustacea: Amphipoda) species complex of Lake Titicaca, using COI and 28S DNA sequences, including samples from the connected Small and Large Lakes that comprise Lake Titicaca as well as from a broader survey of southern South American sites. At least five evolutionarily distant lineages are present within Lake Titicaca, which were estimated to have diverged from one another 12-20 MYA. These major lineages are dispersed throughout the broader South American Hyalella phylogeny, with each lineage representing at least one independent colonization of the lake. Moreover, complex genetic relationships are revealed between Lake Titicaca individuals and those from surrounding water bodies, which may be explained by repeated dispersal into and out of the lake, combined with parallel intralacustrine diversification within two separate clades. Although further work in deeper waters will be required to determine the number of species present and modes of diversification, our results strongly indicate that this amphipod species cloud is polyphyletic with a complex geographic history. Copyright © 2018 Elsevier Inc. All rights reserved.

  20. A Framework for Spatial Risk Assessments: Potential Impacts of Nonindigenous Invasive Species on Native Species

    Directory of Open Access Journals (Sweden)

    Craig R. Allen

    2006-06-01

    Full Text Available Many populations of wild animals and plants are declining and face increasing threats from habitat fragmentation and loss as well as exposure to stressors ranging from toxicants to diseases to invasive nonindigenous species. We describe and demonstrate a spatially explicit ecological risk assessment that allows for the incorporation of a broad array of information that may influence the distribution of an invasive species, toxicants, or other stressors, and the incorporation of landscape variables that may influence the spread of a species or substances. The first step in our analyses is to develop species models and quantify spatial overlap between stressor and target organisms. Risk is assessed as the product of spatial overlap and a hazard index based on target species vulnerabilities to the stressor of interest. We illustrate our methods with an example in which the stressor is the ecologically destructive nonindigenous ant, Solenopsis invicta, and the targets are two declining vertebrate species in the state of South Carolina, USA. A risk approach that focuses on landscapes and that is explicitly spatial is of particular relevance as remaining undeveloped lands become increasingly uncommon and isolated and more important in the management and recovery of species and ecological systems. Effective ecosystem management includes the control of multiple stressors, including invasive species with large impacts, understanding where those impacts may be the most severe, and implementing management strategies to reduce impacts.

  1. Large roads reduce bat activity across multiple species.

    Science.gov (United States)

    Kitzes, Justin; Merenlender, Adina

    2014-01-01

    Although the negative impacts of roads on many terrestrial vertebrate and bird populations are well documented, there have been few studies of the road ecology of bats. To examine the effects of large roads on bat populations, we used acoustic recorders to survey bat activity along ten 300 m transects bordering three large highways in northern California, applying a newly developed statistical classifier to identify recorded calls to the species level. Nightly counts of bat passes were analyzed with generalized linear mixed models to determine the relationship between bat activity and distance from a road. Total bat activity recorded at points adjacent to roads was found to be approximately one-half the level observed at 300 m. Statistically significant road effects were also found for the Brazilian free-tailed bat (Tadarida brasiliensis), big brown bat (Eptesicus fuscus), hoary bat (Lasiurus cinereus), and silver-haired bat (Lasionycteris noctivagans). The road effect was found to be temperature dependent, with hot days both increasing total activity at night and reducing the difference between activity levels near and far from roads. These results suggest that the environmental impacts of road construction may include degradation of bat habitat and that mitigation activities for this habitat loss may be necessary to protect bat populations.

  2. H2DB: a heritability database across multiple species by annotating trait-associated genomic loci.

    Science.gov (United States)

    Kaminuma, Eli; Fujisawa, Takatomo; Tanizawa, Yasuhiro; Sakamoto, Naoko; Kurata, Nori; Shimizu, Tokurou; Nakamura, Yasukazu

    2013-01-01

    H2DB (http://tga.nig.ac.jp/h2db/), an annotation database of genetic heritability estimates for humans and other species, has been developed as a knowledge database to connect trait-associated genomic loci. Heritability estimates have been investigated for individual species, particularly in human twin studies and plant/animal breeding studies. However, there appears to be no comprehensive heritability database for both humans and other species. Here, we introduce an annotation database for genetic heritabilities of various species that was annotated by manually curating online public resources in PUBMED abstracts and journal contents. The proposed heritability database contains attribute information for trait descriptions, experimental conditions, trait-associated genomic loci and broad- and narrow-sense heritability specifications. Annotated trait-associated genomic loci, for which most are single-nucleotide polymorphisms derived from genome-wide association studies, may be valuable resources for experimental scientists. In addition, we assigned phenotype ontologies to the annotated traits for the purposes of discussing heritability distributions based on phenotypic classifications.

  3. A spatial theory for emergent multiple predator-prey interactions in food webs.

    Science.gov (United States)

    Northfield, Tobin D; Barton, Brandon T; Schmitz, Oswald J

    2017-09-01

    Predator-prey interaction is inherently spatial because animals move through landscapes to search for and consume food resources and to avoid being consumed by other species. The spatial nature of species interactions necessitates integrating spatial processes into food web theory and evaluating how predators combine to impact their prey. Here, we present a spatial modeling approach that examines emergent multiple predator effects on prey within landscapes. The modeling is inspired by the habitat domain concept derived from empirical synthesis of spatial movement and interactions studies. Because these principles are motivated by synthesis of short-term experiments, it remains uncertain whether spatial contingency principles hold in dynamical systems. We address this uncertainty by formulating dynamical systems models, guided by core habitat domain principles, to examine long-term multiple predator-prey spatial dynamics. To describe habitat domains, we use classical niche concepts describing resource utilization distributions, and assume species interactions emerge from the degree of overlap between species. The analytical results generally align with those from empirical synthesis and present a theoretical framework capable of demonstrating multiple predator effects that does not depend on the small spatial or temporal scales typical of mesocosm experiments, and help bridge between empirical experiments and long-term dynamics in natural systems.

  4. Development of Biodegradable Poly(citrate)-Polyhedral Oligomeric Silsesquioxanes Hybrid Elastomers with High Mechanical Properties and Osteogenic Differentiation Activity.

    Science.gov (United States)

    Du, Yuzhang; Yu, Meng; Chen, Xiaofeng; Ma, Peter X; Lei, Bo

    2016-02-10

    Biodegradable elastomeric biomaterials have attracted much attention in tissue engineering due to their biomimetic viscoelastic behavior and biocompatibility. However, the low mechanical stability at hydrated state, fast biodegradation in vivo, and poor osteogenic activity greatly limited bioelastomers applications in bone tissue regeneration. Herein, we develop a series of poly(octanediol citrate)-polyhedral oligomeric silsesquioxanes (POC-POSS) hybrids with highly tunable elastomeric behavior (hydrated state) and biodegradation and osteoblasts biocompatibility through a facile one-pot thermal polymerization strategy. POC-POSS hybrids show significantly improved stiffness and ductility in either dry or hydrated conditions, as well as good antibiodegradation ability (20-50% weight loss in 3 months). POC-POSS hybrids exhibit significantly enhanced osteogenic differentiation through upregulating alkaline phosphatase (ALP) activity, calcium deposition, and expression of osteogenic markers (ALPL, BGLAP, and Runx2). The high mechanical stability at hydrated state and enhanced osteogenic activity make POC-POSS hybrid elastomers promising as scaffolds and nanoscale vehicles for bone tissue regeneration and drug delivery. This study may also provide a new strategy (controlling the stiffness under hydrated condition) to design advanced hybrid biomaterials with high mechanical properties under physiological condition for tissue regeneration applications.

  5. Model selection in Bayesian segmentation of multiple DNA alignments.

    Science.gov (United States)

    Oldmeadow, Christopher; Keith, Jonathan M

    2011-03-01

    The analysis of multiple sequence alignments is allowing researchers to glean valuable insights into evolution, as well as identify genomic regions that may be functional, or discover novel classes of functional elements. Understanding the distribution of conservation levels that constitutes the evolutionary landscape is crucial to distinguishing functional regions from non-functional. Recent evidence suggests that a binary classification of evolutionary rates is inappropriate for this purpose and finds only highly conserved functional elements. Given that the distribution of evolutionary rates is multi-modal, determining the number of modes is of paramount concern. Through simulation, we evaluate the performance of a number of information criterion approaches derived from MCMC simulations in determining the dimension of a model. We utilize a deviance information criterion (DIC) approximation that is more robust than the approximations from other information criteria, and show our information criteria approximations do not produce superfluous modes when estimating conservation distributions under a variety of circumstances. We analyse the distribution of conservation for a multiple alignment comprising four primate species and mouse, and repeat this on two additional multiple alignments of similar species. We find evidence of six distinct classes of evolutionary rates that appear to be robust to the species used. Source code and data are available at http://dl.dropbox.com/u/477240/changept.zip.

  6. An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis.

    Science.gov (United States)

    Suatoni, Elizabeth; Vicario, Saverio; Rice, Sean; Snell, Terry; Caccone, Adalgisa

    2006-10-01

    Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.

  7. Live cell imaging unveils multiple domain requirements for in vivo dimerization of the glucocorticoid receptor.

    Directory of Open Access Journals (Sweden)

    Diego M Presman

    2014-03-01

    Full Text Available Glucocorticoids are essential for life, but are also implicated in disease pathogenesis and may produce unwanted effects when given in high doses. Glucocorticoid receptor (GR transcriptional activity and clinical outcome have been linked to its oligomerization state. Although a point mutation within the GR DNA-binding domain (GRdim mutant has been reported as crucial for receptor dimerization and DNA binding, this assumption has recently been challenged. Here we have analyzed the GR oligomerization state in vivo using the number and brightness assay. Our results suggest a complete, reversible, and DNA-independent ligand-induced model for GR dimerization. We demonstrate that the GRdim forms dimers in vivo whereas adding another mutation in the ligand-binding domain (I634A severely compromises homodimer formation. Contrary to dogma, no correlation between the GR monomeric/dimeric state and transcriptional activity was observed. Finally, the state of dimerization affected DNA binding only to a subset of GR binding sites. These results have major implications on future searches for therapeutic glucocorticoids with reduced side effects.

  8. Multiple embryos, multiple nepionts and multiple equatorial layers in Cycloclypeus carpenteri.

    Science.gov (United States)

    Briguglio, Antonino; Kinoshita, Shunichi; Wolfgring, Erik; Hohenegger, Johann

    2016-04-01

    In this study, 17 specimens of Cycloclypeus carpenteri have been analyzed by means of microCT scanning. We used CT scanning technique as it enables the visualization and the quantifications of internal structures of hollow specimens without their destruction. It has been observed that many specimens possessing the natural morphology of this taxon, actually contain multiple embryos (up to 16 in one single specimen) and, in some few cases, multiple nepionts each with its own heterosteginid chambers (up to three separated nepionts). The diameter of each proloculus has been measured, and as a result, they are very variable even within the same specimen, therefore questioning the long known theory that schizonts have smaller proloculi than gamonts and also questioning the fact that proloculi in the same species should all have comparable size. Furthermore, we have observed the presence of additional equatorial planes on several specimens. Such additional planes are always connected to what seems to be the main equatorial plane. Such connections are T-shaped and are located at the junction between two equatorial layers; these junctions are made by a chamberlet, which possesses an unusually higher number of apertures. The connections between equatorial planes are always perfectly synchronized with the relative growth step and the same chamber can be therefore followed along the multiple equatorial planes. Apparently there is a perfect geometric relationship between the creation of additional equatorial planes and the position of the nepionts. Whenever the nepionts are positioned on different planes, additional planes are created and the angle of the nepionts is related to the banding angle of the equatorial planes. The presence of additional planes do not hamper the life of the cell, on the contrary, it seems that the cell is still able to build nicely shaped chamberlets and, after volumetric calculations, it seems all specimens managed to keep their logistic growth

  9. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

    Directory of Open Access Journals (Sweden)

    Gareth D Westrop

    Full Text Available Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

  10. Induction of Apoptosis in Human Multiple Myeloma Cell Lines by Ebselen via Enhancing the Endogenous Reactive Oxygen Species Production

    Directory of Open Access Journals (Sweden)

    Liang Zhang

    2014-01-01

    Full Text Available Ebselen a selenoorganic compound showing glutathione peroxidase like activity is an anti-inflammatory and antioxidative agent. Its cytoprotective activity has been investigated in recent years. However, experimental evidence also shows that ebselen causes cell death in several cancer cell types whose mechanism has not yet been elucidated. In this study, we examined the effect of ebselen on multiple myeloma (MM cell lines in vitro. The results showed that ebselen significantly enhanced the production of reactive oxygen species (ROS accompanied by cell viability decrease and apoptosis rate increase. Further studies revealed that ebselen can induce Bax redistribution from the cytosol to mitochondria leading to mitochondrial membrane potential ΔΨm changes and cytochrome C release from the mitochondria to cytosol. Furtherly, we found that exogenous addition of N-acetyl cysteine (NAC completely diminished the cell damage induced by ebselen. This result suggests that relatively high concentration of ebselen can induce MM cells apoptosis in culture by enhancing the production of endogenous ROS and triggering mitochondria mediated apoptotic pathway.

  11. A Kolmogorov-type competition model with multiple coexistence states and its applications to plant competition for sunlight

    Science.gov (United States)

    Just, Winfried; Nevai, Andrew L.

    2008-12-01

    It is demonstrated that a Kolmogorov-type competition model featuring species allocation and gain functions can possess multiple coexistence statesE Two examples are constructed: one in which the two competing species possess rectangular allocation functions but distinct gain functions, and the other in which one species has a rectangular allocation function, the second species has a bi-rectangular allocation function, and the two species share a common gain function. In both examples, it is shown that the species nullclines may intersect multiple times within the interior of the first quadrant, thus creating both locally stable and unstable equilibrium points. These results have important applications in the study of plant competition for sunlight, in which the allocation functions describe the vertical placement of leaves for two competing species, and the gain functions represent rates of photosynthesis performed by leaves at different heights when shaded by overlying leaves belonging to either species.

  12. Three novel, multiple recombinant types of species of human mastadenovirus D (HAdV-D 73, 74 & 75) isolated from diarrhoeal faeces of immunocompromised patients.

    Science.gov (United States)

    Hage, Elias; Dhingra, Akshay; Liebert, Uwe G; Bergs, Sandra; Ganzenmueller, Tina; Heim, Albert

    2017-11-02

    Species D is the largest of the seven species of human mastadenoviruses (HAdV), but few of its multiple types are associated with asevere disease, e.g. epidemic keratoconjunctivitis. Many other types are hardly ever associated with significant diseases in immunocompetent patients, but have been isolated from the diarrhoeal faeces of terminal AIDS patients suggesting their role as opportunistic pathogens. Three novel HAdV-D strains were isolated from the faeces of three immunocompromised adult patients (clinical diagnoses: lymphoma, myelodysplastic syndrome and AIDS CDC3B, respectively). These strains were not typeable by imputed serology of the hexon and fibre gene and therefore complete genomic sequences were generated by next-generation sequencing (NGS). All three strains were multiple recombinants and fulfilled the criteria for designation as types 73, 74 and 75 with the penton/hexon/fibre genotype codes P67H45F27, P70H74F51 and P75H26F29, respectively. A novel genomic backbone and also a novel hexon neutralization epitope sequence were discovered in type 74, and a novel penton sequence in type 75. At the complete genome level, types 73, 74 and 75 were closely related neither to each other nor to type 70, which was previously isolated in the same region. However, these four HAdV-D types were closely related to each other in single genes and gene regions, e.g. penton, E1 and E4 due to recombination events in their phylogeny. In conclusion, regional co-circulation of opportunistic HAdV-D types facilitated co- and super-infections, which are essential for homologous recombination, and thus resulted in the evolution of novel genotypes by lateral gene transfer.

  13. Multiple mortality events in bats: a global review

    Science.gov (United States)

    O'Shea, Thomas J.; Cryan, Paul; Hayman, David TH; Plowright, Raina K.; Streicker, Daniel G.

    2016-01-01

    Despite conservation concerns for many species of bats, factors causing mortality in bats have not been reviewed since 1970. Here, we review and qualitatively describe trends in the occurrence and apparent causes of multiple mortality events (MMEs) in bats around the world.

  14. Assessing changes on poly(ethylene terephthalate) properties after recycling: Mechanical recycling in laboratory versus postconsumer recycled material

    Energy Technology Data Exchange (ETDEWEB)

    López, María del Mar Castro, E-mail: quimcl02@udc.es [Grupo de Polímeros, Centro de Investigacións Tecnológicas (CIT), Departamento de Física, Escuela Universitaria Politécnica, Universidade de A Coruña, Campus de Ferrol, 15403 Ferrol (Spain); Ares Pernas, Ana Isabel, E-mail: aares@udc.es [Grupo de Polímeros, Centro de Investigacións Tecnológicas (CIT), Departamento de Física, Escuela Universitaria Politécnica, Universidade de A Coruña, Campus de Ferrol, 15403 Ferrol (Spain); Abad López, Ma José, E-mail: mjabad@udc.es [Grupo de Polímeros, Centro de Investigacións Tecnológicas (CIT), Departamento de Física, Escuela Universitaria Politécnica, Universidade de A Coruña, Campus de Ferrol, 15403 Ferrol (Spain); and others

    2014-10-15

    Keeping rheological, mechanical and thermal properties of virgin poly(ethylene terephthalate), PET, is necessary to assure the quality of second-market applications. A comparative study of these properties has been undertaken in virgin, mechanical recycled and commercial recycled PET samples. Viscoelastic characterization was carried out by rheological measurements. Mechanical properties were estimated by tensile and Charpy impact strength tests. Thermal properties and crystallinity were evaluated by differential scanning calorimetry and a deconvolution procedure was applied to study the population of the different crystals. Molecular conformational changes related to crystallinity values were studied by FTIR spectroscopy. Variations in average molecular weight were predicted from rheology. Besides, the presence-absence of linear and cyclic oligomeric species was measured by mass spectrometry techniques, as MALDI-TOF. Mechanical recycled PET undergoes a significant decline in rheological, mechanical and thermal properties upon increasing the number of reprocessing steps. This is due to the cleavage of the ester bonds with reduction in molar mass and raise in cyclic oligomeric species, in particular [GT{sub c}]{sub n} and [GT{sub c}]{sub n}-G type. Chain shortening plus enrichment in trans conformers favour the crystallization process which occurs earlier and faster with modification in crystal populations. Additional physicochemical steps are necessary to preserve the main benefits of PET. - Highlights: • Combination of multiple techniques to characterize the effects of recycling in PET. • Cleavage of ester bonds reduced viscosity, Mw, toughness in mechanical recycled PET. • Virgin, mechanical recycled and commercial recycled PET differ in crystal populations. • Cyclic oligomers [GT{sub c}]{sub n} and [GT{sub c}]{sub n}-G increase from the fourth extrusion cycle onwards.

  15. Equilibrium and extraction mechanism from monomeric and polimeric species of zirconium in solution. part. 2

    International Nuclear Information System (INIS)

    Azevedo, H.L.P. de.

    1980-01-01

    The mechanism of extraction and the equilibrium of chemical species from Zirconium solutions was studied. The multiple extraction method was used to show the species envolved in the extraction process and qualitative informations was obtained about the equilibrium between extractable species (monomers) and non-extractable species (polymers) in the aqueous phase. (M.J.C.) [pt

  16. Association of Nucleotide-binding Oligomerization Domain Receptors with Peptic Ulcer and Gastric Cancer.

    Science.gov (United States)

    Mohammadian Amiri, Rajeeh; Tehrani, Mohsen; Taghizadeh, Shirin; Shokri-Shirvani, Javad; Fakheri, Hafez; Ajami, Abolghasem

    2016-10-01

    Host innate immunity can affect the clinical outcomes of Helicobacter pylori infection, including gastritis, gastric ulcer, gastric adenocarcinoma, and MALT lymphoma. Nucleotide binding oligomerization domain (NOD)-1 and -2 are two molecules of innate immunity which are involved in the host defense against H. pylori. This study aimed to evaluate the effect of the expression level of NOD1 and NOD2 on the susceptibility to gastric cancer as well as peptic ulcer in individuals with H. pylori infection. The gene expression levels of these molecules were compared in three groups of non-ulcer dyspepsia (NUD) as a control group (n=52); peptic ulcer disease (PUD), (n=53); and gastric cancer (GC), (n=39). Relative expression levels of NOD1 in patients with GC were higher than those of NUD and PUD (p<0.001 and P<0.001, respectively). Similarly in case of NOD1, PUD group showed higher level of expression than NUD group (p<0.01). However, there was no significant difference between H. pylori -positive and -negative patients in NUD, PUD, or GC groups. Moreover, the expression levels of NOD2 showed no significant difference among NUD, PUD, or GC groups, while among H. pylori-positive patients, it was higher in GC group than NUD  and PUD groups (p<0.05 and p<0.01, respectively). In addition, positive correlation coefficients were attained between NOD1 and NOD2 expressions in patients with NUD (R2 Linear=0.349, p<0.001), PUD (R2 Linear=0.695, p<0.001), and GC (R2 Linear=0.385, p<0.001). Collectively, the results suggest that the chronic activation of NOD1 and NOD2 receptors might play a role in the development of gastric cancer.

  17. Competitive interactions between co-occurring invaders: identifying asymmetries between two invasive crayfish species

    NARCIS (Netherlands)

    Hudina, S.; Galic, N.G.; Roessink, I.; Hock, K.

    2011-01-01

    Ecosystems today increasingly suffer invasions by multiple invasive species. Complex interactions between invasive species can have different fitness implications for each invader, which can in turn determine the future progression of their invasions and result in differential impacts on native

  18. Species and size diversity in protective services offered by coral guard-crabs

    Directory of Open Access Journals (Sweden)

    C. Seabird McKeon

    2014-09-01

    Full Text Available Coral guard-crabs in the genus Trapezia are well-documented defenders of their pocilloporid coral hosts against coral predators such as the Crown-of-Thorns seastar (Acanthaster planci complex. The objectives of this study were to examine the protective services of six species of Trapezia against corallivory, and the extent of functional diversity among these Trapezia species.Studies conducted in Mo’orea, French Polynesia showed the Trapezia—coral mutualism protected the host corals from multiple predators through functional diversity in the assemblage of crab symbionts. Species differed in their defensive efficacy, but species within similar size classes shared similar abilities. Smaller-size Trapezia species, which were previously thought to be ineffective guards, play important defensive roles against small corallivores.We also measured the benefits of this mutualism to corals in the midst of an Acanthaster outbreak that reduced the live coral cover on the fore reef to less than 4%. The mutualism may positively affect the reef coral demography and potential for recovery during adverse predation events through shelter of multiple species of small corals near the host coral. Our results show that while functional diversity is supported within the genus, some Trapezia species may be functionally equivalent within the same size class, decreasing the threat of gaps in coral protection caused by absence or replacement of any single Trapezia species.

  19. Preparation of genomic DNA from a single species of uncultured magnetotactic bacterium by multiple-displacement amplification.

    Science.gov (United States)

    Arakaki, Atsushi; Shibusawa, Mie; Hosokawa, Masahito; Matsunaga, Tadashi

    2010-03-01

    Magnetotactic bacteria comprise a phylogenetically diverse group that is capable of synthesizing intracellular magnetic particles. Although various morphotypes of magnetotactic bacteria have been observed in the environment, bacterial strains available in pure culture are currently limited to a few genera due to difficulties in their enrichment and cultivation. In order to obtain genetic information from uncultured magnetotactic bacteria, a genome preparation method that involves magnetic separation of cells, flow cytometry, and multiple displacement amplification (MDA) using phi29 polymerase was used in this study. The conditions for the MDA reaction using samples containing 1 to 100 cells were evaluated using a pure-culture magnetotactic bacterium, "Magnetospirillum magneticum AMB-1," whose complete genome sequence is available. Uniform gene amplification was confirmed by quantitative PCR (Q-PCR) when 100 cells were used as a template. This method was then applied for genome preparation of uncultured magnetotactic bacteria from complex bacterial communities in an aquatic environment. A sample containing 100 cells of the uncultured magnetotactic coccus was prepared by magnetic cell separation and flow cytometry and used as an MDA template. 16S rRNA sequence analysis of the MDA product from these 100 cells revealed that the amplified genomic DNA was from a single species of magnetotactic bacterium that was phylogenetically affiliated with magnetotactic cocci in the Alphaproteobacteria. The combined use of magnetic separation, flow cytometry, and MDA provides a new strategy to access individual genetic information from magnetotactic bacteria in environmental samples.

  20. Are trade-offs among species' ecological interactions scale dependent? A test using pitcher-plant inquiline species.

    Science.gov (United States)

    Kneitel, Jamie M

    2012-01-01

    Trade-offs among species' ecological interactions is a pervasive explanation for species coexistence. The traits associated with trade-offs are typically measured to mechanistically explain species coexistence at a single spatial scale. However, species potentially interact at multiple scales and this may be reflected in the traits among coexisting species. I quantified species' ecological traits associated with the trade-offs expected at both local (competitive ability and predator tolerance) and regional (competitive ability and colonization rate) community scales. The most common species (four protozoa and a rotifer) from the middle trophic level of a pitcher plant (Sarracenia purpurea) inquiline community were used to link species traits to previously observed patterns of species diversity and abundance. Traits associated with trade-offs (competitive ability, predator tolerance, and colonization rate) and other ecological traits (size, growth rate, and carrying capacity) were measured for each of the focal species. Traits were correlated with one another with a negative relationship indicative of a trade-off. Protozoan and rotifer species exhibited a negative relationship between competitive ability and predator tolerance, indicative of coexistence at the local community scale. There was no relationship between competitive ability and colonization rate. Size, growth rate, and carrying capacity were correlated with each other and the trade-off traits: Size was related to both competitive ability and predator tolerance, but growth rate and carrying capacity were correlated with predator tolerance. When partial correlations were conducted controlling for size, growth rate and carrying capacity, the trade-offs largely disappeared. These results imply that body size is the trait that provides the basis for ecological interactions and trade-offs. Altogether, this study showed that the examination of species' traits in the context of coexistence at different scales

  1. Bioeconomic analysis supports the endangered species act.

    Science.gov (United States)

    Salau, Kehinde R; Fenichel, Eli P

    2015-10-01

    The United States Endangered Species Act (ESA) was enacted to protect and restore declining fish, wildlife, and plant populations. The ESA mandates endangered species protection irrespective of costs. This translates to the restriction of activities that harm endangered populations. We discuss criticisms of the ESA in the context of public land management and examine under what circumstance banning non-conservation activity on multiple use federal lands can be socially optimal. We develop a bioeconomic model to frame the species management problem under the ESA and identify scenarios where ESA-imposed regulations emerge as optimal strategies. Results suggest that banning harmful activities is a preferred strategy when valued endangered species are in decline or exposed to poor habitat quality. However, it is not optimal to sustain such a strategy in perpetuity. An optimal plan involves a switch to land-use practices characteristic of habitat conservation plans.

  2. Resolved single-molecule detection of individual species within a mixture of anti-biotin antibodies using an engineered monomeric nanopore.

    Science.gov (United States)

    Fahie, Monifa; Chisholm, Christina; Chen, Min

    2015-02-24

    Oligomeric protein nanopores with rigid structures have been engineered for the purpose of sensing a wide range of analytes including small molecules and biological species such as proteins and DNA. We chose a monomeric β-barrel porin, OmpG, as the platform from which to derive the nanopore sensor. OmpG is decorated with seven flexible loops that move dynamically to create a distinct gating pattern when ionic current passes through the pore. Biotin was chemically tethered to the most flexible one of these loops. The gating characteristic of the loop's movement in and out of the porin was substantially altered by analyte protein binding. The gating characteristics of the pore with bound targets were remarkably sensitive to molecular identity, even providing the ability to distinguish between homologues within an antibody mixture. A total of five gating parameters were analyzed for each analyte to create a unique fingerprint for each biotin-binding protein. Our exploitation of gating noise as a molecular identifier may allow more sophisticated sensor design, while OmpG's monomeric structure greatly simplifies nanopore production.

  3. Cartilage oligomeric matrix protein enhances matrix assembly during chondrogenesis of human mesenchymal stem cells.

    Science.gov (United States)

    Haleem-Smith, Hana; Calderon, Raul; Song, Yingjie; Tuan, Rocky S; Chen, Faye H

    2012-04-01

    Cartilage oligomeric matrix protein/thrombospondin-5 (COMP/TSP5) is an abundant cartilage extracellular matrix (ECM) protein that interacts with major cartilage ECM components, including aggrecan and collagens. To test our hypothesis that COMP/TSP5 functions in the assembly of the ECM during cartilage morphogenesis, we have employed mesenchymal stem cell (MSC) chondrogenesis in vitro as a model to examine the effects of COMP over-expression on neo-cartilage formation. Human bone marrow-derived MSCs were transfected with either full-length COMP cDNA or control plasmid, followed by chondrogenic induction in three-dimensional pellet or alginate hydrogel culture. MSC chondrogenesis and ECM production was estimated based on quantitation of sulfated glycosaminoglycan (sGAG) accumulation, immunohistochemistry of the presence and distribution of cartilage ECM proteins, and real-time RT-PCR analyis of mRNA expression of cartilage markers. Our results showed that COMP over-expression resulted in increased total sGAG content during the early phase of MSC chondrogenesis, and increased immuno-detectable levels of aggrecan and collagen type II in the ECM of COMP-transfected pellet and alginate cultures, indicating more abundant cartilaginous matrix. COMP transfection did not significantly increase the transcript levels of the early chondrogenic marker, Sox9, or aggrecan, suggesting that enhancement of MSC cartilage ECM was effected at post-transcriptional levels. These findings strongly suggest that COMP functions in mesenchymal chondrogenesis by enhancing cartilage ECM organization and assembly. The action of COMP is most likely mediated not via direct changes in cartilage matrix gene expression but via interactions of COMP with other cartilage ECM proteins, such as aggrecan and collagens, that result in enhanced assembly and retention.

  4. CARTILAGE OLIGOMERIC MATRIX PROTEIN ENHANCES MATRIX ASSEMBLY DURING CHONDROGENESIS OF HUMAN MESENCHYMAL STEM CELLS

    Science.gov (United States)

    Haleem-Smith, Hana; Calderon, Raul; Song, Yingjie; Tuan, Rocky S.; Chen, Faye H.

    2011-01-01

    Cartilage oligomeric matrix protein/thrombospondin-5 (COMP/TSP5) is an abundant cartilage extracellular matrix (ECM) protein that interacts with major cartilage ECM components, including aggrecan and collagens. To test our hypothesis that COMP/TSP5 functions in the assembly of the ECM during cartilage morphogenesis, we have employed mesenchymal stem cell (MSC) chondrogenesis in vitro as a model to examine the effects of COMP over-expression on neo-cartilage formation. Human bone marrow-derived MSCs were transfected with either full-length COMP cDNA or control plasmid, followed by chondrogenic induction in three-dimensional pellet or alginate-hydrogel culture. MSC chondrogenesis and ECM production was estimated based on quantitation of sulfated glycosaminoglycan (sGAG) accumulation, immunohistochemistry of the presence and distribution of cartilage ECM proteins, and real-time RT-PCR analyis of mRNA expression of cartilage markers. Our results showed that COMP over-expression resulted in increased total sGAG content during the early phase of MSC chondrogenesis, and increased immuno-detectable levels of aggrecan and collagen type II in the ECM of COMP-transfected pellet and alginate cultures, indicating more abundant cartilaginous matrix. COMP transfection did not significantly increase the transcript levels of the early chondrogenic marker, Sox9, or aggrecan, suggesting that enhancement of MSC cartilage ECM was effected at post-transcriptional levels. These findings strongly suggest that COMP functions in mesenchymal chondrogenesis by enhancing cartilage ECM organization and assembly. The action of COMP is most likely mediated not via direct changes in cartilage matrix gene expression but via interactions of COMP with other cartilage ECM proteins, such as aggrecan and collagens, that result in enhanced assembly and retention. PMID:22095699

  5. Discovery of Nanomolar Desmuramylpeptide Agonists of the Innate Immune Receptor Nucleotide-Binding Oligomerization Domain-Containing Protein 2 (NOD2) Possessing Immunostimulatory Properties.

    Science.gov (United States)

    Gobec, Martina; Tomašič, Tihomir; Štimac, Adela; Frkanec, Ruža; Trontelj, Jurij; Anderluh, Marko; Mlinarič-Raščan, Irena; Jakopin, Žiga

    2018-04-12

    Muramyl dipeptide (MDP), a fragment of bacterial peptidoglycan, has long been known as the smallest fragment possessing adjuvant activity, on the basis of its agonistic action on the nucleotide-binding oligomerization domain-containing protein 2 (NOD2). There is a pressing need for novel adjuvants, and NOD2 agonists provide an untapped source of potential candidates. Here, we report the design, synthesis, and characterization of a series of novel acyl tripeptides. A pivotal structural element for molecular recognition by NOD2 has been identified, culminating in the discovery of compound 9, the most potent desmuramylpeptide NOD2 agonist to date. Compound 9 augmented pro-inflammatory cytokine release from human peripheral blood mononuclear cells in synergy with lipopolysaccharide. Furthermore, it was able to induce ovalbumin-specific IgG titers in a mouse model of adjuvancy. These findings provide deeper insights into the structural requirements of desmuramylpeptides for NOD2-activation and highlight the potential use of NOD2 agonists as adjuvants for vaccines.

  6. Chromatographic speciation of Cr(III)-species, inter-species equilibrium isotope fractionation and improved chemical purification strategies for high-precision isotope analysis

    DEFF Research Database (Denmark)

    Larsen, Kirsten Kolbjørn; Wielandt, Daniel Kim Peel; Schiller, Martin

    2016-01-01

    Chromatographic purification of chromium (Cr), which is required for high-precision isotope analysis, is complicated by the presence of multiple Cr-species with different effective charges in the acid digested sample aliquots. The differing ion exchange selectivity and sluggish reaction rates of ...

  7. Multiple-Parameter, Low-False-Alarm Fire-Detection Systems

    Science.gov (United States)

    Hunter, Gary W.; Greensburg, Paul; McKnight, Robert; Xu, Jennifer C.; Liu, C. C.; Dutta, Prabir; Makel, Darby; Blake, D.; Sue-Antillio, Jill

    2007-01-01

    Fire-detection systems incorporating multiple sensors that measure multiple parameters are being developed for use in storage depots, cargo bays of ships and aircraft, and other locations not amenable to frequent, direct visual inspection. These systems are intended to improve upon conventional smoke detectors, now used in such locations, that reliably detect fires but also frequently generate false alarms: for example, conventional smoke detectors based on the blockage of light by smoke particles are also affected by dust particles and water droplets and, thus, are often susceptible to false alarms. In contrast, by utilizing multiple parameters associated with fires, i.e. not only obscuration by smoke particles but also concentrations of multiple chemical species that are commonly generated in combustion, false alarms can be significantly decreased while still detecting fires as reliably as older smoke-detector systems do. The present development includes fabrication of sensors that have, variously, micrometer- or nanometer-sized features so that such multiple sensors can be integrated into arrays that have sizes, weights, and power demands smaller than those of older macroscopic sensors. The sensors include resistors, electrochemical cells, and Schottky diodes that exhibit different sensitivities to the various airborne chemicals of interest. In a system of this type, the sensor readings are digitized and processed by advanced signal-processing hardware and software to extract such chemical indications of fires as abnormally high concentrations of CO and CO2, possibly in combination with H2 and/or hydrocarbons. The system also includes a microelectromechanical systems (MEMS)-based particle detector and classifier device to increase the reliability of measurements of chemical species and particulates. In parallel research, software for modeling the evolution of a fire within an aircraft cargo bay has been developed. The model implemented in the software can

  8. Supplementary Material for: A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein

    KAUST Repository

    Smirnova, Ekaterina; Kwan, Jamie; Siu, Ryan; Gao, Xin; Zoidl, Georg; Demeler, Borries; Saridakis, Vivian; Donaldson, Logan

    2016-01-01

    Abstract Background CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions. Results We demonstrate that the crystal structure of the Sterile Alpha Motif (SAM) domain tandem (SAM1-SAM2) oligomer from CASKIN2 is different than CASKIN1, with the minimal repeating unit being a dimer, rather than a monomer. Analytical ultracentrifugation sedimentation velocity methods revealed differences in monomer/dimer equilibria across a range of concentrations and ionic strengths for the wild type CASKIN2 SAM tandem and a structure-directed double mutant that could not oligomerize. Further distinguishing CASKIN2 from CASKIN1, EGFP-tagged SAM tandem proteins expressed in Neuro2a cells produced punctae that were distinct both in shape and size. Conclusions This study illustrates a new way in which neuronal SAM domains can assemble into large macromolecular assemblies that might concentrate and amplify synaptic responses.

  9. Theoretical Studies of Group IVA and Group IVB Chemistry

    Science.gov (United States)

    2012-01-13

    novel ionic liquids . We have performed very high level CCSD(T) calculations on one such species, Al13- to predict its ionization potential in nearly...Precursors. Polyhedral oligomeric silsesquioxanes (POSS) are three- dimensional Si-O cage compounds that have many uses, because of their resistance

  10. Density dependence governs when population responses to multiple stressors are magnified or mitigated.

    Science.gov (United States)

    Hodgson, Emma E; Essington, Timothy E; Halpern, Benjamin S

    2017-10-01

    Population endangerment typically arises from multiple, potentially interacting anthropogenic stressors. Extensive research has investigated the consequences of multiple stressors on organisms, frequently focusing on individual life stages. Less is known about population-level consequences of exposure to multiple stressors, especially when exposure varies through life. We provide the first theoretical basis for identifying species at risk of magnified effects from multiple stressors across life history. By applying a population modeling framework, we reveal conditions under which population responses from stressors applied to distinct life stages are either magnified (synergistic) or mitigated. We find that magnification or mitigation critically depends on the shape of density dependence, but not the life stage in which it occurs. Stressors are always magnified when density dependence is linear or concave, and magnified or mitigated when it is convex. Using Bayesian numerical methods, we estimated the shape of density dependence for eight species across diverse taxa, finding support for all three shapes. © 2017 by the Ecological Society of America.

  11. Cartilage oligomeric matrix protein associates differentially with erosions and synovitis and has a different temporal course in cyclic citrullinated peptide antibody (anti-CCP)-positive versus anti-CCP-negative early rheumatoid arthritis

    DEFF Research Database (Denmark)

    Christensen, Anne F; Lindegaard, Hanne; Hørslev-Petersen, Kim

    2011-01-01

    -suppressive effect. We aimed to compare circulating cartilage oligomeric matrix protein (COMP), a marker of cartilage turnover, in untreated anti-CCP-positive and anti-CCP-negative RA, and to study the temporal pattern of COMP through 4 years of treatment, including the relationship to imaging and clinical findings.......048). In anti-CCP-positive patients, COMP exhibited a parabolic course over 4 years, while COMP in anti-CCP-negative patients had an almost linear course. In anti-CCP-positive patients, COMP was associated with MRI edema and erosion score, while COMP was correlated with synovitis score in anti...

  12. How much variation can one ant species hold? Species delimitation in the Crematogaster kelleri-group in Madagascar.

    Directory of Open Access Journals (Sweden)

    Bonnie B Blaimer

    Full Text Available We investigated the species-level taxonomy of the Malagasy Crematogaster (Crematogaster kelleri-group and an additional more distantly related species of the same subgenus. Morphological data from worker, queen and male ants, as well as genetic data from three nuclear genes (long wavelength rhodopsin, arginine kinase and carbomoylphosphate synthase and one mitochondrial marker (cytochrome oxidase I led to the recognition of six species. Within the C. kelleri-group, three new species are described: C. hazolava Blaimer sp. n., C. hafahafa Blaimer sp. n. and C. tavaratra Blaimer sp. n. The previously described taxa C. kelleri Forel and C. madagascariensis André are validated by our analysis. Conversely, our data suggests synonymy of C. adrepens Forel (with C. kelleri and C. gibba Emery (with C. madagascariensis. A more distantly related and phylogenetically isolated species, C. tsisitsilo Blaimer sp. n., is further described. We report high levels of morphological and molecular variation in C. kelleri and illustrate that this variation can be explained partly by geography. Species descriptions, images, distribution maps and identification keys based on worker ants, as well as on queen and male ants where available, are presented for all six species. Our work highlights the elevated species richness of Crematogaster ants throughout Madagascar's humid forests, especially in the far northern tip of the island, and the need to use multiple data sources to ensure clear demarcation of this diversity.

  13. Composite polymer electrolyte containing ionic liquid and functionalized polyhedral oligomeric silsesquioxanes for anhydrous PEM applications.

    Science.gov (United States)

    Subianto, Surya; Mistry, Mayur K; Choudhury, Namita Roy; Dutta, Naba K; Knott, Robert

    2009-06-01

    A new type of supported liquid membrane was made by combining an ionic liquid (IL) with a Nafion membrane reinforced with multifunctional polyhedral oligomeric silsesquioxanes (POSSs) using a layer-by-layer strategy for anhydrous proton-exchange membrane (PEM) application. The POSS was functionalized by direct sulfonation, and the sulfonated POSS (S-POSS) was incorporated into Nafion 117 membranes by the infiltration method. The resultant hybrid membrane shows strong ionic interaction between the Nafion matrix and the multifunctional POSS, resulting in increased glass transition temperature and thermal stability at very low loadings of S-POSS (1%). The presence of S-POSS has also improved the proton conductivity especially at low humidities, where it shows a marked increase due to its confinement in the ionic domains and promotes water uptake by capillary condensation. In order to achieve anhydrous conductivity, the IL 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BMI-BTSI) was incorporated into these membranes to provide proton conduction in the absence of water. Although the incorporation of an IL shows a plasticizing effect on the Nafion membrane, the S-POSS composite membrane with an IL shows a higher modulus at high temperatures compared to Nafion 117 and a Nafion-IL membrane, with significantly higher proton conductivity (5 mS/cm at 150 degrees C with 20% IL). This shows the ability of the multifunctional POSS and IL to work symbiotically to achieve the desirable proton conductivity and mechanical properties of such membranes by enhancing the ionic interaction within the material.

  14. Binding and Oligomerization of Modified and Native Bt Toxins in Resistant and Susceptible Pink Bollworm.

    Directory of Open Access Journals (Sweden)

    Josue Ocelotl

    Full Text Available Insecticidal proteins from Bacillus thuringiensis (Bt are used extensively in sprays and transgenic crops for pest control, but their efficacy is reduced when pests evolve resistance. Better understanding of the mode of action of Bt toxins and the mechanisms of insect resistance is needed to enhance the durability of these important alternatives to conventional insecticides. Mode of action models agree that binding of Bt toxins to midgut proteins such as cadherin is essential for toxicity, but some details remain unresolved, such as the role of toxin oligomers. In this study, we evaluated how Bt toxin Cry1Ac and its genetically engineered counterpart Cry1AcMod interact with brush border membrane vesicles (BBMV from resistant and susceptible larvae of Pectinophora gossypiella (pink bollworm, a global pest of cotton. Compared with Cry1Ac, Cry1AcMod lacks 56 amino acids at the amino-terminus including helix α-1; previous work showed that Cry1AcMod formed oligomers in vitro without cadherin and killed P. gossypiella larvae harboring cadherin mutations linked with >1000-fold resistance to Cry1Ac. Here we found that resistance to Cry1Ac was associated with reduced oligomer formation and insertion. In contrast, Cry1AcMod formed oligomers in BBMV from resistant larvae. These results confirm the role of cadherin in oligomerization of Cry1Ac in susceptible larvae and imply that forming oligomers without cadherin promotes toxicity of Cry1AcMod against resistant P. gossypiella larvae that have cadherin mutations.

  15. Role of Nucleotide-Binding Oligomerization Domain-Containing (NOD 2 in Host Defense during Pneumococcal Pneumonia.

    Directory of Open Access Journals (Sweden)

    Tijmen J Hommes

    Full Text Available Streptococcus (S. pneumoniae is the most common causative pathogen in community-acquired pneumonia. Nucleotide-binding oligomerization domain-containing (NOD 2 is a pattern recognition receptor located in the cytosol of myeloid cells that is able to detect peptidoglycan fragments of S. pneumoniae. We here aimed to investigate the role of NOD2 in the host response during pneumococcal pneumonia. Phagocytosis of S. pneumoniae was studied in NOD2 deficient (Nod2-/- and wild-type (Wt alveolar macrophages and neutrophils in vitro. In subsequent in vivo experiments Nod2-/- and Wt mice were inoculated with serotype 2 S. pneumoniae (D39, an isogenic capsule locus deletion mutant (D39Δcps or serotype 3 S. pneumoniae (6303 via the airways, and bacterial growth and dissemination and the lung inflammatory response were evaluated. Nod2-/- alveolar macrophages and blood neutrophils displayed a reduced capacity to internalize pneumococci in vitro. During pneumonia caused by S. pneumoniae D39 Nod2-/- mice were indistinguishable from Wt mice with regard to bacterial loads in lungs and distant organs, lung pathology and neutrophil recruitment. While Nod2-/- and Wt mice also had similar bacterial loads after infection with the more virulent S. pneumoniae 6303 strain, Nod2-/- mice displayed a reduced bacterial clearance of the normally avirulent unencapsulated D39Δcps strain. These results suggest that NOD2 does not contribute to host defense during pneumococcal pneumonia and that the pneumococcal capsule impairs recognition of S. pneumoniae by NOD2.

  16. Oligomerization of Bacillus subtilis DesR is required for fine tuning regulation of membrane fluidity.

    Science.gov (United States)

    Najle, Sebastián R; Inda, María E; de Mendoza, Diego; Cybulski, Larisa E

    2009-10-01

    The DesK-DesR two-component system regulates the order of membrane lipids in the bacterium Bacillus subtilis by controlling the expression of the des gene coding for the delta 5-acyl-lipid desaturase. To activate des transcription, the membrane-bound histidine kinase DesK phosphorylates the response regulator DesR. This covalent modification of the regulatory domain of dimeric DesR promotes, in a cooperative fashion, the hierarchical occupation of two adjacent, non-identical, DesR-P binding sites, so that there is a shift in the equilibrium toward the tetrameric active form of the response regulator. However, the mechanism of regulation of DesR activity by phosphorylation and oligomerization is not well understood. We employed deletion analysis and reporter fusions to study the role of the N-terminal domain on DesR activity. In addition, electromobility shift assays were used to analyze the binding capacity of the transcription factor to deletion mutants of the des promoter. We show that DesR lacking the N-terminal domain is still able to bind to the des promoter. We also demonstrate that if the RA site is moved closer to the -35 region of Pdes, the adjacent site RB is dispensable for activation. Our results indicate that the unphosphorylated regulatory domain of DesR obstructs the access of the recognition helix of DesR to its DNA target. In addition, we present evidence showing that RB is physiologically relevant to control the activation of the des gene when the levels of DesR-P reach a critical threshold.

  17. Fouling behaviors of polybenzimidazole (PBI)-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) hollow fiber membranes for engineering osmosis processes

    KAUST Repository

    Chen, Sicong; Fu, Xiuzhu; Chung, Neal Tai-Shung

    2014-01-01

    This paper investigated the individual effects of reverse salt flux and permeate flux on fouling behaviors of as-spun and annealed polybenzimidazole (PBI)-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) hollow fiber membranes under forward osmosis (FO) and pressure retarded osmosis (PRO) processes. Two types of membrane fouling had been studied; namely, inorganic fouling (CaSO4·2H2O gypsum scaling) during FO operations and organic fouling (sodium alginate fouling) during PRO operations. It is found that gypsum scaling on the membrane surface may be inhibited and even eliminated with an increase in reverse MgCl2 flux due to competitive formations of MgSO4° and CaSO4·2H2O. In contrast, the increase of reverse NaCl flux exhibits a slight enhancement on alginate fouling in both FO and PRO processes. Comparing to the reverse salt flux, the permeate flux always plays a dominant role in fouling. Therefore, lesser fouling has been observed on the membrane surface under the pressurized PRO process than FO process because the reduced initial flux mitigates the fouling phenomena more significantly than the enhancement caused by an increase in reverse NaCl flux. © 2013 Elsevier B.V.

  18. Fouling behaviors of polybenzimidazole (PBI)-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) hollow fiber membranes for engineering osmosis processes

    KAUST Repository

    Chen, Sicong

    2014-02-01

    This paper investigated the individual effects of reverse salt flux and permeate flux on fouling behaviors of as-spun and annealed polybenzimidazole (PBI)-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) hollow fiber membranes under forward osmosis (FO) and pressure retarded osmosis (PRO) processes. Two types of membrane fouling had been studied; namely, inorganic fouling (CaSO4·2H2O gypsum scaling) during FO operations and organic fouling (sodium alginate fouling) during PRO operations. It is found that gypsum scaling on the membrane surface may be inhibited and even eliminated with an increase in reverse MgCl2 flux due to competitive formations of MgSO4° and CaSO4·2H2O. In contrast, the increase of reverse NaCl flux exhibits a slight enhancement on alginate fouling in both FO and PRO processes. Comparing to the reverse salt flux, the permeate flux always plays a dominant role in fouling. Therefore, lesser fouling has been observed on the membrane surface under the pressurized PRO process than FO process because the reduced initial flux mitigates the fouling phenomena more significantly than the enhancement caused by an increase in reverse NaCl flux. © 2013 Elsevier B.V.

  19. Inhibiting α-synuclein oligomerization by stable cell-penetrating β-synuclein fragments recovers phenotype of Parkinson's disease model flies.

    Directory of Open Access Journals (Sweden)

    Ronit Shaltiel-Karyo

    Full Text Available The intracellular oligomerization of α-synuclein is associated with Parkinson's disease and appears to be an important target for disease-modifying treatment. Yet, to date, there is no specific inhibitor for this aggregation process. Using unbiased systematic peptide array analysis, we identified molecular interaction domains within the β-synuclein polypeptide that specifically binds α-synuclein. Adding such peptide fragments to α-synuclein significantly reduced both amyloid fibrils and soluble oligomer formation in vitro. A retro-inverso analogue of the best peptide inhibitor was designed to develop the identified molecular recognition module into a drug candidate. While this peptide shows indistinguishable activity as compared to the native peptide, it is stable in mouse serum and penetrates α-synuclein over-expressing cells. The interaction interface between the D-amino acid peptide and α-synuclein was mapped by Nuclear Magnetic Resonance spectroscopy. Finally, administering the retro-inverso peptide to a Drosophila model expressing mutant A53T α-synuclein in the nervous system, resulted in a significant recovery of the behavioral abnormalities of the treated flies and in a significant reduction in α-synuclein accumulation in the brains of the flies. The engineered retro-inverso peptide can serve as a lead for developing a novel class of therapeutic agents to treat Parkinson's disease.

  20. Continued biological investigations of boron-rich oligomeric phosphate diesters (OPDs). Tumor-selective boron agents for BNCT

    International Nuclear Information System (INIS)

    Lee, Mark W.; Shelly, Kenneth; Kane, Robert R.; Hawthorne, M. Frederick

    2006-01-01

    Clinical success of Boron Neutron Capture Therapy will rely on the selective intracellular delivery of high concentrations of boron-10 to tumor tissue. In order for a boron agent to facilitate clinical success, the simultaneous needs of obtaining a high tumor dose, high tumor selectivity, and low systemic toxicity must be realized. Boron-rich oligomeric phosphate diesters (OPDs) are a class of highly water-soluble compounds containing up to 40% boron by weight. Previous work in our groups demonstrated that once placed in the cytoplasm of tumor cells, OPDs quickly accumulate within the cell nucleus. The objective of the current study was to determine the biodistribution of seven different free OPDs in BALB/c mice bearing EMT6 tumors. Fructose solutions containing between 1.4 and 6.4 micrograms of boron per gram of tissue were interveinously injected in mice seven to ten days after tumor implantation. At intervals during the study, animals were euthanized and samples of tumor, blood, liver, kidney, brain and skin were collected and analyzed for boron content using ICP-AES. Tumor boron concentrations of between 5 and 29 ppm were achieved and maintained over the 72-hour time course of each experiment. Several OPDs demonstrated high tumor selectivity with one oligomer exhibiting a tumor to blood ratio of 35:1. The apparent toxicity of each oligomer was assessed through animal behavior during the experiment and necropsy of each animal upon sacrifice. (author)

  1. Accounting for the ecosystem services of migratory species: Quantifying migration support and spatial subsidies

    Science.gov (United States)

    Semmens, Darius J.; Diffendorfer, James E.; López-Hoffman, Laura; Shapiro, Carl D.

    2011-01-01

    Migratory species support ecosystem process and function in multiple areas, establishing ecological linkages between their different habitats. As they travel, migratory species also provide ecosystem services to people in many different locations. Previous research suggests there may be spatial mismatches between locations where humans use services and the ecosystems that produce them. This occurs with migratory species, between the areas that most support the species' population viability – and hence their long-term ability to provide services – and the locations where species provide the most ecosystem services. This paper presents a conceptual framework for estimating how much a particular location supports the provision of ecosystem services in other locations, and for estimating the extent to which local benefits are dependent upon other locations. We also describe a method for estimating the net payment, or subsidy, owed by or to a location that balances benefits received and support provided by locations throughout the migratory range of multiple species. The ability to quantify these spatial subsidies could provide a foundation for the establishment of markets that incentivize cross-jurisdictional cooperative management of migratory species. It could also provide a mechanism for resolving conflicts over the sustainable and equitable allocation of exploited migratory species.

  2. Collagen XII and XIV, New Partners of Cartilage Oligomeric Matrix Protein in the Skin Extracellular Matrix Suprastructure*

    Science.gov (United States)

    Agarwal, Pallavi; Zwolanek, Daniela; Keene, Douglas R.; Schulz, Jan-Niklas; Blumbach, Katrin; Heinegård, Dick; Zaucke, Frank; Paulsson, Mats; Krieg, Thomas; Koch, Manuel; Eckes, Beate

    2012-01-01

    The tensile and scaffolding properties of skin rely on the complex extracellular matrix (ECM) that surrounds cells, vasculature, nerves, and adnexus structures and supports the epidermis. In the skin, collagen I fibrils are the major structural component of the dermal ECM, decorated by proteoglycans and by fibril-associated collagens with interrupted triple helices such as collagens XII and XIV. Here we show that the cartilage oligomeric matrix protein (COMP), an abundant component of cartilage ECM, is expressed in healthy human skin. COMP expression is detected in the dermal compartment of skin and in cultured fibroblasts, whereas epidermis and HaCaT cells are negative. In addition to binding collagen I, COMP binds to collagens XII and XIV via their C-terminal collagenous domains. All three proteins codistribute in a characteristic narrow zone in the superficial papillary dermis of healthy human skin. Ultrastructural analysis by immunogold labeling confirmed colocalization and further revealed the presence of COMP along with collagens XII and XIV in anchoring plaques. On the basis of these observations, we postulate that COMP functions as an adapter protein in human skin, similar to its function in cartilage ECM, by organizing collagen I fibrils into a suprastructure, mainly in the vicinity of anchoring plaques that stabilize the cohesion between the upper dermis and the basement membrane zone. PMID:22573329

  3. Collagen XII and XIV, new partners of cartilage oligomeric matrix protein in the skin extracellular matrix suprastructure.

    Science.gov (United States)

    Agarwal, Pallavi; Zwolanek, Daniela; Keene, Douglas R; Schulz, Jan-Niklas; Blumbach, Katrin; Heinegård, Dick; Zaucke, Frank; Paulsson, Mats; Krieg, Thomas; Koch, Manuel; Eckes, Beate

    2012-06-29

    The tensile and scaffolding properties of skin rely on the complex extracellular matrix (ECM) that surrounds cells, vasculature, nerves, and adnexus structures and supports the epidermis. In the skin, collagen I fibrils are the major structural component of the dermal ECM, decorated by proteoglycans and by fibril-associated collagens with interrupted triple helices such as collagens XII and XIV. Here we show that the cartilage oligomeric matrix protein (COMP), an abundant component of cartilage ECM, is expressed in healthy human skin. COMP expression is detected in the dermal compartment of skin and in cultured fibroblasts, whereas epidermis and HaCaT cells are negative. In addition to binding collagen I, COMP binds to collagens XII and XIV via their C-terminal collagenous domains. All three proteins codistribute in a characteristic narrow zone in the superficial papillary dermis of healthy human skin. Ultrastructural analysis by immunogold labeling confirmed colocalization and further revealed the presence of COMP along with collagens XII and XIV in anchoring plaques. On the basis of these observations, we postulate that COMP functions as an adapter protein in human skin, similar to its function in cartilage ECM, by organizing collagen I fibrils into a suprastructure, mainly in the vicinity of anchoring plaques that stabilize the cohesion between the upper dermis and the basement membrane zone.

  4. Systematics of Plant-Pathogenic and Related Streptomyces Species Based on Phylogenetic Analyses of Multiple Gene Loci

    Science.gov (United States)

    The 10 species of Streptomyces implicated as the etiological agents in scab disease of potatoes or soft rot disease of sweet potatoes are distributed among 7 different phylogenetic clades in analyses based on 16S rRNA gene sequences, but high sequence similarity of this gene among Streptomyces speci...

  5. A Fusion-Inhibiting Peptide against Rift Valley Fever Virus Inhibits Multiple, Diverse Viruses

    Science.gov (United States)

    2013-09-12

    performance liquid chroma- tography to greater than 95% purity (Bio-synthesis, Inc., Lewisville, TX). Lyophilized peptides were initially resuspended in...lesser extent RVFV-6sc, were found to precipitate Gc (Figure 5); however, in the presence of the non- ionic detergent Triton-X, which will solubilize...Viral membrane fusion. Nat Struct Mol Biol 15: 690–698. 12. Allison SL, Schalich J, Stiasny K, Mandl CW, Kunz C, et al. (1995) Oligomeric rearrangement

  6. Towards an integration of biodiversity-ecosystem functioning and food web theory to evaluate relationships between multiple ecosystem services

    NARCIS (Netherlands)

    Hines, Jes; van der Putten, W.H.; De Deyn, G.B.; Wagg, Cameron; Voigt, Winfried; Mulder, Christian; Weisser, Wolfgang W.; Engel, Jan; Melian, Carlos; Scheu, Stefan; Birkhofer, Klaus; Ebeling, Anne; Scherber, Christoph; Eisenhauer, Nico

    2015-01-01

    Ecosystem responses to changes in species diversity are often studied individually. However, changes in species diversity can simultaneously influence multiple interdependent ecosystem functions. Therefore, an important challenge is to determine when and how changes in species diversity that

  7. In vitro mass multiplication of pomegranate from cotyledonary nodal ...

    African Journals Online (AJOL)

    Maria

    2013-05-15

    May 15, 2013 ... Key words: Establishment, multiplication, rooting, acclimatization, Punica granatum. INTRODUCTION. Pomegranate Punica granatum L. belongs to the family. Punicaceae which comprises only one genus (Punica) and only two species, P. granatum and P. proptopunica. This is popularly known as anar, ...

  8. Telecoupling framework for research on migratory species in the Anthropocene

    Directory of Open Access Journals (Sweden)

    Jacqueline Hulina

    2017-03-01

    Full Text Available Migratory species are an important component of biodiversity and provide essential ecosystem services for humans, but many are threatened and endangered. Numerous studies have been conducted on the biology of migratory species, and there is an increased recognition of the major role of human dimensions in conserving migratory species. However, there is a lack of systematic integration of socioeconomic and environmental factors. Because human activities affect migratory species in multiple places, integrating socioeconomic and environmental factors across space is essential, but challenging. The holistic framework of telecoupling (socioeconomic and environmental interactions over distances has the potential to help meet this challenge because it enables researchers to integrate human and natural interactions across multiple distant places. The use of the telecoupling framework may also lead to new conservation strategies and actions. To demonstrate its potential, we apply the framework to Kirtland’s warblers ('Setophaga kirtlandii' , a conservation-reliant migratory songbird. Results show accomplishments from long-term research and recovery efforts on the warbler in the context of the telecoupling framework. The results also show 24 research gaps even though the species has been relatively well-studied compared to many other species. An important gap is a lack of systematic studies on feedbacks among breeding, wintering, and stopover sites, as well as other “spillover” systems that may affect and be affected by migration (e.g., via tourism, land use, or climate change. The framework integrated scattered information and provided useful insights about new research topics and flow-centered management approaches that encapsulate the full annual cycle of migration. We also illustrate the similarities and differences between Kirtland’s warblers and several other migratory species, indicating the applicability of the telecoupling framework to

  9. Multiple gene genealogies and phenotypic characters differentiate several novel species of Mycosphaerella and related anamorphs on banana.

    Science.gov (United States)

    Arzanlou, M; Groenewald, J Z; Fullerton, R A; Abeln, E C A; Carlier, J; Zapater, M-F; Buddenhagen, I W; Viljoen, A; Crous, P W

    2008-06-01

    Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is known about these taxa, and for the majority of these species no culture or DNA is available for study. In the present study, we collected a global set of Mycosphaerella strains from banana, and compared them by means of morphology and a multi-gene nucleotide sequence data set. The phylogeny inferred from the ITS region and the combined data set containing partial gene sequences of the actin gene, the small subunit mitochondrial ribosomal DNA and the histone H3 gene revealed a rich diversity of Mycosphaerella species on Musa. Integration of morphological and molecular data sets confirmed more than 20 species of Mycosphaerella (incl. anamorphs) to occur on banana. This study reconfirmed the previously described presence of Cercospora apii, M. citri and M. thailandica, and also identified Mycosphaerella communis, M. lateralis and Passalora loranthi on this host. Moreover, eight new species identified from Musa are described, namely Dissoconium musae, Mycosphaerella mozambica, Pseudocercospora assamensis, P. indonesiana, P. longispora, Stenella musae, S. musicola, and S. queenslandica.

  10. Development of the optical sensor for discriminating isomers of fatty acids based on emissive network polymers composed of polyhedral oligomeric silsesquioxane.

    Science.gov (United States)

    Narikiyo, Hayato; Kakuta, Takahiro; Matsuyama, Hiroki; Gon, Masayuki; Tanaka, Kazuo; Chujo, Yoshiki

    2017-07-01

    It was shown that water-soluble network polymers composed of polyhedral oligomeric silsesquioxane (POSS) had hydrophobic spaces inside the network because of strong hydrophobicity of the cubic silica cage. In this study, the water-soluble POSS network polymers connected with triphenylamine derivatives (TPA-POSS) were synthesized, and their functions as a sensor for discriminating the geometric isomers of fatty acids were investigated. Accordingly, in the photoluminescence spectra, different time-courses of intensity and peak wavelengths of the emission bands were detected from the TPA-POSS-containing solution in the presence of cis- or trans-fatty acids during incubation. Furthermore, variable time-dependent changes were obtained by changing coexisting ratios between two geometric isomers. From the mechanistic investigation, it was implied that these changes could be originated from the difference in the degree of interaction between the POSS networks and each fatty acid. Our data could be applicable for constructing a sensing material for generation and proportion of trans-fatty acids in the oil. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Generalized fractional supersymmetry associated to different species of anyons

    International Nuclear Information System (INIS)

    Douari, Jamila; Abdus Salam International Centre for Theoretical Physics, Trieste; Hassouni, Yassine

    2001-01-01

    We consider multiple species of anyons characterized by different statistical parameters. First, we redefine the anyonic algebra and then generalize this definition by constructing the anyonic superalgebra. Finally, we use these tools to generalize the fractional supersymmetry already discussed. (author)

  12. The Effects of Urban Sprawl on Birds at Multiple Levels of Biological Organization

    Directory of Open Access Journals (Sweden)

    Robert Blair

    2004-12-01

    Full Text Available Urban sprawl affects the environment in myriad ways and at multiple levels of biological organization. In this paper I explore the effects of sprawl on native bird communities by comparing the occurrence of birds along gradients of urban land use in southwestern Ohio and northern California and by examining patterns at the individual, species, community, landscape, and continental levels. I do this by assessing the distribution and abundance of all bird species occupying sites of differing land-use intensity in Ohio and California. Additionally, I conducted predation experiments using artificial nests, tracked the nest fate of American Robins and Northern Cardinals, and assessed land cover in these sites. At the individual level, predation on artificial nests decreased with urbanization; however, this trend was not reflected in the nesting success of robins and cardinals, which did not increase with urbanization. At the species level, sprawl affected local patterns of extinction and invasion; the density of different species peaked at different levels of urbanization. At the community level, species richness and diversity peaked at moderate levels of urbanization, and the number of low-nesting species and of species with multiple broods increased with urbanization. The community-level results may reflect both the species-level patterns of local extinction and invasion as well as broader landscape-level patterns. At the landscape level, a linear combination of spatial heterogeneity and density of woody patches accurately predicted both species richness and Shannon Diversity. At the continental level, local extinction of endemic species, followed by the invasion of ubiquitous weedy species, leads to faunal homogenization between ecoregions.

  13. Multiple sclerosis: general features and pharmacologic approach; Esclerosis multiple: aspectos generales y abordaje farmacologico

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen Lagumersindez, Denis; Martinez Sanchez, Gregorio [Instituto de Farmacia y Alimentos, Universidad de La Habana, La Habana (Cuba)

    2009-07-01

    Multiple sclerosis is an autoimmune, inflammatory and desmyelinization disease central nervous system (CNS) of unknown etiology and critical evolution. There different etiological hypotheses talking of a close interrelation among predisposing genetic factors and dissimilar environmental factors, able to give raise to autoimmune response at central nervous system level. Hypothesis of autoimmune pathogeny is based on study of experimental models, and findings in biopsies of affected patients by disease. Accumulative data report that the oxidative stress plays a main role in pathogenesis of multiple sclerosis. Oxygen reactive species generated by macrophages has been involved as mediators of demyelinization and of axon damage, in experimental autoimmune encephalomyelitis and strictly in multiple sclerosis. Disease diagnosis is difficult because of there is not a confirmatory unique test. Management of it covers the treatment of acute relapses, disease modification, and symptoms management. These features require an individualized approach, base on evolution of this affection, and tolerability of treatments. In addition to diet, among non-pharmacologic treatments for multiple sclerosis it is recommended physical therapy. Besides, some clinical assays have been performed in which we used natural extracts, nutrition supplements, and other agents with promising results. Pharmacology allowed neurologists with a broad array of proved effectiveness drugs; however, results of research laboratories in past years make probable that therapeutical possibilities increase notably in future. (Author)

  14. Towards Arctic Resource Governance of Marine Invasive Species

    DEFF Research Database (Denmark)

    Kourantidou, Melina; Kaiser, Brooks; Fernandez, Linda

    2015-01-01

    Scientific and policy-oriented publications highlighting the magnitude of uncertainty in the changing Arctic and the possibilities for effective regional governance are proliferating, yet it remains a challenging task to examine Arctic marine biodiversity. Limited scientific data are currently...... available. Through analysis of marine invasions in the Arctic, we work to identify and assess patterns in the knowledge gaps regarding invasive species in the Arctic that affect the ability to generate improved governance outcomes. These patterns are expected to depend on multiple aspects of scientific...... research into invasive species threats in the Arctic, including the ways in which known marine invasions are related to different stakeholder groups and existing disparate national and international experiences with invasive species. Stakeholdergroups include dominant industries (fishing, shipping, tourism...

  15. Predicting the presence and cover of management relevant invasive plant species on protected areas.

    Science.gov (United States)

    Iacona, Gwenllian; Price, Franklin D; Armsworth, Paul R

    2016-01-15

    Invasive species are a management concern on protected areas worldwide. Conservation managers need to predict infestations of invasive plants they aim to treat if they want to plan for long term management. Many studies predict the presence of invasive species, but predictions of cover are more relevant for management. Here we examined how predictors of invasive plant presence and cover differ across species that vary in their management priority. To do so, we used data on management effort and cover of invasive plant species on central Florida protected areas. Using a zero-inflated multiple regression framework, we showed that protected area features can predict the presence and cover of the focal species but the same features rarely explain both. There were several predictors of either presence or cover that were important across multiple species. Protected areas with three days of frost per year or fewer were more likely to have occurrences of four of the six focal species. When invasive plants were present, their proportional cover was greater on small preserves for all species, and varied with surrounding household density for three species. None of the predictive features were clearly related to whether species were prioritized for management or not. Our results suggest that predictors of cover and presence can differ both within and across species but do not covary with management priority. We conclude that conservation managers need to select predictors of invasion with care as species identity can determine the relationship between predictors of presence and the more management relevant predictors of cover. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Looking beyond rare species as umbrella species: Northern Bobwhites (Colinus virginianus) and conservation of grassland and shrubland birds

    Science.gov (United States)

    Crosby, Andrew D.; Elmore, R.D.; Leslie,, David M.; Will, Rodney E.

    2015-01-01

    Changes in land use and land cover throughout the eastern half of North America have caused substantial declines in populations of birds that rely on grassland and shrubland vegetation types, including socially and economically important game birds such as the Northern Bobwhite (Colinus virginianus; hereafter bobwhites). As much attention is focused on habitat management and restoration for bobwhites, they may act as an umbrella species for other bird species with similar habitat requirements. We quantified the relationship of bobwhites to the overall bird community and evaluated the potential for bobwhites to act as an umbrella species for grassland and shrubland birds. We monitored bobwhite presence and bird community composition within 31 sample units on selected private lands in the south-central United States from 2009 to 2011. Bobwhites were strongly associated with other grassland and shrubland birds and were a significant positive predictor for 9 species. Seven of these, including Bell's Vireo (Vireo bell), Dicksissel (Spiza americana), and Grasshopper Sparrow (Ammodramus savannarum), are listed as species of conservation concern. Species richness and occupancy probability of grassland and shrubland birds were higher relative to the overall bird community in sample units occupied by bobwhites. Our results show that bobwhites can act as an umbrella species for grassland and shrubland birds, although the specific species in any given situation will depend on region and management objectives. These results suggest that efficiency in conservation funding can be increased by using public interest in popular game species to leverage resources to meet multiple conservation objectives.

  17. Sarmentine, a natural herbicide from Piper species with multiple herbicide mechanisms of action

    Science.gov (United States)

    Sarmentine, 1-(1-pyrrolidinyl)-(2E,4E)-2,4-decadien-1-one, is a natural amide isolated from the fruits of Piper species. The compound has a number of interesting biological properties, including its broad-spectrum activity on weeds as a contact herbicide. Initial studies highlighted a similarity in ...

  18. Dynamics of two competing species in the presence of Lévy noise sources

    Science.gov (United States)

    La Cognata, A.; Valenti, D.; Dubkov, A. A.; Spagnolo, B.

    2010-07-01

    We consider a Lotka-Volterra system of two competing species subject to multiplicative α -stable Lévy noise. The interaction parameter between the species is a random process which obeys a stochastic differential equation with a generalized bistable potential in the presence both of a periodic driving term and an additive α -stable Lévy noise. We study the species dynamics, which is characterized by two different regimes, exclusion of one species and coexistence of both. We find quasiperiodic oscillations and stochastic resonance phenomenon in the dynamics of the competing species, analyzing the role of the Lévy noise sources.

  19. Revised species definitions and nomenclature of the rose colored Cithaerias butterflies (Lepidoptera, Nymphalidae, Satyrinae).

    Science.gov (United States)

    Penz, Carla M; Alexander, Laura G; Devries, Philip J

    2014-10-20

    This study provides updated species definitions for five rose-colored Cithaerias butterflies, starting with a historical overview of their taxonomy. Given their mostly transparent wings, genitalia morphology yielded the most reliable characters for species definition and identification. Genitalic divergence is more pronounced when multiple species occur in sympatry than between parapatric taxa. Cithaerias aurorina is granted full species status, C. cliftoni is reinstated as a full species, and one new combination is proposed, i.e. C. aurora tambopata. Two new synonyms are proposed, Callitaera phantoma and Callitaera aura = Cithaerias aurora. 

  20. Bracken: estimating species abundance in metagenomics data

    Directory of Open Access Journals (Sweden)

    Jennifer Lu

    2017-01-01

    Full Text Available Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.