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Sample records for host dh-ph domain

  1. Domain switching and host recognition.

    PubMed

    Tian, Miaoying; Day, Brad

    2006-09-01

    The collective function of secreted pathogen effector molecules is to enhance the virulence and avirulence activity of the pathogen during the infection of its host. While the activity of a majority of pathogen effectors is unknown, several classes of effector molecules have been well characterized. Among these include proteins which function to modulate host defences either through proteolysis, post-translational modifications, or by directly manipulating the host transcriptional machinery that regulates the induction of defence responses. In recent years, several key advances have been made in the characterization of the latter class of effector molecules. Among these include research characterizing the processes associated with host nuclear import and the targeting of host transcriptional defences. While current research is beginning to reveal the biochemical and genetic mechanisms controlling the induction of host resistance, the signalling events that control host specificity remain largely unknown. In this issue of Molecular Microbiology, work by Nissan et al. sheds light onto the molecular-genetic patterns involved in determining host specificity and pathogen virulence in the Pantoea-gypsophila interaction. PMID:16879410

  2. Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides

    PubMed Central

    Salomon, Dor; Guo, Yirui; Kinch, Lisa N.; Grishin, Nick V.; Gardner, Kevin H.; Orth, Kim

    2016-01-01

    Bacterial Type III Secretion Systems deliver effectors into host cells to manipulate cellular processes to the advantage of the pathogen. Many host targets of these effectors are found on membranes. Therefore, to identify their targets, effectors often use specialized membrane-localization domains to localize to appropriate host membranes. However, the molecular mechanisms used by many domains are unknown. Here we identify a conserved bacterial phosphoinositide-binding domain (BPD) that is found in functionally diverse Type III effectors of both plant and animal pathogens. We show that members of the BPD family functionally bind phosphoinositides and mediate localization to host membranes. Moreover, NMR studies reveal that the BPD of the newly identified Vibrio parahaemolyticus Type III effector VopR is unfolded in solution, but folds into a specific structure upon binding its ligand phosphatidylinositol-(4,5)-bisphosphate. Thus, our findings suggest a possible mechanism for promoting refolding of Type III effectors after delivery into host cells. PMID:24346350

  3. A protein domain-based view of the virosphere-host relationship.

    PubMed

    Abroi, Aare

    2015-12-01

    Despite being an important and inseparable part of the biosphere, viruses are too often overlooked in several life sciences, including evolutionary biology, systems biology, and non-marine ecology. In this review, a protein domain-based view of viral proteomes, the proteomes of other organisms and the overlap between them is presented. The data show that in many viral species, viral proteins are not very well annotated with protein domains. Compared with viral proteomes, cellular proteomes are covered quite uniformly with respect to protein domains and show higher coverage. A tremendous number of virally coded domains exist; in fact, the number of protein domains in the characterised virosphere is approaching that found in Archaea, a well-accepted superkingdom. Proteins encoded by viruses contain virosphere-specific domains (i.e., not found in cellular proteomes) and/or many domains shared by viral and cellular proteomes. Virosphere-specific domains are structurally peculiar with respect to different structural measures, making them a clear source of structural and functional novelty. Viral families with RNA genomes tend to harbour more virosphere-specific domains than other viruses. Interestingly, host range preferences of different viral classes are, for the most part, not reflected by domains shared between viruses and different superkingdoms. The role of viruses in the genesis of the cellular domain repertoire is reviewed to bring them more confidently and firmly into the larger biological picture. PMID:26296474

  4. Essential Domains of Anaplasma phagocytophilum Invasins Utilized to Infect Mammalian Host Cells

    PubMed Central

    Seidman, David; Hebert, Kathryn S.; Truchan, Hilary K.; Miller, Daniel P.; Tegels, Brittney K.; Marconi, Richard T.; Carlyon, Jason A.

    2015-01-01

    Anaplasma phagocytophilum causes granulocytic anaplasmosis, an emerging disease of humans and domestic animals. The obligate intracellular bacterium uses its invasins OmpA, Asp14, and AipA to infect myeloid and non-phagocytic cells. Identifying the domains of these proteins that mediate binding and entry, and determining the molecular basis of their interactions with host cell receptors would significantly advance understanding of A. phagocytophilum infection. Here, we identified the OmpA binding domain as residues 59 to 74. Polyclonal antibody generated against a peptide spanning OmpA residues 59 to 74 inhibited A. phagocytophilum infection of host cells and binding to its receptor, sialyl Lewis x (sLex-capped P-selectin glycoprotein ligand 1. Molecular docking analyses predicted that OmpA residues G61 and K64 interact with the two sLex sugars that are important for infection, α2,3-sialic acid and α1,3-fucose. Amino acid substitution analyses demonstrated that K64 was necessary, and G61 was contributory, for recombinant OmpA to bind to host cells and competitively inhibit A. phagocytophilum infection. Adherence of OmpA to RF/6A endothelial cells, which express little to no sLex but express the structurally similar glycan, 6-sulfo-sLex, required α2,3-sialic acid and α1,3-fucose and was antagonized by 6-sulfo-sLex antibody. Binding and uptake of OmpA-coated latex beads by myeloid cells was sensitive to sialidase, fucosidase, and sLex antibody. The Asp14 binding domain was also defined, as antibody specific for residues 113 to 124 inhibited infection. Because OmpA, Asp14, and AipA each contribute to the infection process, it was rationalized that the most effective blocking approach would target all three. An antibody cocktail targeting the OmpA, Asp14, and AipA binding domains neutralized A. phagocytophilum binding and infection of host cells. This study dissects OmpA-receptor interactions and demonstrates the effectiveness of binding domain-specific antibodies

  5. The carboxyl-terminal domain of large T antigen rescues SV40 host range activity in trans independent of acetylation.

    PubMed

    Poulin, Danielle L; DeCaprio, James A

    2006-05-25

    The host range activity of SV40 has been described as the inability of mutant viruses with deletions in the C terminal region of large T Ag to replicate in certain types of African green monkey kidney cells. We constructed new mutant viruses expressing truncated T Ag proteins and found that these mutant viruses exhibited the host range phenotype. The host range phenotype was independent of acetylation of T Ag at lysine 697. Co-expression of the C terminal domain of T Ag (aa 627-708) in trans increased both T Ag and VP1 mRNA as well as protein levels for host range mutant viruses in the restrictive cell type. In addition, the T Ag 627-708 fragment promoted the productive lytic infection of host range mutant viruses in the nonpermissive cell type. The carboxyl-terminal region of T Ag contains a biological function essential for the SV40 viral life cycle. PMID:16510165

  6. Thermodynamic properties of the effector domains of MARTX toxins suggest their unfolding for translocation across the host membrane.

    PubMed

    Kudryashova, Elena; Heisler, David; Zywiec, Andrew; Kudryashov, Dmitri S

    2014-06-01

    MARTX (multifunctional autoprocessing repeats-in-toxin) family toxins are produced by Vibrio cholerae, Vibrio vulnificus, Aeromonas hydrophila and other Gram-negative bacteria. Effector domains of MARTX toxins cross the cytoplasmic membrane of a host cell through a putative pore formed by the toxin's glycine-rich repeats. The structure of the pore is unknown and the translocation mechanism of the effector domains is poorly understood. We examined the thermodynamic stability of the effector domains of V. cholerae and A. hydrophila MARTX toxins to elucidate the mechanism of their translocation. We found that all but one domain in each toxin are thermodynamically unstable and several acquire a molten globule state near human physiological temperatures. Fusion of the most stable cysteine protease domain to the adjacent effector domain reduces its thermodynamic stability ∼ 1.4-fold (from D G H 2 O 21.8 to 16.1 kJ mol(-1) ). Precipitation of several individual domains due to thermal denaturation is reduced upon their fusion into multi-domain constructs. We speculate that low thermostability of the MARTX effector domains correlates with that of many other membrane-penetrating toxins and implies their unfolding for cell entry. This study extends the list of thermolabile bacterial toxins, suggesting that this quality is essential and could be susceptible for selective targeting of pathogenic toxins. PMID:24724536

  7. N-Terminal Domain of Feline Calicivirus (FCV) Proteinase-Polymerase Contributes to the Inhibition of Host Cell Transcription.

    PubMed

    Wu, Hongxia; Zu, Shaopo; Sun, Xue; Liu, Yongxiang; Tian, Jin; Qu, Liandong

    2016-01-01

    Feline Calicivirus (FCV) infection results in the inhibition of host protein synthesis, known as "shut-off". However, the precise mechanism of shut-off remains unknown. Here, we found that the FCV strain 2280 proteinase-polymerase (PP) protein can suppress luciferase reporter gene expression driven by endogenous and exogenous promoters. Furthermore, we found that the N-terminal 263 aa of PP (PPN-263) determined its shut-off activity using the expression of truncated proteins. However, the same domain of the FCV strain F9 PP protein failed to inhibit gene expression. A comparison between strains 2280 and F9 indicated that Val27, Ala96 and Ala98 were key sites for the inhibition of host gene expression by strain 2280 PPN-263, and PPN-263 exhibited the ability to shut off host gene expression as long as it contained any two of the three amino acids. Because the N-terminus of the PP protein is required for its proteinase and shut-off activities, we investigated the ability of norovirus 3C-like proteins (3CLP) from the GII.4-1987 and -2012 isolates to interfere with host gene expression. The results showed that 3CLP from both isolates was able to shut off host gene expression, but 3CLP from GII.4-2012 had a stronger inhibitory activity than that from GII.4-1987. Finally, we found that 2280 PP and 3CLP significantly repressed reporter gene transcription but did not affect mRNA translation. Our results provide new insight into the mechanism of the FCV-mediated inhibition of host gene expression. PMID:27447663

  8. N-Terminal Domain of Feline Calicivirus (FCV) Proteinase-Polymerase Contributes to the Inhibition of Host Cell Transcription

    PubMed Central

    Wu, Hongxia; Zu, Shaopo; Sun, Xue; Liu, Yongxiang; Tian, Jin; Qu, Liandong

    2016-01-01

    Feline Calicivirus (FCV) infection results in the inhibition of host protein synthesis, known as “shut-off”. However, the precise mechanism of shut-off remains unknown. Here, we found that the FCV strain 2280 proteinase-polymerase (PP) protein can suppress luciferase reporter gene expression driven by endogenous and exogenous promoters. Furthermore, we found that the N-terminal 263 aa of PP (PPN-263) determined its shut-off activity using the expression of truncated proteins. However, the same domain of the FCV strain F9 PP protein failed to inhibit gene expression. A comparison between strains 2280 and F9 indicated that Val27, Ala96 and Ala98 were key sites for the inhibition of host gene expression by strain 2280 PPN-263, and PPN-263 exhibited the ability to shut off host gene expression as long as it contained any two of the three amino acids. Because the N-terminus of the PP protein is required for its proteinase and shut-off activities, we investigated the ability of norovirus 3C-like proteins (3CLP) from the GII.4-1987 and -2012 isolates to interfere with host gene expression. The results showed that 3CLP from both isolates was able to shut off host gene expression, but 3CLP from GII.4-2012 had a stronger inhibitory activity than that from GII.4-1987. Finally, we found that 2280 PP and 3CLP significantly repressed reporter gene transcription but did not affect mRNA translation. Our results provide new insight into the mechanism of the FCV-mediated inhibition of host gene expression. PMID:27447663

  9. Molecular interfaces of the galactose-binding protein Tectonin domains in host-pathogen interaction.

    PubMed

    Low, Diana Hooi Ping; Frecer, Vladimir; Le Saux, Agnès; Srinivasan, Ganesh Anand; Ho, Bow; Chen, Jianzhu; Ding, Jeak Ling

    2010-03-26

    Beta-propeller proteins function in catalysis, protein-protein interaction, cell cycle regulation, and innate immunity. The galactose-binding protein (GBP) from the plasma of the horseshoe crab, Carcinoscorpius rotundicauda, is a beta-propeller protein that functions in antimicrobial defense. Studies have shown that upon binding to Gram-negative bacterial lipopolysaccharide (LPS), GBP interacts with C-reactive protein (CRP) to form a pathogen-recognition complex, which helps to eliminate invading microbes. However, the molecular basis of interactions between GBP and LPS and how it interplays with CRP remain largely unknown. By homology modeling, we showed that GBP contains six beta-propeller/Tectonin domains. Ligand docking indicated that Tectonin domains 6 to 1 likely contain the LPS binding sites. Protein-protein interaction studies demonstrated that Tectonin domain 4 interacts most strongly with CRP. Hydrogen-deuterium exchange mass spectrometry mapped distinct sites of GBP that interact with LPS and with CRP, consistent with in silico predictions. Furthermore, infection condition (lowered Ca(2+) level) increases GBP-CRP affinity by 1000-fold. Resupplementing the system with a physiological level of Ca(2+) did not reverse the protein-protein affinity to the basal state, suggesting that the infection-induced complex had undergone irreversible conformational change. We propose that GBP serves as a bridging molecule, participating in molecular interactions, GBP-LPS and GBP-CRP, to form a stable pathogen-recognition complex. The interaction interfaces in these two partners suggest that Tectonin domains can differentiate self/nonself, crucial to frontline defense against infection. In addition, GBP shares architectural and functional homologies to a human protein, hTectonin, suggesting its evolutionarily conservation for approximately 500 million years, from horseshoe crab to human. PMID:20118243

  10. Role of Nucleotide-Binding Oligomerization Domain-Containing (NOD) 2 in Host Defense during Pneumococcal Pneumonia

    PubMed Central

    Hommes, Tijmen J.; van Lieshout, Miriam H.; van ‘t Veer, Cornelis; Florquin, Sandrine; Bootsma, Hester J.; Hermans, Peter W.; de Vos, Alex F.; van der Poll, Tom

    2015-01-01

    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. PMID:26673231

  11. Biophysical studies on calcium and carbohydrate binding to carbohydrate recognition domain of Gal/GalNAc lectin from Entamoeba histolytica: insights into host cell adhesion.

    PubMed

    Yadav, Rupali; Verma, Kuldeep; Chandra, Mintu; Mukherjee, Madhumita; Datta, Sunando

    2016-09-01

    Entamoeba histolytica, an enteric parasite expresses a Gal/GalNAc-specific lectin that contributes to its virulence by establishing adhesion to host cell. In this study, carbohydrate recognition domain of Hgl (EhCRD) was purified and biophysical studies were conducted to understand the thermodynamic basis of its binding to carbohydrate and Ca(++) Here, we show that carbohydrate recognition domain (CRD) of the lectin binds to calcium through DPN motif. To decipher the role of calcium in carbohydrate binding and host cell adhesion, biophysical and cell-based studies were carried out. We demonstrated that the presence of the cation neither change the affinity of the lectin for carbohydrates nor alters its conformation. Mutation of the calcium-binding motif in EhCRD resulted in complete loss of ability to bind calcium but retained its affinity for carbohydrates. Purified EhCRD significantly diminished adhesion of the amebic trophozoites to Chinese Hamster Ovary (CHO) cells as well as triggered red blood cell agglutination. The calcium-binding defective mutant abrogated amebic adhesion to CHO cells similar to the wild-type protein, but it failed to agglutinate RBCs suggesting a differential role of the cation in these two processes. This study provides the first molecular description of the role of calcium in Gal/GalNAc mediated host cell adhesion. PMID:27008865

  12. TIR domain-containing adaptor SARM is a late addition to the ongoing microbe–host dialog

    PubMed Central

    Zhang, Qing; Zmasek, Christian M.; Cai, Xiaohui; Godzik, Adam

    2011-01-01

    Toll/interleukin-1 receptor (TIR) domain-containing proteins play important roles in defense against pathogens in both animals and plants, connecting the immunity signaling pathways via a chain of specific protein–protein interactions. Among them is SARM, the only TIR domain-containing adaptor that can negatively regulate TLR signaling. By extensive phylogenetic analysis, we show here that SARM is closely related to bacterial proteins with TIR domains, suggesting that this family has a different evolutionary history from other animal TIR-containing adaptors, possibly emerging via a lateral gene transfer from bacteria to animals. We also show evidence of several similar, independent transfer events, none of which, however, survived in vertebrates. An evolutionary relationship between the animal SARM adaptor and bacterial proteins with TIR domains illustrates the possible role that bacterial TIR-containing proteins play in regulating eukaryotic immune responses and how this mechanism was possibly adapted by the eukaryotes themselves. PMID:21110998

  13. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges.

    PubMed

    Monier, Adam; Welsh, Rory M; Gentemann, Chelle; Weinstock, George; Sodergren, Erica; Armbrust, E Virginia; Eisen, Jonathan A; Worden, Alexandra Z

    2012-01-01

    Phosphate (PO(4)) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO(4) using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO(4) transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO(4) uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO(4) -availability may not serve as a simple bottom-up control of marine phytoplankton. PMID:21914098

  14. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges

    PubMed Central

    Monier, Adam; Welsh, Rory M; Gentemann, Chelle; Weinstock, George; Sodergren, Erica; Armbrust, E Virginia; Eisen, Jonathan A; Worden, Alexandra Z

    2012-01-01

    Phosphate (PO4) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO4 using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO4 transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO4 uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO4-availability may not serve as a simple bottom-up control of marine phytoplankton. PMID:21914098

  15. The C-terminal domain is sufficient for host-binding activity of the Mu phage tail-spike protein.

    PubMed

    Suzuki, Hidetaka; Yamada, Seiko; Toyama, Yoshiharu; Takeda, Shigeki

    2010-09-01

    The Mu phage virion contains tail-spike proteins beneath the baseplate, which it uses to adsorb to the outer membrane of Escherichia coli during the infection process. The tail spikes are composed of gene product 45 (gp45), which contains 197 amino acid residues. In this study, we purified and characterized both the full-length and the C-terminal domains of recombinant gp45 to identify the functional and structural domains. Limited proteolysis resulted in a Ser64-Gln197 sequence, which was composed of a stable C-terminal domain. Analytical ultracentrifugation of the recombinant C-terminal domain (gp45-C) indicated that the molecular weight of gp45-C was about 58 kDa and formed a trimeric protomer in solution. Coprecipitation experiments and a quartz crystal microbalance (QCM) demonstrated that gp45-C irreversibly binds to the E. coli membrane. These results indicate that gp45 shows behaviors similar to tail-spike proteins of other phages; however, gp45 did not show significant sequence homology with the other phage tail-spike structures that have been identified. PMID:20478417

  16. RNA-Free and Ribonucleoprotein-Associated Influenza Virus Polymerases Directly Bind the Serine-5-Phosphorylated Carboxyl-Terminal Domain of Host RNA Polymerase II

    PubMed Central

    Martínez-Alonso, Mónica; Hengrung, Narin

    2016-01-01

    ABSTRACT Influenza viruses subvert the transcriptional machinery of their hosts to synthesize their own viral mRNA. Ongoing transcription by cellular RNA polymerase II (Pol II) is required for viral mRNA synthesis. By a process known as cap snatching, the virus steals short 5′ capped RNA fragments from host capped RNAs and uses them to prime viral transcription. An interaction between the influenza A virus RNA polymerase and the C-terminal domain (CTD) of the large subunit of Pol II has been established, but the molecular details of this interaction remain unknown. We show here that the influenza virus ribonucleoprotein (vRNP) complex binds to the CTD of transcriptionally engaged Pol II. Furthermore, we provide evidence that the viral polymerase binds directly to the serine-5-phosphorylated form of the Pol II CTD, both in the presence and in the absence of viral RNA, and show that this interaction is conserved in evolutionarily distant influenza viruses. We propose a model in which direct binding of the viral RNA polymerase in the context of vRNPs to Pol II early in infection facilitates cap snatching, while we suggest that binding of free viral polymerase to Pol II late in infection may trigger Pol II degradation. IMPORTANCE Influenza viruses cause yearly epidemics and occasional pandemics that pose a threat to human health, as well as represent a large economic burden to health care systems globally. Existing vaccines are not always effective, as they may not exactly match the circulating viruses. Furthermore, there are a limited number of antivirals available, and development of resistance to these is a concern. New measures to combat influenza are needed, but before they can be developed, it is necessary to better understand the molecular interactions between influenza viruses and their host cells. By providing further insights into the molecular details of how influenza viruses hijack the host transcriptional machinery, we aim to uncover novel targets for

  17. Two TIR-like domain containing proteins in a newly emerging zoonotic Staphylococcus aureus strain sequence type 398 are potential virulence factors by impacting on the host innate immune response

    PubMed Central

    Patterson, Nicholas J.; Günther, Juliane; Gibson, Amanda J.; Offord, Victoria; Coffey, Tracey J.; Splitter, Gary; Monk, Ian; Seyfert, Hans-Martin; Werling, Dirk

    2014-01-01

    Staphylococcus aureus, sequence type (ST) 398, is an emerging pathogen and the leading cause of livestock-associated methicillin-resistant S. aureus infections in Europe and North America. This strain is characterized by high promiscuity in terms of host-species and also lacks several traditional S. aureus virulence factors. This does not, however, explain the apparent ease with which it crosses species-barriers. Recently, TIR-domain containing proteins (Tcps) which inhibit the innate immune response were identified in some Gram-negative bacteria. Here we report the presence of two proteins, S. aureus TIR-like Protein 1 (SaTlp1) and S. aureus TIR-like Protein 2 (SaTlp2), expressed by ST398 which contain domain of unknown function 1863 (DUF1863), similar to the Toll/IL-1 receptor (TIR) domain. In contrast to the Tcps in Gram-negative bacteria, our data suggest that SaTlp1 and SaTlp2 increase activation of the transcription factor NF-κB as well as downstream pro-inflammatory cytokines and immune effectors. To assess the role of both proteins as potential virulence factors knock-out mutants were created. These showed a slightly enhanced survival rate in a murine infectious model compared to the wild-type strain at one dose. Our data suggest that both proteins may act as factors contributing to the enhanced ability of ST398 to cross species-barriers. PMID:25538689

  18. The N-terminal domain of EspF induces host cell apoptosis after infection with enterohaemorrhagic Escherichia coli O157:H7.

    PubMed

    Zhao, Suhui; Zhou, Ying; Wang, Chunhui; Yang, Yu; Wu, Xianbo; Wei, Yao; Zhu, Li; Zhao, Wei; Zhang, Qiwei; Wan, Chengsong

    2013-01-01

    Enterohemorrhagic Escherichia coli (EHEC) employs a type III secretion system (TTSS) to export the translocator and effector proteins required for mucosal colonization. As an important bacterial effector protein in locus of enterocyte effacement four, the EspF protein causes F-actin filament aggregations to form attaching and effacing (A/E) lesions, and induces the destruction of brush-border microvilli and cytoskeletal rearrangements to form pedestals. However, the molecular pathogenesis of A/E lesions due to EHEC O157:H7 infection is unclear. In this study, we constructed an espF-deficient mutant (ΔespF) with a 162-bp deletion in the N-terminal domain by using overlap extension PCR. The results showed that EHEC EspF translocated into intestinal epithelial cells, targeted mitochondria and induced apoptosis. The ΔespF mutant, compared to EHEC prototype Guangzhou strain, had lower cell attachment and effacement abilities, lower caspase-9/3 and lactate dehydrogenase levels, lower bacterial adhesion, weaker mitochondria apoptosis, and a higher mouse survival rate. Our results demonstrate the probable function of the EspF N-terminal domain, which targets mitochondria and binds mitochondria heat shock protein 70 to induce cell apoptosis via A/E lesions. These findings may be invaluable in clarifying the molecular pathogenesis of EspF of EHEC O157:H7. PMID:23372831

  19. A cupin domain-containing protein with a quercetinase activity (VdQase) regulates Verticillium dahliae's pathogenicity and contributes to counteracting host defenses

    PubMed Central

    El Hadrami, Abdelbasset; Islam, Md. Rashidul; Adam, Lorne R.; Daayf, Fouad

    2015-01-01

    We previously identified rutin as part of potato root responses to its pathogen Verticillium dahliae. Rutin was directly toxic to the pathogen at doses greater than 160 μM, a threshold below which many V. dahliae pathogenicity-related genes were up-regulated. We identified and characterized a cupin domain-containing protein (VdQase) with a dioxygenase activity and a potential role in V. dahliae-potato interactions. The pathogenicity of VdQase knock-out mutants generated through Agrobacterium tumefasciens-mediated transformation was significantly reduced on susceptible potato cultivar Kennebec compared to wild type isolates. Fluorescence microscopy revealed a higher accumulation of flavonols in the stems of infected potatoes and a higher concentration of rutin in the leaves in response to the VdQase mutants as compared to wild type isolates. This, along with the HPLC characterization of high residual and non-utilized quercetin in presence of the knockout mutants, indicates the involvement of VdQase in the catabolism of quercetin and possibly other flavonols in planta. Quantification of Salicylic and Jasmonic Acids (SA, JA) in response to the mutants vs. wild type isolates revealed involvement of VdQase in the interference with signaling, suggesting a role in pathogenicity. It is hypothesized that the by-product of dioxygenation 2-protocatechuoylphloroglucinolcarboxylic acid, after dissociating into phloroglucinol and protocatechuoyl moieties, becomes a starting point for benzoic acid and SA, thereby interfering with the JA pathway and affecting the interaction outcome. These events may be key factors for V. dahliae in countering potato defenses and becoming notorious in the rhizosphere. PMID:26113857

  20. Analysis of Host Gene Expression Changes Reveals Distinct Roles for the Cytoplasmic Domain of the Epstein-Barr Virus Receptor/CD21 in B-Cell Maturation, Activation, and Initiation of Virus Infection

    PubMed Central

    Arredouani, Mohamed S.; Bhasin, Manoj K.; Sage, David R.; Dunn, Laura K.; Gill, Michael B.; Agnani, Deep; Libermann, Towia A.

    2014-01-01

    ABSTRACT Epstein-Barr virus (EBV) attachment to human CD21 on the B-cell surface initiates infection. Whether CD21 is a simple tether or conveys vital information to the cell interior for production of host factors that promote infection of primary B cells is controversial, as the cytoplasmic fragment of CD21 is short, though highly conserved. The ubiquity of CD21 on normal B cells, the diversity of this population, and the well-known resistance of primary B cells to gene transfer technologies have all impeded resolution of this question. To uncover the role(s) of the CD21 cytoplasmic domain during infection initiation, the full-length receptor (CD21 = CR), a mutant lacking the entire cytoplasmic tail (CT), and a control vector (NEO) were stably expressed in two pre-B-cell lines that lack endogenous receptor. Genome-wide transcriptional analysis demonstrated that stable CD21 surface expression alone (either CR or CT) produced multiple independent changes in gene expression, though both dramatically decreased class I melanoma-associated antigen (MAGE) family RNAs and upregulated genes associated with B-cell differentiation (e.g., C2TA, HLA-II, IL21R, MIC2, CD48, and PTPRCAP/CD45-associated protein). Temporal analysis spanning 72 h revealed that not only CR- but also CT-expressing lines initiated latency. In spite of this, the number and spectrum of transcripts altered in CR- compared with CT-bearing lines at 1 h after infection further diverged. Differential modulation of immediate early cellular transcripts (e.g., c-Jun and multiple histones), both novel and previously linked to CD21-initiated signaling, as well as distinct results from pathway analyses support a separate role for the cytoplasmic domain in initiation of intracellular signals. IMPORTANCE Membrane proteins that mediate virus attachment tether virus particles to the cell surface, initiating infection. In addition, upon virus interaction such proteins may transmit signals to the interior of the cell

  1. Domain Engineering

    NASA Astrophysics Data System (ADS)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  2. Methods for production of proteins in host cells

    DOEpatents

    Donnelly, Mark; Joachimiak, Andrzej

    2004-01-13

    The present invention provides methods for the production of proteins, particularly toxic proteins, in host cells. The invention provides methods which use a fusion protein comprising a chaperonin binding domain in host cells induced or regulated to have increased levels of chaperonin which binds the chaperonin binding domain.

  3. Specific N-linked and O-linked glycosylation modifications in the envelope V1 domain of simian immunodeficiency virus variants that evolve in the host alter recognition by neutralizing antibodies.

    PubMed Central

    Chackerian, B; Rudensey, L M; Overbaugh, J

    1997-01-01

    During progression to AIDS in simian immunodeficiency virus (SIV) Mne-infected macaques, viral variants are selected that encode sequences with serine and threonine changes in variable region 1 (V1) of the surface component of the viral envelope protein (Env-SU). Because these serine and threonine amino acid changes are characteristic of sites for O-linked and N-linked glycosylation, we examined whether they were targets for modification by carbohydrates. For this purpose, we used several biochemical methods for analyzing the Env-SU protein encoded by chimeras of SIVMneCL8 and envelope sequences cloned from an SIVMneCL8-infected Macaca nemestrina during clinical latency and just after the onset of AIDS. The addition of an N-linked glycan was demonstrated by changes in the electrophoretic mobility of Env-SU, and this was verified by specific glycanase digestions and a detailed analysis of the molecular mass of partially purified Env-SU by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Molecular mass calculations by MALDI-TOF MS also demonstrated an increased mass, from 102.3 to 103.5 kDa, associated with serine and threonine residues predicted to be O-linked glycosylation sites. Together, these data provide the first direct evidence that the carbohydrate profile of Env-SU is distinct in SIV variants that evolve during infection of the host. Moreover, our studies show that these changes in glycosylation in V1 were directly associated with changes in antigenicity. Specifically, serine and threonine changes in V1 allowed the virus to escape neutralization by macaque sera that contained antibodies that could neutralize the parental virus, SIVMneCL8. The escape from antibody recognition appeared to be influenced by either O-linked or N-linked carbohydrate additions in V1. Moreover, when glycine residues were engineered at the positions where serine and threonine changes evolve in V1 of SIVMneCL8, there was no change in

  4. A Unified Approach to Intra-Domain Security

    SciTech Connect

    Shue, Craig A; Kalafut, Andrew J.; Gupta, Prof. Minaxi

    2009-01-01

    While a variety of mechanisms have been developed for securing individual intra-domain protocols, none address the issue in a holistic manner. We develop a unified framework to secure prominent networking protocols within a single domain. We begin with a secure version of the DHCP protocol, which has the additional feature of providing each host with a certificate. We then leverage these certificates to secure ARP, prevent spoofing within the domain, and secure SSH and VPN connections between the domain and hosts which have previously interacted with it locally. In doing so, we also develop an incrementally deployable public key infrastructure which can later be leveraged to support inter-domain authentication.

  5. Solution structure of leptospiral LigA4 Big domain.

    PubMed

    Mei, Song; Zhang, Jiahai; Zhang, Xuecheng; Tu, Xiaoming

    2015-11-13

    Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca(2+) binding property of LigA4 Big domain. PMID:26449456

  6. Microsporidia-Host Interactions

    PubMed Central

    Szumowski, Suzannah C.; Troemel, Emily R.

    2015-01-01

    Microsporidia comprise one of the largest groups of obligate intracellular pathogens and can infect virtually all animals, but host response to these fungal-related microbes has been poorly understood. Several new studies of the host transcriptional response to microsporidia infection have found infection-induced regulation of genes involved in innate immunity, ubiquitylation, metabolism, and hormonal signaling. In addition, microsporidia have recently been shown to exploit host recycling endocytosis for exit from intestinal cells, and to interact with host degradation pathways. Microsporidia infection has also been shown to profoundly affect behavior in insect hosts. Altogether, these and other recent findings are providing much-needed insight into the underlying mechanisms of microsporidia interaction with host animals. PMID:25847674

  7. Glob-Hosts

    Energy Science and Technology Software Center (ESTSC)

    2007-08-31

    The glob-hosts utility manipulates hostlist strings in UNIX shell scripts. Hostlists are a parseable string representatin of list of hosts, which compress nicely when a group of hosts are named with contiguous numeric suffixes. For example, the hosts blue1, blue2, and blue3 can be represented by the hostlist string "blue1, blue2, blue3" or equivalently "blue[1-3]". The globhost utility cn peform the following operations on a hostlist string: count, size, expand, nth, union, minus, intersection, andmore » exclude.« less

  8. Extending Black Domain Name List by Using Co-occurrence Relation between DNS Queries

    NASA Astrophysics Data System (ADS)

    Sato, Kazumichi; Ishibashi, Keisuke; Toyono, Tsuyoshi; Hasegawa, Haruhisa; Yoshino, Hideaki

    Botnet threats, such as server attacks or sending of spam e-mail, have been increasing. Therefore, infected hosts must be found and their malicious activities mitigated. An effective method for finding infected hosts is to use a blacklist of domain names. When a bot receives attack commands from a Command and Control (C&C) server, it attempts to resolve domain names of C&C servers. We can thus detect infected hosts by finding these that send queries on black domain names. However, we cannot find all infected hosts because of the inaccuracy of blacklists. There are many black domain names, and the lifetimes of these domain names are short; therefore a blacklist cannot cover all black domain names. We thus present a method for finding unknown black domain names by using DNS query data and an existing blacklist of known black domain names. To achieve this, we focus on DNS queries sent by infected hosts. One bot sends several queries on black domain names due to C&C server redundancy. We use the co-occurrence relation of two different domain names to find unknown black domain names and extend the blacklist. If a domain name frequently co-occurs with a known black name, we assume that the domain name is also black. A cross-validation evaluation of the proposed method showed that 91.2% of domain names that are on the validation list scored in the top 1%.

  9. Data hosting infrastructure for primary biodiversity data

    PubMed Central

    2011-01-01

    Background Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects tasked with collecting them. To get the most value out of these data it is imperative to seek a solution whereby these data are rescued, archived and made available to the biodiversity community. To this end, the biodiversity informatics community requires investment in processes and infrastructure to mitigate data loss and provide solutions for long-term hosting and sharing of biodiversity data. Discussion We review the current state of biodiversity data hosting and investigate the technological and sociological barriers to proper data management. We further explore the rescuing and re-hosting of legacy data, the state of existing toolsets and propose a future direction for the development of new discovery tools. We also explore the role of data standards and licensing in the context of data hosting and preservation. We provide five recommendations for the biodiversity community that will foster better data preservation and access: (1) encourage the community's use of data standards, (2) promote the public domain licensing of data, (3) establish a community of those involved in data hosting and archival, (4) establish hosting centers for biodiversity data, and (5) develop tools for data discovery. Conclusion The community's adoption of standards and development of tools to enable data discovery is essential to sustainable data preservation. Furthermore, the increased adoption of open content licensing, the establishment of data hosting infrastructure and the creation of a data hosting and archiving community are all necessary steps towards the community ensuring that data archival policies become standardized. PMID:22373257

  10. Host-to-host encryption using commercial networking products

    SciTech Connect

    Not Available

    1980-10-06

    The report considers three commercial devices in a setting of host-to-host encryption. The basic questions considered are: (1) can this local networking product be modified to provide host-to-host encryption; (2) how could host-to-host encryption be achieved without modifying this local networking product. The HYPERchannel adapter from Network Systems Corporation, the Net/One from Ungermann-Bass, and the Computrol's Megalink product are each be examined. Section 2 discusses the general issues of host-to-host encryption. A generic host-to-host cryptosystem is developed, to be used later in the analysis of the specific products. Section 3 presents in turn the HYPERchannel, Net/One, and Megalink, considering the possibilities of host-to-host encryption with and without product modification. The report's conclusions are summarized in Section 4.

  11. Asteroseismology and Exoplanet Hosts

    NASA Astrophysics Data System (ADS)

    Huber, Daniel

    2015-08-01

    Asteroseismology is among the most powerful observational tools to determine fundamental properties of stars. Space-based photometry has recently enabled the systematic detection of oscillations in exoplanet host stars, allowing a combination of asteroseismology with transit and radial-velocity measurements to precisely characterize planetary systems. In this talk I will review the latest asteroseismic detections in exoplanet host stars spanning from the main sequence to the red-giant branch, focusing in particular on radii and ages of stars hosting small (sub-Neptune sized) planets discovered by the Kepler mission. I will furthermore discuss applications of asteroseismology to measure spin-orbit inclinations in multiplanet systems, and their implications for formation theories of hot Jupiters. Finally I will give an outlook on asteroseismic studies of exoplanet hosts with current and future space- and ground-based facilities such as K2, SONG, TESS, and PLATO.

  12. Association and Host Selectivity in Multi-Host Pathogens

    PubMed Central

    Malpica, José M.; Sacristán, Soledad; Fraile, Aurora; García-Arenal, Fernando

    2006-01-01

    The distribution of multi-host pathogens over their host range conditions their population dynamics and structure. Also, host co-infection by different pathogens may have important consequences for the evolution of hosts and pathogens, and host-pathogen co-evolution. Hence it is of interest to know if the distribution of pathogens over their host range is random, or if there are associations between hosts and pathogens, or between pathogens sharing a host. To analyse these issues we propose indices for the observed patterns of host infection by pathogens, and for the observed patterns of co-infection, and tests to analyse if these patterns conform to randomness or reflect associations. Applying these tests to the prevalence of five plant viruses on 21 wild plant species evidenced host-virus associations: most hosts and viruses were selective for viruses and hosts, respectively. Interestingly, the more host-selective viruses were the more prevalent ones, suggesting that host specialisation is a successful strategy for multi-host pathogens. Analyses also showed that viruses tended to associate positively in co-infected hosts. The developed indices and tests provide the tools to analyse how strong and common are these associations among different groups of pathogens, which will help to understand and model the population biology of multi-host pathogens. PMID:17183670

  13. Host Responses to Biofilm.

    PubMed

    Watters, C; Fleming, D; Bishop, D; Rumbaugh, K P

    2016-01-01

    From birth to death the human host immune system interacts with bacterial cells. Biofilms are communities of microbes embedded in matrices composed of extracellular polymeric substance (EPS), and have been implicated in both the healthy microbiome and disease states. The immune system recognizes many different bacterial patterns, molecules, and antigens, but these components can be camouflaged in the biofilm mode of growth. Instead, immune cells come into contact with components of the EPS matrix, a diverse, hydrated mixture of extracellular DNA (bacterial and host), proteins, polysaccharides, and lipids. As bacterial cells transition from planktonic to biofilm-associated they produce small molecules, which can increase inflammation, induce cell death, and even cause necrosis. To survive, invading bacteria must overcome the epithelial barrier, host microbiome, complement, and a variety of leukocytes. If bacteria can evade these initial cell populations they have an increased chance at surviving and causing ongoing disease in the host. Planktonic cells are readily cleared, but biofilms reduce the effectiveness of both polymorphonuclear neutrophils and macrophages. In addition, in the presence of these cells, biofilm formation is actively enhanced, and components of host immune cells are assimilated into the EPS matrix. While pathogenic biofilms contribute to states of chronic inflammation, probiotic Lactobacillus biofilms cause a negligible immune response and, in states of inflammation, exhibit robust antiinflammatory properties. These probiotic biofilms colonize and protect the gut and vagina, and have been implicated in improved healing of damaged skin. Overall, biofilms stimulate a unique immune response that we are only beginning to understand. PMID:27571696

  14. Parasite host range and the evolution of host resistance.

    PubMed

    Gorter, F A; Hall, A R; Buckling, A; Scanlan, P D

    2015-05-01

    Parasite host range plays a pivotal role in the evolution and ecology of hosts and the emergence of infectious disease. Although the factors that promote host range and the epidemiological consequences of variation in host range are relatively well characterized, the effect of parasite host range on host resistance evolution is less well understood. In this study, we tested the impact of parasite host range on host resistance evolution. To do so, we used the host bacterium Pseudomonas fluorescens SBW25 and a diverse suite of coevolved viral parasites (lytic bacteriophage Φ2) with variable host ranges (defined here as the number of host genotypes that can be infected) as our experimental model organisms. Our results show that resistance evolution to coevolved phages occurred at a much lower rate than to ancestral phage (approximately 50% vs. 100%), but the host range of coevolved phages did not influence the likelihood of resistance evolution. We also show that the host range of both single parasites and populations of parasites does not affect the breadth of the resulting resistance range in a naïve host but that hosts that evolve resistance to single parasites are more likely to resist other (genetically) more closely related parasites as a correlated response. These findings have important implications for our understanding of resistance evolution in natural populations of bacteria and viruses and other host-parasite combinations with similar underlying infection genetics, as well as the development of phage therapy. PMID:25851735

  15. NASA HOST project overview

    NASA Technical Reports Server (NTRS)

    Sokolowski, Daniel E.

    1989-01-01

    NASA's Hot Section Technology (HOST) program has developed improved analytical models for the aerothermal environment, thermomechanical loading, material behavior, structural response, and service life of aircraft gas turbine engines' hot section components. These models, in conjunction with sophisticated computer codes, can be used in design analyses of critical combustor and turbine elements. Toward these ends, efforts were undertaken in instrumentation, combustion, turbine heat transfer, structural analysis, fatigue-fracture, and surface protection. Attention is presently given to the organization of HOST activities and their specific subject matter.

  16. Host age modulates within-host parasite competition.

    PubMed

    Izhar, Rony; Routtu, Jarkko; Ben-Ami, Frida

    2015-05-01

    In many host populations, one of the most striking differences among hosts is their age. While parasite prevalence differences in relation to host age are well known, little is known on how host age impacts ecological and evolutionary dynamics of diseases. Using two clones of the water flea Daphnia magna and two clones of its bacterial parasite Pasteuria ramosa, we examined how host age at exposure influences within-host parasite competition and virulence. We found that multiply-exposed hosts were more susceptible to infection and suffered higher mortality than singly-exposed hosts. Hosts oldest at exposure were least often infected and vice versa. Furthermore, we found that in young multiply-exposed hosts competition was weak, allowing coexistence and transmission of both parasite clones, whereas in older multiply-exposed hosts competitive exclusion was observed. Thus, age-dependent parasite exposure and host demography (age structure) could together play an important role in mediating parasite evolution. At the individual level, our results demonstrate a previously unnoticed interaction of the host's immune system with host age, suggesting that the specificity of immune function changes as hosts mature. Therefore, evolutionary models of parasite virulence might benefit from incorporating age-dependent epidemiological parameters. PMID:25994010

  17. Tricholoma vaccinum host communication during ectomycorrhiza formation.

    PubMed

    Wagner, Katharina; Linde, Jörg; Krause, Katrin; Gube, Matthias; Koestler, Tina; Sammer, Dominik; Kniemeyer, Olaf; Kothe, Erika

    2015-11-01

    The genome sequence of Tricholoma vaccinum was obtained to predict its secretome in order to elucidate communication of T. vaccinum with its host tree spruce (Picea abies) in interkingdom signaling. The most prominent protein domains within the 206 predicted secreted proteins belong to energy and nutrition (52%), cell wall degradation (19%) and mycorrhiza establishment (9%). Additionally, we found small secreted proteins that show typical features of effectors potentially involved in host communication. From the secretome, 22 proteins could be identified, two of which showed higher protein abundances after spruce root exudate exposure, while five were downregulated in this treatment. The changes in T. vaccinum protein excretion with first recognition of the partner were used to identify small secreted proteins with the potential to act as effectors in the mutually beneficial symbiosis. Our observations support the hypothesis of a complex communication network including a cocktail of communication molecules induced long before physical contact of the partners. PMID:26449385

  18. Conducting Ferroelectric Walls, Domain Topology, and Domain Switching Kinetics in a Hybrid Improper Ferroelectric

    NASA Astrophysics Data System (ADS)

    Cheong, Sang-Wook; Rutgers Center For Emergent Materials Team

    Charged polar interfaces such as charged ferroelectric domain walls or heterostructured interfaces of ZnO/(Zn,Mg)O and LaAlO 3 /SrTiO 3 , across which the normal component of electric polarization changes suddenly, can host large two-dimensional conduction. Charged ferroelectric domain walls can be highly conducting but energetically unfavored; however, they were found to be mysteriously abundant in hybrid improper ferroelectric (Ca,Sr) 3 Ti 2 O 7 single crystals. From the exploration of antiphase domain boundaries, which are hidden in piezoresponse force microscopy, using dark-field electron microscopy, we have explored the macroscopic topology of polarization domains and antiphase domains. We found that the macroscopic domain topology is directly responsible for the presence of charged domain walls, and is closely related with the polarization domain switching mechanism in (Ca,Sr) 3 Ti 2 O 7 . Rutgers Center for Emergent Materials and Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, USA.

  19. Probiotics-host communication

    PubMed Central

    Thomas, Carissa M

    2010-01-01

    The intestinal microbiota includes a diverse group of functional microorganisms, including candidate probiotics or viable microorganisms that benefit the host. Beneficial effects of probiotics include enhancing intestinal epithelial cell function, protecting against physiologic stress, modulating cytokine secretion profiles, influencing T-lymphocyte populations, and enhancing antibody secretion. Probiotics have demonstrated significant potential as therapeutic options for a variety of diseases, but the mechanisms responsible for these effects remain to be fully elucidated. Accumulating evidence demonstrates that probiotics communicate with the host by modulating key signaling pathways, such as NFκB and MAPK, to either enhance or suppress activation and influence downstream pathways. Beneficial microbes can profoundly alter the physiology of the gastrointestinal tract, and understanding these mechanisms may result in new diagnostic and therapeutic strategies. PMID:20672012

  20. Hosting a Katrina Evacuee.

    NASA Astrophysics Data System (ADS)

    Hoagland, David

    2008-03-01

    No individual or institution anticipated the impact on the academic research community of hurricane Katrina. When Tulane physicist Wayne Reed asked me to host his research group just a day or two after the disaster, with no authorization or understanding of the commitment, I agreed immediately and then pondered implications. Fortunately, colleagues helped in making the commitment real, only the bureaucracy of my public university posing small hindrances. Industry was remarkably generous in providing Reed with significant ``loaner'' equipment, and amazingly, a suite of custom Reed experiments was running within weeks. At the end, the most productive collaborations for Reed seemed not to have been with my group, with its similar research, but to other groups at my institution, particularly the synthetic chemists, who gained access to methods previously unique to Tulane while offering samples previously unique to UMass. Quickly designed projects exploiting this match turned out remarkably productive. Although begun with trepidation, hosting of Reed had huge positive benefits to me and UMass, and I believe, also to Reed and Tulane. Some key lessons for the future: (i) industry has capacity and willingness to help academic research during disruption (ii) commitment of a host institution must be immediate, without a wait for formal approvals or arrangement of special funding -- delay leads only to discouragement, (iii) continuing academic progress of displaced students must come first, and (iv) intellectual synergy rather than overlap should be the basis for seeking a host. Lastly, NSF or other funding agency should consider a program directly addressing the research needs of unexpectedly disrupted academic scientists, and most particularly, graduate students who face greatly extended studies.

  1. Fatty acid-producing hosts

    SciTech Connect

    Pfleger, Brian F; Lennen, Rebecca M

    2013-12-31

    Described are hosts for overproducing a fatty acid product such as a fatty acid. The hosts include an exogenous nucleic acid encoding a thioesterase and, optionally, an exogenous nucleic acid encoding an acetyl-CoA carboxylase, wherein an acyl-CoA synthetase in the hosts are functionally delected. The hosts prefereably include the nucleic acid encoding the thioesterase at an intermediate copy number. The hosts are preferably recominantly stable and growth-competent at 37.degree. C. Methods of producing a fatty acid product comprising culturing such hosts at 37.degree. C. are also described.

  2. Domains and Naive Theories

    PubMed Central

    Gelman, Susan A.; Noles, Nicholaus S.

    2013-01-01

    Human cognition entails domain-specific cognitive processes that influence memory, attention, categorization, problem-solving, reasoning, and knowledge organization. This review examines domain-specific causal theories, which are of particular interest for permitting an examination of how knowledge structures change over time. We first describe the properties of commonsense theories, and how commonsense theories differ from scientific theories, illustrating with children’s classification of biological and non-biological kinds. We next consider the implications of domain-specificity for broader issues regarding cognitive development and conceptual change. We then examine the extent to which domain-specific theories interact, and how people reconcile competing causal frameworks. Future directions for research include examining how different content domains interact, the nature of theory change, the role of context (including culture, language, and social interaction) in inducing different frameworks, and the neural bases for domain-specific reasoning. PMID:24187603

  3. Dispersal of a defensive symbiont depends on contact between hosts, host health, and host size.

    PubMed

    Hopkins, Skylar R; Boyle, Lindsey J; Belden, Lisa K; Wojdak, Jeremy M

    2015-10-01

    Symbiont dispersal is necessary for the maintenance of defense mutualisms in space and time, and the distribution of symbionts among hosts should be intricately tied to symbiont dispersal behaviors. However, we know surprisingly little about how most defensive symbionts find and choose advantageous hosts or what cues trigger symbionts to disperse from their current hosts. In a series of six experiments, we explored the dispersal ecology of an oligochaete worm (Chaetogaster limnaei) that protects snail hosts from infection by larval trematode parasites. Specifically, we determined the factors that affected net symbiont dispersal from a current "donor" host to a new "receiver" host. Symbionts rarely dispersed unless hosts directly came in contact with one another. However, symbionts overcame their reluctance to disperse across the open environment if the donor host died. When hosts came in direct contact, net symbiont dispersal varied with both host size and trematode infection status, whereas symbiont density did not influence the probability of symbiont dispersal. Together, these experiments show that symbiont dispersal is not a constant, random process, as is often assumed in symbiont dispersal models, but rather the probability of dispersal varies with ecological conditions and among individual hosts. The observed heterogeneity in dispersal rates among hosts may help to explain symbiont aggregation among snail hosts in nature. PMID:25964062

  4. Learning and Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mansour, Yishay

    Domain adaptation is a fundamental learning problem where one wishes to use labeled data from one or several source domains to learn a hypothesis performing well on a different, yet related, domain for which no labeled data is available. This generalization across domains is a very significant challenge for many machine learning applications and arises in a variety of natural settings, including NLP tasks (document classification, sentiment analysis, etc.), speech recognition (speakers and noise or environment adaptation) and face recognition (different lighting conditions, different population composition).

  5. HostPhinder: A Phage Host Prediction Tool

    PubMed Central

    Villarroel, Julia; Kleinheinz, Kortine Annina; Jurtz, Vanessa Isabell; Zschach, Henrike; Lund, Ole; Nielsen, Morten; Larsen, Mette Voldby

    2016-01-01

    The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry [2]. PMID:27153081

  6. Comparing mechanisms of host manipulation across host and parasite taxa

    USGS Publications Warehouse

    Lafferty, Kevin D.; Shaw, Jenny C.

    2013-01-01

    Parasites affect host behavior in several ways. They can alter activity, microhabitats or both. For trophically transmitted parasites (the focus of our study), decreased activity might impair the ability of hosts to respond to final-host predators, and increased activity and altered microhabitat choice might increase contact rates between hosts and final-host predators. In an analysis of trophically transmitted parasites, more parasite groups altered activity than altered microhabitat choice. Parasites that infected vertebrates were more likely to impair the host’s reaction to predators, whereas parasites that infected invertebrates were more likely to increase the host’s contact with predators. The site of infection might affect how parasites manipulate their hosts. For instance, parasites in the central nervous system seem particularly suited to manipulating host behavior. Manipulative parasites commonly occupy the body cavity, muscles and central nervous systems of their hosts. Acanthocephalans in the data set differed from other taxa in that they occurred exclusively in the body cavity of invertebrates. In addition, they were more likely to alter microhabitat choice than activity. Parasites in the body cavity (across parasite types) were more likely to be associated with increased host contact with predators. Parasites can manipulate the host through energetic drain, but most parasites use more sophisticated means. For instance, parasites target four physiological systems that shape behavior in both invertebrates and vertebrates: neural, endocrine, neuromodulatory and immunomodulatory. The interconnections between these systems make it difficult to isolate specific mechanisms of host behavioral manipulation.

  7. HostPhinder: A Phage Host Prediction Tool.

    PubMed

    Villarroel, Julia; Kleinheinz, Kortine Annina; Jurtz, Vanessa Isabell; Zschach, Henrike; Lund, Ole; Nielsen, Morten; Larsen, Mette Voldby

    2016-01-01

    The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry [2]. PMID:27153081

  8. Allergic host defences.

    PubMed

    Palm, Noah W; Rosenstein, Rachel K; Medzhitov, Ruslan

    2012-04-26

    Allergies are generally thought to be a detrimental outcome of a mistargeted immune response that evolved to provide immunity to macroparasites. Here we present arguments to suggest that allergic immunity has an important role in host defence against noxious environmental substances, including venoms, haematophagous fluids, environmental xenobiotics and irritants. We argue that appropriately targeted allergic reactions are beneficial, although they can become detrimental when excessive. Furthermore, we suggest that allergic hypersensitivity evolved to elicit anticipatory responses and to promote avoidance of suboptimal environments. PMID:22538607

  9. Thioaptamers Targeting Dengue Virus Type-2 Envelope Protein Domain III

    PubMed Central

    Gandham, Sai Hari A.; Volk, David E.; Rao, Lokesh G. L.; Neerathilingam, Muniasamy; Gorenstein, David G.

    2014-01-01

    Thioaptamers targeting the dengue-2 virus (DENV-2) envelope protein domain III (EDIII) were developed. EDIII, which contains epitopes for binding neutralizing antibodies, is the putative host-receptor binding domain and is thus an attractive target for development of vaccines, anti-viral therapeutic and diagnostic agents. Thioaptamer DENTA-1 bound to DENV-2 EDIII adjacent to a known neutralizing antibody binding site with a dissociation constant of 154 nM. PMID:25261724

  10. Host Specificity of Bacterial Pathogens

    PubMed Central

    Bäumler, Andreas; Fang, Ferric C.

    2013-01-01

    Most pathogens are able to infect multiple hosts but some are highly adapted to a single-host species. A detailed understanding of the basis of host specificity can provide important insights into molecular pathogenesis, the evolution of pathogenic microbes, and the potential for pathogens to cross the species barrier to infect new hosts. Comparative genomics and the development of humanized mouse models have provided important new tools with which to explore the basis of generalism and specialism. This review will examine host specificity of bacterial pathogens with a focus on generalist and specialist serovars of Salmonella enterica. PMID:24296346

  11. Causal Learning Across Domains

    ERIC Educational Resources Information Center

    Schulz, Laura E.; Gopnik, Alison

    2004-01-01

    Five studies investigated (a) children's ability to use the dependent and independent probabilities of events to make causal inferences and (b) the interaction between such inferences and domain-specific knowledge. In Experiment 1, preschoolers used patterns of dependence and independence to make accurate causal inferences in the domains of…

  12. Modeling Protein Domain Function

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  13. Domain wall filters

    SciTech Connect

    Baer, Oliver; Narayanan, Rajamani; Neuberger, Herbert; Witzel, Oliver

    2007-03-15

    We propose using the extra dimension separating the domain walls carrying lattice quarks of opposite handedness to gradually filter out the ultraviolet fluctuations of the gauge fields that are felt by the fermionic excitations living in the bulk. This generalization of the homogeneous domain wall construction has some theoretical features that seem nontrivial.

  14. Host range, host specificity and hypothesized host shift events among viruses of lower vertebrates

    PubMed Central

    2011-01-01

    The successful replication of a viral agent in a host is a complex process that often leads to a species specificity of the virus and can make interspecies transmission difficult. Despite this difficulty, natural host switch seems to have been frequent among viruses of lower vertebrates, especially fish viruses, since there are several viruses known to be able to infect a wide range of species. In the present review we will focus on well documented reports of broad host range, variations in host specificity, and host shift events hypothesized for viruses within the genera Ranavirus, Novirhabdovirus, Betanodavirus, Isavirus, and some herpesvirus. PMID:21592358

  15. Fungal sensing of host environment.

    PubMed

    Braunsdorf, C; Mailänder-Sánchez, D; Schaller, M

    2016-09-01

    To survive inside a host, fungi have to adapt to a changing and often hostile environment and therefore need the ability to recognize what is going on around them. To adapt to different host niches, they need to sense external conditions such as temperature, pH and to recognize specific host factors. The ability to respond to physiological changes inside the host, independent of being in a commensal, pathogenic or even symbiotic context, implicates mechanisms for sensing of specific host factors. Because the cell wall is constantly in contact with the surrounding, fungi express receptors on the surface of their cell wall, such as pheromone receptors, which have important roles, besides mediating chemotropism for mating. We are not restricting the discussion to the human host because the receptors and mechanisms used by different fungal species to sense their environment are often similar even for plant pathogens. Furthermore, the natural habitat of opportunistic pathogenic fungi with the potential to cause infection in a human host is in soil and on plants. While the hosts' mechanisms of sensing fungal pathogens have been addressed in the literature, the focus of this review is to fill the gap, giving an overview on fungal sensing of a host-(ile) environment. Expanding our knowledge on host-fungal interactions is extremely important to prevent and treat diseases of pathogenic fungi, which are important issues in human health and agriculture but also to understand the delicate balance of fungal symbionts in our ecosystem. PMID:27155351

  16. Optical Frequency Domain Imaging

    NASA Astrophysics Data System (ADS)

    Bouma, Brett E.; Tearney, Guillermo J.; Vakoc, Benjamin; Yun, Seok Hyun

    In this chapter, we discuss a frequency-domain approach, optical frequency-domain imaging (OFDI), which is based on optical frequency-domain reflectometry and uses a wavelength-swept laser and standard single-element photodetectors. The chapter begins with an overview of the fundamental aspects of the technology, including the detected signal, sensitivity, depth range, and resolution, and then goes on to discuss specific component technologies including the light source, interferometer and acquisition electronics, and image processing. The final section of the chapter provides a brief glimpse at some of the biomedical applications that most directly take advantage of the improved speed and sensitivity of OFDI.

  17. Host Stress Drives Salmonella Recrudescence

    PubMed Central

    Verbrugghe, Elin; Dhaenens, Maarten; Leyman, Bregje; Boyen, Filip; Shearer, Neil; Van Parys, Alexander; Haesendonck, Roel; Bert, Wim; Favoreel, Herman; Deforce, Dieter; Thompson, Arthur; Haesebrouck, Freddy; Pasmans, Frank

    2016-01-01

    Host stress is well known to result in flare-ups of many bacterial, viral and parasitic infections. The mechanism by which host stress is exploited to increase pathogen loads, is poorly understood. Here we show that Salmonella enterica subspecies enterica serovar Typhimurium employs a dedicated mechanism, driven by the scsA gene, to respond to the host stress hormone cortisol. Through this mechanism, cortisol increases Salmonella proliferation inside macrophages, resulting in increased intestinal infection loads in DBA/2J mice. ScsA directs overall Salmonella virulence gene expression under conditions that mimic the intramacrophagic environment of Salmonella, and stimulates the host cytoskeletal alterations that are required for increased Salmonella proliferation inside cortisol exposed macrophages. We thus provide evidence that in a stressed host, the complex interplay between a pathogen and its host endocrine and innate immune system increases intestinal pathogen loads to facilitate pathogen dispersal. PMID:26857846

  18. Visualizing Knowledge Domains.

    ERIC Educational Resources Information Center

    Borner, Katy; Chen, Chaomei; Boyack, Kevin W.

    2003-01-01

    Reviews visualization techniques for scientific disciplines and information retrieval and classification. Highlights include historical background of scientometrics, bibliometrics, and citation analysis; map generation; process flow of visualizing knowledge domains; measures and similarity calculations; vector space model; factor analysis;…

  19. Oscillons and domain walls

    SciTech Connect

    Hindmarsh, Mark; Salmi, Petja

    2008-05-15

    Oscillons, extremely long-lived localized oscillations of a scalar field, are shown to be produced by evolving domain wall networks in {phi}{sup 4} theory in two spatial dimensions. We study the oscillons in frequency space using the classical spectral function at zero momentum, and obtain that the velocity distribution is suppressed as {gamma}{sup -2} at large Lorentz factor {gamma}, with oscillons produced up to at least {gamma}{approx}10. This leads us to speculate that oscillons are produced at cusps, regions of the domain wall travelling near the speed of light. In order to gain some insight onto the dilute oscillon 'gas' produced by the domain walls, we prepare a denser gas by filling the simulation volume with oscillons boosted in random directions. We finish the study by revisiting collisions between oscillons and between an oscillon and a domain wall, showing that in the latter case they can pass straight through with minimal distortion.

  20. Anisotropy of Silicate-Hosted Magnetite Inclusions

    NASA Astrophysics Data System (ADS)

    Scott, G. R.; Feinberg, J. M.; Renne, P. R.

    2004-12-01

    Anisotropy of magnetic properties is a hallmark of silicate crystals with oriented iron-oxide inclusions. Strongly magnetic magnetite-bearing silicates (10-1 A m-1) are common components of gabbros and layered intrusions, contributing to local and regional magnetic anomalies. Additionally, these iron-oxide silicates hold the promise of being exceptional paleomagnetic recorders owing to their features of: physical/chemical isolation from altering fluids, chemical equilibrium with their silicate host, and long relaxation times (enhanced coercivity). However, anisotropy of remanence must be understood before these advantageous features can be utilized. Measurements of single crystals of clinopyroxene and plagioclase (10-4 g) show anisotropy in direction and intensity that directly reflect the crystallography of the silicate host. The host controls both the crystallographic orientation of the magnetite (magnetocrystalline anisotropy) and the elongation direction of the magnetite inclusion (shape anisotropy). We have found another source of anisotropy that involves an internal exsolution of ulvöspinel within titanomagnetite inclusions. This also reflects a host control as this second exsolution occurs along the magnetite \\{100\\}. This fixed wall shape anisotropy creates an array of interacting single domain magnetite parallelepipeds, parallel to \\{100\\}. Each of these anisotropies contributes to enhanced coercivity of remanence, which significantly exceeds the IRM saturation magnetization for magnetite (300 mT). The anisotropy of IRM (aIRM@ 1.1 T) of magnetite-bearing clinopyroxene and plagioclase shows clustering of directions, reflecting the mixture of variables that include: inclusion elongation direction and abundance, orientation of magnetite easy axes relative to the applied field, inclusion aspect ratio and diameter, and pre-existing magnetic domain structure. For pyroxene (monoclinic) with two arrays of needle-shaped magnetite inclusions, the aIRM is

  1. Tandem BRCT Domains

    PubMed Central

    Mesquita, Rafael D.; Woods, Nicholas T.; Seabra-Junior, Eloy S.; Monteiro, Alvaro N.A.

    2010-01-01

    The cell’s ability to sense and respond to specific stimuli is a complex system derived from precisely regulated protein-protein interactions. Some of these protein-protein interactions are mediated by the recognition of linear peptide motifs by protein modular domains. BRCT (BRCA1 C-terminal) domains and their linear motif counterparts, which contain phosphoserines, are one such pair-wise interaction system that seems to have evolved to serve as a surveillance system to monitor threats to the cell’s genetic integrity. Evidence indicates that BRCT domains found in tandem can cooperate to provide sequence-specific binding of phosphorylated peptides as is the case for the breast and ovarian cancer susceptibility gene BRCA1 and the PAX transcription factor–interacting protein PAXIP1. Particular interest has been paid to tandem BRCT domains as “readers” of signaling events in the form of phosphorylated serine moieties induced by the activation of DNA damage response kinases ATM, ATR, and DNA-PK. However, given the diversity of tandem BRCT-containing proteins, questions remain as to the origin and evolution of this domain. Here, we discuss emerging views of the origin and evolving roles of tandem BRCT domain repeats in the DNA damage response. PMID:21533002

  2. [Tuberculosis in compromised hosts].

    PubMed

    2003-11-01

    Recent development of tuberculosis in Japan tends to converge on a specific high risk group. The proportion of tuberculosis developing particularly from the compromised hosts in the high risk group is especially high. At this symposium, therefore, we took up diabetes mellitus, gastrectomy, dialysis, AIDS and the elderly for discussion. Many new findings and useful reports for practical medical treatment are submitted; why these compromised hosts are predisposed to tuberculosis, tuberculosis diagnostic and remedial notes of those compromised hosts etc. It is an important question for the future to study how to prevent tuberculosis from these compromised hosts. 1. Tuberculosis in diabetes mellitus: aggravation and its immunological mechanism: Kazuyoshi KAWAKAMI (Department of Internal Medicine, Division of Infectious Diseases, Graduate School and Faculty of Medicine, University of the Ryukyus). It has been well documented that diabetes mellitus (DM) is a major aggravating factor in tuberculosis. The onset of this disease is more frequent in DM patients than in individuals with any underlying diseases. However, the precise mechanism of this finding remains to be fully understood. Earlier studies reported that the migration, phagocytosis and bactericidal activity of neutrophils are all impaired in DM patients, which is related to their reduced host defense to infection with extracellular bacteria, such as S. aureus and E. colli. Host defense to mycobacterial infection is largely mediated by cellular immunity, and Th1-related cytokines, such as IFN-gamma and IL-12, play a central role in this response. It is reported that serum level of these cytokines and their production by peripheral blood mononuclear cells (PBMC) are reduced in tuberculosis patients with DM, and this is supposed to be involved in the high incidence of tuberculosis in DM. Our study observed similar findings and furthermore indicated that IFN-gamma and IL-12 production by BCG-stimulated PBMC was lower

  3. Intersectin-2L regulates caveola endocytosis secondary to Cdc42-mediated actin polymerization.

    PubMed

    Klein, Irene K; Predescu, Dan N; Sharma, Tiffany; Knezevic, Ivana; Malik, Asrar B; Predescu, Sanda

    2009-09-18

    Here we addressed the role of intersectin-2L (ITSN-2L), a guanine nucleotide exchange factor for the Rho GTPase Cdc42, in the mechanism of caveola endocytosis in endothelial cells (ECs). Immunoprecipitation and co-localization studies showed that ITSN-2L associates with members of the Cdc42-WASp-Arp2/3 actin polymerization pathway. Expression of Dbl homology-pleckstrin homology (DH-PH) region of ITSN-2L (DH-PH(ITSN-2L)) induced specific activation of Cdc42, resulting in formation of extensive filopodia, enhanced cortical actin, as well as a shift from G-actin to F-actin. The "catalytically dead" DH-PH domain reversed these effects and induced significant stress fiber formation, without a detectable shift in actin pools. A biotin assay for caveola internalization indicated a significant decrease in the uptake of biotinylated proteins in DH-PH(ITSN-2L)-transfected cells compared with control and 1 microM jasplakinolide-treated cells. ECs depleted of ITSN-2L by small interfering RNA, however, showed decreased Cdc42 activation and actin remodeling similar to the defective DH-PH, resulting in 62% increase in caveola-mediated uptake compared with controls. Thus, ITSN-2L, a guanine nucleotide exchange factor for Cdc42, regulates different steps of caveola endocytosis in ECs by controlling the temporal and spatial actin polymerization and remodeling sub-adjacent to the plasma membrane. PMID:19622753

  4. Determination of host RNA helicases activity in viral replication

    PubMed Central

    Sharma, Amit; Boris-Lawrie, Kathleen

    2016-01-01

    RNA helicases are encoded by all eukaryotic and prokaryotic cells and a minority of viruses. Activity of RNA helicases is necessary for all steps in the expression of cells and viruses and the host innate response to virus infection. Their vast functional repertoire is attributable to the core ATPase-dependent helicase domain in conjunction with flanking domains that are interchangeable and engage viral and cellular cofactors. Here, we address the important issue of host RNA helicases that are necessary for replication of a virus. The chapter covers approaches to identification and characterization of candidate helicases and methods to define the biochemical and biophysical parameters of specificity and functional activity of the enzymes. We discuss the context of cellular RNA helicase activity and virion-associated RNA helicases. The methodology and choice of controls fosters the assessment of the virologic scope of RNA helicases across divergent cell lineages and viral replication cycles. PMID:22713331

  5. Increased magnetic damping of a single domain wall and adjacent magnetic domains detected by spin torque diode in a nanostripe

    NASA Astrophysics Data System (ADS)

    Lequeux, Steven; Sampaio, Joao; Bortolotti, Paolo; Devolder, Thibaut; Matsumoto, Rie; Yakushiji, Kay; Kubota, Hitoshi; Fukushima, Akio; Yuasa, Shinji; Nishimura, Kazumasa; Nagamine, Yoshinori; Tsunekawa, Koji; Cros, Vincent; Grollier, Julie

    2015-11-01

    Spin torque resonance has been used to simultaneously probe the dynamics of a magnetic domain wall and of magnetic domains in a nanostripe magnetic tunnel junction. Due to the large associated resistance variations, we are able to analyze quantitatively the resonant properties of these single nanoscale magnetic objects. In particular, we find that the magnetic damping of both the domains and the domain wall is doubled compared to the damping value of the host magnetic layer. We estimate the contributions to the damping arising from the dipolar couplings between the different layers in the junction and from the intralayer spin pumping effect, and find that they cannot explain the large damping enhancement that we observe. We conclude that the measured increased damping is intrinsic to large amplitudes excitations of spatially localized modes or solitons such as vibrating or propagating domain walls.

  6. Increased magnetic damping of a single domain wall and adjacent magnetic domains detected by spin torque diode in a nanostripe

    SciTech Connect

    Lequeux, Steven; Sampaio, Joao; Bortolotti, Paolo; Cros, Vincent; Grollier, Julie; Matsumoto, Rie; Yakushiji, Kay; Kubota, Hitoshi; Fukushima, Akio; Yuasa, Shinji; Nishimura, Kazumasa; Nagamine, Yoshinori; Tsunekawa, Koji

    2015-11-02

    Spin torque resonance has been used to simultaneously probe the dynamics of a magnetic domain wall and of magnetic domains in a nanostripe magnetic tunnel junction. Due to the large associated resistance variations, we are able to analyze quantitatively the resonant properties of these single nanoscale magnetic objects. In particular, we find that the magnetic damping of both the domains and the domain wall is doubled compared to the damping value of the host magnetic layer. We estimate the contributions to the damping arising from the dipolar couplings between the different layers in the junction and from the intralayer spin pumping effect, and find that they cannot explain the large damping enhancement that we observe. We conclude that the measured increased damping is intrinsic to large amplitudes excitations of spatially localized modes or solitons such as vibrating or propagating domain walls.

  7. Domains in Ferroelectric Nanostructures

    NASA Astrophysics Data System (ADS)

    Gregg, Marty

    2010-03-01

    Ferroelectric materials have great potential in influencing the future of small scale electronics. At a basic level, this is because ferroelectric surfaces are charged, and so interact strongly with charge-carrying metals and semiconductors - the building blocks for all electronic systems. Since the electrical polarity of the ferroelectric can be reversed, surfaces can both attract and repel charges in nearby materials, and can thereby exert complete control over both charge distribution and movement. It should be no surprise, therefore, that microelectronics industries have already looked very seriously at harnessing ferroelectric materials in a variety of applications, from solid state memory chips (FeRAMs) to field effect transistors (FeFETs). In all such applications, switching the direction of the polarity of the ferroelectric is a key aspect of functional behavior. The mechanism for switching involves the field-induced nucleation and growth of domains. Domain coarsening, through domain wall propagation, eventually causes the entire ferroelectric to switch its polar direction. It is thus the existence and behavior of domains that determine the switching response, and ultimately the performance of the ferroelectric device. A major issue, associated with the integration of ferroelectrics into microelectronic devices, has been that the fundamental properties associated with ferroelectrics, when in bulk form, appear to change quite dramatically and unpredictably when at the nanoscale: new modes of behaviour, and different functional characteristics from those seen in bulk appear. For domains, in particular, the proximity of surfaces and boundaries have a dramatic effect: surface tension and depolarizing fields both serve to increase the equilibrium density of domains, such that minor changes in scale or morphology can have major ramifications for domain redistribution. Given the importance of domains in dictating the overall switching characteristics of a device

  8. Ethanol production by recombinant hosts

    DOEpatents

    Ingram, Lonnie O.; Beall, David S.; Burchhardt, Gerhard F. H.; Guimaraes, Walter V.; Ohta, Kazuyoshi; Wood, Brent E.; Shanmugam, Keelnatham T.

    1995-01-01

    Novel plasmids comprising genes which code for the alcohol dehydrogenase and pyruvate decarboxylase are described. Also described are recombinant hosts which have been transformed with genes coding for alcohol dehydrogenase and pyruvate. By virtue of their transformation with these genes, the recombinant hosts are capable of producing significant amounts of ethanol as a fermentation product. Also disclosed are methods for increasing the growth of recombinant hosts and methods for reducing the accumulation of undesirable metabolic products in the growth medium of these hosts. Also disclosed are recombinant host capable of producing significant amounts of ethanol as a fermentation product of oligosaccharides and plasmids comprising genes encoding polysaccharases, in addition to the genes described above which code for the alcohol dehydrogenase and pyruvate decarboxylase. Further, methods are described for producing ethanol from oligomeric feedstock using the recombinant hosts described above. Also provided is a method for enhancing the production of functional proteins in a recombinant host comprising overexpressing an adhB gene in the host. Further provided are process designs for fermenting oligosaccharide-containing biomass to ethanol.

  9. Ethanol production by recombinant hosts

    DOEpatents

    Fowler, David E.; Horton, Philip G.; Ben-Bassat, Arie

    1996-01-01

    Novel plasmids comprising genes which code for the alcohol dehydrogenase and pyruvate decarboxylase are described. Also described are recombinant hosts which have been transformed with genes coding for alcohol dehydrogenase and pyruvate. By virtue of their transformation with these genes, the recombinant hosts are capable of producing significant amounts of ethanol as a fermentation product. Also disclosed are methods for increasing the growth of recombinant hosts and methods for reducing the accumulation of undesirable metabolic products in the growth medium of these hosts. Also disclosed are recombinant host capable of producing significant amounts of ethanol as a fermentation product of oligosaccharides and plasmids comprising genes encoding polysaccharases, in addition to the genes described above which code for the alcohol dehydrogenase and pyruvate decarboxylase. Further, methods are described for producing ethanol from oligomeric feedstock using the recombinant hosts described above. Also provided is a method for enhancing the production of functional proteins in a recombinant host comprising overexpressing an adhB gene in the host. Further provided are process designs for fermenting oligosaccharide-containing biomass to ethanol.

  10. Host defenses trigger salmonella's arsenal.

    PubMed

    Keestra, A Marijke; Bäumler, Andreas J

    2011-03-17

    Salmonella survives in macrophages by using a molecular syringe to deliver proteins into the host-cell cytosol where they manipulate phagocyte physiology. Arpaia and colleagues (Arpaia et al., 2011) show that deployment of this virulence factor is triggered by the very responses that are intended to confer host resistance. PMID:21402352

  11. Stennis hosts 2010 Special Olympics

    NASA Technical Reports Server (NTRS)

    2010-01-01

    Sarah Johnson, 28, of Gulfport, carries in the Olympic torch to signal the start of the 2010 Area III Special Olympic games at NASA's John C. Stennis Space Center on March 27. Stennis volunteers hosted special needs athletes from across the area for the event. Stennis is an annual host of the games.

  12. Emerging Supramolecular Therapeutic Carriers Based on Host-Guest Interactions.

    PubMed

    Karim, Anis Abdul; Dou, Qingqing; Li, Zibiao; Loh, Xian Jun

    2016-05-01

    Recent advances in host-guest chemistry have significantly influenced the construction of supramolecular soft biomaterials. The highly selective and non-covalent interactions provide vast possibilities of manipulating supramolecular self-assemblies at the molecular level, allowing a rational design to control the sizes and morphologies of the resultant objects as carrier vehicles in a delivery system. In this Focus Review, the most recent developments of supramolecular self-assemblies through host-guest inclusion, including nanoparticles, micelles, vesicles, hydrogels, and various stimuli-responsive morphology transition materials are presented. These sophisticated materials with diverse functions, oriented towards therapeutic agent delivery, are further summarized into several active domains in the areas of drug delivery, gene delivery, co-delivery and site-specific targeting deliveries. Finally, the possible strategies for future design of multifunctional delivery carriers by combining host-guest chemistry with biological interface science are proposed. PMID:26833861

  13. Axion domain wall baryogenesis

    SciTech Connect

    Daido, Ryuji; Kitajima, Naoya; Takahashi, Fuminobu

    2015-07-28

    We propose a new scenario of baryogenesis, in which annihilation of axion domain walls generates a sizable baryon asymmetry. Successful baryogenesis is possible for a wide range of the axion mass and decay constant, m≃10{sup 8}–10{sup 13} GeV and f≃10{sup 13}–10{sup 16} GeV. Baryonic isocurvature perturbations are significantly suppressed in our model, in contrast to various spontaneous baryogenesis scenarios in the slow-roll regime. In particular, the axion domain wall baryogenesis is consistent with high-scale inflation which generates a large tensor-to-scalar ratio within the reach of future CMB B-mode experiments. We also discuss the gravitational waves produced by the domain wall annihilation and its implications for the future gravitational wave experiments.

  14. Frequency and Fitness Consequences of Bacteriophage Φ6 Host Range Mutations

    PubMed Central

    Ford, Brian E.; Sun, Bruce; Carpino, James; Chapler, Elizabeth S.; Ching, Jane; Choi, Yoon; Jhun, Kevin; Kim, Jung D.; Lallos, Gregory G.; Morgenstern, Rachelle; Singh, Shalini; Theja, Sai; Dennehy, John J.

    2014-01-01

    Viruses readily mutate and gain the ability to infect novel hosts, but few data are available regarding the number of possible host range-expanding mutations allowing infection of any given novel host, and the fitness consequences of these mutations on original and novel hosts. To gain insight into the process of host range expansion, we isolated and sequenced 69 independent mutants of the dsRNA bacteriophage Φ6 able to infect the novel host, Pseudomonas pseudoalcaligenes. In total, we found at least 17 unique suites of mutations among these 69 mutants. We assayed fitness for 13 of 17 mutant genotypes on P. pseudoalcaligenes and the standard laboratory host, P. phaseolicola. Mutants exhibited significantly lower fitnesses on P. pseudoalcaligenes compared to P. phaseolicola. Furthermore, 12 of the 13 assayed mutants showed reduced fitness on P. phaseolicola compared to wildtype Φ6, confirming the prevalence of antagonistic pleiotropy during host range expansion. Further experiments revealed that the mechanistic basis of these fitness differences was likely variation in host attachment ability. In addition, using computational protein modeling, we show that host-range expanding mutations occurred in hotspots on the surface of the phage's host attachment protein opposite a putative hydrophobic anchoring domain. PMID:25409341

  15. Cucumis melo endornavirus: Genome organization, host range and co-divergence with the host.

    PubMed

    Sabanadzovic, Sead; Wintermantel, William M; Valverde, Rodrigo A; McCreight, James D; Aboughanem-Sabanadzovic, Nina

    2016-03-01

    A high molecular weight dsRNA was isolated from a Cucumis melo L. plant (referred to as 'CL01') of an unknown cultivar and completely sequenced. Sequence analyses showed that dsRNA is associated with an endornavirus for which a name Cucumis melo endornavirus (CmEV) is proposed. The genome of CmEV-CL01 consists of 15,078 nt, contains a single, 4939 codons-long ORF and terminates with a stretch of 10 cytosine residues. Comparisons of the putative CmEV-encoded polyprotein with available references in protein databases revealed a unique genome organization characterized by the presence of the following domains: viral helicase Superfamily 1 (Hel-1), three glucosyltransferases (doublet of putative capsular polysaccharide synthesis proteins and a putative C_28_Glycosyltransferase), and an RNA-dependent RNA polymerase (RdRp). The presence of three glycome-related domains of different origin makes the genome organization of CmEV unique among endornaviruses. Phylogenetic analyses of viral RdRp domains showed that CmEV belongs to a specific lineage within the family Endornaviridae made exclusively of plant-infecting endornaviruses. An RT-PCR based survey demonstrated high incidence of CmEV among melon germplasm accession (>87% of tested samples). Analyses of partial genome sequences of CmEV isolates from 26 different melon genotypes suggest fine-tuned virus adaptation and co-divergence with the host. Finally, results of the present study revealed that CmEV is present in plants belonging to three different genera in the family Cucurbitaceae. Such diverse host range is unreported for known endornaviruses and suggests a long history of CmEV association with cucurbits predating their speciation. PMID:26805037

  16. Predicting domain-domain interactions using a parsimony approach

    PubMed Central

    Guimarães, Katia S; Jothi, Raja; Zotenko, Elena; Przytycka, Teresa M

    2006-01-01

    We propose a novel approach to predict domain-domain interactions from a protein-protein interaction network. In our method we apply a parsimony-driven explanation of the network, where the domain interactions are inferred using linear programming optimization, and false positives in the protein network are handled by a probabilistic construction. This method outperforms previous approaches by a considerable margin. The results indicate that the parsimony principle provides a correct approach for detecting domain-domain contacts. PMID:17094802

  17. Hosts and parasites as aliens.

    PubMed

    Taraschewski, H

    2006-06-01

    Over the past decades, various free-living animals (hosts) and their parasites have invaded recipient areas in which they had not previously occurred, thus gaining the status of aliens or exotics. In general this happened to a low extent for hundreds of years. With variable frequency, invasions have been followed by the dispersal and establishment of non-indigenous species, whether host or parasite. In the literature thus far, colonizations by both hosts and parasites have not been treated and reviewed together, although both are usually interwoven in various ways. As to those factors permitting invasive success and colonization strength, various hypotheses have been put forward depending on the scientific background of respective authors and on the conspicuousness of certain invasions. Researchers who have tried to analyse characteristic developmental patterns, the speed of dispersal or the degree of genetic divergence in populations of alien species have come to different conclusions. Among parasitologists, the applied aspects of parasite invasions, such as the negative effects on economically important hosts, have long been at the centre of interest. In this contribution, invasions by hosts as well as parasites are considered comparatively, revealing many similarities and a few differences. Two helminths, the liver fluke, Fasciola hepatica, of cattle and sheep and the swimbladder nematode, Anguillicola crassus, of eels are shown to be useful as model parasites for the study of animal invasions and environmental global change. Introductions of F. hepatica have been associated with imports of cattle or other grazing animals. In various target areas, susceptible lymnaeid snails serving as intermediate hosts were either naturally present and/or were introduced from the donor continent of the parasite (Europe) and/or from other regions which were not within the original range of the parasite, partly reflecting progressive stages of a global biota change. In several

  18. Time-domain imaging

    NASA Technical Reports Server (NTRS)

    Tolliver, C. L.

    1989-01-01

    The quest for the highest resolution microwave imaging and principle of time-domain imaging has been the primary motivation for recent developments in time-domain techniques. With the present technology, fast time varying signals can now be measured and recorded both in magnitude and in-phase. It has also enhanced our ability to extract relevant details concerning the scattering object. In the past, the interface of object geometry or shape for scattered signals has received substantial attention in radar technology. Various scattering theories were proposed to develop analytical solutions to this problem. Furthermore, the random inversion, frequency swept holography, and the synthetic radar imaging, have two things in common: (1) the physical optic far-field approximation, and (2) the utilization of channels as an extra physical dimension, were also advanced. Despite the inherent vectorial nature of electromagnetic waves, these scalar treatments have brought forth some promising results in practice with notable examples in subsurface and structure sounding. The development of time-domain techniques are studied through the theoretical aspects as well as experimental verification. The use of time-domain imaging for space robotic vision applications has been suggested.

  19. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  20. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  1. MURINE CYTOMEGALOVIRUS HOST RESISTANCE MODELS

    EPA Science Inventory

    Mouse cytomegalovirus (MCMV) is a well developed and extremely useful and relevant host resistance model for immunotoxicity testing. at cytomegalovirus (RCMV) is currently under development and may have similar applications. ytomegaloviruses are species specific; RCMV is a distin...

  2. Asteroseismology of Exoplanet Host Stars

    NASA Astrophysics Data System (ADS)

    Kayhan, Cenk; Çelik Orhan, Zeynep; Yildiz, Mutlu

    2016-07-01

    Exoplanet studies are one of the most interesting and attractive topics in astrophysics. Besides of ground-based observations, Kepler and CoRoT space missions improved our knowledge by providing unprecedented data of exoplanets and host stars. Precise determination of basic properties of planets depends on how we accurately determine fundamental properties of host stars. Asteroseismology is a powerful tool to study stellar structure and evolution and provides us radius, mass and age of the host stars. In this study, we construct stellar interior models of these stars with the MESA evolution code and compare model frequencies with the oscillation frequencies derived from Kepler data. Then, we obtain fundamental parameters of the host stars. Finally, fundamental parameters of exoplanets are reevaluated.

  3. Stennis hosts 2010 Special Olympics

    NASA Technical Reports Server (NTRS)

    2010-01-01

    B.J. Matherne, 27, of Gulfport, scores a soccer goal during one of the 2010 Special Olympic games at NASA's John C. Stennis Space Center on March 27. Stennis serves as an annual host for the special needs event. Each year, local, regional and national Special Olympics events are hosted in more than 150 countries for persons with special needs. An international Special Olympics competition is held every two years.

  4. Crystal Structures of the Outer Membrane Domain of Intimin and Invasin from Enterohemorrhagic E. coli and Enteropathogenic Y. pseudotuberculosis

    SciTech Connect

    Fairman, James W.; Dautin, Nathalie; Wojtowicz, Damian; Liu, Wei; Noinaj, Nicholas; Barnard, Travis J.; Udho, Eshwar; Przytycka, Teresa M.; Cherezov, Vadim; Buchanan, Susan K.

    2012-12-10

    Intimins and invasins are virulence factors produced by pathogenic Gram-negative bacteria. They contain C-terminal extracellular passenger domains that are involved in adhesion to host cells and N-terminal {beta} domains that are embedded in the outer membrane. Here, we identify the domain boundaries of an E. coli intimin {beta} domain and use this information to solve its structure and the {beta} domain structure of a Y. pseudotuberculosis invasin. Both {beta} domain structures crystallized as monomers and reveal that the previous range of residues assigned to the {beta} domain also includes a protease-resistant domain that is part of the passenger. Additionally, we identify 146 nonredundant representative members of the intimin/invasin family based on the boundaries of the highly conserved intimin and invasin {beta} domains. We then use this set of sequences along with our structural data to find and map the evolutionarily constrained residues within the {beta} domain.

  5. Simplified Parallel Domain Traversal

    SciTech Connect

    Erickson III, David J

    2011-01-01

    Many data-intensive scientific analysis techniques require global domain traversal, which over the years has been a bottleneck for efficient parallelization across distributed-memory architectures. Inspired by MapReduce and other simplified parallel programming approaches, we have designed DStep, a flexible system that greatly simplifies efficient parallelization of domain traversal techniques at scale. In order to deliver both simplicity to users as well as scalability on HPC platforms, we introduce a novel two-tiered communication architecture for managing and exploiting asynchronous communication loads. We also integrate our design with advanced parallel I/O techniques that operate directly on native simulation output. We demonstrate DStep by performing teleconnection analysis across ensemble runs of terascale atmospheric CO{sub 2} and climate data, and we show scalability results on up to 65,536 IBM BlueGene/P cores.

  6. Magnetic bubble domain memories

    NASA Technical Reports Server (NTRS)

    Ypma, J. E.

    1974-01-01

    Some attractive features of Bubble Domain Memory and its relation to existing technologies are discussed. Two promising applications are block access mass memory and tape recorder replacement. The required chip capabilities for these uses are listed, and the specifications for a block access mass memory designed to fit between core and HPT disk are presented. A feasibility model for a tape recorder replacement is introduced.

  7. Public domain optical character recognition

    NASA Astrophysics Data System (ADS)

    Garris, Michael D.; Blue, James L.; Candela, Gerald T.; Dimmick, Darrin L.; Geist, Jon C.; Grother, Patrick J.; Janet, Stanley A.; Wilson, Charles L.

    1995-03-01

    A public domain document processing system has been developed by the National Institute of Standards and Technology (NIST). The system is a standard reference form-based handprint recognition system for evaluating optical character recognition (OCR), and it is intended to provide a baseline of performance on an open application. The system's source code, training data, performance assessment tools, and type of forms processed are all publicly available. The system recognizes the handprint entered on handwriting sample forms like the ones distributed with NIST Special Database 1. From these forms, the system reads hand-printed numeric fields, upper and lowercase alphabetic fields, and unconstrained text paragraphs comprised of words from a limited-size dictionary. The modular design of the system makes it useful for component evaluation and comparison, training and testing set validation, and multiple system voting schemes. The system contains a number of significant contributions to OCR technology, including an optimized probabilistic neural network (PNN) classifier that operates a factor of 20 times faster than traditional software implementations of the algorithm. The source code for the recognition system is written in C and is organized into 11 libraries. In all, there are approximately 19,000 lines of code supporting more than 550 subroutines. Source code is provided for form registration, form removal, field isolation, field segmentation, character normalization, feature extraction, character classification, and dictionary-based postprocessing. The recognition system has been successfully compiled and tested on a host of UNIX workstations. This paper gives an overview of the recognition system's software architecture, including descriptions of the various system components along with timing and accuracy statistics.

  8. Identification of FAM111A as an SV40 Host Range Restriction and Adenovirus Helper Factor

    PubMed Central

    Padi, Megha; Korkhin, Anna; James, Robert L.; Adelmant, Guillaume; Yoon, Rosa; Guo, Luxuan; Berrios, Christian; Zhang, Ying; Calderwood, Michael A.; Velmurgan, Soundarapandian; Cheng, Jingwei; Marto, Jarrod A.; Hill, David E.; Cusick, Michael E.; Vidal, Marc; Florens, Laurence; Washburn, Michael P.; Litovchick, Larisa; DeCaprio, James A.

    2012-01-01

    The small genome of polyomaviruses encodes a limited number of proteins that are highly dependent on interactions with host cell proteins for efficient viral replication. The SV40 large T antigen (LT) contains several discrete functional domains including the LXCXE or RB-binding motif, the DNA binding and helicase domains that contribute to the viral life cycle. In addition, the LT C-terminal region contains the host range and adenovirus helper functions required for lytic infection in certain restrictive cell types. To understand how LT affects the host cell to facilitate viral replication, we expressed full-length or functional domains of LT in cells, identified interacting host proteins and carried out expression profiling. LT perturbed the expression of p53 target genes and subsets of cell-cycle dependent genes regulated by the DREAM and the B-Myb-MuvB complexes. Affinity purification of LT followed by mass spectrometry revealed a specific interaction between the LT C-terminal region and FAM111A, a previously uncharacterized protein. Depletion of FAM111A recapitulated the effects of heterologous expression of the LT C-terminal region, including increased viral gene expression and lytic infection of SV40 host range mutants and adenovirus replication in restrictive cells. FAM111A functions as a host range restriction factor that is specifically targeted by SV40 LT. PMID:23093934

  9. Identification of FAM111A as an SV40 host range restriction and adenovirus helper factor.

    PubMed

    Fine, Debrah A; Rozenblatt-Rosen, Orit; Padi, Megha; Korkhin, Anna; James, Robert L; Adelmant, Guillaume; Yoon, Rosa; Guo, Luxuan; Berrios, Christian; Zhang, Ying; Calderwood, Michael A; Velmurgan, Soundarapandian; Cheng, Jingwei; Marto, Jarrod A; Hill, David E; Cusick, Michael E; Vidal, Marc; Florens, Laurence; Washburn, Michael P; Litovchick, Larisa; DeCaprio, James A

    2012-01-01

    The small genome of polyomaviruses encodes a limited number of proteins that are highly dependent on interactions with host cell proteins for efficient viral replication. The SV40 large T antigen (LT) contains several discrete functional domains including the LXCXE or RB-binding motif, the DNA binding and helicase domains that contribute to the viral life cycle. In addition, the LT C-terminal region contains the host range and adenovirus helper functions required for lytic infection in certain restrictive cell types. To understand how LT affects the host cell to facilitate viral replication, we expressed full-length or functional domains of LT in cells, identified interacting host proteins and carried out expression profiling. LT perturbed the expression of p53 target genes and subsets of cell-cycle dependent genes regulated by the DREAM and the B-Myb-MuvB complexes. Affinity purification of LT followed by mass spectrometry revealed a specific interaction between the LT C-terminal region and FAM111A, a previously uncharacterized protein. Depletion of FAM111A recapitulated the effects of heterologous expression of the LT C-terminal region, including increased viral gene expression and lytic infection of SV40 host range mutants and adenovirus replication in restrictive cells. FAM111A functions as a host range restriction factor that is specifically targeted by SV40 LT. PMID:23093934

  10. Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein

    NASA Astrophysics Data System (ADS)

    Gruszka, Dominika T.; Whelan, Fiona; Farrance, Oliver E.; Fung, Herman K. H.; Paci, Emanuele; Jeffries, Cy M.; Svergun, Dmitri I.; Baldock, Clair; Baumann, Christoph G.; Brockwell, David J.; Potts, Jennifer R.; Clarke, Jane

    2015-06-01

    Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed `clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length.

  11. Domain Specific vs Domain General: Implications for Dynamic Assessment

    ERIC Educational Resources Information Center

    Kaniel, Shlomo

    2010-01-01

    The article responds to the need for evidence-based dynamic assessment. The article is divided into two sections: In Part 1 we examine the scientific answer to the question of how far human mental activities and capabilities are domain general (DG) / domain specific (DS). A highly complex answer emerges from the literature review of domains such…

  12. Effects of basic human values on host community acculturation orientations.

    PubMed

    Sapienza, Irene; Hichy, Zira; Guarnera, Maria; Nuovo, Santo Di

    2010-08-01

    Although literature provides evidence for the relationship between values and acculturation, the relationship between host community acculturation orientations has not yet been investigated. In this study we tested the effects of four high-order values (openness to change, self-transcendence, conservation, and self-enhancement, devised according to Schwartz's model) on host community acculturation orientations towards immigrants (devised according the interactive acculturation model) in the public domain of employment and the private domain of endogamy/exogamy. Participants were 264 Italian University students, who completed a questionnaire containing the Portrait Values Questionnaire, a measure of personal values, and the Host Community Acculturation Scale, aimed at measuring Italian acculturation strategies towards three groups of immigrants: Immigrants (the general category), Chinese (the valued immigrant group), and Albanians (the devalued immigrant group). Results showed that personal values are related to the adoption of acculturation orientations: In particular, the values that mostly impacted on acculturation orientations were self-transcendence and conservation. Values concerning self-transcendence encourage the adoption of integrationism, integrationism-transformation, and individualism and reduce the adoption of assimilationism, segregationism, and exclusionism. Values concerning conservation encourage the adoption of assimilation, segregation and exclusion orientations and reduce the adoption of both types of integrationism and individualism. Minor effects were found regarding self-enhancement and openness to change. PMID:22044017

  13. Host receptors for bacteriophage adsorption.

    PubMed

    Bertozzi Silva, Juliano; Storms, Zachary; Sauvageau, Dominic

    2016-02-01

    The adsorption of bacteriophages (phages) onto host cells is, in all but a few rare cases, a sine qua non condition for the onset of the infection process. Understanding the mechanisms involved and the factors affecting it is, thus, crucial for the investigation of host-phage interactions. This review provides a survey of the phage host receptors involved in recognition and adsorption and their interactions during attachment. Comprehension of the whole infection process, starting with the adsorption step, can enable and accelerate our understanding of phage ecology and the development of phage-based technologies. To assist in this effort, we have established an open-access resource--the Phage Receptor Database (PhReD)--to serve as a repository for information on known and newly identified phage receptors. PMID:26755501

  14. Supernovae in paired host galaxies

    NASA Astrophysics Data System (ADS)

    Nazaryan, T. A.; Petrosian, A. R.; Hakobyan, A. A.; Adibekyan, V. Zh.; Kunth, D.; Mamon, G. A.; Turatto, M.; Aramyan, L. S.

    2014-12-01

    We investigate the influence of close neighbor galaxies on the properties of supernovae (SNe) and their host galaxies using 56 SNe located in pairs of galaxies with different levels of star formation (SF) and nuclear activity. The mean distance of type II SNe from nuclei of hosts is greater by about a factor of 2 than that of type Ibc SNe. For the first time it is shown that SNe Ibc are located in pairs with significantly smaller difference of radial velocities between components than pairs containing SNe Ia and II. We consider this as a result of higher star formation rate (SFR) of these closer systems of galaxies. SN types are not correlated with the luminosity ratio of host and neighbor galaxies in pairs. The orientation of SNe with respect to the preferred direction toward neighbor galaxy is found to be isotropic and independent of kinematical properties of the galaxy pair.

  15. Infected cell protein 0 functional domains and their coordination in herpes simplex virus replication.

    PubMed

    Gu, Haidong

    2016-02-12

    Herpes simplex virus 1 (HSV-1) is a ubiquitous human pathogen that establishes latent infection in ganglia neurons. Its unique life cycle requires a balanced "conquer and compromise" strategy to deal with the host anti-viral defenses. One of HSV-1 α (immediate early) gene products, infected cell protein 0 (ICP0), is a multifunctional protein that interacts with and modulates a wide range of cellular defensive pathways. These pathways may locate in different cell compartments, which then migrate or exchange factors upon stimulation, for the purpose of a concerted and effective defense. ICP0 is able to simultaneously attack multiple host pathways by either degrading key restrictive factors or modifying repressive complexes. This is a viral protein that contains an E3 ubiquitin ligase, translocates among different cell compartments and interacts with major defensive complexes. The multiple functional domains of ICP0 can work independently and at the same time coordinate with each other. Dissecting the functional domains of ICP0 and delineating the coordination of these domains will help us understand HSV-1 pathogenicity as well as host defense mechanisms. This article focuses on describing individual ICP0 domains, their biochemical properties and their implication in HSV-1 infection. By putting individual domain functions back into the picture of host anti-viral defense network, this review seeks to elaborate the complex interactions between HSV-1 and its host. PMID:26870669

  16. Infected cell protein 0 functional domains and their coordination in herpes simplex virus replication

    PubMed Central

    Gu, Haidong

    2016-01-01

    Herpes simplex virus 1 (HSV-1) is a ubiquitous human pathogen that establishes latent infection in ganglia neurons. Its unique life cycle requires a balanced “conquer and compromise” strategy to deal with the host anti-viral defenses. One of HSV-1 α (immediate early) gene products, infected cell protein 0 (ICP0), is a multifunctional protein that interacts with and modulates a wide range of cellular defensive pathways. These pathways may locate in different cell compartments, which then migrate or exchange factors upon stimulation, for the purpose of a concerted and effective defense. ICP0 is able to simultaneously attack multiple host pathways by either degrading key restrictive factors or modifying repressive complexes. This is a viral protein that contains an E3 ubiquitin ligase, translocates among different cell compartments and interacts with major defensive complexes. The multiple functional domains of ICP0 can work independently and at the same time coordinate with each other. Dissecting the functional domains of ICP0 and delineating the coordination of these domains will help us understand HSV-1 pathogenicity as well as host defense mechanisms. This article focuses on describing individual ICP0 domains, their biochemical properties and their implication in HSV-1 infection. By putting individual domain functions back into the picture of host anti-viral defense network, this review seeks to elaborate the complex interactions between HSV-1 and its host. PMID:26870669

  17. Molecular Dynamics Studies on the HIV-1 Integrase Catalytic Domain

    SciTech Connect

    Lins, Roberto D.; Briggs, J. M.; Straatsma, TP; Carlson, Heather A.; Greenwald, Jason; Choe, Senyon; Mccammon, Andy

    1999-06-30

    The HIV-1 integrase, which is essential for viral replication, catalyzes the insertion of viral DNA into the host chromosome, thereby recruiting host cell machinery into making viral proteins. It represents the third main HIV enzyme target for inhibitor design, the first two being the reverse transcriptase and the protease. Two 1-ns molecular dynamics simulations have been carried out on completely hydrated models of the HIV-1 integrase catalytic domain, one with no metal ions and another with one magnesium ion in the catalytic site. The simulations predict that the region of the active site that is missing in the published crystal structures has (at the time of this work) more secondary structure than previously thought. The flexibility of this region has been discussed with respect to the mechanistic function of the enzyme. The results of these simulations will be used as part of inhibitor design projects directed against the catalytic domain of the enzyme.

  18. Structure of NS1A effector domain from the influenza A/Udorn/72 virus

    SciTech Connect

    Xia, Shuangluo; Monzingo, Arthur F.; Robertus, Jon D.

    2009-01-01

    The structure of the effector domain of the influenza protein NS1, a validated antiviral drug target, has been solved in two space groups. The nonstructural protein NS1A from influenza virus is a multifunctional virulence factor and a potent inhibitor of host immunity. It has two functional domains: an N-terminal 73-amino-acid RNA-binding domain and a C-terminal effector domain. Here, the crystallographic structure of the NS1A effector domain of influenza A/Udorn/72 virus is presented. Structure comparison with the NS1 effector domain from mouse-adapted influenza A/Puerto Rico/8/34 (PR8) virus strain reveals a similar monomer conformation but a different dimer interface. Further analysis and evaluation shows that the dimer interface observed in the structure of the PR8 NS1 effector domain is likely to be a crystallographic packing effect. A hypothetical model of the intact NS1 dimer is presented.

  19. Frequency domain nonlinear optics

    NASA Astrophysics Data System (ADS)

    Legare, Francois

    2016-05-01

    The universal dilemma of gain narrowing occurring in fs amplifiers prevents ultra-high power lasers from delivering few-cycle pulses. This problem is overcome by a new amplification concept: Frequency domain Optical Parametric Amplification - FOPA. It enables simultaneous up-scaling of peak power and amplified spectral bandwidth and can be performed at any wavelength range of conventional amplification schemes, however, with the capability to amplify single cycles of light. The key idea for amplification of octave-spanning spectra without loss of spectral bandwidth is to amplify the broad spectrum ``slice by slice'' in the frequency domain, i.e. in the Fourier plane of a 4f-setup. The striking advantages of this scheme, are its capability to amplify (more than) one octave of bandwidth without shorting the corresponding pulse duration. This is because ultrabroadband phase matching is not defined by the properties of the nonlinear crystal employed but the number of crystals employed. In the same manner, to increase the output energy one simply has to increase the spectral extension in the Fourier plane and to add one more crystal. Thus, increasing pulse energy and shortening its duration accompany each other. A proof of principle experiment was carried out at ALLS on the sub-two cycle IR beam line and yielded record breaking performance in the field of few-cycle IR lasers. 100 μJ two-cycle pulses from a hollow core fibre compression setup were amplified to 1.43mJ without distorting spatial or temporal properties. Pulse duration at the input of FOPA and after FOPA remains the same. Recently, we have started upgrading this system to be pumped by 250 mJ to reach 40 mJ two-cycle IR few-cycle pulses and latest results will be presented at the conference. Furthermore, the extension of the concept of FOPA to other nonlinear optical processes will be discussed. Frequency domain nonlinear optics.

  20. On Probability Domains III

    NASA Astrophysics Data System (ADS)

    Frič, Roman; Papčo, Martin

    2015-12-01

    Domains of generalized probability have been introduced in order to provide a general construction of random events, observables and states. It is based on the notion of a cogenerator and the properties of product. We continue our previous study and show how some other quantum structures fit our categorical approach. We discuss how various epireflections implicitly used in the classical probability theory are related to the transition to fuzzy probability theory and describe the latter probability theory as a genuine categorical extension of the former. We show that the IF-probability can be studied via the fuzzy probability theory. We outline a "tensor modification" of the fuzzy probability theory.

  1. Host diversity begets parasite diversity: Bird final hosts and trematodes in snail intermediate hosts

    USGS Publications Warehouse

    Hechinger, R.F.; Lafferty, K.D.

    2005-01-01

    An unappreciated facet of biodiversity is that rich communities and high abundance may foster parasitism. For parasites that sequentially use different host species throughout complex life cycles, parasite diversity and abundance in 'downstream' hosts should logically increase with the diversity and abundance of 'upstream' hosts (which carry the preceding stages of parasites). Surprisingly, this logical assumption has little empirical support, especially regarding metazoan parasites. Few studies have attempted direct tests of this idea and most have lacked the appropriate scale of investigation. In two different studies, we used time-lapse videography to quantify birds at fine spatial scales, and then related bird communities to larval trematode communities in snail populations sampled at the same small spatial scales. Species richness, species heterogeneity and abundance of final host birds were positively correlated with species richness, species heterogeneity and abundance of trematodes in host snails. Such community-level interactions have rarely been demonstrated and have implications for community theory, epidemiological theory and ecosystem management. ?? 2005 The Royal Society.

  2. Transfer of high domain knowledge to a similar domain.

    PubMed

    Jessup, Ryan K

    2009-01-01

    Researchers have widely examined domain knowledge yet rarely investigate the transfer of knowledge from one domain to another. This study sought to fill in the literature gap concerning the impact of domain knowledge on memory in a similar situation. Specifically, this study examined whether high knowledge of baseball could enhance memory for the similar yet unknown domain of cricket, using a 2 (knowledge) x 2 (prime) design. An interaction occurred, indicating that when primed, baseball knowledge improves memory for cricket events in participants with high baseball knowledge but reduces memory in their low-knowledge counterparts. These results suggest that extensive knowledge in one domain allows it to serve as an organizational framework for incoming information in a similar domain; conversely, priming poorly understood domain knowledge results in negative transfer. PMID:19353932

  3. An internal thioester in a pathogen surface protein mediates covalent host binding.

    PubMed

    Walden, Miriam; Edwards, John M; Dziewulska, Aleksandra M; Bergmann, Rene; Saalbach, Gerhard; Kan, Su-Yin; Miller, Ona K; Weckener, Miriam; Jackson, Rosemary J; Shirran, Sally L; Botting, Catherine H; Florence, Gordon J; Rohde, Manfred; Banfield, Mark J; Schwarz-Linek, Ulrich

    2015-01-01

    To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a 'chemical harpoon'. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. PMID:26032562

  4. Host specificity and specialization in eriophyoid mites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We analyzed a database containing 3957 records of eriophyoid species and 7699 records of host plants. About 80% of eriophyoids were found on only one host plant species, 95% on hosts within one genus, and 99% on hosts within one family. Thus, most eriophyoid species are monophagous (feed on only on...

  5. Visual mimicry of host nestlings by cuckoos

    PubMed Central

    Langmore, Naomi E.; Stevens, Martin; Maurer, Golo; Heinsohn, Robert; Hall, Michelle L.; Peters, Anne; Kilner, Rebecca M.

    2011-01-01

    Coevolution between antagonistic species has produced instances of exquisite mimicry. Among brood-parasitic cuckoos, host defences have driven the evolution of mimetic eggs, but the evolutionary arms race was believed to be constrained from progressing to the chick stage, with cuckoo nestlings generally looking unlike host young. However, recent studies on bronze-cuckoos have confounded theoretical expectations by demonstrating cuckoo nestling rejection by hosts. Coevolutionary theory predicts reciprocal selection for visual mimicry of host young by cuckoos, although this has not been demonstrated previously. Here we show that, in the eyes of hosts, nestlings of three bronze-cuckoo species are striking visual mimics of the young of their morphologically diverse hosts, providing the first evidence that coevolution can select for visual mimicry of hosts in cuckoo chicks. Bronze-cuckoos resemble their own hosts more closely than other host species, but the accuracy of mimicry varies according to the diversity of hosts they exploit. PMID:21227972

  6. Host Event Based Network Monitoring

    SciTech Connect

    Jonathan Chugg

    2013-01-01

    The purpose of INL’s research on this project is to demonstrate the feasibility of a host event based network monitoring tool and the effects on host performance. Current host based network monitoring tools work on polling which can miss activity if it occurs between polls. Instead of polling, a tool could be developed that makes use of event APIs in the operating system to receive asynchronous notifications of network activity. Analysis and logging of these events will allow the tool to construct the complete real-time and historical network configuration of the host while the tool is running. This research focused on three major operating systems commonly used by SCADA systems: Linux, WindowsXP, and Windows7. Windows 7 offers two paths that have minimal impact on the system and should be seriously considered. First is the new Windows Event Logging API, and, second, Windows 7 offers the ALE API within WFP. Any future work should focus on these methods.

  7. Undiscovered Bat Hosts of Filoviruses.

    PubMed

    Han, Barbara A; Schmidt, John Paul; Alexander, Laura W; Bowden, Sarah E; Hayman, David T S; Drake, John M

    2016-07-01

    Ebola and other filoviruses pose significant public health and conservation threats by causing high mortality in primates, including humans. Preventing future outbreaks of ebolavirus depends on identifying wildlife reservoirs, but extraordinarily high biodiversity of potential hosts in temporally dynamic environments of equatorial Africa contributes to sporadic, unpredictable outbreaks that have hampered efforts to identify wild reservoirs for nearly 40 years. Using a machine learning algorithm, generalized boosted regression, we characterize potential filovirus-positive bat species with estimated 87% accuracy. Our model produces two specific outputs with immediate utility for guiding filovirus surveillance in the wild. First, we report a profile of intrinsic traits that discriminates hosts from non-hosts, providing a biological caricature of a filovirus-positive bat species. This profile emphasizes traits describing adult and neonate body sizes and rates of reproductive fitness, as well as species' geographic range overlap with regions of high mammalian diversity. Second, we identify several bat species ranked most likely to be filovirus-positive on the basis of intrinsic trait similarity with known filovirus-positive bats. New bat species predicted to be positive for filoviruses are widely distributed outside of equatorial Africa, with a majority of species overlapping in Southeast Asia. Taken together, these results spotlight several potential host species and geographical regions as high-probability targets for future filovirus surveillance. PMID:27414412

  8. AVTC Hosts TechnoCamp

    ERIC Educational Resources Information Center

    Miner, Brenda

    2006-01-01

    The Area Vo-Tech Center (AVTC) in Russellville, Arkansas, recently hosted its first TechnoCamp to encourage enrollment based on the aptitude and interest level of the students enrolling in the various programs. The center currently offers student enrollment in auto technology, computer engineering, cosmetology, construction technology, drafting…

  9. Undiscovered Bat Hosts of Filoviruses

    PubMed Central

    Schmidt, John Paul; Alexander, Laura W.; Bowden, Sarah E.; Hayman, David T. S.; Drake, John M.

    2016-01-01

    Ebola and other filoviruses pose significant public health and conservation threats by causing high mortality in primates, including humans. Preventing future outbreaks of ebolavirus depends on identifying wildlife reservoirs, but extraordinarily high biodiversity of potential hosts in temporally dynamic environments of equatorial Africa contributes to sporadic, unpredictable outbreaks that have hampered efforts to identify wild reservoirs for nearly 40 years. Using a machine learning algorithm, generalized boosted regression, we characterize potential filovirus-positive bat species with estimated 87% accuracy. Our model produces two specific outputs with immediate utility for guiding filovirus surveillance in the wild. First, we report a profile of intrinsic traits that discriminates hosts from non-hosts, providing a biological caricature of a filovirus-positive bat species. This profile emphasizes traits describing adult and neonate body sizes and rates of reproductive fitness, as well as species’ geographic range overlap with regions of high mammalian diversity. Second, we identify several bat species ranked most likely to be filovirus-positive on the basis of intrinsic trait similarity with known filovirus-positive bats. New bat species predicted to be positive for filoviruses are widely distributed outside of equatorial Africa, with a majority of species overlapping in Southeast Asia. Taken together, these results spotlight several potential host species and geographical regions as high-probability targets for future filovirus surveillance. PMID:27414412

  10. Biosignatures of Pathogen and Host

    SciTech Connect

    Fitch, J P; Chromy, B A; Forde, C E; Garcia, E; Gardner, S N; Gu, P P; Kuczmarksi, T A; Melius, C F; McCutchen-Maloney, S L; Milanovich, F P; Motin, V L; Ott, L L; Quong, A A; Quong, J N; Rocco, J M; Slezak, T R; Sokhansanj, B A; Vitalis, E A; Zemla, A T; McCready, P M

    2002-08-27

    In information theory, a signature is characterized by the information content as well as noise statistics of the communication channel. Biosignatures have analogous properties. A biosignature can be associated with a particular attribute of a pathogen or a host. However, the signature may be lost in backgrounds of similar or even identical signals from other sources. In this paper, we highlight statistical and signal processing challenges associated with identifying good biosignatures for pathogens in host and other environments. In some cases it may be possible to identify useful signatures of pathogens through indirect but amplified signals from the host. Discovery of these signatures requires new approaches to modeling and data interpretation. For environmental biosignal collections, it is possible to use signal processing techniques from other applications (e.g., synthetic aperture radar) to track the natural progression of microbes over large areas. We also present a computer-assisted approach to identify unique nucleic-acid based microbial signatures. Finally, an understanding of host-pathogen interactions will result in better detectors as well as opportunities in vaccines and therapeutics.

  11. Cellular Host Responses to Gliomas

    PubMed Central

    Barish, Michael E.; Garcia, Elizabeth; Metz, Marianne Z.; Myers, Sarah M.; Gutova, Margarita; Frank, Richard T.; Miletic, Hrvoje; Kendall, Stephen E.; Glackin, Carlotta A.; Bjerkvig, Rolf; Aboody, Karen S.

    2012-01-01

    Background Glioblastoma multiforme (GBM) is the most aggressive type of malignant primary brain tumors in adults. Molecular and genetic analysis has advanced our understanding of glioma biology, however mapping the cellular composition of the tumor microenvironment is crucial for understanding the pathology of this dreaded brain cancer. In this study we identified major cell populations attracted by glioma using orthotopic rodent models of human glioma xenografts. Marker-specific, anatomical and morphological analyses revealed a robust influx of host cells into the main tumor bed and tumor satellites. Methodology/Principal Findings Human glioma cell lines and glioma spheroid orthotopic implants were used in rodents. In both models, the xenografts recruited large numbers of host nestin-expressing cells, which formed a ‘network’ with glioma. The host nestin-expressing cells appeared to originate in the subventricular zone ipsilateral to the tumor, and were clearly distinguishable from pericytes that expressed smooth muscle actin. These distinct cell populations established close physical contact in a ‘pair-wise’ manner and migrated together to the deeper layers of tumor satellites and gave rise to tumor vasculature. The GBM biopsy xenografts displayed two different phenotypes: (a) low-generation tumors (first in vivo passage in rats) were highly invasive and non-angiogenic, and host nestin-positive cells that infiltrated into these tumors displayed astrocytic or elongated bipolar morphology; (b) high-generation xenografts (fifth passage) had pronounced cellularity, were angiogenic with ‘glomerulus-like’ microvascular proliferations that contained host nestin-positive cells. Stromal cell-derived factor-1 and its receptor CXCR4 were highly expressed in and around glioma xenografts, suggesting their role in glioma progression and invasion. Conclusions/Significance Our data demonstrate a robust migration of nestin-expressing host cells to glioma, which

  12. STAS Domain Structure and Function

    PubMed Central

    Sharma, Alok K.; Rigby, Alan C.; Alper, Seth L.

    2011-01-01

    Pendrin shares with nearly all SLC26/SulP anion transporters a carboxy-terminal cytoplasmic segment organized around a Sulfate Transporter and Anti-Sigma factor antagonist (STAS) domain. STAS domains of divergent amino acid sequence exhibit a conserved fold of 4 β strands interspersed among 5 α helices. The first STAS domain proteins studied were single-domain anti-sigma factor antagonists (anti-anti-σ). These anti-anti-σ indirectly stimulate bacterial RNA polymerase by inactivating inhibitory anti-σ kinases, liberating σ factors to direct specific transcription of target genes or operons. Some STAS domains are nucleotide-binding phosphoproteins or nucleotidases. Others are interaction/transduction modules within multidomain sensors of light, oxygen and other gasotransmitters, cyclic nucleotides, inositol phosphates, and G proteins. Additional multidomain STAS protein sequences suggest functions in sensing, metabolism, or transport of nutrients such as sugars, amino acids, lipids, anions, vitamins, or hydrocarbons. Still other multidomain STAS polypeptides include histidine and serine/threonine kinase domains and ligand-activated transcription factor domains. SulP/SLC26 STAS domains and adjacent sequences interact with other transporters, cytoskeletal scaffolds, and with enzymes metabolizing transported anion substrates, forming putative metabolons. STAS domains are central to membrane targeting of many SulP/SLC26 anion transporters, and STAS domain mutations are associated with at least three human recessive diseases. This review summarizes STAS domain structure and function. PMID:22116355

  13. Host Cell Factors in Filovirus Entry: Novel Players, New Insights

    PubMed Central

    Hofmann-Winkler, Heike; Kaup, Franziska; Pöhlmann, Stefan

    2012-01-01

    Filoviruses cause severe hemorrhagic fever in humans with high case-fatality rates. The cellular factors exploited by filoviruses for their spread constitute potential targets for intervention, but are incompletely defined. The viral glycoprotein (GP) mediates filovirus entry into host cells. Recent studies revealed important insights into the host cell molecules engaged by GP for cellular entry. The binding of GP to cellular lectins was found to concentrate virions onto susceptible cells and might contribute to the early and sustained infection of macrophages and dendritic cells, important viral targets. Tyrosine kinase receptors were shown to promote macropinocytic uptake of filoviruses into a subset of susceptible cells without binding to GP, while interactions between GP and human T cell Ig mucin 1 (TIM-1) might contribute to filovirus infection of mucosal epithelial cells. Moreover, GP engagement of the cholesterol transporter Niemann-Pick C1 was demonstrated to be essential for GP-mediated fusion of the viral envelope with a host cell membrane. Finally, mutagenic and structural analyses defined GP domains which interact with these host cell factors. Here, we will review the recent progress in elucidating the molecular interactions underlying filovirus entry and discuss their implications for our understanding of the viral cell tropism. PMID:23342362

  14. Pathogens and host immunity in the ancient human oral cavity

    PubMed Central

    Warinner, Christina; Matias Rodrigues, João F.; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y.; Tito, Raul Y.; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C.; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars; Samaniego Castruita, José Alfredo; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian; Olsen, Jesper V.; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M.; Collins, Matthew J.; Gilbert, M. Thomas P.; Rühli, Frank; Cappellini, Enrico

    2014-01-01

    Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize: (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) the first evidence of ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, “red-complex” pathogens, and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity, and diet, thereby extending the direct investigation of common diseases into the human evolutionary past. PMID:24562188

  15. Pathogens and host immunity in the ancient human oral cavity.

    PubMed

    Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars H; Castruita, José Alfredo Samaniego; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian D; Olsen, Jesper V; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M; Collins, Matthew J; Gilbert, M Thomas P; Rühli, Frank; Cappellini, Enrico

    2014-04-01

    Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past. PMID:24562188

  16. Protecting software agents from malicious hosts using quantum computing

    NASA Astrophysics Data System (ADS)

    Reisner, John; Donkor, Eric

    2000-07-01

    We evaluate how quantum computing can be applied to security problems for software agents. Agent-based computing, which merges technological advances in artificial intelligence and mobile computing, is a rapidly growing domain, especially in applications such as electronic commerce, network management, information retrieval, and mission planning. System security is one of the more eminent research areas in agent-based computing, and the specific problem of protecting a mobile agent from a potentially hostile host is one of the most difficult of these challenges. In this work, we describe our agent model, and discuss the capabilities and limitations of classical solutions to the malicious host problem. Quantum computing may be extremely helpful in addressing the limitations of classical solutions to this problem. This paper highlights some of the areas where quantum computing could be applied to agent security.

  17. Legionella pneumophila glucosyltransferase inhibits host elongation factor 1A

    PubMed Central

    Belyi, Yury; Niggeweg, Ricarda; Opitz, Bastian; Vogelsgesang, Martin; Hippenstiel, Stefan; Wilm, Matthias; Aktories, Klaus

    2006-01-01

    Legionella pneumophila, the causal agent of Legionnaires' disease, is an intracellular parasite and invades and proliferates within different eukaryotic cells, including human alveolar macrophages. After several 100-fold multiplication within host cells, the pathogens are released for new invasion by induction of apoptosis or necrosis. Here we report that L. pneumophila produces a glucosyltransferase, which selectively modifies an ≈50-kDa mammalian protein by using UDP-glucose as a cosubstrate. MS analysis identified the protein substrate as the mammalian elongation factor (EF)1A. Legionella glucosyltransferase modifies its eukaryotic protein substrate at serine-53, which is located in the GTPase domain of the EF. Glucosylation of EF1A results in inhibition of eukaryotic protein synthesis and death of target cells. Our findings show a mode of inhibition of protein synthesis by microbial pathogens and offer a perspective for understanding of the host-pathogen interaction of L. pneumophila. PMID:17068130

  18. MPEG-4 AVC domain watermarking transparency

    NASA Astrophysics Data System (ADS)

    Duta, S.; Mitrea, M.; Prêteux, F.; Belhaj, M.

    2008-04-01

    The ever-increasing Internet distribution of video content is echoed in ever-increasing efforts to devise systems balancing copyright protection and user rights. Watermarking is such an example: by persistently and imperceptibly associating some data with the host video, it offers at the same time a reliable and user-friendly solution for copyright infringement tracking. This paper takes a closer look at the apparent contradiction between watermarking (using the visual redundancy of the video to embed the data) and compression (eliminating the visual redundancy in order to speed up distribution and to alleviate storage requirements). In this respect, the viability of compressed domain watermarking is evaluated by analysing the visual effects of the MPEG-4 AVC stream alteration. The corpus consists of 10 video sequences of about 25 minutes each, coded at 256kbps and 64 kbps.

  19. Multiple effects of host-species diversity on coexisting host-specific and host-opportunistic microbes.

    PubMed

    Kedem, Hadar; Cohen, Carmit; Messika, Irit; Einav, Monica; Pilosof, Shai; Hawlena, Hadas

    2014-05-01

    While host-species diversity often influences microbial prevalence, there may be multiple mechanisms causing such effects that may also depend on the foraging strategy of the microbes. We employed a natural gradient of rodent-species richness to examine competing hypotheses describing possible mechanisms mediating the relationship between host-species richness and the prevalence of the most dominant microbes, along with microbe specificity to the different rodent host species. We sampled blood from three gerbil species in plots differing in terms of the proportion of the different species and screened for the most dominant bacteria. Two dominant bacterial lineages were detected: host-specific bacteria and host-opportunistic bacteria. Using a model selection approach, we detected evidence for both direct and indirect effects of host-species richness on the prevalence of these bacteria. Infection probability of the host-specific lineage was lower in richer host communities, most likely due to increased frequency and density of the least suitable host species. In contrast, field observations suggest that the effect of host-species richness on infection probability of the opportunistic lineage was both direct and indirect, mostly mediated by changes in flea densities on the host and by the presence of the host-specific lineage. Our results thus suggest that host-species richness has multiple effects on microbial prevalence, depending on the degree of host-specificity of the microbe in question. PMID:25000749

  20. Beyond the Number Domain

    PubMed Central

    Cantlon, Jessica F.; Platt, Michael L.; Brannon, Elizabeth M.

    2009-01-01

    In a world without numbers, we would be unable to build a skyscraper, hold a national election, plan a wedding, or pay for a chicken at the market. The numerical symbols used in all these behaviors build on the approximate number system (ANS) which represents the number of discrete objects or events as a continuous mental magnitude. In this review, we first discuss evidence that the ANS bears a set of behavioral and brain signatures that are universally displayed across animal species, human cultures, and development. We then turn to the question of whether the ANS constitutes a specialized cognitive and neural domain--a question central to understanding how this system works, the nature of its evolutionary and developmental trajectory, and its physical instantiation in the brain. PMID:19131268

  1. Crystallization of PTP Domains.

    PubMed

    Levy, Colin; Adams, James; Tabernero, Lydia

    2016-01-01

    Protein crystallography is the most powerful method to obtain atomic resolution information on the three-dimensional structure of proteins. An essential step towards determining the crystallographic structure of a protein is to produce good quality crystals from a concentrated sample of purified protein. These crystals are then used to obtain X-ray diffraction data necessary to determine the 3D structure by direct phasing or molecular replacement if the model of a homologous protein is available. Here, we describe the main approaches and techniques to obtain suitable crystals for X-ray diffraction. We include tools and guidance on how to evaluate and design the protein construct, how to prepare Se-methionine derivatized protein, how to assess the stability and quality of the sample, and how to crystallize and prepare crystals for diffraction experiments. While general strategies for protein crystallization are summarized, specific examples of the application of these strategies to the crystallization of PTP domains are discussed. PMID:27514806

  2. Parasites, immunology of hosts, and host sexual selection.

    PubMed

    Møller, A P; Saino, N

    1994-12-01

    Parasite-mediated sexual selection is reviewed with special emphasis on the bird literature. Choosy females may benefit from choosing parasite-free mates if such males provide better parental care, do not transmit contagious parasites, or provide resistance genes to offspring. There is evidence in support of each of these mechanisms. The immunocompetence handicap hypothesis posits that secondary sexual characters reliably reveal the ability of males to resist parasites due to the immunosuppressive effects of testosterone and other biochemicals. Several aspects of these negative feedback mechanisms are supported by laboratory studies, but evidence from free-living animals is almost completely absent. Corticosterone rather than testosterone may potentially mediate the immunocompetence handicap mechanism. A simple version of the immunocompetence handicap is developed suggesting that body condition of male hosts is a sufficient mediator of the handicap mechanism of reliable sexual signaling. Sexual selection appears to be more intense in sexually dichromatic bird species, and comparative studies using pairwise comparisons of closely related taxa reveal that sexually dichromatic bird species have larger spleens, larger bursa of Fabricius, and higher concentrations of leukocytes than monochromatic species. Parasite-mediated sexual selection is proposed to affect parasite biology by increasing (1) the variance-to-mean ratio in parasite abundance, (2) variance in the intensity of natural selection affecting hosts, and (3) speciation rates among parasites exploiting hosts subject to intense sexual selection as compared to those subject to less intense selection. PMID:7799157

  3. Location of Host and Host Habitat by Fruit Fly Parasitoids

    PubMed Central

    Quilici, Serge; Rousse, Pascal

    2012-01-01

    Augmentative releases of parasitoids may be a useful tool for the area-wide management of tephritid pests. The latter are parasitized by many wasp species, though only a few of them are relevant for augmentative biocontrol purposes. To date, nearly all the actual or potential biocontrol agents for such programs are egg or larval Opiinae parasitoids (Hymenoptera: Braconidae). Here, we review the literature published on their habitat and host location behavior, as well as the factors that modulate this behavior, which is assumed to be sequential; parasitoids forage first for the host habitat and then for the host itself. Parasitoids rely on chemical, visual, and mechanical stimuli, often strongly related to their ecology. Behavioral modulation factors include biotic and abiotic factors including learning, climatic conditions and physiological state of the insect. Finally, conclusions and perspectives for future research are briefly highlighted. A detailed knowledge of this behavior may be very useful for selecting the release sites for both inundative/augmentative releases of mass-reared parasitoids and inoculative releases for classical biocontrol. PMID:26466736

  4. Twinning, Epitaxy and Domain Switching in Ferroelastic Inclusion Compounds

    NASA Technical Reports Server (NTRS)

    Hollingsworth, Mark D.; Peterson, Matthew L.

    2003-01-01

    Our research is in the area of solid-state organic chemistry, which lies at the interface between physical organic chemistry and materials science. We use crystalline solids as models to probe fundamental issues about physical processes, molecular interactions and chemical reactions that are important for fabrication, stabilization and application of technological materials. Much of our most recent work has focused on the phenomena of ferroelastic and ferroelectric domain switching, in which application of an external force or electric field to a crystal causes the molecules inside the crystal to reorient, in tandem, to a new orientational state. To better understand and control the domain switching process, we have designed and synthesized over twenty closely related, ferroelastic organic crystals. Our approach has been to use crystalline inclusion compounds, in which one molecule (the guest) is trapped within the crystalline framework of a second molecule (the host). By keeping the host constant and varying the proportions and kinds of guests, it has been possible to tailor these materials so that domain switching is rapid and reversible (which is desirable for high technology applications). Inclusion compounds therefore serve as powerful systems for understanding the specific molecular mechanisms that control domain switching.

  5. Identification of sequence motifs involved in Dengue virus-host interactions.

    PubMed

    Asnet Mary, J; Paramasivan, R; Shenbagarathai, R

    2016-03-01

    Dengue fever is a rapidly spreading mosquito-borne virus infection, which remains a serious global public health problem. As there is no specific treatment or commercial vaccine available for effective control of the disease, the attempts on developing novel control strategies are underway. Viruses utilize the surface receptor proteins of host to enter into the cells. Though various proteins were said to be receptors of Dengue virus (DENV) using Virus Overlay Protein Binding Assay, the precise interaction between DENV and host is not explored. Understanding the structural features of domain III envelope glycoprotein would help in developing efficient antiviral inhibitors. Therefore, an attempt was made to identify the sequence motifs present in domain III envelope glycoprotein of Dengue virus. Computational analysis revealed that the NGR motif is present in the domain III envelope glycoprotein of DENV-1 and DENV-3. Similarly, DENV-1, DENV-2 and DENV-4 were found to contain Yxxphi motif which is a tyrosine-based sorting signal responsible for the interaction with a mu subunit of adaptor protein complex. High-throughput virtual screening resulted in five compounds as lead molecules based on glide score, which ranges from -4.664 to -6.52 kcal/Mol. This computational prediction provides an additional tool for understanding the virus-host interactions and helps to identify potential targets in the host. Further, experimental evidence is warranted to confirm the virus-host interactions and also inhibitory activity of reported lead compounds. PMID:25905427

  6. Tandem immunoprecipitation approach to identify HIV-1 Gag associated host factors.

    PubMed

    Gao, Wei; Li, Min; Zhang, Jingxin

    2014-07-01

    HIV-1 Gag by itself is able to assemble and release from host cells and thus serves as a simplified model to identify host factors involved in this stage of the HIV-1 life cycle. In this study, a tandem immunoprecipitation approach is taken to immunoprecipitate Gag-interacting host proteins from transfected 293T cells. It is demonstrated that with the tandem immunoprecipitation method Gag-interacting host factors can be precipitated more efficiently than by single-step immunoprecipitation. Gag proteins are found to interact with multiple RNA-binding proteins such as hnRNPs, nucleolin, EF1a and ribosomal proteins. Such interactions are mediated by cellular RNAs and the Gag Nuclear Capsid (NC) domain. Deletion of the NC domain results in removal of most of the RNA-binding proteins, as well as a reduction of the Gag releasing capability, which can be restored by replacing the deleted NC domain with another multimerization motif. Importantly, interactions between Gag and host factors are relevant functionally, as evidenced by significantly increased nucleolin protein in the cytoplasm where it is recruited into the Gag complex, and enhanced Gag release when nucleolin is over-expressed. PMID:24690621

  7. WAP domain proteins as modulators of mucosal immunity.

    PubMed

    Wilkinson, Thomas S; Roghanian, Ali; Simpson, Alexander John; Sallenave, Jean-Michel

    2011-10-01

    WAP (whey acidic protein) is an important whey protein present in milk of mammals. This protein has characteristic domains, rich in cysteine residues, called 4-DSC (four-disulfide core domain). Other proteins, mainly present at mucosal surfaces, have been shown to also possess these characteristic WAP-4-DSC domains. The present review will focus on two WAP-4-DSC containing proteins, namely SLPI (secretory leucocyte protease inhibitor) and trappin-2/elafin. Although first described as antiproteases able to inhibit in particular host neutrophil proteases [NE (neutrophil elastase), cathepsin-G and proteinase-3] and as such, able to limit maladaptive tissue damage during inflammation, it has become apparent that these molecules have a variety of other functions (direct antimicrobial activity, bacterial opsonization, induction of adaptive immune responses, promotion of tissue repair, etc.). After providing information about the 'classical' antiproteasic role of these molecules, we will discuss the evidence pertaining to their pleiotropic functions in inflammation and immunity. PMID:21936824

  8. AGN and their host galaxies

    NASA Astrophysics Data System (ADS)

    Steinborn, L. K.; Dolag, K.; Hirschmann, M.; Remus, R.-S.; Teklu, A. F.

    2016-06-01

    Large scale cosmological hydrodynamic simulations are an important tool to study the co-evolution between black holes (BHs) and their host galaxies. However, in order to model the accretion onto BHs and AGN feedback we need sub-grid models which contain several free parameters. The choice of these parameters has a significant impact on the properties of the BHs and their host galaxies. Therefore, we improve the accretion model and the AGN feedback model based on both theory and observations to eliminate most free parameters. In that way, the slope of the observed relation between BH mass and stellar mass is reproduced self-consistently. We performed a few extremely large simulation runs as part of the Magneticum Pathfinder simulation set, combining a high resolution with very large cosmological volumes, enabling us to study for example dual AGN, the role of galaxy mergers and AGN clustering properties.

  9. Exoplanets and their Host Stars

    NASA Astrophysics Data System (ADS)

    Schmitt, J.

    2016-06-01

    Among the most fundamental astrophysical discoveries are clearly the detections of many thousands of ``extrasolar'' planets orbiting their hosts. The majority of these new planetary systems have properties dramatically different from those in our solar system. The large distances to extrasolar planets imply that they can only be observed together with their hosts. Modern observations have shown that stars and planets are not merely accidental celestial neighbors bound by the force of gravity, rather they influence each other in a variety of ways. This also and specifically applies to the X-ray properties of exoplanet systems which I will review in my talk and give some ideas for future work in this area.

  10. Host thin films incorporating nanoparticles

    NASA Astrophysics Data System (ADS)

    Qureshi, Uzma

    The focus of this research project was the investigation of the functional properties of thin films that incorporate a secondary nanoparticulate phase. In particular to assess if the secondary nanoparticulate material enhanced a functional property of the coating on glass. In order to achieve this, new thin film deposition methods were developed, namely use of nanopowder precursors, an aerosol assisted transport technique and an aerosol into atmospheric pressure chemical vapour deposition system. Aerosol assisted chemical vapour deposition (AACVD) was used to deposit 8 series of thin films on glass. Five different nanoparticles silver, gold, ceria, tungsten oxide and zinc oxide were tested and shown to successfully deposit thin films incorporating nanoparticles within a host matrix. Silver nanoparticles were synthesised and doped within a titania film by AACVD. This improved solar control properties. A unique aerosol assisted chemical vapour deposition (AACVD) into atmospheric pressure chemical vapour deposition (APCVD) system was used to deposit films of Au nanoparticles and thin films of gold nanoparticles incorporated within a host titania matrix. Incorporation of high refractive index contrast metal oxide particles within a host film altered the film colour. The key goal was to test the potential of nanopowder forms and transfer the suspended nanopowder via an aerosol to a substrate in order to deposit a thin film. Discrete tungsten oxide nanoparticles or ceria nanoparticles within a titanium dioxide thin film enhanced the self-cleaning and photo-induced super-hydrophilicity. The nanopowder precursor study was extended by deposition of zinc oxide thin films incorporating Au nanoparticles and also ZnO films deposited from a ZnO nanopowder precursor. Incorporation of Au nanoparticles within a VO: host matrix improved the thermochromic response, optical and colour properties. Composite VC/TiC and Au nanoparticle/V02/Ti02 thin films displayed three useful

  11. Multifunctionalities driven by ferroic domains

    SciTech Connect

    Yang, J. C.; Huang, Y. L.; Chu, Y. H.; He, Q.

    2014-08-14

    Considerable attention has been paid to ferroic systems in pursuit of advanced applications in past decades. Most recently, the emergence and development of multiferroics, which exhibit the coexistence of different ferroic natures, has offered a new route to create functionalities in the system. In this manuscript, we step from domain engineering to explore a roadmap for discovering intriguing phenomena and multifunctionalities driven by periodic domain patters. As-grown periodic domains, offering exotic order parameters, periodic local perturbations and the capability of tailoring local spin, charge, orbital and lattice degrees of freedom, are introduced as modeling templates for fundamental studies and novel applications. We discuss related significant findings on ferroic domain, nanoscopic domain walls, and conjunct heterostructures based on the well-organized domain patterns, and end with future prospects and challenges in the field.

  12. Bats host major mammalian paramyxoviruses

    PubMed Central

    Drexler, Jan Felix; Corman, Victor Max; Müller, Marcel Alexander; Maganga, Gael Darren; Vallo, Peter; Binger, Tabea; Gloza-Rausch, Florian; Rasche, Andrea; Yordanov, Stoian; Seebens, Antje; Oppong, Samuel; Sarkodie, Yaw Adu; Pongombo, Célestin; Lukashev, Alexander N.; Schmidt-Chanasit, Jonas; Stöcker, Andreas; Carneiro, Aroldo José Borges; Erbar, Stephanie; Maisner, Andrea; Fronhoffs, Florian; Buettner, Reinhard; Kalko, Elisabeth K.V.; Kruppa, Thomas; Franke, Carlos Roberto; Kallies, René; Yandoko, Emmanuel R.N.; Herrler, Georg; Reusken, Chantal; Hassanin, Alexandre; Krüger, Detlev H.; Matthee, Sonja; Ulrich, Rainer G.; Leroy, Eric M.; Drosten, Christian

    2012-01-01

    The large virus family Paramyxoviridae includes some of the most significant human and livestock viruses, such as measles-, distemper-, mumps-, parainfluenza-, Newcastle disease-, respiratory syncytial virus and metapneumoviruses. Here we identify an estimated 66 new paramyxoviruses in a worldwide sample of 119 bat and rodent species (9,278 individuals). Major discoveries include evidence of an origin of Hendra- and Nipah virus in Africa, identification of a bat virus conspecific with the human mumps virus, detection of close relatives of respiratory syncytial virus, mouse pneumonia- and canine distemper virus in bats, as well as direct evidence of Sendai virus in rodents. Phylogenetic reconstruction of host associations suggests a predominance of host switches from bats to other mammals and birds. Hypothesis tests in a maximum likelihood framework permit the phylogenetic placement of bats as tentative hosts at ancestral nodes to both the major Paramyxoviridae subfamilies (Paramyxovirinae and Pneumovirinae). Future attempts to predict the emergence of novel paramyxoviruses in humans and livestock will have to rely fundamentally on these data. PMID:22531181

  13. Bats host major mammalian paramyxoviruses.

    PubMed

    Drexler, Jan Felix; Corman, Victor Max; Müller, Marcel Alexander; Maganga, Gael Darren; Vallo, Peter; Binger, Tabea; Gloza-Rausch, Florian; Cottontail, Veronika M; Rasche, Andrea; Yordanov, Stoian; Seebens, Antje; Knörnschild, Mirjam; Oppong, Samuel; Adu Sarkodie, Yaw; Pongombo, Célestin; Lukashev, Alexander N; Schmidt-Chanasit, Jonas; Stöcker, Andreas; Carneiro, Aroldo José Borges; Erbar, Stephanie; Maisner, Andrea; Fronhoffs, Florian; Buettner, Reinhard; Kalko, Elisabeth K V; Kruppa, Thomas; Franke, Carlos Roberto; Kallies, René; Yandoko, Emmanuel R N; Herrler, Georg; Reusken, Chantal; Hassanin, Alexandre; Krüger, Detlev H; Matthee, Sonja; Ulrich, Rainer G; Leroy, Eric M; Drosten, Christian

    2012-01-01

    The large virus family Paramyxoviridae includes some of the most significant human and livestock viruses, such as measles-, distemper-, mumps-, parainfluenza-, Newcastle disease-, respiratory syncytial virus and metapneumoviruses. Here we identify an estimated 66 new paramyxoviruses in a worldwide sample of 119 bat and rodent species (9,278 individuals). Major discoveries include evidence of an origin of Hendra- and Nipah virus in Africa, identification of a bat virus conspecific with the human mumps virus, detection of close relatives of respiratory syncytial virus, mouse pneumonia- and canine distemper virus in bats, as well as direct evidence of Sendai virus in rodents. Phylogenetic reconstruction of host associations suggests a predominance of host switches from bats to other mammals and birds. Hypothesis tests in a maximum likelihood framework permit the phylogenetic placement of bats as tentative hosts at ancestral nodes to both the major Paramyxoviridae subfamilies (Paramyxovirinae and Pneumovirinae). Future attempts to predict the emergence of novel paramyxoviruses in humans and livestock will have to rely fundamentally on these data. PMID:22531181

  14. Nucleation of holin domains and holes optimizes lysis timing of E. coli by phage λ

    NASA Astrophysics Data System (ADS)

    Ryan, Gillian; Rutenberg, Andrew

    2007-03-01

    Holin proteins regulate the precise scheduling of Escherichia coli lysis during infection by bacteriophage λ. Inserted into the host bacterium's inner membrane during infection, holins aggregate to form rafts and then holes within those rafts. We present a two-stage nucleation model of holin action, with the nucleation of condensed holin domains followed by the nucleation of holes within these domains. Late nucleation of holin rafts leads to a weak dependence of lysis timing on host cell size, though both nucleation events contribute equally to timing errors. Our simulations recover the accurate scheduling observed experimentally, and also suggest that phage-λ lysis of E.coli is optimized.

  15. Domain topology and domain switching kinetics in a hybrid improper ferroelectric

    PubMed Central

    Huang, F. -T.; Xue, F.; Gao, B.; Wang, L. H.; Luo, X.; Cai, W.; Lu, X. -Z.; Rondinelli, J. M.; Chen, L. Q.; Cheong, S. -W.

    2016-01-01

    Charged polar interfaces such as charged ferroelectric walls or heterostructured interfaces of ZnO/(Zn,Mg)O and LaAlO3/SrTiO3, across which the normal component of electric polarization changes suddenly, can host large two-dimensional conduction. Charged ferroelectric walls, which are energetically unfavourable in general, were found to be mysteriously abundant in hybrid improper ferroelectric (Ca,Sr)3Ti2O7 crystals. From the exploration of antiphase boundaries in bilayer-perovskites, here we discover that each of four polarization-direction states is degenerate with two antiphase domains, and these eight structural variants form a Z4 × Z2 domain structure with Z3 vortices and five distinct types of domain walls, whose topology is directly relevant to the presence of abundant charged walls. We also discover a zipper-like nature of antiphase boundaries, which are the reversible creation/annihilation centres of pairs of two types of ferroelectric walls (and also Z3-vortex pairs) in 90° and 180° polarization switching. Our results demonstrate the unexpectedly rich nature of hybrid improper ferroelectricity. PMID:27215944

  16. Domain topology and domain switching kinetics in a hybrid improper ferroelectric.

    PubMed

    Huang, F-T; Xue, F; Gao, B; Wang, L H; Luo, X; Cai, W; Lu, X-Z; Rondinelli, J M; Chen, L Q; Cheong, S-W

    2016-01-01

    Charged polar interfaces such as charged ferroelectric walls or heterostructured interfaces of ZnO/(Zn,Mg)O and LaAlO3/SrTiO3, across which the normal component of electric polarization changes suddenly, can host large two-dimensional conduction. Charged ferroelectric walls, which are energetically unfavourable in general, were found to be mysteriously abundant in hybrid improper ferroelectric (Ca,Sr)3Ti2O7 crystals. From the exploration of antiphase boundaries in bilayer-perovskites, here we discover that each of four polarization-direction states is degenerate with two antiphase domains, and these eight structural variants form a Z4 × Z2 domain structure with Z3 vortices and five distinct types of domain walls, whose topology is directly relevant to the presence of abundant charged walls. We also discover a zipper-like nature of antiphase boundaries, which are the reversible creation/annihilation centres of pairs of two types of ferroelectric walls (and also Z3-vortex pairs) in 90° and 180° polarization switching. Our results demonstrate the unexpectedly rich nature of hybrid improper ferroelectricity. PMID:27215944

  17. Dynamical domain wall and localization

    NASA Astrophysics Data System (ADS)

    Toyozato, Yuta; Higuchi, Masafumi; Nojiri, Shin'ichi

    2016-03-01

    Based on the previous works (Toyozato et al., 2013 [24]; Higuchi and Nojiri, 2014 [25]), we investigate the localization of the fields on the dynamical domain wall, where the four-dimensional FRW universe is realized on the domain wall in the five-dimensional space-time. Especially we show that the chiral spinor can localize on the domain wall, which has not been succeeded in the past works as the seminal work in George et al. (2009) [23].

  18. Domain transfer multiple kernel learning.

    PubMed

    Duan, Lixin; Tsang, Ivor W; Xu, Dong

    2012-03-01

    Cross-domain learning methods have shown promising results by leveraging labeled patterns from the auxiliary domain to learn a robust classifier for the target domain which has only a limited number of labeled samples. To cope with the considerable change between feature distributions of different domains, we propose a new cross-domain kernel learning framework into which many existing kernel methods can be readily incorporated. Our framework, referred to as Domain Transfer Multiple Kernel Learning (DTMKL), simultaneously learns a kernel function and a robust classifier by minimizing both the structural risk functional and the distribution mismatch between the labeled and unlabeled samples from the auxiliary and target domains. Under the DTMKL framework, we also propose two novel methods by using SVM and prelearned classifiers, respectively. Comprehensive experiments on three domain adaptation data sets (i.e., TRECVID, 20 Newsgroups, and email spam data sets) demonstrate that DTMKL-based methods outperform existing cross-domain learning and multiple kernel learning methods. PMID:21646679

  19. Hydrophilic Domains Enhance Nanobubble Stability.

    PubMed

    Nishiyama, Takashi; Takahashi, Koji; Ikuta, Tatsuya; Yamada, Yutaka; Takata, Yasuyuki

    2016-05-18

    Highly stable nanoscale gas states at solid/liquid interfaces, referred to as nanobubbles, have been widely studied for over a decade. In this study, nanobubbles generated on a hydrophobic Teflon amorphous fluoroplastic thin film in the presence and absence of hydrophilic carbon domains are investigated by peak force quantitative nanomechanics. On the hydrophobic surface without hydrophilic domains, a small number of nanobubbles are generated and then rapidly decrease in size. On the hydrophobic surface with hydrophilic domains, the hydrophilic domains have a significant effect on the generation and stability of nanobubbles, with bubbles remaining on the surface for up to three days. PMID:26864857

  20. Conformational Analysis of Isolated Domains of Helicobacter pylori CagA

    PubMed Central

    Alonso, Hernan; Saijo-Hamano, Yumiko; Kwok, Terry; Roujeinikova, Anna

    2013-01-01

    The CagA protein of Helicobacter pylori is associated with increased virulence and gastric cancer risk. CagA is translocated into the host cell by a H. pylori type IV secretion system via mechanisms that are poorly understood. Translocated CagA interacts with numerous host factors, altering a variety of host signalling pathways. The recently determined crystal structure of C-terminally-truncated CagA indicated the presence of two domains: the smaller, flexible N-terminal domain and the larger, middle domain. In this study, we have investigated the conformation, oligomeric state and stability of the N-terminal, middle and glutamate-proline-isoleucine-tyrosine-alanine (EPIYA)-repeats domains. All three domains are monomeric, suggesting that the multimerisation of CagA observed in infected cells is likely to be mediated not by CagA itself but by its interacting partners. The middle and the C-terminal domains, but not the N-terminal domain, are capable of refolding spontaneously upon heat denaturation, lending support to the hypothesis that unfolded CagA is threaded C-terminus first through the type IV secretion channel with its N-terminal domain, which likely requires interactions with other domains to refold, being threaded last. Our findings also revealed that the C-terminal EPIYA-repeats domain of CagA exists in an intrinsically disordered premolten globule state with regions in PPII conformation - a feature that is shared by many scaffold proteins that bind multiple protein components of signalling pathways. Taken together, these results provide a deeper understanding of the physicochemical properties of CagA that underpin its complex cellular and oncogenic functions. PMID:24223932

  1. Host compatibility rather than vector–host-encounter rate determines the host range of avian Plasmodium parasites

    PubMed Central

    Medeiros, Matthew C. I.; Hamer, Gabriel L.; Ricklefs, Robert E.

    2013-01-01

    Blood-feeding arthropod vectors are responsible for transmitting many parasites between vertebrate hosts. While arthropod vectors often feed on limited subsets of potential host species, little is known about the extent to which this influences the distribution of vector-borne parasites in some systems. Here, we test the hypothesis that different vector species structure parasite–host relationships by restricting access of certain parasites to a subset of available hosts. Specifically, we investigate how the feeding patterns of Culex mosquito vectors relate to distributions of avian malaria parasites among hosts in suburban Chicago, IL, USA. We show that Plasmodium lineages, defined by cytochrome b haplotypes, are heterogeneously distributed across avian hosts. However, the feeding patterns of the dominant vectors (Culex restuans and Culex pipiens) are similar across these hosts, and do not explain the distributions of Plasmodium parasites. Phylogenetic similarity of avian hosts predicts similarity in their Plasmodium parasites. This effect was driven primarily by the general association of Plasmodium parasites with particular host superfamilies. Our results suggest that a mosquito-imposed encounter rate does not limit the distribution of avian Plasmodium parasites across hosts. This implies that compatibility between parasites and their avian hosts structure Plasmodium host range. PMID:23595266

  2. Mapping the Moral Domain

    PubMed Central

    Graham, Jesse; Nosek, Brian A.; Haidt, Jonathan; Iyer, Ravi; Koleva, Spassena; Ditto, Peter H.

    2010-01-01

    The moral domain is broader than the empathy and justice concerns assessed by existing measures of moral competence, and it is not just a subset of the values assessed by value inventories. To fill the need for reliable and theoretically-grounded measurement of the full range of moral concerns, we developed the Moral Foundations Questionnaire (MFQ) based on a theoretical model of five universally available (but variably developed) sets of moral intuitions: Harm/care, Fairness/reciprocity, Ingroup/loyalty, Authority/respect, and Purity/sanctity. We present evidence for the internal and external validity of the scale and the model, and in doing so present new findings about morality: 1. Comparative model fitting of confirmatory factor analyses provides empirical justification for a five-factor structure of moral concerns. 2. Convergent/discriminant validity evidence suggests that moral concerns predict personality features and social group attitudes not previously considered morally relevant. 3. We establish pragmatic validity of the measure in providing new knowledge and research opportunities concerning demographic and cultural differences in moral intuitions. These analyses provide evidence for the usefulness of Moral Foundations Theory in simultaneously increasing the scope and sharpening the resolution of psychological views of morality. PMID:21244182

  3. Ontology development for Sufism domain

    NASA Astrophysics Data System (ADS)

    Iqbal, Rizwan

    2012-01-01

    Domain ontology is a descriptive representation of any particular domain which in detail describes the concepts in a domain, the relationships among those concepts and organizes them in a hierarchal manner. It is also defined as a structure of knowledge, used as a means of knowledge sharing to the community. An Important aspect of using ontologies is to make information retrieval more accurate and efficient. Thousands of domain ontologies from all around the world are available online on ontology repositories. Ontology repositories like SWOOGLE currently have over 1000 ontologies covering a wide range of domains. It was found that up to date there was no ontology available covering the domain of "Sufism". This unavailability of "Sufism" domain ontology became a motivation factor for this research. This research came up with a working "Sufism" domain ontology as well a framework, design of the proposed framework focuses on the resolution to problems which were experienced while creating the "Sufism" ontology. The development and working of the "Sufism" domain ontology are covered in detail in this research. The word "Sufism" is a term which refers to Islamic mysticism. One of the reasons to choose "Sufism" for ontology creation is its global curiosity. This research has also managed to create some individuals which inherit the concepts from the "Sufism" ontology. The creation of individuals helps to demonstrate the efficient and precise retrieval of data from the "Sufism" domain ontology. The experiment of creating the "Sufism" domain ontology was carried out on a tool called Protégé. Protégé is a tool which is used for ontology creation, editing and it is open source.

  4. Ontology development for Sufism domain

    NASA Astrophysics Data System (ADS)

    Iqbal, Rizwan

    2011-12-01

    Domain ontology is a descriptive representation of any particular domain which in detail describes the concepts in a domain, the relationships among those concepts and organizes them in a hierarchal manner. It is also defined as a structure of knowledge, used as a means of knowledge sharing to the community. An Important aspect of using ontologies is to make information retrieval more accurate and efficient. Thousands of domain ontologies from all around the world are available online on ontology repositories. Ontology repositories like SWOOGLE currently have over 1000 ontologies covering a wide range of domains. It was found that up to date there was no ontology available covering the domain of "Sufism". This unavailability of "Sufism" domain ontology became a motivation factor for this research. This research came up with a working "Sufism" domain ontology as well a framework, design of the proposed framework focuses on the resolution to problems which were experienced while creating the "Sufism" ontology. The development and working of the "Sufism" domain ontology are covered in detail in this research. The word "Sufism" is a term which refers to Islamic mysticism. One of the reasons to choose "Sufism" for ontology creation is its global curiosity. This research has also managed to create some individuals which inherit the concepts from the "Sufism" ontology. The creation of individuals helps to demonstrate the efficient and precise retrieval of data from the "Sufism" domain ontology. The experiment of creating the "Sufism" domain ontology was carried out on a tool called Protégé. Protégé is a tool which is used for ontology creation, editing and it is open source.

  5. Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography.

    PubMed

    Leuthold, Mila M; Koromyslova, Anna D; Singh, Bishal K; Hansman, Grant S

    2016-01-01

    The norovirus capsid is composed of a single major structural protein, termed VP1. VP1 is subdivided into a shell (S) domain and a protruding (P) domain. The S domain forms a contiguous scaffold around the viral RNA, whereas the P domain forms viral spikes on the S domain and contains determinants for antigenicity and host-cell interactions. The P domain binds carbohydrate structures, i.e., histo-blood group antigens, which are thought to be important for norovirus infections. In this protocol, we describe a method for producing high quality norovirus P domains in high yields. These proteins can then be used for X-ray crystallography and ELISA in order to study antigenicity and host-cell interactions. The P domain is firstly cloned into an expression vector and then expressed in bacteria. The protein is purified using three steps that involve immobilized metal-ion affinity chromatography and size exclusion chromatography. In principle, it is possible to clone, express, purify, and crystallize proteins in less than four weeks, which makes this protocol a rapid system for analyzing newly emerging norovirus strains. PMID:27167457

  6. Signatures of Pleiotropy, Economy and Convergent Evolution in a Domain-Resolved Map of Human–Virus Protein–Protein Interaction Networks

    PubMed Central

    Garamszegi, Sara; Franzosa, Eric A.; Xia, Yu

    2013-01-01

    A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution, treating proteins as nodes and interactions as edges. Here, we construct a domain-resolved map of human-virus and within-human protein-protein interaction networks by annotating protein interactions with high-coverage, high-accuracy, domain-centric interaction mechanisms: (1) domain-domain interactions, in which a domain in one protein binds to a domain in a second protein, and (2) domain-motif interactions, in which a domain in one protein binds to a short, linear peptide motif in a second protein. Analysis of these domain-resolved networks reveals, for the first time, significant mechanistic differences between virus-human and within-human interactions at the resolution of single domains. While human proteins tend to compete with each other for domain binding sites by means of sequence similarity, viral proteins tend to compete with human proteins for domain binding sites in the absence of sequence similarity. Independent of their previously established preference for targeting human protein hubs, viral proteins also preferentially target human proteins containing linear motif-binding domains. Compared to human proteins, viral proteins participate in more domain-motif interactions, target more unique linear motif-binding domains per residue, and contain more unique linear motifs per residue. Together, these results suggest that viruses surmount genome size constraints by convergently evolving multiple short linear motifs in order to effectively mimic, hijack, and manipulate complex host processes for their survival. Our domain-resolved analyses reveal unique signatures of pleiotropy, economy, and convergent evolution in viral-host interactions that are

  7. Understanding host switching through ecological fitting

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Despite the fact that parasites are highly specialized to their hosts, extensive empirical evidence demonstrates that host switching rather than co-speciation is the most important factor influencing the origin of host-parasite associations. Ecological fitting in sloppy fitness space has been propos...

  8. Structure of a two-CAP-domain protein from the human hookworm parasite Necator americanus

    SciTech Connect

    Asojo, Oluwatoyin A.

    2011-05-01

    The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite N. americanus refined to a resolution limit of 2.2 Å is presented. Major proteins secreted by the infective larval stage hookworms upon host entry include Ancylostoma secreted proteins (ASPs), which are characterized by one or two CAP (cysteine-rich secretory protein/antigen 5/pathogenesis related-1) domains. The CAP domain has been reported in diverse phylogenetically unrelated proteins, but has no confirmed function. The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite Necator americanus was refined to a resolution limit of 2.2 Å. The structure was solved by molecular replacement (MR) using Na-ASP-2, a one-CAP-domain ASP, as the search model. The correct MR solution could only be obtained by truncating the polyalanine model of Na-ASP-2 and removing several loops. The structure reveals two CAP domains linked by an extended loop. Overall, the carboxyl-terminal CAP domain is more similar to Na-ASP-2 than to the amino-terminal CAP domain. A large central cavity extends from the amino-terminal CAP domain to the carboxyl-terminal CAP domain, encompassing the putative CAP-binding cavity. The putative CAP-binding cavity is a characteristic cavity in the carboxyl-terminal CAP domain that contains a His and Glu pair. These residues are conserved in all single-CAP-domain proteins, but are absent in the amino-terminal CAP domain. The conserved His residues are oriented such that they appear to be capable of directly coordinating a zinc ion as observed for CAP proteins from reptile venoms. This first structure of a two-CAP-domain ASP can serve as a template for homology modeling of other two-CAP-domain proteins.

  9. Fractional diffusion on bounded domains

    DOE PAGESBeta

    Defterli, Ozlem; D'Elia, Marta; Du, Qiang; Gunzburger, Max Donald; Lehoucq, Richard B.; Meerschaert, Mark M.

    2015-03-13

    We found that the mathematically correct specification of a fractional differential equation on a bounded domain requires specification of appropriate boundary conditions, or their fractional analogue. In this paper we discuss the application of nonlocal diffusion theory to specify well-posed fractional diffusion equations on bounded domains.

  10. Digesting blood of an auxiliary host in fleas: effect of phylogenetic distance from a principal host.

    PubMed

    Khokhlova, Irina S; Fielden, Laura J; Degen, A Allan; Krasnov, Boris R

    2012-04-15

    Fleas are haematophagous ectoparasites that exhibit varying degrees of host specificity. Flea abundance is highest on principal hosts and lower on auxiliary hosts but may vary greatly among auxiliary hosts. We investigated the feeding and energy expenditure for digestion in two flea species Parapulex chephrenis and Xenopsylla ramesis on a principal host (Acomys cahirinus and Meriones crassus, respectively) and eight auxiliary host species. We predicted that fleas would perform better - that is (i) a higher proportion of fleas would take a blood meal, (ii) fleas would take larger blood meals and (iii) fleas would spend less energy on digestion - if they fed on (i) a principal host compared with an auxiliary host and (ii) an auxiliary host phylogenetically close to a principal host compared with an auxiliary host phylogenetically distant from a principal host. Energy costs of digestion were estimated using CO(2) emission and represented energy cost during the first stage of blood digestion. Contrary to our predictions, fleas did not always perform better on a principal than on an auxiliary host or on auxiliary hosts phylogenetically closer to the principal host than on auxiliary hosts phylogenetically distant from a principal host. Variation in flea feeding performance may result from the interplay of several factors including co-occurrence between hosts and susceptibility of a host to flea attacks, the species-specific level of immunocompetence of a host and the level of host specificity of a flea. This study describes the first investigation into the metabolic expenditure of parasitism and its relationship to phylogenetic relationships amongst hosts. PMID:22442362

  11. Generic Model Host System Design

    SciTech Connect

    Chu, Chungming; Wu, Juhao; Qiang, Ji; Shen, Guobao; /Brookhaven

    2012-06-22

    There are many simulation codes for accelerator modelling; each one has some strength but not all. A platform which can host multiple modelling tools would be ideal for various purposes. The model platform along with infrastructure support can be used not only for online applications but also for offline purposes. Collaboration is formed for the effort of providing such a platform. In order to achieve such a platform, a set of common physics data structure has to be set. Application Programming Interface (API) for physics applications should also be defined within a model data provider. A preliminary platform design and prototype is discussed.

  12. HostDesigner, Version 3

    SciTech Connect

    Hay, Benjamin; McCann, Billy Wayne

    2015-09-18

    HostDesigner is a computer-aided molecular design code that enables the general application of de novo structure-based methods to problems in chemistry and material science. Its purpose is to identify organic molecules with 3D structures that match user-input specifications. To accomplish this, the code connects chemical fragments to build millions of potential molecules, evaluates the resulting structures based on geometric constraints, and outputs a rank-ordered list of candidates. Example applications include the design of metal ion sequestering agents for use in separations processes, molecules that form self-assembled nanoscale containers, and molecular building blocks for metal-organic frameworks.

  13. Polarized domains of myelinated axons.

    PubMed

    Salzer, James L

    2003-10-01

    The entire length of myelinated axons is organized into a series of polarized domains that center around nodes of Ranvier. These domains, which are crucial for normal saltatory conduction, consist of distinct multiprotein complexes of cell adhesion molecules, ion channels, and scaffolding molecules; they also differ in their diameter, organelle content, and rates of axonal transport. Juxtacrine signals from myelinating glia direct their sequential assembly. The composition, mechanisms of assembly, and function of these molecular domains will be reviewed. I also discuss similarities of this domain organization to that of polarized epithelia and present emerging evidence that disorders of domain organization and function contribute to the axonopathies of myelin and other neurologic disorders. PMID:14556710

  14. The monocyte binding domain(s) on human immunoglobulin G.

    PubMed

    Woof, J M; Nik Jaafar, M I; Jefferis, R; Burton, D R

    1984-06-01

    Monocyte binding has previously been assigned to the C gamma 3 domain of human immunoglobulin G (IgG) largely on the ability of the pFc' fragment to inhibit the monocyte-IgG interaction. This ability is markedly reduced compared to the intact parent IgG. We find this result with a conventional pFc' preparation but this preparation is found to contain trace contamination of parent IgG as demonstrated by reactivity with monoclonal antibodies directed against C gamma 2 domain and light-chain epitopes of human IgG. Extensive immunoaffinity purification of the pFc' preparation removes its inhibitory ability indicating that this originates in the trace contamination of parent IgG (or Fc). Neither of the human IgG1 paraproteins TIM, lacking the C gamma 2 domain, or SIZ, lacking the C gamma 3 domain, are found to inhibit the monocyte-IgG interaction. The hinge-deleted IgG1 Dob protein shows little or no inhibitory ability. Indirect evidence for the involvement of the C gamma 2 domain in monocyte binding is considered. We suggest finally that the site of interaction is found either on the C gamma 2 domain alone or between the C gamma 2 and C gamma 3 domains. PMID:6235444

  15. The Diversity and Evolution of Wolbachia Ankyrin Repeat Domain Genes

    PubMed Central

    Siozios, Stefanos; Ioannidis, Panagiotis; Klasson, Lisa; Andersson, Siv G. E.; Braig, Henk R.; Bourtzis, Kostas

    2013-01-01

    Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions. PMID:23390535

  16. Majorana Fermion Rides on a Magnetic Domain Wall

    NASA Astrophysics Data System (ADS)

    Kim, Se Kwon; Tewari, Sumanta; Tserkovnyak, Yaroslav

    Owing to the recent progress on endowing the electronic structure of magnetic nanowires with topological properties, the associated topological solitons in the magnetic texture--magnetic domain walls--appear as very natural hosts for exotic electronic excitations. Here, we propose to use the magnetic domain walls to engender Majorana fermions, which has several notable advantages compared to the existing approaches. First of all, the local tunneling density-of-states anomaly associated with the Majorana zero mode bound to a smooth magnetic soliton is immune to most of parasitic artifacts associated with the abrupt physical ends of a wire, which mar the existing experimental probes. Second, a viable route to move and braid Majorana fermions is offered by domain-wall motion. In particular, we envision the recently demonstrated heat-current induced motion of domain walls in insulating ferromagnets as a promising tool for nonintrusive displacement of Majorana modes. This leads us to propose a feasible scheme for braiding domain walls within a magnetic nanowire network, which manifests the nob-Abelian exchange statistics within the Majorana subspace. This work has been supported in part by the U.S. DOE-BES, FAME, and AFOSR grants.

  17. Yersinia type III effectors perturb host innate immune responses

    PubMed Central

    Pha, Khavong; Navarro, Lorena

    2016-01-01

    The innate immune system is the first line of defense against invading pathogens. Innate immune cells recognize molecular patterns from the pathogen and mount a response to resolve the infection. The production of proinflammatory cytokines and reactive oxygen species, phagocytosis, and induced programmed cell death are processes initiated by innate immune cells in order to combat invading pathogens. However, pathogens have evolved various virulence mechanisms to subvert these responses. One strategy utilized by Gram-negative bacterial pathogens is the deployment of a complex machine termed the type III secretion system (T3SS). The T3SS is composed of a syringe-like needle structure and the effector proteins that are injected directly into a target host cell to disrupt a cellular response. The three human pathogenic Yersinia spp. (Y. pestis, Y. enterocolitica, and Y. pseudotuberculosis) are Gram-negative bacteria that share in common a 70 kb virulence plasmid which encodes the T3SS. Translocation of the Yersinia effector proteins (YopE, YopH, YopT, YopM, YpkA/YopO, and YopP/J) into the target host cell results in disruption of the actin cytoskeleton to inhibit phagocytosis, downregulation of proinflammatory cytokine/chemokine production, and induction of cellular apoptosis of the target cell. Over the past 25 years, studies on the Yersinia effector proteins have unveiled tremendous knowledge of how the effectors enhance Yersinia virulence. Recently, the long awaited crystal structure of YpkA has been solved providing further insights into the activation of the YpkA kinase domain. Multisite autophosphorylation by YpkA to activate its kinase domain was also shown and postulated to serve as a mechanism to bypass regulation by host phosphatases. In addition, novel Yersinia effector protein targets, such as caspase-1, and signaling pathways including activation of the inflammasome were identified. In this review, we summarize the recent discoveries made on Yersinia

  18. Yersinia type III effectors perturb host innate immune responses.

    PubMed

    Pha, Khavong; Navarro, Lorena

    2016-02-26

    The innate immune system is the first line of defense against invading pathogens. Innate immune cells recognize molecular patterns from the pathogen and mount a response to resolve the infection. The production of proinflammatory cytokines and reactive oxygen species, phagocytosis, and induced programmed cell death are processes initiated by innate immune cells in order to combat invading pathogens. However, pathogens have evolved various virulence mechanisms to subvert these responses. One strategy utilized by Gram-negative bacterial pathogens is the deployment of a complex machine termed the type III secretion system (T3SS). The T3SS is composed of a syringe-like needle structure and the effector proteins that are injected directly into a target host cell to disrupt a cellular response. The three human pathogenic Yersinia spp. (Y. pestis, Y. enterocolitica, and Y. pseudotuberculosis) are Gram-negative bacteria that share in common a 70 kb virulence plasmid which encodes the T3SS. Translocation of the Yersinia effector proteins (YopE, YopH, YopT, YopM, YpkA/YopO, and YopP/J) into the target host cell results in disruption of the actin cytoskeleton to inhibit phagocytosis, downregulation of proinflammatory cytokine/chemokine production, and induction of cellular apoptosis of the target cell. Over the past 25 years, studies on the Yersinia effector proteins have unveiled tremendous knowledge of how the effectors enhance Yersinia virulence. Recently, the long awaited crystal structure of YpkA has been solved providing further insights into the activation of the YpkA kinase domain. Multisite autophosphorylation by YpkA to activate its kinase domain was also shown and postulated to serve as a mechanism to bypass regulation by host phosphatases. In addition, novel Yersinia effector protein targets, such as caspase-1, and signaling pathways including activation of the inflammasome were identified. In this review, we summarize the recent discoveries made on Yersinia

  19. The host and the flora.

    PubMed

    Nuding, S; Antoni, L; Stange, E F

    2013-01-01

    To prevent bacterial overgrowth, colonization of the epithelium and subsequent translocation, the gastrointestinal tract maintains an effective mucosal barrier. Besides mucus the most important components of this protective system are epithelial antimicrobial peptides such as defensins, the cathelicidin LL-37, lysozyme, phospholipase A, and proteins with additional antimicrobial properties such as ubiquicidin, ribosomal proteins or histones. Commensal species may tolerate intestinal antimicrobial peptides, for example Bacteroides ssp. or Parabacteroides ssp. as major species in the human colon were highly resistant to the constitutive defensin HBD-1 and only susceptible to the inducible defensin HBD-3. Reduction of disulfide bonds is an important mechanism activating HBD-1. As several studies show, alterations in the expression of antimicrobial peptides directly influence the composition of the intestinal flora. Correspondingly, an increased production of defensins or inhibition of the processing of mouse defensins to their active form led to a quantitative shift of luminal and mucosal bacterial species. On the other hand, microorganisms also modulate the synthesis of host defensins by induction or inhibition of specific peptides. Lactobacilli, the probiotic strain Escherichia coli Nissle and Salmonella enteritica stimulate HBD-2 expression, whereas Shigella flexneri downregulates the synthesis of HBD-1, HBD-3 and LL-37. Thus, the proper balance between the luminal flora and the mucosa is a permanently dynamic, sensitive and host-specific relationship. PMID:24246976

  20. Host Evasion by Burkholderia cenocepacia

    PubMed Central

    Ganesan, Shyamala; Sajjan, Umadevi S.

    2012-01-01

    Burkholderia cenocepacia is an opportunistic respiratory pathogen of individuals with cystic fibrosis (CF). Some strains of B. cenocepacia are highly transmissible and resistant to almost all antibiotics. Approximately one-third of B. cenocepacia infected CF patients go on to develop fatal “cepacia syndrome.” During the last two decades, substantial progress has been made with regards to evasion of host innate defense mechanisms by B. cenocepacia. Almost all strains of B. cenocepacia have the capacity to survive and replicate intracellularly in both airway epithelial cells and macrophages, which are primary sentinels of the lung and play a pivotal role in clearance of infecting bacteria. Those strains of B. cenocepacia, which express both cable pili and the associated 22 kDa adhesin are also capable of transmigrating across airway epithelium and persist in mouse models of infection. In this review, we will discuss how this type of interaction between B. cenocepacia and host may lead to persistence of bacteria as well as lung inflammation in CF patients. PMID:22919590

  1. Host defences against Giardia lamblia.

    PubMed

    Lopez-Romero, G; Quintero, J; Astiazarán-García, H; Velazquez, C

    2015-08-01

    Giardia spp. is a protozoan parasite that inhabits the upper small intestine of mammals and other species and is the aetiological agent of giardiasis. It has been demonstrated that nitric oxide, mast cells and dendritic cells are the first line of defence against Giardia. IL-6 and IL-17 play an important role during infection. Several cytokines possess overlapping functions in regulating innate and adaptive immune responses. IgA and CD4(+) T cells are fundamental to the process of Giardia clearance. It has been suggested that CD4(+) T cells play a double role during the anti-Giardia immune response. First, they activate and stimulate the differentiation of B cells to generate Giardia-specific antibodies. Second, they act through a B-cell-independent mechanism that is probably mediated by Th17 cells. Several Giardia proteins that stimulate humoral and cellular immune responses have been described. Variant surface proteins, α-1 giardin, and cyst wall protein 2 can induce host protective responses to future Giardia challenges. The characterization and evaluation of the protective potential of the immunogenic proteins that are associated with Giardia will offer new insights into host-parasite interactions and may aid in the development of an effective vaccine against the parasite. PMID:26072999

  2. Host evasion by Burkholderia cenocepacia.

    PubMed

    Ganesan, Shyamala; Sajjan, Umadevi S

    2011-01-01

    Burkholderia cenocepacia is an opportunistic respiratory pathogen of individuals with cystic fibrosis (CF). Some strains of B. cenocepacia are highly transmissible and resistant to almost all antibiotics. Approximately one-third of B. cenocepacia infected CF patients go on to develop fatal "cepacia syndrome." During the last two decades, substantial progress has been made with regards to evasion of host innate defense mechanisms by B. cenocepacia. Almost all strains of B. cenocepacia have the capacity to survive and replicate intracellularly in both airway epithelial cells and macrophages, which are primary sentinels of the lung and play a pivotal role in clearance of infecting bacteria. Those strains of B. cenocepacia, which express both cable pili and the associated 22 kDa adhesin are also capable of transmigrating across airway epithelium and persist in mouse models of infection. In this review, we will discuss how this type of interaction between B. cenocepacia and host may lead to persistence of bacteria as well as lung inflammation in CF patients. PMID:22919590

  3. Domain walls riding the wave.

    SciTech Connect

    Karapetrov, G.; Novosad, V.; Materials Science Division

    2010-11-01

    Recent years have witnessed a rapid proliferation of electronic gadgets around the world. These devices are used for both communication and entertainment, and it is a fact that they account for a growing portion of household energy consumption and overall world consumption of electricity. Increasing the energy efficiency of these devices could have a far greater and immediate impact than a gradual switch to renewable energy sources. The advances in the area of spintronics are therefore very important, as gadgets are mostly comprised of memory and logic elements. Recent developments in controlled manipulation of magnetic domains in ferromagnet nanostructures have opened opportunities for novel device architectures. This new class of memories and logic gates could soon power millions of consumer electronic devices. The attractiveness of using domain-wall motion in electronics is due to its inherent reliability (no mechanical moving parts), scalability (3D scalable architectures such as in racetrack memory), and nonvolatility (retains information in the absence of power). The remaining obstacles in widespread use of 'racetrack-type' elements are the speed and the energy dissipation during the manipulation of domain walls. In their recent contribution to Physical Review Letters, Oleg Tretiakov, Yang Liu, and Artem Abanov from Texas A&M University in College Station, provide a theoretical description of domain-wall motion in nanoscale ferromagnets due to the spin-polarized currents. They find exact conditions for time-dependent resonant domain-wall movement, which could speed up the motion of domain walls while minimizing Ohmic losses. Movement of domain walls in ferromagnetic nanowires can be achieved by application of external magnetic fields or by passing a spin-polarized current through the nanowire itself. On the other hand, the readout of the domain state is done by measuring the resistance of the wire. Therefore, passing current through the ferromagnetic wire is

  4. Structural and evolutionary divergence of cyclic nucleotide binding domains in eukaryotic pathogens: Implications for drug design.

    PubMed

    Mohanty, Smita; Kennedy, Eileen J; Herberg, Friedrich W; Hui, Raymond; Taylor, Susan S; Langsley, Gordon; Kannan, Natarajan

    2015-10-01

    Many cellular functions in eukaryotic pathogens are mediated by the cyclic nucleotide binding (CNB) domain, which senses second messengers such as cyclic AMP and cyclic GMP. Although CNB domain-containing proteins have been identified in many pathogenic organisms, an incomplete understanding of how CNB domains in pathogens differ from other eukaryotic hosts has hindered the development of selective inhibitors for CNB domains associated with infectious diseases. Here, we identify and classify CNB domain-containing proteins in eukaryotic genomes to understand the evolutionary basis for CNB domain functional divergence in pathogens. We identify 359 CNB domain-containing proteins in 31 pathogenic organisms and classify them into distinct subfamilies based on sequence similarity within the CNB domain as well as functional domains associated with the CNB domain. Our study reveals novel subfamilies with pathogen-specific variations in the phosphate-binding cassette. Analyzing these variations in light of existing structural and functional data provides new insights into ligand specificity and promiscuity and clues for drug design. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases. PMID:25847873

  5. Evolution of host range in Coleosporium ipomoeae, a plant pathogen with multiple hosts.

    PubMed

    Chappell, Thomas M; Rausher, Mark D

    2016-05-10

    Plants and their pathogens coevolve locally. Previous investigations of one host-one pathogen systems have demonstrated that natural selection favors pathogen genotypes that are virulent on a broad range of host genotypes. In the present study, we examine a system consisting of one pathogen species that infects three host species in the morning glory genus Ipomoea. We show that many pathogen genotypes can infect two or three of the host species when tested on plants from nonlocal communities. By contrast, pathogen genotypes are highly host-specific, infecting only one host species, when tested on host species from the local community. This pattern indicates that within-community evolution narrows the host breadth of pathogen genotypes. Possible evolutionary mechanisms include direct selection for narrow host breadth due to costs of virulence and evolution of ipomoea resistance in the host species. PMID:27114547

  6. Modeling software systems by domains

    NASA Technical Reports Server (NTRS)

    Dippolito, Richard; Lee, Kenneth

    1992-01-01

    The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

  7. Information Fusion: Moving from domain independent to domain literate approaches

    NASA Astrophysics Data System (ADS)

    McGuinness, D.

    2008-12-01

    Information Fusion has been a focus of research within the field of computer science for a number of years. Numerous environments aimed at general schema evaluation, diagnosis, and evolution have evolved within those communities including for example the Chimaera Ontology Evolution Environment and the Prompt environment for mapping schema alignment. General (domain independent) efforts have produced useful research results and numerous tools, however these results have predominantly been generated and used by computer scientists and have been focused largely on information schema integration and diagnosis. More recently semantically-enabled web-centric approaches have emerged that utilize domain knowledge to provide tools and services aimed at natural scientists needs for data fusion. In this talk, we will introduce some foundations for information fusion and provide deployed examples of how these foundations and evolving tools have been and are being used today in natural science domains by domain scientists. Some examples will be provided from deployed virtual observatory settings.

  8. Matching Recommendation Technologies and Domains

    NASA Astrophysics Data System (ADS)

    Burke, Robin; Ramezani, Maryam

    Recommender systems form an extremely diverse body of technologies and approaches. The chapter aims to assist researchers and developers to identify the recommendation technologies that are most likely to be applicable to different domains of recommendation. Unlike other taxonomies of recommender systems, our approach is centered on the question of knowledge: what knowledge does a recommender system need in order to function, and where does that knowledge come from? Different recommendation domains (books vs condominiums, for example) provide different opportunities for the gathering and application of knowledge. These considerations give rise to a mapping between domain characteristics and recommendation technologies.

  9. Concerted Action of Two Formins in Gliding Motility and Host Cell Invasion by Toxoplasma gondii

    PubMed Central

    Daher, Wassim; Plattner, Fabienne; Carlier, Marie-France; Soldati-Favre, Dominique

    2010-01-01

    The invasive forms of apicomplexan parasites share a conserved form of gliding motility that powers parasite migration across biological barriers, host cell invasion and egress from infected cells. Previous studies have established that the duration and direction of gliding motility are determined by actin polymerization; however, regulators of actin dynamics in apicomplexans remain poorly characterized. In the absence of a complete ARP2/3 complex, the formin homology 2 domain containing proteins and the accessory protein profilin are presumed to orchestrate actin polymerization during host cell invasion. Here, we have undertaken the biochemical and functional characterization of two Toxoplasma gondii formins and established that they act in concert as actin nucleators during invasion. The importance of TgFRM1 for parasite motility has been assessed by conditional gene disruption. The contribution of each formin individually and jointly was revealed by an approach based upon the expression of dominant mutants with modified FH2 domains impaired in actin binding but still able to dimerize with their respective endogenous formin. These mutated FH2 domains were fused to the ligand-controlled destabilization domain (DD-FKBP) to achieve conditional expression. This strategy proved unique in identifying the non-redundant and critical roles of both formins in invasion. These findings provide new insights into how controlled actin polymerization drives the directional movement required for productive penetration of parasites into host cells. PMID:20949068

  10. HOST structural analysis program overview

    NASA Technical Reports Server (NTRS)

    Thompson, Robert L.

    1986-01-01

    Hot-section components of aircraft gas turbine engines are subjected to severe thermal structural loading conditions, especially during the startup and takeoff portions of the engine cycle. The most severe and damaging stresses and strains are those induced by the steep thermal gradients induced during the startup transient. These transient stresses and strains are also the most difficult to predict, in part because the temperature gradients and distributions are not well known or readily predictable and, in part, because the cyclic elastic-viscoplastic behavior of the materials at these extremes of temperature and strain are not well known or readily predictable. A broad spectrum of structures related technology programs is underway to address these deficiencies at the basic as well as the applied level. The three key program elements in the HOST structural analysis program are computations, constitutive modeling, and experiments for each research activity. Also shown are tables summarizing each of the activities.

  11. HostDesigner, Version 3

    Energy Science and Technology Software Center (ESTSC)

    2015-09-18

    HostDesigner is a computer-aided molecular design code that enables the general application of de novo structure-based methods to problems in chemistry and material science. Its purpose is to identify organic molecules with 3D structures that match user-input specifications. To accomplish this, the code connects chemical fragments to build millions of potential molecules, evaluates the resulting structures based on geometric constraints, and outputs a rank-ordered list of candidates. Example applications include the design of metal ionmore » sequestering agents for use in separations processes, molecules that form self-assembled nanoscale containers, and molecular building blocks for metal-organic frameworks.« less

  12. VLA Hosts "Flag Across America"

    NASA Astrophysics Data System (ADS)

    2001-11-01

    The National Radio Astronomy Observatory (NRAO) hosted the runners and support personnel of the "Americans United Flag Across America" run as the transcontinental memorial and fundraising effort came through New Mexico. The flag run arrived at NRAO's Very Large Array (VLA) radio telescope west of Socorro, NM, early in the post-Midnight morning of Monday, November 5, and departed after sunrise that morning en route to the Arizona border. Drivers, runners and support personnel stayed overnight at the VLA. During the night, a "VLA Night Owl Run" kept the flag moving around the VLA area until the westward trek resumed after dawn. The run began Oct. 11, one month after the terrorist attacks on New York and Washington. Organized by employees of American and United Airlines to honor the flight crews lost in those attacks, to show support for U.S. troops and to raise funds to help the victims' families, the run will take an American flag from Boston Logan Airport to Los Angeles International Airport. The Boston-to-Los Angeles trip represents the intended journey of American Flight 11 and United Flight 175, both of which were crashed by terrorists into the World Trade Center. "Our observatory was proud to host this group and honored that they brought this flag through our facility," said Miller Goss, NRAO's director of VLA operations. The runners carried a flag that flew in a U.S. F-16 over Iraq in support of Operation Southern Watch on Oct. 2, and has visited Ground Zero in Manhattan. The flag is scheduled to arrive in Los Angeles on Veterans Day, Nov. 11. The National Radio Astronomy Observatory is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.

  13. Host Genomics in Infectious Diseases

    PubMed Central

    2013-01-01

    Understanding mechanisms by which genetic variants predispose to complications of infectious diseases can lead to important benefits including the development of biomarkers to prioritize vaccination or prophylactic therapy. Family studies, candidate genes in animal models, and the absence of well-defined risks where the complications are rare all can point to genetic predisposition. The most common approach to assessing genetic risk is to conduct an association study, which is a case control study using either a candidate gene approach or a genome wide approach. Although candidate gene variants may focus on potentially causal variants, because other variants across the genome are not tested these studies frequently cannot be replicated. Genome wide association studies need a sizable sample and usually do not identify causal variants but variants which may be in linkage disequilibrium to the actual causal variant. There are many pitfalls that can lead to bias in such studies, including misclassification of cases and controls, use of improper phenotypes, and genotyping errors. These studies have been limited to common genes and rare variants may not be detected. As the use of next generation sequencing becomes more common, it can be anticipated that more variants will be confirmed. The purpose of this review article is to address the issue of genomics in infectious diseases with an emphasis on the host. Although there are a plentitude of studies that focus on the molecular characteristics of pathogens, there are far fewer studies that address the role of human genetics in the predisposition to infection or more commonly its complications. This paper will review both the approaches used to study host genetics in humans and the pitfalls associated with some of these methods. The focus will be on human disease and therefore discussion of the use of animal models will be limited to those where there are genes that have been replicated in humans. The paper will focus on

  14. Understanding Host-Switching by Ecological Fitting.

    PubMed

    Araujo, Sabrina B L; Braga, Mariana Pires; Brooks, Daniel R; Agosta, Salvatore J; Hoberg, Eric P; von Hartenthal, Francisco W; Boeger, Walter A

    2015-01-01

    Despite the fact that parasites are highly specialized with respect to their hosts, empirical evidence demonstrates that host switching rather than co-speciation is the dominant factor influencing the diversification of host-parasite associations. Ecological fitting in sloppy fitness space has been proposed as a mechanism allowing ecological specialists to host-switch readily. That proposal is tested herein using an individual-based model of host switching. The model considers a parasite species exposed to multiple host resources. Through time host range expansion can occur readily without the prior evolution of novel genetic capacities. It also produces non-linear variation in the size of the fitness space. The capacity for host colonization is strongly influenced by propagule pressure early in the process and by the size of the fitness space later. The simulations suggest that co-adaptation may be initiated by the temporary loss of less fit phenotypes. Further, parasites can persist for extended periods in sub-optimal hosts, and thus may colonize distantly related hosts by a "stepping-stone" process. PMID:26431199

  15. Penetration of Bdellovibrio bacteriovorus into Host Cells

    PubMed Central

    Abram, Dinah; e Melo, J. Castro; Chou, D.

    1974-01-01

    Electron microscopy reveals that, in Bdellovibrio infection, after the formation of a passage pore in the host cell wall, the differentiated parasite penetration pole is associated with the host protoplast. This firm contact persists throughout the parasite penetration and after this process is completed. In penetrated hosts this contact is also apparent by phase microscopy. The association between the walls of the parasite and the host at the passage pore, on the other hand, is transient. Bdellovibrio do not penetrate hosts whose protoplast and cell walls are separated by plasmolysis, or in which the membrane-wall relationship is affected by low turgor pressure. It is concluded, therefore, that for penetration to occur it is essential that the host protoplast be within reach of the parasite, so that a firm contact can be established between them. A penetration mechanism is proposed that is effected by forces generated by fluxes of water and solutes due to structural changes in the infected host envelope. These forces cause a differential expansion of the host protoplast and cell wall and their separation from each other around the entry site, while the parasite remains firmly anchored to the host protoplast. Consequently, the parasite ends up enclosed in the expanded host periplasm. The actual entry, therefore, is a passive act of the parasite. Images PMID:4208138

  16. Understanding Host-Switching by Ecological Fitting

    PubMed Central

    Araujo, Sabrina B. L.; Braga, Mariana Pires; Brooks, Daniel R.; Agosta, Salvatore J.; Hoberg, Eric P.; von Hartenthal, Francisco W.; Boeger, Walter A.

    2015-01-01

    Despite the fact that parasites are highly specialized with respect to their hosts, empirical evidence demonstrates that host switching rather than co-speciation is the dominant factor influencing the diversification of host-parasite associations. Ecological fitting in sloppy fitness space has been proposed as a mechanism allowing ecological specialists to host-switch readily. That proposal is tested herein using an individual-based model of host switching. The model considers a parasite species exposed to multiple host resources. Through time host range expansion can occur readily without the prior evolution of novel genetic capacities. It also produces non-linear variation in the size of the fitness space. The capacity for host colonization is strongly influenced by propagule pressure early in the process and by the size of the fitness space later. The simulations suggest that co-adaptation may be initiated by the temporary loss of less fit phenotypes. Further, parasites can persist for extended periods in sub-optimal hosts, and thus may colonize distantly related hosts by a "stepping-stone" process. PMID:26431199

  17. Engineered CH2 domains (nanoantibodies).

    PubMed

    Dimitrov, Dimiter S

    2009-01-01

    Currently, almost all FDA approved therapeutic antibodies (except ReoPro, Lucentis and Cimzia which are Fabs), and the vast majority of those in clinical trials are full-size antibodies mostly in IgG1 format of about 150 kDa size. A fundamental problem for such large molecules is their poor penetration into tissues (e.g., solid tumors) and poor or absent binding to regions on the surface of some molecules (e.g., on the HIV envelope glycoprotein) which are fully accessible only by molecules of smaller size. Therefore, much work especially during the last decade has been aimed at developing novel scaffolds of much smaller size and high stability. Here I briefly describe a proposition to use the immunoglobulin (Ig) constant CH2 domain (CH3 for IgE and IgM) as a scaffold. CH2 is critical for the Ig effector functions. Isolated CH2 is stable monomer in contrast to all other constant domains and most of the variable domains. CH2 and engineered CH2 domains with improved stability can be used as scaffolds for construction of libraries containing diverse binders to various antigens. Such binders based on a CH2 scaffold could also confer some effector functions. Because the CH2 domains are the smallest independently folded antibody domains that can be engineered to contain simultaneously antigen-binding sites and binding sites mediating effector and stability functions, and to distinguish them from domain antibodies which are used to denote engineered VH or VL domains or nanobodies which are used to denote camelid VHH, I termed them nanoantibodies (nAbs). PMID:20046570

  18. Domain Walls with Strings Attached

    SciTech Connect

    Shmakova, Marina

    2001-08-20

    We have constructed a bulk and brane action of IIA theory which describes a pair of BPS domain walls on S{sub 1}/Z{sub 2}, with strings attached. The walls are given by two orientifold O8-planes with coincident D8-branes and F1-D0-strings are stretched between the walls. This static configuration satisfies all matching conditions for the string and domain wall sources and has 1/4 of unbroken supersymmetry.

  19. The role of the polymer host on reversible photodegradation in Disperse Orange 11 dye

    NASA Astrophysics Data System (ADS)

    Hung, Sheng-Ting; Ramini, Shiva K.; Wyrick, David G.; Clays, Koen; Kuzyk, Mark G.

    2012-10-01

    The photodegradation and recovery process in anthraquinone chromophores have been characterized using am­ plified spontaneous emission (ASE) in several Anthraquinone derivatives doped in poly(methyl methacrylate) (PMMA). To understand the mechanisms of self healing in disperse orange 11 (DOll) doped in PMMA and the role of the host polymer, we investigated reversible photodegradation in DOll doped in copolymer composed of different percentages of methyl methacrylate (MMA) and Styrene. The results suggest that the host polymer is an important factor in determining the distribution of domain sizes of dye molecules.

  20. Repeated targeting of the same hosts by a brood parasite compromises host egg rejection

    PubMed Central

    Stevens, Martin; Troscianko, Jolyon; Spottiswoode, Claire N.

    2013-01-01

    Cuckoo eggs famously mimic those of their foster parents to evade rejection from discriminating hosts. Here we test whether parasites benefit by repeatedly parasitizing the same host nest. This should make accurate rejection decisions harder, regardless of the mechanism that hosts use to identify foreign eggs. Here we find strong support for this prediction in the African tawny-flanked prinia (Prinia subflava), the most common host of the cuckoo finch (Anomalospiza imberbis). We show experimentally that hosts reject eggs that differ from an internal template, but crucially, as the proportion of foreign eggs increases, hosts are less likely to reject them and require greater differences in appearance to do so. Repeated parasitism by the same cuckoo finch female is common in host nests and likely to be an adaptation to increase the probability of host acceptance. Thus, repeated parasitism interacts with egg mimicry to exploit cognitive and sensory limitations in host defences. PMID:24064931

  1. Host-to-host variation of ecological interactions in polymicrobial infections

    NASA Astrophysics Data System (ADS)

    Mukherjee, Sayak; Weimer, Kristin E.; Seok, Sang-Cheol; Ray, Will C.; Jayaprakash, C.; Vieland, Veronica J.; Swords, W. Edward; Das, Jayajit

    2015-02-01

    Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevolution of hosts and microbes, are based on averages across a host population. By assuming that observed variations are random and independent, these models overlook the role of differences between hosts. Here, we analyze mechanisms underlying host-to-host variations of bacterial infection kinetics, using the well characterized experimental infection model of polymicrobial otitis media (OM) in chinchillas, in combination with population dynamic models and a maximum entropy (MaxEnt) based inference scheme. We find that the nature of the interactions between bacterial species critically regulates host-to-host variations in these interactions. Surprisingly, seemingly unrelated phenomena, such as the efficiency of individual bacterial species in utilizing nutrients for growth, and the microbe-specific host immune response, can become interdependent in a host population. The latter finding suggests a potential mechanism that could lead to selection of specific strains of bacterial species during the coevolution of the host immune response and the bacterial species.

  2. Local host specialization, host-switching, and dispersal shape the regional distributions of avian haemosporidian parasites

    PubMed Central

    Ellis, Vincenzo A.; Collins, Michael D.; Medeiros, Matthew C. I.; Sari, Eloisa H. R.; Coffey, Elyse D.; Dickerson, Rebecca C.; Lugarini, Camile; Stratford, Jeffrey A.; Henry, Donata R.; Merrill, Loren; Matthews, Alix E.; Hanson, Alison A.; Roberts, Jackson R.; Joyce, Michael; Kunkel, Melanie R.; Ricklefs, Robert E.

    2015-01-01

    The drivers of regional parasite distributions are poorly understood, especially in comparison with those of free-living species. For vector-transmitted parasites, in particular, distributions might be influenced by host-switching and by parasite dispersal with primary hosts and vectors. We surveyed haemosporidian blood parasites (Plasmodium and Haemoproteus) of small land birds in eastern North America to characterize a regional parasite community. Distributions of parasite populations generally reflected distributions of their hosts across the region. However, when the interdependence between hosts and parasites was controlled statistically, local host assemblages were related to regional climatic gradients, but parasite assemblages were not. Moreover, because parasite assemblage similarity does not decrease with distance when controlling for host assemblages and climate, parasites evidently disperse readily within the distributions of their hosts. The degree of specialization on hosts varied in some parasite lineages over short periods and small geographic distances independently of the diversity of available hosts and potentially competing parasite lineages. Nonrandom spatial turnover was apparent in parasite lineages infecting one host species that was well-sampled within a single year across its range, plausibly reflecting localized adaptations of hosts and parasites. Overall, populations of avian hosts generally determine the geographic distributions of haemosporidian parasites. However, parasites are not dispersal-limited within their host distributions, and they may switch hosts readily. PMID:26305975

  3. Host-to-host variation of ecological interactions in polymicrobial infections

    PubMed Central

    Mukherjee, Sayak; Weimer, Kristin E.; Seok, Sang-Cheol; Ray, Will C.; Jayaprakash, C.; Vieland, Veronica J.; Swords, W. Edward

    2014-01-01

    Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevolution of hosts and microbes, are based on averages across a host population. By assuming that observed variations are random and independent, these models overlook the role of differences between hosts. Here, we analyze mechanisms underlying host-to-host variations of bacterial infection kinetics, using the well characterized experimental infection model of polymicrobial otitis media (OM) in chinchillas, in combination with population dynamic models and a Maximum Entropy (MaxEnt) based inference scheme. We find that the nature of the interactions between bacterial species critically regulates host-to-host variations in these interactions. Surprisingly, seemingly unrelated phenomena, such as the efficiency of individual bacterial species in utilizing nutrients for growth, and the microbe-specific host immune response, can become interdependent in a host population. The latter finding suggests a potential mechanism that could lead to selection of specific strains of bacterial species during the coevolution of the host immune response and the bacterial species. PMID:25473880

  4. Structural basis for antagonizing a host restriction factor by C7 family of poxvirus host-range proteins

    PubMed Central

    Meng, Xiangzhi; Krumm, Brian; Li, Yongchao; Deng, Junpeng; Xiang, Yan

    2015-01-01

    Human sterile alpha motif domain-containing 9 (SAMD9) protein is a host restriction factor for poxviruses, but it can be overcome by some poxvirus host-range proteins that share homology with vaccinia virus C7 protein. To understand the mechanism of action for this important family of host-range factors, we determined the crystal structures of C7 and myxoma virus M64, a C7 family member that is unable to antagonize SAMD9. Despite their different functions and only 23% sequence identity, the two proteins have very similar overall structures, displaying a previously unidentified fold comprised of a compact 12-stranded antiparallel β-sandwich wrapped in two short α helices. Extensive structure-guided mutagenesis of C7 identified three loops clustered on one edge of the β sandwich as critical for viral replication and binding with SAMD9. The loops are characterized with functionally important negatively charged, positively charged, and hydrophobic residues, respectively, together forming a unique “three-fingered molecular claw.” The key residues of the claw are not conserved in two C7 family members that do not antagonize SAMD9 but are conserved in distantly related C7 family members from four poxvirus genera that infect diverse mammalian species. Indeed, we found that all in the latter group of proteins bind SAMD9. Taken together, our data indicate that diverse mammalian poxviruses use a conserved molecular claw in a C7-like protein to target SAMD9 and overcome host restriction. PMID:26578811

  5. Host shifts and evolutionary radiations of butterflies

    PubMed Central

    Fordyce, James A.

    2010-01-01

    Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today. PMID:20610430

  6. Host Selection of Microbiota via Differential Adhesion.

    PubMed

    McLoughlin, Kirstie; Schluter, Jonas; Rakoff-Nahoum, Seth; Smith, Adrian L; Foster, Kevin R

    2016-04-13

    The host epithelium is the critical interface with microbial communities, but the mechanisms by which the host regulates these communities are poorly understood. Here we develop the hypothesis that hosts use differential adhesion to select for and against particular members of their microbiota. We use an established computational, individual-based model to study the impact of host factors that regulate adhesion at the epithelial surface. Our simulations predict that host-mediated adhesion can increase the competitive advantage of microbes and create ecological refugia for slow-growing species. We show how positive selection via adhesion can be transformed into negative selection if the host secretes large quantities of a matrix such as mucus. Our work predicts that adhesion is a powerful mechanism for both positive and negative selection within the microbiota. We discuss molecules-mucus glycans and IgA-that affect microbe adhesion and identify testable predictions of the adhesion-as-selection model. PMID:27053168

  7. Recognition of additional roles for immunoglobulin domains in immune function

    PubMed Central

    Cannon, John P.; Dishaw, Larry J.; Haire, Robert N.; Litman, Ronda T.; Ostrov, David A.; Litman, Gary W.

    2010-01-01

    Characterization of immune receptors found in phylogenetically disparate species at the genetic, structural and functional levels has provided unique insight into the evolutionary acquisition of immune function. The roles of variable- and intermediate-type immunoglobulin (Ig) domains in direct recognition of ligands and other functions are far wider than previously anticipated. Common mechanisms of multigene family diversification and expansion as well as unique adaptations that relate to function continue to provide unique insight into the numerous patterns, processes and complex interactions that regulate the host response to infectious challenge. PMID:20004115

  8. Sputnik, a virophage infecting the viral domain of life.

    PubMed

    Desnues, Christelle; Boyer, Mickaël; Raoult, Didier

    2012-01-01

    This chapter discusses the astonishing discovery of the Sputnik virophage, a new virus infecting giant viruses of the genera Mimivirus and Mamavirus. While other virophages have also since been described, this chapter focuses mainly on Sputnik, which is the best described. We detail the general properties of the virophage life cycle, as well as its hosts, genomic characteristics, ecology, and origin. In addition to genetic, phylogenetic, and structural evidence, the existence of virophages has deeply altered our view of the tripartite division of life to include the addition of a fourth domain constituted of the nucleocytoplasmic large DNA viruses, an important point that is discussed. PMID:22420851

  9. Induction of promyelocytic leukemia (PML) oncogenic domains (PODs) by papillomavirus

    SciTech Connect

    Nakahara, Tomomi; Lambert, Paul F.

    2007-09-30

    Promyelocytic leukemia oncogenic domains (PODs), also called nuclear domain 10 (ND10), are subnuclear structures that have been implicated in a variety of cellular processes as well as the life cycle of DNA viruses including papillomaviruses. In order to investigate the interplay between papillomaviruses and PODs, we analyzed the status of PODs in organotypic raft cultures of human keratinocytes harboring HPV genome that support the differentiation-dependent HPV life cycle. The number of PODs per nucleus was increased in the presence of HPV genomes selectively within the poorly differentiated layers but was absent in the terminally differentiated layers of the stratified epithelium. This increase in PODs was correlated with an increase in abundance of post-translationally modified PML protein. Neither the E2-dependent transcription nor viral DNA replication was reliant upon the presence of PML. Implications of these findings in terms of HPV's interaction with its host are discussed.

  10. Domain and Specification Models for Software Engineering

    NASA Technical Reports Server (NTRS)

    Iscoe, Neil; Liu, Zheng-Yang; Feng, Guohui

    1992-01-01

    This paper discusses our approach to representing application domain knowledge for specific software engineering tasks. Application domain knowledge is embodied in a domain model. Domain models are used to assist in the creation of specification models. Although many different specification models can be created from any particular domain model, each specification model is consistent and correct with respect to the domain model. One aspect of the system-hierarchical organization is described in detail.

  11. The Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens

    SciTech Connect

    Geisbrecht, B V; Hamaoka, B Y; Perman, B; Zemla, A; Leahy, D J

    2005-10-14

    The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 {angstrom} resolution, respectively. These structures reveal a core fold that is comprised of an {alpha}-helix lying diagonally across a five-stranded, mixed {beta}-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the {beta}-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

  12. Host Plant Adaptation in Drosophila mettleri Populations

    PubMed Central

    Castrezana, Sergio; Bono, Jeremy M.

    2012-01-01

    The process of local adaptation creates diversity among allopatric populations, and may eventually lead to speciation. Plant-feeding insect populations that specialize on different host species provide an excellent opportunity to evaluate the causes of ecological specialization and the subsequent consequences for diversity. In this study, we used geographically separated Drosophila mettleri populations that specialize on different host cacti to examine oviposition preference for and larval performance on an array of natural and non-natural hosts (eight total). We found evidence of local adaptation in performance on saguaro cactus (Carnegiea gigantea) for populations that are typically associated with this host, and to chemically divergent prickly pear species (Opuntia spp.) in a genetically isolated population on Santa Catalina Island. Moreover, each population exhibited reduced performance on the alternative host. This finding is consistent with trade-offs associated with adaptation to these chemically divergent hosts, although we also discuss alternative explanations for this pattern. For oviposition preference, Santa Catalina Island flies were more likely to oviposit on some prickly pear species, but all populations readily laid eggs on saguaro. Experiments with non-natural hosts suggest that factors such as ecological opportunity may play a more important role than host plant chemistry in explaining the lack of natural associations with some hosts. PMID:22493678

  13. Host plant adaptation in Drosophila mettleri populations.

    PubMed

    Castrezana, Sergio; Bono, Jeremy M

    2012-01-01

    The process of local adaptation creates diversity among allopatric populations, and may eventually lead to speciation. Plant-feeding insect populations that specialize on different host species provide an excellent opportunity to evaluate the causes of ecological specialization and the subsequent consequences for diversity. In this study, we used geographically separated Drosophila mettleri populations that specialize on different host cacti to examine oviposition preference for and larval performance on an array of natural and non-natural hosts (eight total). We found evidence of local adaptation in performance on saguaro cactus (Carnegiea gigantea) for populations that are typically associated with this host, and to chemically divergent prickly pear species (Opuntia spp.) in a genetically isolated population on Santa Catalina Island. Moreover, each population exhibited reduced performance on the alternative host. This finding is consistent with trade-offs associated with adaptation to these chemically divergent hosts, although we also discuss alternative explanations for this pattern. For oviposition preference, Santa Catalina Island flies were more likely to oviposit on some prickly pear species, but all populations readily laid eggs on saguaro. Experiments with non-natural hosts suggest that factors such as ecological opportunity may play a more important role than host plant chemistry in explaining the lack of natural associations with some hosts. PMID:22493678

  14. Localization of resistive domains in inhomogeneous superconductors

    SciTech Connect

    Gurevich, A.V.; Mints, R.G.

    1981-01-01

    The properties of resistive domains due to the Joule heating in inhomogeneous superconductors with transport currents are studied. The equilibrium of a domain at an inhomogeneity of arbitrary type and with dimensions much smaller than the dimensions of the domain is investigated. It is shown that resistive domains can become localized at inhomogeneities. The temperature distribution in a domain and the current--voltage characteristic of the domain are determined. The stability of localized domains is discussed. It is shown that such domains give rise to a hysteresis in the destruction (recovery) of the superconductivity by the transport current.

  15. An acanthocephalan parasite boosts the escape performance of its intermediate host facing non-host predators.

    PubMed

    Medoc, V; Beisel, J-N

    2008-07-01

    Among the potential effects of parasitism on host condition, the 'increased host abilities' hypothesis is a counterintuitive pattern which might be predicted in complex-life-cycle parasites. In the case of trophic transmission, a parasite increasing its intermediate host's performance facing non-host predators improves its probability of transmission to an adequate, definitive host. In the present study, we investigated the cost of infection with the acanthocephalan Polymorphus minutus on the locomotor/escape performance of its intermediate host, the crustacean Gammarus roeseli. This parasite alters the behaviour of its intermediate host making it more vulnerable to predation by avian definitive hosts. We assessed the swimming speeds of gammarids using a stressful treatment and their escape abilities under predation pressure. Despite the encystment of P. minutus in the abdomen of its intermediate host, infected amphipods had significantly higher swimming speeds than uninfected ones (increases of up to 35%). Furthermore, when interacting with the non-host crustacean predator Dikerogammarus villosus, the highest escape speeds and greatest distances covered by invertebrates were observed for parasitized animals. The altered behaviour observed among the manipulated invertebrates supported the 'increased host abilities' hypothesis, which has until now remained untested experimentally. The tactic of increasing the ability of infected intermediate hosts to evade potential predation attempts by non-host species is discussed. PMID:18477417

  16. Functional domain walls in multiferroics

    NASA Astrophysics Data System (ADS)

    Meier, Dennis

    2015-11-01

    During the last decade a wide variety of novel and fascinating correlation phenomena has been discovered at domain walls in multiferroic bulk systems, ranging from unusual electronic conductance to inseparably entangled spin and charge degrees of freedom. The domain walls represent quasi-2D functional objects that can be induced, positioned, and erased on demand, bearing considerable technological potential for future nanoelectronics. Most of the challenges that remain to be solved before turning related device paradigms into reality, however, still fall in the field of fundamental condensed matter physics and materials science. In this topical review seminal experimental findings gained on electric and magnetic domain walls in multiferroic bulk materials are addressed. A special focus is put on the physical properties that emerge at so-called charged domain walls and the added functionality that arises from coexisting magnetic order. The research presented in this review highlights that we are just entering a whole new world of intriguing nanoscale physics that is yet to be explored in all its details. The goal is to draw attention to the persistent challenges and identify future key directions for the research on functional domain walls in multiferroics.

  17. Functional domain walls in multiferroics.

    PubMed

    Meier, Dennis

    2015-11-25

    During the last decade a wide variety of novel and fascinating correlation phenomena has been discovered at domain walls in multiferroic bulk systems, ranging from unusual electronic conductance to inseparably entangled spin and charge degrees of freedom. The domain walls represent quasi-2D functional objects that can be induced, positioned, and erased on demand, bearing considerable technological potential for future nanoelectronics. Most of the challenges that remain to be solved before turning related device paradigms into reality, however, still fall in the field of fundamental condensed matter physics and materials science. In this topical review seminal experimental findings gained on electric and magnetic domain walls in multiferroic bulk materials are addressed. A special focus is put on the physical properties that emerge at so-called charged domain walls and the added functionality that arises from coexisting magnetic order. The research presented in this review highlights that we are just entering a whole new world of intriguing nanoscale physics that is yet to be explored in all its details. The goal is to draw attention to the persistent challenges and identify future key directions for the research on functional domain walls in multiferroics. PMID:26523728

  18. Predicting cognitive change within domains

    PubMed Central

    Duff, Kevin; Beglinger, Leigh J.; Moser, David J.; Paulsen, Jane S.

    2010-01-01

    Standardized regression based (SRB) formulas, a method for predicting cognitive change across time, traditionally use baseline performance on a neuropsychological measure to predict future performance on that same measure. However, there are instances in which the same tests may not be given at follow-up assessments (e.g., lack of continuity of provider, avoiding practice effects). The current study sought to expand this methodology by developing SRBs to predict performance on different tests within the same cognitive domain. Using a sample of 127 non-demented community-dwelling older adults assessed at baseline and after one year, two sets of SRBs were developed: 1. those predicting performance on the same test, and 2. those predicting performance on a different test within the same cognitive domain. The domains examined were learning and memory, processing speed, and language. Across both sets of SRBs, one year scores were significantly predicted by baseline scores, especially for the learning and memory and processing speed measures. Although SRBs developed for the same test were comparable to those developed for different tests within the same domain, less variance was accounted for as tests became less similar. The current results lend preliminary support for additional development of SRBs, both for same- and different-tests, as well as beginning to examine domain-based SRBs. PMID:20358479

  19. Seasonal and spatial heterogeneities in host and vector abundances impact the spatiotemporal spread of bluetongue

    PubMed Central

    2013-01-01

    Bluetongue (BT) can cause severe livestock losses and large direct and indirect costs for farmers. To propose targeted control strategies as alternative to massive vaccination, there is a need to better understand how BT virus spread in space and time according to local characteristics of host and vector populations. Our objective was to assess, using a modelling approach, how spatiotemporal heterogeneities in abundance and distribution of hosts and vectors impact the occurrence and amplitude of local and regional BT epidemics. We built a reaction–diffusion model accounting for the seasonality in vector abundance and the active dispersal of vectors. Because of the scale chosen, and movement restrictions imposed during epidemics, host movements and wind-induced passive vector movements were neglected. Four levels of complexity were addressed using a theoretical approach, from a homogeneous to a heterogeneous environment in abundance and distribution of hosts and vectors. These scenarios were illustrated using data on abundance and distribution of hosts and vectors in a real geographical area. We have shown that local epidemics can occur earlier and be larger in scale far from the primary case rather than close to it. Moreover, spatial heterogeneities in hosts and vectors delay the epidemic peak and decrease the infection prevalence. The results obtained on a real area confirmed those obtained on a theoretical domain. Although developed to represent BTV spatiotemporal spread, our model can be used to study other vector-borne diseases of animals with a local to regional spread by vector diffusion. PMID:23782421

  20. Ehrlichia chaffeensis TRP32 Interacts with Host Cell Targets That Influence Intracellular Survival

    PubMed Central

    Luo, Tian

    2012-01-01

    Ehrlichia chaffeensis is an obligately intracellular bacterium that exhibits tropism for mononuclear phagocytes and survives by evading host cell defense mechanisms. Recently, molecular interactions of E. chaffeensis tandem repeat proteins 47 and 120 (TRP47 and -120) and the eukaryotic host cell have been described. In this investigation, yeast two-hybrid analysis demonstrated that an E. chaffeensis type 1 secretion system substrate, TRP32, interacts with a diverse group of human proteins associated with major biological processes of the host cell, including protein synthesis, trafficking, degradation, immune signaling, cell signaling, iron metabolism, and apoptosis. Eight target proteins, including translation elongation factor 1 alpha 1 (EF1A1), deleted in azoospermia (DAZ)-associated protein 2 (DAZAP2), ferritin light polypeptide (FTL), CD63, CD14, proteasome subunit beta type 1 (PSMB1), ring finger and CCCH-type domain 1 (RC3H1), and tumor protein p53-inducible protein 11 (TP53I11) interacted with TRP32 as determined by coimmunoprecipitation assays, colocalization with TRP32 in HeLa and THP-1 cells, and/or RNA interference. Interactions between TRP32 and host targets localized to the E. chaffeensis morulae or in the host cell cytoplasm adjacent to morulae. Common or closely related interacting partners of E. chaffeensis TRP32, TRP47, and TRP120 demonstrate a molecular convergence on common cellular processes and molecular cross talk between Ehrlichia TRPs and host targets. These findings further support the role of TRPs as effectors that promote intracellular survival. PMID:22547548

  1. Faraday instability in deformable domains

    NASA Astrophysics Data System (ADS)

    Pucci, Giuseppe; Ben Amar, Martine; Couder, Yves

    2014-11-01

    We investigate the Faraday instability in floating liquid lenses, as an example of hydrodynamic instability that develops in a domain with flexible boundaries. We show that a mutual adaptation of the instability pattern and the domain shape occurs, as a result of the competition between the wave radiation pressure and the capillary response of the lens border. Two archetypes of behaviour are observed. In the first, stable shapes are obtained experimentally and predicted theoretically as the exact solutions of a Riccati equation, and they result from the equilibrium between wave radiation pressure and capillarity. In the second, the radiation pressure exceeds the capillary response of the lens border and leads to non-equilibrium behaviours, with breaking into smaller domains that have a complex dynamics including spontaneous propagation. The authors are grateful to Université Franco-Italienne (UFI) for financial support.

  2. Domain walls inside localised orientifolds

    NASA Astrophysics Data System (ADS)

    Blåbäck, J.; van der Woerd, E.; Van Riet, T.; Williams, M.

    2015-12-01

    The equations of motion of toroidal orientifold compactifications with fluxes are in one-to-one correspondence with gauged supergravity if the orientifold (and D-brane) sources are smeared over the compact space. This smeared limit is identical to the approximation that ignores warping. It is therefore relevant to compare quantities obtained from the gauged supergravity with the true 10d solution with localised sources. In this paper we find the correspondence between BPS domain walls in gauged SUGRA and 10D SUGRA with localised sources. Our model is the simplest orientifold with fluxes we are aware of: an O6/D6 compactification on {T}^3/{Z}_2 in massive IIA with H 3-flux. The BPS domain walls correspond to a O6/D6/NS5/D8 bound state. Our analysis reveals that the domain wall energy computed in gauged SUGRA is unaffected by the localisation of the O6/D6 sources.

  3. The Bordetella Adenylate Cyclase Repeat-in-Toxin (RTX) Domain Is Immunodominant and Elicits Neutralizing Antibodies*

    PubMed Central

    Wang, Xianzhe; Maynard, Jennifer A.

    2015-01-01

    The adenylate cyclase toxin (ACT) is a multifunctional virulence factor secreted by Bordetella species. Upon interaction of its C-terminal hemolysin moiety with the cell surface receptor αMβ2 integrin, the N-terminal cyclase domain translocates into the host cell cytosol where it rapidly generates supraphysiological cAMP concentrations, which inhibit host cell anti-bacterial activities. Although ACT has been shown to induce protective immunity in mice, it is not included in any current acellular pertussis vaccines due to protein stability issues and a poor understanding of its role as a protective antigen. Here, we aimed to determine whether any single domain could recapitulate the antibody responses induced by the holo-toxin and to characterize the dominant neutralizing antibody response. We first immunized mice with ACT and screened antibody phage display libraries for binding to purified ACT. The vast majority of unique antibodies identified bound the C-terminal repeat-in-toxin (RTX) domain. Representative antibodies binding two nonoverlapping, neutralizing epitopes in the RTX domain prevented ACT association with J774A.1 macrophages and soluble αMβ2 integrin, suggesting that these antibodies inhibit the ACT-receptor interaction. Sera from mice immunized with the RTX domain showed similar neutralizing activity as ACT-immunized mice, indicating that this domain induced an antibody response similar to that induced by ACT. These data demonstrate that RTX can elicit neutralizing antibodies and suggest it may present an alternative to ACT. PMID:25505186

  4. Host selection by the shiny cowbird

    USGS Publications Warehouse

    Wiley, J.W.

    1988-01-01

    Factors important in Shiny Cowbird (Molothrus bonariensis) host selection were examined within the mangrove community in Puerto Rico. Cowbirds did not parasitize birds in proportion to their abundance. The cowbird breeding season coincided with those of its major hosts, which were 'high-quality' foster species (i.e., species that fledge .gtoreq. 55% of cowbirds hatched: Yellow Warbler, Dendroica petechia; Yellow-shouldered Blackbird, Agelaius xanthomus; Black-whiskered Vireo, Vireo altiloquus; Black-cowled Oriole, Icterus dominicensis; Peurto Rican Flycatcher, Myiarchus antillarum; Troupial, Icterus icterus), and did not extend into other periods even though nests of 'low-quality: species (i.e., species that fledge < 55% of cowbird chicks that hatched: Bronze Mannikin, Lonchura cucullata; Greater Antillean Grackle, Quiscalus niger; Gray Kingbird, Tyrannus dominicensis; Northern Mockingbird, Mimus polyglottos; Red-legged Thrush, Turdus plumbeus) were available. Shiny Cowbird food habits and egg size were similar to those of their hosts, suggesting that cowbirds choose hosts partly on the basis of this combination. Cowbirds located host nests primarily by cryptically watching activities of birds in likely habitats. Other nest locating strategies were active searching of suitable habitat and 'flushing' of hosts by the cowbird's noisy approach. Cowbirds closely monitored nest status with frequent visits that peaked on the host's first day of egg laying. Hosts using covered nests (e.g., cavities, domed nests) were as vulnerable to cowbird parasitism as those building open nests.

  5. Host-parasitoid associations in Strepsiptera.

    PubMed

    Kathirithamby, Jeyaraney

    2009-01-01

    Strepsiptera are obligate endoparasitoids that exhibit extreme sexual dimorphism and parasitize seven orders and 33 families of Insecta. The adult males and the first instar larvae in the Mengenillidia and Stylopidia are free-living, whereas the adult females in Mengenillidia are free-living but in the suborder Stylopidia they remain endoparasitic in the host. Parasitism occurs at the host larval/nymphal stage and continues in a mobile host until that host's adult stage. The life of the host is lengthened to allow the male strepsipteran to complete maturation and the viviparous female to release the first instar larvae when the next generation of the host's larvae/nymphs has been produced. The ability of strepsipterans to parasitize a wide range of hosts, in spite of being endoparasitoids, is perhaps due to their unique immune avoidance system. Aspects of virulence, heterotrophic heteronomy in the family Myrmecolacidae, cryptic species, genomics, immune response, and behavior of stylopized hosts are discussed in this chapter. PMID:18817508

  6. Social Host Ordinances and Policies. Prevention Update

    ERIC Educational Resources Information Center

    Higher Education Center for Alcohol, Drug Abuse, and Violence Prevention, 2011

    2011-01-01

    Social host liability laws (also known as teen party ordinances, loud or unruly gathering ordinances, or response costs ordinances) target the location in which underage drinking takes place. Social host liability laws hold noncommercial individuals responsible for underage drinking events on property they own, lease, or otherwise control. They…

  7. Specification and installation of a MILNET host

    SciTech Connect

    George, M.

    1986-04-01

    A MILNET host computer was specified and installed to meet the needs of the growing user community at Sandia. The configuration of this host is described from specification through installation and testing. Also included are descriptions of the MILNET network and administrative procedures for the system. 5 figs.

  8. Endosymbiont Tolerance and Control within Insect Hosts

    PubMed Central

    Ratzka, Carolin; Gross, Roy; Feldhaar, Heike

    2012-01-01

    Bacterial endosymbioses are very common in insects and can range from obligate to facultative as well as from mutualistic to pathogenic associations. Several recent studies provide new insight into how endosymbionts manage to establish chronic infections of their hosts without being eliminated by the host immune system. Endosymbiont tolerance may be achieved either by specific bacterial adaptations or by host measurements shielding bacteria from innate defense mechanisms. Nevertheless, insect hosts also need to sustain control mechanisms to prevent endosymbionts from unregulated proliferation. Emerging evidence indicates that in some cases the mutual adaptations of the two organisms may have led to the integration of the endosymbionts as a part of the host immune system. In fact, endosymbionts may provide protective traits against pathogens and predators and may even be required for the proper development of the host immune system during host ontogeny. This review gives an overview of current knowledge of molecular mechanisms ensuring maintenance of chronic infections with mutualistic endosymbionts and the impact of endosymbionts on host immune competence. PMID:26466544

  9. Mycobacterium tuberculosis and the host response

    PubMed Central

    Kaufmann, Stefan H.E.; Cole, Stewart T.; Mizrahi, Valerie; Rubin, Eric; Nathan, Carl

    2005-01-01

    Mycobacterium tuberculosis remains a leading cause of morbidity and mortality worldwide. Advances reported at a recent international meeting highlight insights and controversies in the genetics of M. tuberculosis and the infected host, the nature of protective immune responses, adaptation of the bacillus to host-imposed stresses, animal models, and new techniques. PMID:15939785

  10. Genetics, experience, and host-plant preference in Eurosta solidaginis: implications for host shifts and speciation.

    PubMed

    Craig, T P; Horner, J D; Itami, J K

    2001-04-01

    Host-associated mating is crucial in maintaining the partial reproductive isolation between the host races of Eurosta solidaginis (Diptera: Tephritidae), a fly that forms galls on Solidago altissima and S. gigantea. (We refer to flies reared from S. gigantea as gigantea flies and those reared from S. altissima as altissima flies.) We measured the host preference of males and females of both host races, F1 hybrids between the host races, F2, and backcrosses to both host races. Male and female altissima flies and female gigantea flies had high host fidelity, whereas male gigantea flies had low host fidelity. This result suggests that there may be gene flow between the host races due to nonassortative mating that occurs when male gigantea mate with altissima females on S. altissima. This indicates assortative-mating mechanisms in addition to host-associated mating are required to produce the partial reproductive isolation between the host races that has been observed. Nongenetic factors had no influence on host preference. Larval conditioning did not influence host preference: reciprocal F1 hybrids reared in S. altissima and S. gigantea both preferred S. gigantea. Adult experience had no impact on host preference: females preferred their natal host plant regardless of which host they encountered first as an adult. The hypothesis that maternal effects influence preferences was rejected because male and female flies did not show a consistent preference for the host plant of their mother. We also found no evidence that preference was a sex-linked trait because F1 and backcrosses to the host races with different combinations of X chromosomes from the two host races preferred S. gigantea. Our results indicate that host preference is not determined by a large number of genes because preference of hybrids did not correspond to the proportion of the genome derived from each host race. The strength of the ovipuncture preference for S. gigantea by gigantea females, the females

  11. Are three colonies of Neostromboceros albicomus, a candidate biological control agent for Lygodium microphyllum, the same host biotype?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three colonies of Neostromboceros albicomus, a candidate biological control agent of Lygodium microphyllum, were barcoded using the D2 expansion domain, to determine which of two biotypes they represented. The first colony, collected in 2005 & 2007, was used for the initial host range testing. Colon...

  12. The Role of Within-Host Competition for Coexistence in Multiparasitoid-Host Systems.

    PubMed

    van Velzen, Ellen; Pérez-Vila, Saleta; Etienne, Rampal S

    2016-01-01

    Multiparasitism (females of multiple species parasitizing the same host) is a ubiquitous phenomenon in parasitoids, yet the role of within-host competition has been mostly ignored in multiparasitoid-host models. Here we study the effect of varying the degree of competition at different life stages: competition over oviposition sites (between-adult competition) and larval competition over resources within the host (within-host competition). We adapt a Nicholson-Bailey model to allow for varying levels of between-adult competition (varying the overlap in species distributions) and within-host competition (varying the number of offspring that can successfully emerge from a host). Surprisingly, while stronger between-adult competition reduces coexistence, stronger within-host competition promotes it. Asymmetric between-adult competition (a fecundity difference between the two species) reduces coexistence when compared to symmetric competition; this can be counteracted by asymmetric within-host competition (within-host competitive advantage of the lower-fecundity species), but only when within-host competition is strong and the correlation between the parasitoids' distributions is intermediate. We discuss our results in the context of the interaction between two parasitoid species, Nasonia vitripennis and Nasonia giraulti, which have strongly correlated distributions and high levels of multiparasitism in the field. We conclude that either low or asymmetric within-host competition is unlikely to explain their coexistence. PMID:27277402

  13. Host selection by the autoparasitoid Encarsia pergandiella on primary (Bemisia tabaci) and secondary (Eretmocerus mundus) hosts.

    PubMed

    Zhang, Yi-Bo; Castañé, Cristina; Gabarra, Rosa; Albajes, Ramon; Wan, Fang-Hao

    2015-12-01

    In autoparasitoids, females are generally primary endoparasitoids of Hemiptera, while males are hyperparasitoids developing in or on conspecific females or other primary parasitoids. Female-host acceptance can be influenced by extrinsic and/or intrinsic factors. In this paper, we are concerned with intrinsic factors such as nutritional status, mating status, etc. We observed the behavior of Encarsia pergandiella Howard (Hymenoptera: Aphelinidae) females when parasitizing primary (3rd instar larvae of Bemisia tabaci Gennadius [Homoptera: Aleyrodidae]) and secondary hosts (3rd instar larvae and pupae of Eretmocerus mundus Mercet [Hymenoptera: Aphelinidae]) for a period of 1 h. Females had different reproductive (virgin or mated younger) and physiological (fed elder or mated elder) status. Virgin females killed a large number of secondary hosts while investing a long time per host. However, they did not feed upon them. Mated females killed a lower number of secondary hosts and host feeding was observed in both consuming primary and secondary hosts. It was common to observe host examining females of all physiological statues tested repeatedly stinging the same hosts when parasitizing, killing or rejecting them. Fed elder females parasitized more B. tabaci larvae than E. mundus larvae or pupae, while investing less time on the primary host than on the secondary host. They also parasitized more B. tabaci larvae than mated elder females, while investing less time per host. The access of females to honey allowed them to lay more eggs. PMID:24992443

  14. Coevolutionary interactions between host and parasite genotypes.

    PubMed

    Lambrechts, Louis; Fellous, Simon; Koella, Jacob C

    2006-01-01

    More than 20 years after Dawkins introduced the concept of "extended phenotype" (i.e. phenotypes of hosts and parasites result from interactions between the two genomes) and although this idea has now reached contemporary textbooks of evolutionary biology, most studies of the evolution of host-parasite systems still focus solely on either the host or the parasite, neglecting the role of the other partner. It is important to consider that host and parasite genotypes share control of the epidemiological parameters of their relationship. Moreover, not only the traits of the infection but also the genetic correlations among these and other traits that determine fitness might be controlled by interactions between host and parasite genotypes. PMID:16310412

  15. Host Sexual Dimorphism and Parasite Adaptation

    PubMed Central

    Duneau, David; Ebert, Dieter

    2012-01-01

    In species with separate sexes, parasite prevalence and disease expression is often different between males and females. This effect has mainly been attributed to sex differences in host traits, such as immune response. Here, we make the case for how properties of the parasites themselves can also matter. Specifically, we suggest that differences between host sexes in many different traits, such as morphology and hormone levels, can impose selection on parasites. This selection can eventually lead to parasite adaptations specific to the host sex more commonly encountered, or to differential expression of parasite traits depending on which host sex they find themselves in. Parasites adapted to the sex of the host in this way can contribute to differences between males and females in disease prevalence and expression. Considering those possibilities can help shed light on host–parasite interactions, and impact epidemiological and medical science. PMID:22389630

  16. Protein Kinase B (PknB) of Mycobacterium tuberculosis Is Essential for Growth of the Pathogen in Vitro as well as for Survival within the Host*

    PubMed Central

    Chawla, Yogesh; Upadhyay, Sandeep; Khan, Shazia; Nagarajan, Sathya Narayanan; Forti, Francesca; Nandicoori, Vinay Kumar

    2014-01-01

    The Mycobacterium tuberculosis protein kinase B (PknB) comprises an intracellular kinase domain, connected through a transmembrane domain to an extracellular region that contains four PASTA domains. The present study describes the comprehensive analysis of different domains of PknB in the context of viability in avirulent and virulent mycobacteria. We find stringent regulation of PknB expression necessary for cell survival, with depletion or overexpression of PknB leading to cell death. Although PknB-mediated kinase activity is essential for cell survival, active kinase lacking the transmembrane or extracellular domain fails to complement conditional mutants not expressing PknB. By creating chimeric kinases, we find that the intracellular kinase domain has unique functions in the virulent strain, which cannot be substituted by other kinases. Interestingly, we find that although the presence of the C-terminal PASTA domain is dispensable in the avirulent M. smegmatis, all four PASTA domains are essential in M. tuberculosis. The differential behavior of PknB vis-à-vis the number of essential PASTA domains and the specificity of kinase domain functions suggest that PknB-mediated growth and signaling events differ in virulent compared with avirulent mycobacteria. Mouse infection studies performed to determine the role of PknB in mediating pathogen survival in the host demonstrate that PknB is not only critical for growth of the pathogen in vitro but is also essential for the survival of the pathogen in the host. PMID:24706757

  17. Selecting soluble/foldable protein domains through single-gene or genomic ORF filtering: structure of the head domain of Burkholderia pseudomallei antigen BPSL2063.

    PubMed

    Gourlay, Louise J; Peano, Clelia; Deantonio, Cecilia; Perletti, Lucia; Pietrelli, Alessandro; Villa, Riccardo; Matterazzo, Elena; Lassaux, Patricia; Santoro, Claudio; Puccio, Simone; Sblattero, Daniele; Bolognesi, Martino

    2015-11-01

    The 1.8 Å resolution crystal structure of a conserved domain of the potential Burkholderia pseudomallei antigen and trimeric autotransporter BPSL2063 is presented as a structural vaccinology target for melioidosis vaccine development. Since BPSL2063 (1090 amino acids) hosts only one conserved domain, and the expression/purification of the full-length protein proved to be problematic, a domain-filtering library was generated using β-lactamase as a reporter gene to select further BPSL2063 domains. As a result, two domains (D1 and D2) were identified and produced in soluble form in Escherichia coli. Furthermore, as a general tool, a genomic open reading frame-filtering library from the B. pseudomallei genome was also constructed to facilitate the selection of domain boundaries from the entire ORFeome. Such an approach allowed the selection of three potential protein antigens that were also produced in soluble form. The results imply the further development of ORF-filtering methods as a tool in protein-based research to improve the selection and production of soluble proteins or domains for downstream applications such as X-ray crystallography. PMID:26527140

  18. Uncovering Wolbachia Diversity upon Artificial Host Transfer

    PubMed Central

    Schneider, Daniela I.; Riegler, Markus; Arthofer, Wolfgang; Merçot, Hervé; Stauffer, Christian; Miller, Wolfgang J.

    2013-01-01

    The common endosymbiotic Wolbachia bacteria influence arthropod hosts in multiple ways. They are mostly recognized for their manipulations of host reproduction, yet, more recent studies demonstrate that Wolbachia also impact host behavior, metabolic pathways and immunity. Besides their biological and evolutionary roles, Wolbachia are new potential biological control agents for pest and vector management. Importantly, Wolbachia-based control strategies require controlled symbiont transfer between host species and predictable outcomes of novel Wolbachia-host associations. Theoretically, this artificial horizontal transfer could inflict genetic changes within transferred Wolbachia populations. This could be facilitated through de novo mutations in the novel recipient host or changes of haplotype frequencies of polymorphic Wolbachia populations when transferred from donor to recipient hosts. Here we show that Wolbachia resident in the European cherry fruit fly, Rhagoletis cerasi, exhibit ancestral and cryptic sequence polymorphism in three symbiont genes, which are exposed upon microinjection into the new hosts Drosophila simulans and Ceratitis capitata. Our analyses of Wolbachia in microinjected D. simulans over 150 generations after microinjection uncovered infections with multiple Wolbachia strains in trans-infected lines that had previously been typed as single infections. This confirms the persistence of low-titer Wolbachia strains in microinjection experiments that had previously escaped standard detection techniques. Our study demonstrates that infections by multiple Wolbachia strains can shift in prevalence after artificial host transfer driven by either stochastic or selective processes. Trans-infection of Wolbachia can claim fitness costs in new hosts and we speculate that these costs may have driven the shifts of Wolbachia strains that we saw in our model system. PMID:24376534

  19. Codivergence of Mycoviruses with Their Hosts

    PubMed Central

    Göker, Markus; Scheuner, Carmen; Klenk, Hans-Peter; Stielow, J. Benjamin; Menzel, Wulf

    2011-01-01

    Background The associations between pathogens and their hosts are complex and can result from any combination of evolutionary events such as codivergence, switching, and duplication of the pathogen. Mycoviruses are RNA viruses which infect fungi and for which natural vectors are so far unknown. Thus, lateral transfer might be improbable and codivergence their dominant mode of evolution. Accordingly, mycoviruses are a suitable target for statistical tests of virus-host codivergence, but inference of mycovirus phylogenies might be difficult because of low sequence similarity even within families. Methodology We analyzed here the evolutionary dynamics of all mycovirus families by comparing virus and host phylogenies. Additionally, we assessed the sensitivity of the co-phylogenetic tests to the settings for inferring virus trees from their genome sequences and approximate, taxonomy-based host trees. Conclusions While sequence alignment filtering modes affected branch support, the overall results of the co-phylogenetic tests were significantly influenced only by the number of viruses sampled per family. The trees of the two largest families, Partitiviridae and Totiviridae, were significantly more similar to those of their hosts than expected by chance, and most individual host-virus links had a significant positive impact on the global fit, indicating that codivergence is the dominant mode of virus diversification. However, in this regard mycoviruses did not differ from closely related viruses sampled from non-fungus hosts. The remaining virus families were either dominated by other evolutionary modes or lacked an apparent overall pattern. As this negative result might be caused by insufficient taxon sampling, the most parsimonious hypothesis still is that host-parasite evolution is basically the same in all mycovirus families. This is the first study of mycovirus-host codivergence, and the results shed light not only on how mycovirus biology affects their co

  20. Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

    PubMed Central

    Khor, Susan

    2014-01-01

    Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains. PMID:24586450

  1. Function of Nod-like Receptors in Microbial Recognition and Host Defense

    PubMed Central

    Franchi, Luigi; Warner, Neil; Viani, Kyle; Nuñez, Gabriel

    2009-01-01

    Summary Nucleotide oligomerization domain (NOD)-like receptors (NLRs) are a specialized group of intracellular proteins that play a critical role in the regulation of the host innate immune response. NLRs act as scaffolding proteins that assemble signaling platforms that trigger nuclear factor-κB and mitogen-activated protein kinase signaling pathways and control the activation of inflammatory caspases. Importantly, mutations in several members of the NLR family have been linked to a variety of inflammatory diseases consistent with these molecules playing an important role in host-pathogen interactions and the inflammatory response. In this review, we focus on the role of Nod1 and Nod2 in host defense and in particular discuss recent finding regarding the role of Nlrc4, Nlpr1, and Nlrp3 inflammasomes in caspase-1 activation and subsequent release of proinflammatory cytokines such as interleukin-1β. PMID:19120480

  2. A Method to Examine Content Domain Structures

    ERIC Educational Resources Information Center

    D'Agostino, Jerome; Karpinski, Aryn; Welsh, Megan

    2011-01-01

    After a test is developed, most content validation analyses shift from ascertaining domain definition to studying domain representation and relevance because the domain is assumed to be set once a test exists. We present an approach that allows for the examination of alternative domain structures based on extant test items. In our example based on…

  3. Ectoparasitism and stress hormones: strategy of host exploitation, common host-parasite history and energetics matter.

    PubMed

    St Juliana, Justin R; Khokhlova, Irina S; Wielebnowski, Nadja; Kotler, Burt P; Krasnov, Boris R

    2014-09-01

    Parasites are thought to have numerous negative effects on their hosts. These negative effects may be associated with stress in a host. We evaluated the effects of four species of flea ectoparasites (Parapulex chephrenis, Synosternus cleopatrae, Xenopsylla conformis and Xenopsylla ramesis) on non-specific responses of eight species of rodents (Meriones crassus, Gerbillus dasyurus, Gerbillus andersoni, Gerbillus pyramidum, Gerbillus nanus, Acomys cahirinus, Acomys russatus and Mesocricetus auratus) and measured faecal glucocorticoid metabolites concentrations (FGMC) produced by the hosts. We found no effect of body mass of an individual rodent on FGMCs. Parasitism by fleas with a 'stay on the host body' exploitation strategy was associated with higher host FGMCs than parasitism by fleas that spent most of their life 'off-host'. FGMCs among rodents infested by the same flea species were correlated positively with the phylogenetic distance of a given rodent from the principal host of this flea; changes in FGMCs were lower in the host species more closely related to the flea's principal host. Changes in FMGCs of a host while parasitized were correlated with a host's change in body mass, where hosts that lost more body mass had higher FGMCs. Our results suggest that ectoparasitism can be stressful to their hosts. However, the occurrence of parasite-induced stress seems to depend on the identity of both host and parasite species and the evolutionary history of a host-parasite association. To our knowledge, this is the first multispecies study to evaluate the effect of ectoparasites on glucocorticoid hormones in small mammals. PMID:24661039

  4. Mosquito Host Selection Varies Seasonally with Host Availability and Mosquito Density

    PubMed Central

    Thiemann, Tara C.; Wheeler, Sarah S.; Barker, Christopher M.; Reisen, William K.

    2011-01-01

    Host selection by vector mosquitoes is a critical component of virus proliferation, particularly for viruses such as West Nile (WNV) that are transmitted enzootically to a variety of avian hosts, and tangentially to dead-end hosts such as humans. Culex tarsalis is a principal vector of WNV in rural areas of western North America. Based on previous work, Cx. tarsalis utilizes a variety of avian and mammalian hosts and tends to feed more frequently on mammals in the late summer than during the rest of the year. To further explore this and other temporal changes in host selection, bloodfed females were collected at a rural farmstead and heron nesting site in Northern California from May 2008 through May 2009, and bloodmeal hosts identified using either a microsphere-based array or by sequencing of the mitochondrial cytochrome c oxidase I (COI) gene. Host composition during summer was dominated by four species of nesting Ardeidae. In addition, the site was populated with various passerine species as well as domestic farm animals and humans. When present, Cx. tarsalis fed predominantly (>80%) upon the ardeids, with Black-crowned Night-Herons, a highly competent WNV host, the most prevalent summer host. As the ardeids fledged and left the area and mosquito abundance increased in late summer, Cx. tarsalis feeding shifted to include more mammals, primarily cattle, and a high diversity of avian species. In the winter, Yellow-billed Magpies and House Sparrows were the predominant hosts, and Yellow-billed Magpies and American Robins were fed upon more frequently than expected given their relative abundance. These data demonstrated that host selection was likely based both on host availability and differences in utilization, that the shift of bloodfeeding to include more mammalian hosts was likely the result of both host availability and increased mosquito abundance, and that WNV-competent hosts were fed upon by Cx. tarsalis throughout the year. PMID:22206038

  5. Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

    PubMed

    Klemm, Elizabeth J; Gkrania-Klotsas, Effrossyni; Hadfield, James; Forbester, Jessica L; Harris, Simon R; Hale, Christine; Heath, Jennifer N; Wileman, Thomas; Clare, Simon; Kane, Leanne; Goulding, David; Otto, Thomas D; Kay, Sally; Doffinger, Rainer; Cooke, Fiona J; Carmichael, Andrew; Lever, Andrew M L; Parkhill, Julian; MacLennan, Calman A; Kumararatne, Dinakantha; Dougan, Gordon; Kingsley, Robert A

    2016-01-01

    Host adaptation is a key factor contributing to the emergence of new bacterial, viral and parasitic pathogens. Many pathogens are considered promiscuous because they cause disease across a range of host species, while others are host-adapted, infecting particular hosts(1). Host adaptation can potentially progress to host restriction, where the pathogen is strictly limited to a single host species and is frequently associated with more severe symptoms. Host-adapted and host-restricted bacterial clades evolve from within a broader host-promiscuous species and sometimes target different niches within their specialist hosts, such as adapting from a mucosal to a systemic lifestyle. Genome degradation, marked by gene inactivation and deletion, is a key feature of host adaptation, although the triggers initiating genome degradation are not well understood. Here, we show that a chronic systemic non-typhoidal Salmonella infection in an immunocompromised human patient resulted in genome degradation targeting genes that are expendable for a systemic lifestyle. We present a genome-based investigation of a recurrent blood-borne Salmonella enterica serotype Enteritidis (S. Enteritidis) infection covering 15 years in an interleukin-12 β1 receptor-deficient individual that developed into an asymptomatic chronic infection. The infecting S. Enteritidis harboured a mutation in the mismatch repair gene mutS that accelerated the genomic mutation rate. Phylogenetic analysis and phenotyping of multiple patient isolates provides evidence for a remarkable level of within-host evolution that parallels genome changes present in successful host-restricted bacterial pathogens but never before observed on this timescale. Our analysis identifies common pathways of host adaptation and demonstrates the role that immunocompromised individuals can play in this process. PMID:27572160

  6. Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host

    PubMed Central

    Klemm, Elizabeth J; Gkrania-Klotsas, Effrossyni; Hadfield, James; Forbester, Jessica L; Harris, Simon R; Hale, Christine; Heath, Jennifer N; Wileman, Thomas; Clare, Simon; Kane, Leanne; Goulding, David; Otto, Thomas D; Kay, Sally; Doffinger, Rainer; Cooke, Fiona J; Carmichael, Andrew; Lever, Andrew ML; Parkhill, Julian; MacLennan, Calman A; Kumararatne, Dinakantha

    2016-01-01

    Summary Host adaptation is a key factor contributing to the emergence of new bacterial, viral and parasitic pathogens. Many pathogens are considered promiscuous because they cause disease across a range of host species, while others are host-adapted, infecting particular hosts1. Host adaptation can potentially progress to host restriction where the pathogen is strictly limited to a single host species and is frequently associated with more severe symptoms. Host-adapted and host-restricted bacterial clades evolve from within a broader host-promiscuous species and sometimes target different niches within their specialist hosts, such as adapting from a mucosal to a systemic lifestyle. Genome degradation, marked by gene inactivation and deletion, is a key feature of host adaptation, although the triggers initiating genome degradation are not well understood. Here, we show that a chronic systemic non-typhoidal Salmonella infection in an immunocompromised human patient resulted in genome degradation targeting genes that are expendable for a systemic lifestyle. We present a genome-based investigation of a recurrent blood-borne Salmonella enterica serotype Enteritidis (S. Enteritidis) infection covering 15 years in an interleukin (IL)-12 β-1 receptor-deficient individual that developed into an asymptomatic chronic infection. The infecting S. Enteritidis harbored a mutation in the mismatch repair gene mutS that accelerated the genomic mutation rate. Phylogenetic analysis and phenotyping of multiple patient isolates provides evidence for a remarkable level of within-host evolution that parallels genome changes present in successful host-restricted bacterial pathogens but never before observed on this timescale. Our analysis identifies common pathways of host adaptation and demonstrates the role that immunocompromised individuals can play in this process. PMID:27127642

  7. Mosquito host selection varies seasonally with host availability and mosquito density.

    PubMed

    Thiemann, Tara C; Wheeler, Sarah S; Barker, Christopher M; Reisen, William K

    2011-12-01

    Host selection by vector mosquitoes is a critical component of virus proliferation, particularly for viruses such as West Nile (WNV) that are transmitted enzootically to a variety of avian hosts, and tangentially to dead-end hosts such as humans. Culex tarsalis is a principal vector of WNV in rural areas of western North America. Based on previous work, Cx. tarsalis utilizes a variety of avian and mammalian hosts and tends to feed more frequently on mammals in the late summer than during the rest of the year. To further explore this and other temporal changes in host selection, bloodfed females were collected at a rural farmstead and heron nesting site in Northern California from May 2008 through May 2009, and bloodmeal hosts identified using either a microsphere-based array or by sequencing of the mitochondrial cytochrome c oxidase I (COI) gene. Host composition during summer was dominated by four species of nesting Ardeidae. In addition, the site was populated with various passerine species as well as domestic farm animals and humans. When present, Cx. tarsalis fed predominantly (>80%) upon the ardeids, with Black-crowned Night-Herons, a highly competent WNV host, the most prevalent summer host. As the ardeids fledged and left the area and mosquito abundance increased in late summer, Cx. tarsalis feeding shifted to include more mammals, primarily cattle, and a high diversity of avian species. In the winter, Yellow-billed Magpies and House Sparrows were the predominant hosts, and Yellow-billed Magpies and American Robins were fed upon more frequently than expected given their relative abundance. These data demonstrated that host selection was likely based both on host availability and differences in utilization, that the shift of bloodfeeding to include more mammalian hosts was likely the result of both host availability and increased mosquito abundance, and that WNV-competent hosts were fed upon by Cx. tarsalis throughout the year. PMID:22206038

  8. Tensor distinction of domains in ferroic crystals

    NASA Astrophysics Data System (ADS)

    Litvin, D. B.

    2009-10-01

    Ferroic crystals contain two or more domains and may be distinguished by the values of components of tensorial physical properties of the domains. We have extended Aizu’s global tensor distinction by magnetization, polarization, and strain of all domains which arise in a ferroic phase transition to include distinction by toroidal moment, and from phases invariant under time reversal to domains which arise in transitions from all magnetic and non-magnetic phases. For determining possible switching of domains, a domain pair tensor distinction is also considered for all pairs of domains which arise in each ferroic phase transition.

  9. Protein structural domains: definition and prediction.

    PubMed

    Ezkurdia, Iakes; Tress, Michael L

    2011-11-01

    Recognition and prediction of structural domains in proteins is an important part of structure and function prediction. This unit lists the range of tools available for domain prediction, and describes sequence and structural analysis tools that complement domain prediction methods. Also detailed are the basic domain prediction steps, along with suggested strategies for different protein sequences and potential pitfalls in domain boundary prediction. The difficult problem of domain orientation prediction is also discussed. All the resources necessary for domain boundary prediction are accessible via publicly available Web servers and databases and do not require computational expertise. PMID:22045561

  10. The Luminosity Function of QSO Host Galaxies

    NASA Technical Reports Server (NTRS)

    Hamilton, Timothy S.; Casertano, Stefano; Turnshek, David A.; White, Nicholas E. (Technical Monitor)

    2002-01-01

    We present some results from our HST archival image study of 71 QSO host galaxies. The objects are selected to have z less than or equal to 0.46 and total absolute magnitude M(sub v) less than or equal to -23 in our adopted cosmology (H(sub 0) = 50 kilometers per second Mpc(sup-1), q(sub 0) = 0.5, lambda = 0)). The aim of this initial study is to investigate the composition of the sample with respect to host morphology and radio loudness, as well as derive the QSO host galaxy luminosity function. We have analyzed available WFPC2 images in R or I band (U in one case), using a uniform set of procedures. The host galaxies span a narrow range of luminosities and are exceptionally bright, much more so than normal galaxies, usually L greater than L*(sub v). The QSOs are almost equally divided among three subclasses: radio-loud QSOs with elliptical hosts, radio-quiet QSOs with elliptical hosts, and radio-quiet QSOs with spiral hosts. Radio-loud QSOs with spiral hosts are extremely rare. Using a weighting procedure, we derive the combined luminosity function of QSO host galaxies. We find that the luminosity function of QSO hosts differs in shape from that of normal galaxies but that they coincide at the highest luminosities. The ratio of the number of quasar hosts to the number of normal galaxies at a luminosity L*(sub v) is R = (Lv/11.48L*(sub v))(sup 2.46), where L*(sub v) corresponds to M*(sub v)= -22.35, and a QSO is defined to be an object with total nuclear plus host light M(sub v) less than or equal to -23. This ratio can be interpreted as the probability that a galaxy with luminosity L(sub V) will host a QSO at redshift z approximately equal to 0.26.

  11. THE LOCAL HOSTS OF TYPE Ia SUPERNOVAE

    SciTech Connect

    Neill, James D.; Martin, D. Christopher; Barlow, Tom A.; Foster, Karl; Friedman, Peter G.; Morrissey, Patrick; Wyder, Ted K.; Sullivan, Mark; Howell, D. Andrew; Conley, Alex; Seibert, Mark; Madore, Barry F.; Neff, Susan G.; Schiminovich, David; Bianchi, Luciana; Donas, Jose; Milliard, Bruno; Heckman, Timothy M.; Lee, Young-Wook; Rich, R. Michael

    2009-12-20

    We use multi-wavelength, matched aperture, integrated photometry from the Galaxy Evolution Explorer (GALEX), the Sloan Digital Sky Survey, and the RC3 to estimate the physical properties of 166 nearby galaxies hosting 168 well-observed Type Ia supernovae (SNe Ia). The ultraviolet (UV) imaging of local SN Ia hosts from GALEX allows a direct comparison with higher-redshift hosts measured at optical wavelengths that correspond to the rest-frame UV. Our data corroborate well-known features that have been seen in other SN Ia samples. Specifically, hosts with active star formation produce brighter and slower SNe Ia on average, and hosts with luminosity-weighted ages older than 1 Gyr produce on average more faint, fast, and fewer bright, slow SNe Ia than younger hosts. New results include that in our sample, the faintest and fastest SNe Ia occur only in galaxies exceeding a stellar mass threshold of approx10{sup 10} M{sub sun}, leading us to conclude that their progenitors must arise in populations that are older and/or more metal rich than the general SN Ia population. A low host extinction subsample hints at a residual trend in peak luminosity with host age, after correcting for light-curve shape, giving the appearance that older hosts produce less-extincted SNe Ia on average. This has implications for cosmological fitting of SNe Ia, and suggests that host age could be useful as a parameter in the fitting. Converting host mass to metallicity and computing {sup 56}Ni mass from the supernova light curves, we find that our local sample is consistent with a model that predicts a shallow trend between stellar metallicity and the {sup 56}Ni mass that powers the explosion, but we cannot rule out the absence of a trend. We measure a correlation between {sup 56}Ni mass and host age in the local universe that is shallower and not as significant as that seen at higher redshifts. The details of the age-{sup 56}Ni mass correlations at low and higher redshift imply a luminosity

  12. Development in the Food Domain.

    ERIC Educational Resources Information Center

    Rozin, Paul

    1990-01-01

    Discusses problems of general interest in developmental psychology that can be successfully studied in the domain of food; these include (1) development of food likes and dislikes; (2) establishment of the edible/inedible distinction; (3) disgust and contagion; (4) transgenerational communication of preferences; and (5) transition to food…

  13. Cellulose binding domain fusion proteins

    DOEpatents

    Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1998-02-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  14. Cellulose binding domain fusion proteins

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  15. Enabling Interoperability in Heliophysical Domains

    NASA Astrophysics Data System (ADS)

    Bentley, Robert

    2013-04-01

    There are many aspects of science in the Solar System that are overlapping - phenomena observed in one domain can have effects in other domains. However, there are many problems related to exploiting the data in cross-disciplinary studies because of lack of interoperability of the data and services. The CASSIS project is a Coordination Action funded under FP7 that has the objective of improving the interoperability of data and services related Solar System science. CASSIS has been investigating how the data could be made more accessible with some relatively minor changes to the observational metadata. The project has been looking at the services that are used within the domain and determining whether they are interoperable with each other and if not what would be required make them so. It has also been examining all types of metadata that are used when identifying and using observations and trying to make them more compliant with techniques and standards developed by bodies such as the International Virtual Observatory Alliance (IVOA). Many of the lessons that are being learnt in the study are applicable to domains that go beyond those directly involved in heliophysics. Adopting some simple standards related to the design of the services interfaces and metadata that are used would make it much easier to investigate interdisciplinary science topics. We will report on our finding and describe a roadmap for the future. For more information about CASSIS, please visit the project Web site on cassis-vo.eu

  16. Identification of alternative topological domains in chromatin

    PubMed Central

    2014-01-01

    Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The ensemble of domains we identify allows us to quantify the degree to which the domain structure is hierarchical as opposed to overlapping, and our analysis reveals a pronounced hierarchical structure in which larger stable domains tend to completely contain smaller domains. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone marks at the boundaries. PMID:24868242

  17. Exclusion and spatial segregation in the apparent competition between two hosts sharing macroparasites.

    PubMed

    Manica, Mattia; Rosà, Roberto; Pugliese, Andrea; Bolzoni, Luca

    2013-06-01

    In this paper we investigate the spatial dynamics of a deterministic model describing two host species that partially share a common spatial domain, experiencing apparent competition mediated by macroparasites. The aim of this work is to understand the mechanisms underlying apparent competition processes in a spatially structured environment, which have been generally overlooked up to now. First, we analyse the behaviour of a single-host macroparasite partial differential equation (PDE) model, both in the cases of uniform or spatially-dependent vital rates of the host, focusing on the role of spatial diffusion on parasite persistence and host abundance. We obtained the threshold condition for parasite persistence, and (in contrast to what occurs in reaction-diffusion models for an isolated population) we found that, in the case of spatially-dependent vital rates, increasing the host diffusion coefficient results in an increase of the overall host population. Then, a PDE model featuring spatial diffusion and apparent competition mediated via shared macroparasites between two species is analysed in order to understand the role of spatial heterogeneity in host coexistence. We assumed a partial overlap among the habitats of the two species and found that the shared parasites could cause, depending on the values of the diffusion coefficients and differences in induced mortality among host species, a decrease of the realized habitat and, eventually, the extinction of the species less tolerant to parasite infection. This shows that the presence of regulating parasites complicates the effect of dispersal on population dynamics and that the dynamics of apparent competition cannot be adequately understood from spatially-independent models. PMID:23524023

  18. Diversity in protein recognition by PTB domains.

    PubMed

    Forman-Kay, J D; Pawson, T

    1999-12-01

    Phosphotyrosine-binding (PTB) domains were originally identified as modular domains that recognize phosphorylated Asn-Pro-Xxx-p Tyr-containing proteins. Recent binding and structural studies of PTB domain complexes with target peptides have revealed a number of deviations from the previously described mode of interaction, with respect to both the sequences of possible targets and their structures within the complexes. This diversity of recognition by PTB domains extends and strengthens our general understanding of modular binding domain recognition. PMID:10607674

  19. A venom metalloproteinase from the parasitic wasp Eulophus pennicornis is toxic towards its host, tomato moth (Lacanobia oleracae).

    PubMed

    Price, D R G; Bell, H A; Hinchliffe, G; Fitches, E; Weaver, R; Gatehouse, J A

    2009-04-01

    Three genes encoding clan MB metalloproteinases (EpMP1-3) were identified from venom glands of the ectoparasitic wasp Eulophus pennicornis. The derived amino acid sequences predict mature proteins of approximately 46 kDa, with a novel two-domain structure comprising a C-terminal reprolysin domain, and an N-terminal domain of unknown function. EpMP3 expressed as a recombinant protein in Pichia pastoris had gelatinase activity, which was inhibited by EDTA. Injection of recombinant EpMP3 into fifth instar Lacanobia oleracea (host) larvae resulted in partial insect mortality associated with the moult to sixth instar, with surviving insects showing retarded development and growth. EpMP3 is expressed specifically in venom glands. These results suggest that EpMP3 is a functional component of Eulophus venom, which is able to manipulate host development. PMID:19320760

  20. Bacillus anthracis TIR Domain-Containing Protein Localises to Cellular Microtubule Structures and Induces Autophagy

    PubMed Central

    Carlsson, Emil; Thwaite, Joanne E.; Jenner, Dominic C.; Spear, Abigail M.; Flick-Smith, Helen; Atkins, Helen S.; Ding, Jeak Ling

    2016-01-01

    Toll-like receptors (TLRs) recognise invading pathogens and mediate downstream immune signalling via Toll/IL-1 receptor (TIR) domains. TIR domain proteins (Tdps) have been identified in multiple pathogenic bacteria and have recently been implicated as negative regulators of host innate immune activation. A Tdp has been identified in Bacillus anthracis, the causative agent of anthrax. Here we present the first study of this protein, designated BaTdp. Recombinantly expressed and purified BaTdp TIR domain interacted with several human TIR domains, including that of the key TLR adaptor MyD88, although BaTdp expression in cultured HEK293 cells had no effect on TLR4- or TLR2- mediated immune activation. During expression in mammalian cells, BaTdp localised to microtubular networks and caused an increase in lipidated cytosolic microtubule-associated protein 1A/1B-light chain 3 (LC3), indicative of autophagosome formation. In vivo intra-nasal infection experiments in mice showed that a BaTdp knockout strain colonised host tissue faster with higher bacterial load within 4 days post-infection compared to the wild type B. anthracis. Taken together, these findings indicate that BaTdp does not play an immune suppressive role, but rather, its absence increases virulence. BaTdp present in wild type B. anthracis plausibly interact with the infected host cell, which undergoes autophagy in self-defence. PMID:27391310

  1. Bacillus anthracis TIR Domain-Containing Protein Localises to Cellular Microtubule Structures and Induces Autophagy.

    PubMed

    Carlsson, Emil; Thwaite, Joanne E; Jenner, Dominic C; Spear, Abigail M; Flick-Smith, Helen; Atkins, Helen S; Byrne, Bernadette; Ding, Jeak Ling

    2016-01-01

    Toll-like receptors (TLRs) recognise invading pathogens and mediate downstream immune signalling via Toll/IL-1 receptor (TIR) domains. TIR domain proteins (Tdps) have been identified in multiple pathogenic bacteria and have recently been implicated as negative regulators of host innate immune activation. A Tdp has been identified in Bacillus anthracis, the causative agent of anthrax. Here we present the first study of this protein, designated BaTdp. Recombinantly expressed and purified BaTdp TIR domain interacted with several human TIR domains, including that of the key TLR adaptor MyD88, although BaTdp expression in cultured HEK293 cells had no effect on TLR4- or TLR2- mediated immune activation. During expression in mammalian cells, BaTdp localised to microtubular networks and caused an increase in lipidated cytosolic microtubule-associated protein 1A/1B-light chain 3 (LC3), indicative of autophagosome formation. In vivo intra-nasal infection experiments in mice showed that a BaTdp knockout strain colonised host tissue faster with higher bacterial load within 4 days post-infection compared to the wild type B. anthracis. Taken together, these findings indicate that BaTdp does not play an immune suppressive role, but rather, its absence increases virulence. BaTdp present in wild type B. anthracis plausibly interact with the infected host cell, which undergoes autophagy in self-defence. PMID:27391310

  2. Contrasting Lifestyles Within the Host Cell.

    PubMed

    Di Russo Case, Elizabeth; Samuel, James E

    2016-02-01

    Intracellular bacterial pathogens have evolved to exploit the protected niche provided within the boundaries of a eukaryotic host cell. Upon entering a host cell, some bacteria can evade the adaptive immune response of its host and replicate in a relatively nutrient-rich environment devoid of competition from other host flora. Growth within a host cell is not without their hazards, however. Many pathogens enter their hosts through receptor-mediated endocytosis or phagocytosis, two intracellular trafficking pathways that terminate in a highly degradative organelle, the phagolysosome. This usually deadly compartment is maintained at a low pH and contains degradative enzymes and reactive oxygen species, resulting in an environment to which few bacterial species are adapted. Some intracellular pathogens, such as Shigella, Listeria, Francisella, and Rickettsia, escape the phagosome to replicate within the cytosol of the host cell. Bacteria that remain within a vacuole either alter the trafficking of their initial phagosomal compartment or adapt to survive within the harsh environment it will soon become. In this chapter, we focus on the mechanisms by which different vacuolar pathogens either evade lysosomal fusion, as in the case of Mycobacterium and Chlamydia, or allow interaction with lysosomes to varying degrees, such as Brucella and Coxiella, and their specific adaptations to inhabit a replicative niche. PMID:26999394

  3. Contrasting Lifestyles Within the Host Cell

    PubMed Central

    Case, Elizabeth Di Russo; Samuel, James E.

    2015-01-01

    CHAPTER SUMMARY Intracellular bacterial pathogens have evolved to exploit the protected niche provided within the boundaries of a eukaryotic host cell. Upon entering a host cell, some bacteria can evade the adaptive immune response of its host, and replicate in a relatively nutrient-rich environment devoid of competition from other host flora. Growth within a host cell is not without its hazards, however. Many pathogens enter their hosts through receptor-mediated endocytosis or phagocytosis, two intracellular trafficking pathways that terminate in a highly degradative organelle, the phagolysosome. This usually deadly compartment is maintained at a low pH, and contains degradative enzymes, and reactive oxygen species resulting in an environment to which few bacterial species are adapted. Some intracellular pathogens, like Shigella, Listeria, Francisella, and Rickettsia escape the phagosome to replicate within the cytosol of the host cell. Bacteria that remain within a vacuole either alter the trafficking of their initial phagosomal compartment or adapt to survive within the harsh environment it will soon become. In this chapter, we focus on the mechanisms by which different vacuolar pathogens either evade lysosomal fusion, as in the case of Mycobacterium and Chlamydia, or allow interaction with lysosomes to varying degrees, such as Brucella and Coxiella, and their specific adaptations to inhabit a replicative niche. PMID:26999394

  4. Host defence mediates interspecific competition in ectoparasites.

    PubMed

    Bush, Sarah E; Malenke, Jael R

    2008-05-01

    1. Interspecific competition influences which, how many and where species coexist in biological communities. Interactions between species in different trophic levels can mediate interspecific competition; e.g. predators are known to reduce competition between prey species by suppressing their population sizes. A parallel phenomenon may take place in host-parasite systems, with host defence mediating competition between parasite species. 2. We experimentally investigated the impact of host defence (preening) on competitive interactions between two species of feather-feeding lice: 'wing' lice Columbicola columbae and 'body' lice Campanulotes compar. Both species are host-specific parasites that co-occur on rock pigeons Columba livia. 3. We show that wing lice and body lice compete and that host defence mediates the magnitude of this competitive interaction. 4. Competition is asymmetrical; wing louse populations are negatively impacted by body lice, but not vice versa. This competitive asymmetry is consistent with the fact that body lice predominate in microhabitats on the host's body that offer the most food and the most space. 5. Our results indicate that host-defence-mediated competition can influence the structure of parasite communities and may play a part in the evolution of parasite diversity. PMID:18194262

  5. Mechanisms of host seeking by parasitic nematodes.

    PubMed

    Gang, Spencer S; Hallem, Elissa A

    2016-07-01

    The phylum Nematoda comprises a diverse group of roundworms that includes parasites of vertebrates, invertebrates, and plants. Human-parasitic nematodes infect more than one billion people worldwide and cause some of the most common neglected tropical diseases, particularly in low-resource countries [1]. Parasitic nematodes of livestock and crops result in billions of dollars in losses each year [1]. Many nematode infections are treatable with low-cost anthelmintic drugs, but repeated infections are common in endemic areas and drug resistance is a growing concern with increasing therapeutic and agricultural administration [1]. Many parasitic nematodes have an environmental infective larval stage that engages in host seeking, a process whereby the infective larvae use sensory cues to search for hosts. Host seeking is a complex behavior that involves multiple sensory modalities, including olfaction, gustation, thermosensation, and humidity sensation. As the initial step of the parasite-host interaction, host seeking could be a powerful target for preventative intervention. However, host-seeking behavior remains poorly understood. Here we review what is currently known about the host-seeking behaviors of different parasitic nematodes, including insect-parasitic nematodes, mammalian-parasitic nematodes, and plant-parasitic nematodes. We also discuss the neural bases of these behaviors. PMID:27211240

  6. Analysis of multi-domain protein dynamics

    PubMed Central

    Roy, Amitava; Hua, Duy P; Post, Carol Beth

    2016-01-01

    Proteins with a modular architecture of multiple domains connected by linkers often exhibit diversity in the relative positions of domains while the domain tertiary structure remains unchanged. The biological function of these modular proteins, or the regulation of their activity depends on the variation in domain orientation and separation. Accordingly, careful characterization of inter-domain motion and correlated fluctuations of multi-domain systems is relevant for understanding the functional behavior of modular proteins. Molecular dynamics (MD) simulations provides a powerful approach to study these motions in atomic detail. Nevertheless, the common procedure for analyzing fluctuations from MD simulations after overall rigid-body alignment fails for multi-domain proteins; it greatly overestimates correlated positional fluctuations in the presence of relative domain motion. We show here that expressing the atomic motions of a multi-domain protein as a combination of displacement within the domain reference frame and motion of the relative domains correctly separates the internal motions to allow a useful description of correlated fluctuations. We illustrate the methodology of separating the domain fluctuations and local fluctuations by application to the tandem SH2 domains of human Syk protein kinase and by characterizing an effect of phosphorylation on the dynamics. Correlated motions are assessed from a distance covariance rather than the more common vector-coordinate covariance. The approach makes it possible to calculate the proper correlations in fluctuations internal to a domain as well as between domains. PMID:26675644

  7. THE EXTREME HOSTS OF EXTREME SUPERNOVAE

    SciTech Connect

    Neill, James D.; Quimby, Robert; Ofek, Eran; Wyder, Ted K.; Martin, D. Christopher; Barlow, Tom A.; Foster, Karl; Friedman, Peter G.; Morrissey, Patrick; Sullivan, Mark; Gal-Yam, Avishay; Howell, D. Andrew; Nugent, Peter; Seibert, Mark; Overzier, Roderik; Neff, Susan G.; Schiminovich, David; Bianchi, Luciana; Donas, Jose; Heckman, Timothy M.

    2011-01-20

    We use GALEX ultraviolet (UV) and optical integrated photometry of the hosts of 17 luminous supernovae (LSNe, having peak M{sub V} < -21) and compare them to a sample of 26, 000 galaxies from a cross-match between the SDSS DR4 spectral catalog and GALEX interim release 1.1. We place the LSN hosts on the galaxy NUV - r versus M{sub r} color-magnitude diagram (CMD) with the larger sample to illustrate how extreme they are. The LSN hosts appear to favor low-density regions of the galaxy CMD falling on the blue edge of the blue cloud toward the low-luminosity end. From the UV-optical photometry, we estimate the star formation history of the LSN hosts. The hosts have moderately low star formation rates (SFRs) and low stellar masses (M{sub *}) resulting in high specific star formation rates (sSFR). Compared with the larger sample, the LSN hosts occupy low-density regions of a diagram plotting sSFR versus M{sub *} in the area having higher sSFR and lower M{sub *}. This preference for low M{sub *}, high sSFR hosts implies that the LSNe are produced by an effect having to do with their local environment. The correlation of mass with metallicity suggests that perhaps wind-driven mass loss is the factor that prevents LSNe from arising in higher-mass, higher-metallicity hosts. The massive progenitors of the LSNe (>100 M{sub sun}), by appearing in low-SFR hosts, are potential tests for theories of the initial mass function that limit the maximum mass of a star based on the SFR.

  8. Host conservatism or host specialization? Patterns of fungal diversification are influenced by host specificity in Ophiognomonia (Gnomoniaceae, Diaporthales)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species of Ophiognomonia (Gnomoniaceae) are perithecial fungi that occur as endophytes, pathogens, and latent saprobes on leaf and stem tissue of plants in the Betulaceae, Fagaceae, Juglandaceae, Lauraceae, Malvaceae, Platanaceae, Rosaceae, Salicaceae, and Sapindaceae. In this study host plant patte...

  9. Hepatitis E virus ORF1 encoded non structural protein-host protein interaction network.

    PubMed

    Ojha, Nishant Kumar; Lole, Kavita S

    2016-02-01

    Hepatitis E virus ORF1 encoded non-structural polyprotein (nsP) consist of multiple domains, namely: Methyltransferase, Y-domain, Protease, X-domain, Helicase and RNA dependent RNA polymerase. We have attempted to identify human liver cell proteins that are interacting with HEV ORF1 encoded functional domains by using Y2H screening. A total of 155 protein-protein interactions between HEV-ORF1 and human proteins were identified. Comparative analysis of the HEV-ORF1-Human interaction network with reconstructed human interactome showed that the cellular proteins interacting with HEV-ORF1 are central and interconnected. Enrichment analysis of Gene Ontology and cellular pathways showed that the viral proteins preferentially interacted with the proteins of metabolism and energy generation along with host immune response and ubiquitin proteasomal pathways. The mTOR and focal adhesion pathways were also targeted by the virus. These interactions suggest that HEV probably utilizes important proteins in carbohydrate metabolism, energy generation and iron homoeostasis in the host cells during its establishment. PMID:26689634

  10. Host restriction factors for hepatitis C virus

    PubMed Central

    Zhou, Li-Ya; Zhang, Lei-Liang

    2016-01-01

    Host-hepatitis C virus (HCV) interactions have both informed fundamental concepts of viral replication and pathogenesis and provided novel insights into host cell biology. These findings are illustrated by the recent discovery of host-encoded factors that restrict HCV infection. In this review, we briefly discuss these restriction factors in different steps of HCV infection. In each case, we discuss how these restriction factors were identified, the mechanisms by which they inhibit HCV infection and their potential contribution to viral pathogenesis. PMID:26819515

  11. Integral field spectroscopy of QSO host galaxies

    NASA Astrophysics Data System (ADS)

    Jahnke, K.; Wisotzki, L.; Sánchez, S. F.; Christensen, L.; Becker, T.; Kelz, A.; Roth, M. M.

    2004-02-01

    We describe a project to study the state of the ISM in ˜20 low redshift (z<0.3) QSO host galaxies observed with the PMAS integral field spectrograph. We describe the development of the method to access the stellar and gas components of the spectrum without the strong nuclear emission, in order to access the host galaxy properties in the central region. It shows that integral field spectroscopy promises to be very efficient in studying the gas distribution and its velocity field, and also the spatially resolved stellar population in the host galaxies of luminous AGN.

  12. Iron homeostasis in host defence and inflammation

    PubMed Central

    Ganz, Tomas; Nemeth, Elizabeta

    2016-01-01

    Iron is an essential trace element for multicellular organisms and nearly all microorganisms. Although iron is abundant in the environment, common forms of iron are minimally soluble and therefore poorly accessible to biological organisms. Microorganisms entering a mammalian host face multiple mechanisms that further restrict their ability to obtain iron and thereby limit their pathogenicity. Iron levels also modulate host defence, as iron content in macrophages regulates their cytokine production. Here, we review recent advances that highlight the role of systemic and cellular iron-regulating mechanisms in protecting hosts from infection, emphasizing aspects that are applicable to human health and disease. PMID:26160612

  13. Direct imaging of topological edge states at a bilayer graphene domain wall.

    PubMed

    Yin, Long-Jing; Jiang, Hua; Qiao, Jia-Bin; He, Lin

    2016-01-01

    The AB-BA domain wall in gapped graphene bilayers is a rare naked structure hosting topological electronic states. Although it has been extensively studied in theory, a direct imaging of its topological edge states is still missing. Here we image the topological edge states at the graphene bilayer domain wall by using scanning tunnelling microscope. The simultaneously obtained atomic-resolution images of the domain wall provide us unprecedented opportunities to measure the spatially varying edge states within it. The one-dimensional conducting channels are observed to be mainly located around the two edges of the domain wall, which is reproduced quite well by our theoretical calculations. Our experiment further demonstrates that the one-dimensional topological states are quite robust even in the presence of high magnetic fields. The result reported here may raise hopes of graphene-based electronics with ultra-low dissipation. PMID:27312315

  14. Direct imaging of topological edge states at a bilayer graphene domain wall

    NASA Astrophysics Data System (ADS)

    Yin, Long-Jing; Jiang, Hua; Qiao, Jia-Bin; He, Lin

    2016-06-01

    The AB-BA domain wall in gapped graphene bilayers is a rare naked structure hosting topological electronic states. Although it has been extensively studied in theory, a direct imaging of its topological edge states is still missing. Here we image the topological edge states at the graphene bilayer domain wall by using scanning tunnelling microscope. The simultaneously obtained atomic-resolution images of the domain wall provide us unprecedented opportunities to measure the spatially varying edge states within it. The one-dimensional conducting channels are observed to be mainly located around the two edges of the domain wall, which is reproduced quite well by our theoretical calculations. Our experiment further demonstrates that the one-dimensional topological states are quite robust even in the presence of high magnetic fields. The result reported here may raise hopes of graphene-based electronics with ultra-low dissipation.

  15. Modulated helical metals at magnetic domain walls of pyrochlore iridium oxides

    NASA Astrophysics Data System (ADS)

    Yamaji, Youhei; Imada, Masatoshi

    2016-05-01

    Spontaneous symmetry breakings, metal-insulator transitions, and transport properties of magnetic-domain-wall states in pyrochlore iridium oxides are studied by employing a symmetry-adapted effective Hamiltonian with a slab perpendicular to the (111) direction of the pyrochlore structure. Emergent metallic domain wall, which has an unconventional topological nature with a controllable and mobile metallic layer, is shown to host Fermi surfaces with modulated helical spin textures resembling Rashba metals. The helical nature of the domain-wall Fermi surfaces is experimentally detectable by anomalous Hall conductivity, circular dichroism, and optical Hall conductivity under external magnetic fields. Possible applications of the domain-wall metals to spin-current generation and "half-metallic" conduction are also discussed.

  16. Direct imaging of topological edge states at a bilayer graphene domain wall

    PubMed Central

    Yin, Long-Jing; Jiang, Hua; Qiao, Jia-Bin; He, Lin

    2016-01-01

    The AB–BA domain wall in gapped graphene bilayers is a rare naked structure hosting topological electronic states. Although it has been extensively studied in theory, a direct imaging of its topological edge states is still missing. Here we image the topological edge states at the graphene bilayer domain wall by using scanning tunnelling microscope. The simultaneously obtained atomic-resolution images of the domain wall provide us unprecedented opportunities to measure the spatially varying edge states within it. The one-dimensional conducting channels are observed to be mainly located around the two edges of the domain wall, which is reproduced quite well by our theoretical calculations. Our experiment further demonstrates that the one-dimensional topological states are quite robust even in the presence of high magnetic fields. The result reported here may raise hopes of graphene-based electronics with ultra-low dissipation. PMID:27312315

  17. Host-Specific Parvovirus Evolution in Nature Is Recapitulated by In Vitro Adaptation to Different Carnivore Species

    PubMed Central

    Allison, Andrew B.; Kohler, Dennis J.; Ortega, Alicia; Hoover, Elizabeth A.; Grove, Daniel M.; Holmes, Edward C.; Parrish, Colin R.

    2014-01-01

    Canine parvovirus (CPV) emerged as a new pandemic pathogen of dogs in the 1970s and is closely related to feline panleukopenia virus (FPV), a parvovirus of cats and related carnivores. Although both viruses have wide host ranges, analysis of viral sequences recovered from different wild carnivore species, as shown here, demonstrated that >95% were derived from CPV-like viruses, suggesting that CPV is dominant in sylvatic cycles. Many viral sequences showed host-specific mutations in their capsid proteins, which were often close to sites known to control binding to the transferrin receptor (TfR), the host receptor for these carnivore parvoviruses, and which exhibited frequent parallel evolution. To further examine the process of host adaptation, we passaged parvoviruses with alternative backgrounds in cells from different carnivore hosts. Specific mutations were selected in several viruses and these differed depending on both the background of the virus and the host cells in which they were passaged. Strikingly, these in vitro mutations recapitulated many specific changes seen in viruses from natural populations, strongly suggesting they are host adaptive, and which were shown to result in fitness advantages over their parental virus. Comparison of the sequences of the transferrin receptors of the different carnivore species demonstrated that many mutations occurred in and around the apical domain where the virus binds, indicating that viral variants were likely selected through their fit to receptor structures. Some of the viruses accumulated high levels of variation upon passage in alternative hosts, while others could infect multiple different hosts with no or only a few additional mutations. Overall, these studies demonstrate that the evolutionary history of a virus, including how long it has been circulating and in which hosts, as well as its phylogenetic background, has a profound effect on determining viral host range. PMID:25375184

  18. Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species.

    PubMed

    Allison, Andrew B; Kohler, Dennis J; Ortega, Alicia; Hoover, Elizabeth A; Grove, Daniel M; Holmes, Edward C; Parrish, Colin R

    2014-11-01

    Canine parvovirus (CPV) emerged as a new pandemic pathogen of dogs in the 1970s and is closely related to feline panleukopenia virus (FPV), a parvovirus of cats and related carnivores. Although both viruses have wide host ranges, analysis of viral sequences recovered from different wild carnivore species, as shown here, demonstrated that>95% were derived from CPV-like viruses, suggesting that CPV is dominant in sylvatic cycles. Many viral sequences showed host-specific mutations in their capsid proteins, which were often close to sites known to control binding to the transferrin receptor (TfR), the host receptor for these carnivore parvoviruses, and which exhibited frequent parallel evolution. To further examine the process of host adaptation, we passaged parvoviruses with alternative backgrounds in cells from different carnivore hosts. Specific mutations were selected in several viruses and these differed depending on both the background of the virus and the host cells in which they were passaged. Strikingly, these in vitro mutations recapitulated many specific changes seen in viruses from natural populations, strongly suggesting they are host adaptive, and which were shown to result in fitness advantages over their parental virus. Comparison of the sequences of the transferrin receptors of the different carnivore species demonstrated that many mutations occurred in and around the apical domain where the virus binds, indicating that viral variants were likely selected through their fit to receptor structures. Some of the viruses accumulated high levels of variation upon passage in alternative hosts, while others could infect multiple different hosts with no or only a few additional mutations. Overall, these studies demonstrate that the evolutionary history of a virus, including how long it has been circulating and in which hosts, as well as its phylogenetic background, has a profound effect on determining viral host range. PMID:25375184

  19. Bridge hosts, a missing link for disease ecology in multi-host systems.

    PubMed

    Caron, Alexandre; Cappelle, Julien; Cumming, Graeme S; de Garine-Wichatitsky, Michel; Gaidet, Nicolas

    2015-01-01

    In ecology, the grouping of species into functional groups has played a valuable role in simplifying ecological complexity. In epidemiology, further clarifications of epidemiological functions are needed: while host roles may be defined, they are often used loosely, partly because of a lack of clarity on the relationships between a host's function and its epidemiological role. Here we focus on the definition of bridge hosts and their epidemiological consequences. Bridge hosts provide a link through which pathogens can be transmitted from maintenance host populations or communities to receptive populations that people want to protect (i.e., target hosts). A bridge host should (1) be competent for the pathogen or able to mechanically transmit it; and (2) come into direct contact or share habitat with both maintenance and target populations. Demonstration of bridging requires an operational framework that integrates ecological and epidemiological approaches. We illustrate this framework using the example of the transmission of Avian Influenza Viruses across wild bird/poultry interfaces in Africa and discuss a range of other examples that demonstrate the usefulness of our definition for other multi-host systems. Bridge hosts can be particularly important for understanding and managing infectious disease dynamics in multi-host systems at wildlife/domestic/human interfaces, including emerging infections. PMID:26198845

  20. Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species.

    PubMed

    Zhong, Zhenhui; Norvienyeku, Justice; Chen, Meilian; Bao, Jiandong; Lin, Lianyu; Chen, Liqiong; Lin, Yahong; Wu, Xiaoxian; Cai, Zena; Zhang, Qi; Lin, Xiaoye; Hong, Yonghe; Huang, Jun; Xu, Linghong; Zhang, Honghong; Chen, Long; Tang, Wei; Zheng, Huakun; Chen, Xiaofeng; Wang, Yanli; Lian, Bi; Zhang, Liangsheng; Tang, Haibao; Lu, Guodong; Ebbole, Daniel J; Wang, Baohua; Wang, Zonghua

    2016-01-01

    One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants. PMID:27151494

  1. The plastic response of Manduca sexta to host and non-host plants.

    PubMed

    Koenig, Christopher; Bretschneider, Anne; Heckel, David G; Grosse-Wilde, Ewald; Hansson, Bill S; Vogel, Heiko

    2015-08-01

    Specialist insect herbivores have evolved efficient ways to adapt to the major defenses of their host plants. Although Manduca sexta, specialized on Solanaceous plants, has become a model organism for insect molecular biology, little is known about its adaptive responses to the chemical defenses of its hosts. To study larval performance and transcriptomic responses to host and non-host plants, we conducted developmental assays and replicated RNAseq experiments with Manduca larvae fed on different Solanaceous plants as well as on a Brassicaceous non-host plant, Brassica napus. Manduca larvae developed fastest on Nicotiana attenuata, but no significant differences in performance were found on larvae fed on other Solanaceae or the non-host B. napus. The RNAseq experiments revealed that Manduca larvae display plastic responses at the gene expression level, and transcriptional signatures specific to the challenges of each host- and non-host plant. Our observations are not consistent with expectations that specialist herbivores would perform poorly on non-host plants. Instead, our findings demonstrate the ability of this specialized insect herbivore to efficiently use a larger repertoire of host plants than it utilizes in the field. PMID:26070471

  2. Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species

    PubMed Central

    Zhong, Zhenhui; Norvienyeku, Justice; Chen, Meilian; Bao, Jiandong; Lin, Lianyu; Chen, Liqiong; Lin, Yahong; Wu, Xiaoxian; Cai, Zena; Zhang, Qi; Lin, Xiaoye; Hong, Yonghe; Huang, Jun; Xu, Linghong; Zhang, Honghong; Chen, Long; Tang, Wei; Zheng, Huakun; Chen, Xiaofeng; Wang, Yanli; Lian, Bi; Zhang, Liangsheng; Tang, Haibao; Lu, Guodong; Ebbole, Daniel J.; Wang, Baohua; Wang, Zonghua

    2016-01-01

    One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants. PMID:27151494

  3. Microbiome influences on insect host vector competence

    PubMed Central

    Weiss, Brian

    2011-01-01

    Insect symbioses lack the complexity and diversity of those associated with higher eukaryotic hosts. Symbiotic microbiomes are beneficial to their insect hosts in many ways, including dietary supplementation, tolerance to environmental perturbations and maintenance and/or enhancement of host immune system homeostasis. Recent studies have also highlighted the importance of the microbiome in the context of host pathogen transmission processes. Here we provide an overview of the relationship between insect disease vectors, such as tsetse flies and mosquitoes, and their associated microbiome. Several mechanisms are discussed through which symbiotic microbes may influence their host’s ability to transmit pathogens, as well as potential disease control strategies that harness symbiotic microbes to reduce pathogen transmission through an insect vector. PMID:21697014

  4. Towards host-directed therapies for tuberculosis.

    PubMed

    Zumla, Alimuddin; Maeurer, Markus; Chakaya, Jeremiah; Hoelscher, Michael; Ntoumi, Francine; Rustomjee, Roxana; Vilaplana, Cristina; Yeboah-Manu, Dorothy; Rasolof, Voahangy; Munderi, Paula; Singh, Nalini; Aklillu, Eleni; Padayatchi, Nesri; Macete, Eusebio; Kapata, Nathan; Mulenga, Modest; Kibiki, Gibson; Mfinanga, Sayoki; Nyirenda, Thomas; Maboko, Leonard; Garcia-Basteiro, Alberto; Rakotosamimanana, Niaina; Bates, Matthew; Mwaba, Peter; Reither, Klaus; Gagneux, Sebastien; Edwards, Sarah; Mfinanga, Elirehema; Abdulla, Salim; Cardona, Pere-Joan; Russell, James B W; Gant, Vanya; Noursadeghi, Mahdad; Elkington, Paul; Bonnet, Maryline; Menendez, Clara; Dieye, Tandakha N; Diarra, Bassirou; Maiga, Almoustapha; Aseffa, Abraham; Parida, Shreemanta; Wejse, Christian; Petersen, Eskild; Kaleebu, Pontiano; Oliver, Matt; Craig, Gill; Corrah, Tumena; Tientcheu, Leopold; Antonio, Martin; Rao, Martin; McHugh, Timothy D; Sheikh, Aziz; Ippolito, Giuseppe; Ramjee, Gita; Kaufmann, Stefan H E; Churchyard, Gavin; Steyn, Andrie; Grobusch, Martin; Sanne, Ian; Martinson, Neil; Madansein, Rajhmun; Wilkinson, Robert J; Mayosi, Bongani; Schito, Marco; Wallis, Robert S

    2015-08-01

    The treatment of tuberculosis is based on combinations of drugs that directly target Mycobacterium tuberculosis. A new global initiative is now focusing on a complementary approach of developing adjunct host-directed therapies. PMID:26184493

  5. Communication between Bacteria and Their Hosts

    PubMed Central

    2013-01-01

    It is clear that a dialogue is occurring between microbes and their hosts and that chemical signals are the language of this interkingdom communication. Microbial endocrinology shows that, through their long coexistence with animals and plants, microorganisms have evolved sensors for detecting eukaryotic hormones, which the microbe uses to determine that they are within proximity of a suitable host and to optimally time the expression of genes needed for host colonisation. It has also been shown that some prokaryotic chemical communication signals are recognized by eukaryotes. Deciphering what is being said during the cross-talk between microbe and host is therefore important, as it could lead to new strategies for preventing or treating bacterial infections. PMID:24381789

  6. The virome in host health and disease

    PubMed Central

    Cadwell, Ken

    2015-01-01

    The mammalian virome includes diverse commensal and pathogenic viruses that evoke a broad range of immune responses from the host. Sustained viral immunomodulation is implicated in a variety of inflammatory diseases, but also confers unexpected benefits to the host. These outcomes of viral infections are often dependent on host genotype. Moreover, it is becoming clear that the virome is part of a dynamic network of microorganisms that inhabit the body. Therefore, viruses can be viewed as a component of the microbiome, and interactions with commensal bacteria and other microbial agents influence their behavior. In this article, our current understanding of how the virome, together with other components of the microbiome, affects the function of the host immune system to regulate health and disease is reviewed. PMID:25992857

  7. Host compounds for red phosphorescent OLEDs

    SciTech Connect

    Xia, Chuanjun; Cheon, Kwang -Ohk

    2015-08-25

    Novel compounds containing a triphenylene moiety linked to an .alpha..beta. connected binaphthyl ring system are provided. These compounds have surprisingly good solubility in organic solvents and are useful as host compounds in red phosphorescent OLEDs.

  8. The Swift GRB Host Galaxy Legacy Survey

    NASA Astrophysics Data System (ADS)

    Perley, Daniel A.

    2015-01-01

    I introduce the Swift Host Galaxy Legacy Survey (SHOALS), a comprehensive multiwavelength program to characterize the demographics of the GRB host population across its entire redshift range. Using unbiased selection criteria we have designated a subset of 130 Swift gamma-ray bursts which are now being targeted with intensive observational follow-up. Deep Spitzer imaging of every field has already been obtained and analyzed, with major programs ongoing at Keck, GTC, and Gemini to obtain complementary optical/NIR photometry to enable full SED modeling and derivation of fundamental physical parameters such as mass, extinction, and star-formation rate. Using these data I will present an unbiased measurement of the GRB host-galaxy luminosity and mass functions and their evolution with redshift between z=0 and z=5, compare GRB hosts to other star-forming galaxy populations, and discuss implications for the nature of the GRB progenitor and the ability of GRBs to probe cosmic star-formation.

  9. Host-Microbe Interactions in Caenorhabditis elegans

    PubMed Central

    Hou, Aixin

    2013-01-01

    A good understanding of how microbes interact with hosts has a direct bearing on our capability of fighting infectious microbial pathogens and making good use of beneficial ones. Among the model organisms used to study reciprocal actions among microbes and hosts, C. elegans may be the most advantageous in the context of its unique attributes such as the short life cycle, easiness of laboratory maintenance, and the availability of different genetic mutants. This review summarizes the recent advances in understanding host-microbe interactions in C. elegans. Although these investigations have greatly enhanced our understanding of C. elegans-microbe relationships, all but one of them involve only one or few microbial species. We argue here that more research is needed for exploring the evolution and establishment of a complex microbial community in the worm's intestine and its interaction with the host. PMID:23984180

  10. Viral and host control of cytomegalovirus maturation

    PubMed Central

    Tandon, Ritesh; Mocarski, Edward S.

    2012-01-01

    Maturation in herpesviruses initiates in the nucleus of the infected cell with encapsidation of viral DNA to form nucleocapsids and concludes with envelopment in the cytoplasm to form infectious virions that egress the cell. The entire process of virus maturation is orchestrated by protein-protein interactions and enzymatic activities of viral and host origin. Viral tegument proteins play important roles in maintaining the structural stability of capsids and directing the acquisition of virus envelope. Envelopment occurs at modified host membranes and exploits host vesicular trafficking. In this review, we summarize the current knowledge and concepts in human cytomegalovirus (HCMV) maturation and their parallels in other herpesviruses with an emphasis on viral and host factors regulating this process. PMID:22633075

  11. Host Density and Competency Determine the Effects of Host Diversity on Trematode Parasite Infection

    PubMed Central

    Wojdak, Jeremy M.; Edman, Robert M.; Wyderko, Jennie A.; Zemmer, Sally A.; Belden, Lisa K.

    2014-01-01

    Variation in host species composition can dramatically alter parasite transmission in natural communities. Whether diverse host communities dilute or amplify parasite transmission is thought to depend critically on species traits, particularly on how hosts affect each other’s densities, and their relative competency as hosts. Here we studied a community of potential hosts and/or decoys (i.e. non-competent hosts) for two trematode parasite species, Echinostoma trivolvis and Ribeiroia ondatrae, which commonly infect wildlife across North America. We manipulated the density of a focal host (green frog tadpoles, Rana clamitans), in concert with manipulating the diversity of alternative species, to simulate communities where alternative species either (1) replace the focal host species so that the total number of individuals remains constant (substitution) or (2) add to total host density (addition). For E. trivolvis, we found that total parasite transmission remained roughly equal (or perhaps decreased slightly) when alternative species replaced focal host individuals, but parasite transmission was higher when alternative species were added to a community without replacing focal host individuals. Given the alternative species were roughly equal in competency, these results are consistent with current theory. Remarkably, both total tadpole and per-capita tadpole infection intensity by E. trivolvis increased with increasing intraspecific host density. For R. ondatrae, alternative species did not function as effective decoys or hosts for parasite infective stages, and the diversity and density treatments did not produce clear changes in parasite transmission, although high tank to tank variation in R. ondatrae infection could have obscured patterns. PMID:25119568

  12. Host reproductive phenology drives seasonal patterns of host use in mosquitoes.

    PubMed

    Burkett-Cadena, Nathan D; McClure, Christopher J W; Ligon, Russell A; Graham, Sean P; Guyer, Craig; Hill, Geoffrey E; Ditchkoff, Stephen S; Eubanks, Micky D; Hassan, Hassan K; Unnasch, Thomas R

    2011-01-01

    Seasonal shifts in host use by mosquitoes from birds to mammals drive the timing and intensity of annual epidemics of mosquito-borne viruses, such as West Nile virus, in North America. The biological mechanism underlying these shifts has been a matter of debate, with hypotheses falling into two camps: (1) the shift is driven by changes in host abundance, or (2) the shift is driven by seasonal changes in the foraging behavior of mosquitoes. Here we explored the idea that seasonal changes in host use by mosquitoes are driven by temporal patterns of host reproduction. We investigated the relationship between seasonal patterns of host use by mosquitoes and host reproductive phenology by examining a seven-year dataset of blood meal identifications from a site in Tuskegee National Forest, Alabama USA and data on reproduction from the most commonly utilized endothermic (white-tailed deer, great blue heron, yellow-crowned night heron) and ectothermic (frogs) hosts. Our analysis revealed that feeding on each host peaked during periods of reproductive activity. Specifically, mosquitoes utilized herons in the spring and early summer, during periods of peak nest occupancy, whereas deer were fed upon most during the late summer and fall, the period corresponding to the peak in births for deer. For frogs, however, feeding on early- and late-season breeders paralleled peaks in male vocalization. We demonstrate for the first time that seasonal patterns of host use by mosquitoes track the reproductive phenology of the hosts. Peaks in relative mosquito feeding on each host during reproductive phases are likely the result of increased tolerance and decreased vigilance to attacking mosquitoes by nestlings and brooding adults (avian hosts), quiescent young (avian and mammalian hosts), and mate-seeking males (frogs). PMID:21408172

  13. Gabor domain optical coherence microscopy

    NASA Astrophysics Data System (ADS)

    Murali, Supraja

    Time domain Optical Coherence Tomography (TD-OCT), first reported in 1991, makes use of the low temporal coherence properties of a NIR broadband laser to create depth sectioning of up to 2mm under the surface using optical interferometry and point to point scanning. Prior and ongoing work in OCT in the research community has concentrated on improving axial resolution through the development of broadband sources and speed of image acquisition through new techniques such as Spectral domain OCT (SD-OCT). In SD-OCT, an entire depth scan is acquired at once with a low numerical aperture (NA) objective lens focused at a fixed point within the sample. In this imaging geometry, a longer depth of focus is achieved at the expense of lateral resolution, which is typically limited to 10 to 20 mum. Optical Coherence Microscopy (OCM), introduced in 1994, combined the advantages of high axial resolution obtained in OCT with high lateral resolution obtained by increasing the NA of the microscope placed in the sample arm. However, OCM presented trade-offs caused by the inverse quadratic relationship between the NA and the DOF of the optics used. For applications requiring high lateral resolution, such as cancer diagnostics, several solutions have been proposed including the periodic manual re-focusing of the objective lens in the time domain as well as the spectral domain C-mode configuration in order to overcome the loss in lateral resolution outside the DOF. In this research, we report for the first time, high speed, sub-cellular imaging (lateral resolution of 2 mum) in OCM using a Gabor domain image processing algorithm with a custom designed and fabricated dynamic focus microscope interfaced to a Ti:Sa femtosecond laser centered at 800 nm within an SD-OCM configuration. It is envisioned that this technology will provide a non-invasive replacement for the current practice of multiple biopsies for skin cancer diagnosis. The research reported here presents three important advances

  14. Spline interpolation on unbounded domains

    NASA Astrophysics Data System (ADS)

    Skeel, Robert D.

    2016-06-01

    Spline interpolation is a splendid tool for multiscale approximation on unbounded domains. In particular, it is well suited for use by the multilevel summation method (MSM) for calculating a sum of pairwise interactions for a large set of particles in linear time. Outlined here is an algorithm for spline interpolation on unbounded domains that is efficient and elegant though not so simple. Further gains in efficiency are possible via quasi-interpolation, which compromises collocation but with minimal loss of accuracy. The MSM, which may also be of value for continuum models, embodies most of the best features of both hierarchical clustering methods (tree methods, fast multipole methods, hierarchical matrix methods) and FFT-based 2-level methods (particle-particle particle-mesh methods, particle-mesh Ewald methods).

  15. Certifying Domain-Specific Policies

    NASA Technical Reports Server (NTRS)

    Lowry, Michael; Pressburger, Thomas; Rosu, Grigore; Koga, Dennis (Technical Monitor)

    2001-01-01

    Proof-checking code for compliance to safety policies potentially enables a product-oriented approach to certain aspects of software certification. To date, previous research has focused on generic, low-level programming-language properties such as memory type safety. In this paper we consider proof-checking higher-level domain -specific properties for compliance to safety policies. The paper first describes a framework related to abstract interpretation in which compliance to a class of certification policies can be efficiently calculated Membership equational logic is shown to provide a rich logic for carrying out such calculations, including partiality, for certification. The architecture for a domain-specific certifier is described, followed by an implemented case study. The case study considers consistency of abstract variable attributes in code that performs geometric calculations in Aerospace systems.

  16. Frequency domain optical parametric amplification

    PubMed Central

    Schmidt, Bruno E.; Thiré, Nicolas; Boivin, Maxime; Laramée, Antoine; Poitras, François; Lebrun, Guy; Ozaki, Tsuneyuki; Ibrahim, Heide; Légaré, François

    2014-01-01

    Today’s ultrafast lasers operate at the physical limits of optical materials to reach extreme performances. Amplification of single-cycle laser pulses with their corresponding octave-spanning spectra still remains a formidable challenge since the universal dilemma of gain narrowing sets limits for both real level pumped amplifiers as well as parametric amplifiers. We demonstrate that employing parametric amplification in the frequency domain rather than in time domain opens up new design opportunities for ultrafast laser science, with the potential to generate single-cycle multi-terawatt pulses. Fundamental restrictions arising from phase mismatch and damage threshold of nonlinear laser crystals are not only circumvented but also exploited to produce a synergy between increased seed spectrum and increased pump energy. This concept was successfully demonstrated by generating carrier envelope phase stable, 1.43 mJ two-cycle pulses at 1.8 μm wavelength. PMID:24805968

  17. Pyramidal inversion domain boundaries revisited

    SciTech Connect

    Remmele, T.; Albrecht, M.; Irmscher, K.; Fornari, R.; Strassburg, M.

    2011-10-03

    The structure of pyramidal inversion domain boundaries in GaN:Mg was investigated by aberration corrected transmission electron microscopy. The analysis shows the upper (0001) boundary to consist of a single Mg layer inserted between polarity inverted GaN layers in an abcab stacking. The Mg bound in these defects is at least one order of magnitude lower than the chemical Mg concentration. Temperature dependent Hall effect measurements show that up to 27% of the Mg acceptors is electrically compensated.

  18. System time-domain simulation

    NASA Technical Reports Server (NTRS)

    Dawson, C. T.; Eggleston, T. W.; Goris, A. C.; Fashano, M.; Paynter, D.; Tranter, W. H.

    1980-01-01

    Complex systems are simulated by engineers without extensive computer experience. Analyst uses free-form engineering-oriented language to input "black box" description. System Time Domain (SYSTID) Simulation Program generates appropriate algorithms and proceeds with simulation. Program is easily linked to postprocessing routines. SYSTID program is written in FORTRAN IV for batch execution and has been implemented on UNIVAC 1110 under control of EXEC 8, Level 31.

  19. Flexible time domain averaging technique

    NASA Astrophysics Data System (ADS)

    Zhao, Ming; Lin, Jing; Lei, Yaguo; Wang, Xiufeng

    2013-09-01

    Time domain averaging(TDA) is essentially a comb filter, it cannot extract the specified harmonics which may be caused by some faults, such as gear eccentric. Meanwhile, TDA always suffers from period cutting error(PCE) to different extent. Several improved TDA methods have been proposed, however they cannot completely eliminate the waveform reconstruction error caused by PCE. In order to overcome the shortcomings of conventional methods, a flexible time domain averaging(FTDA) technique is established, which adapts to the analyzed signal through adjusting each harmonic of the comb filter. In this technique, the explicit form of FTDA is first constructed by frequency domain sampling. Subsequently, chirp Z-transform(CZT) is employed in the algorithm of FTDA, which can improve the calculating efficiency significantly. Since the signal is reconstructed in the continuous time domain, there is no PCE in the FTDA. To validate the effectiveness of FTDA in the signal de-noising, interpolation and harmonic reconstruction, a simulated multi-components periodic signal that corrupted by noise is processed by FTDA. The simulation results show that the FTDA is capable of recovering the periodic components from the background noise effectively. Moreover, it can improve the signal-to-noise ratio by 7.9 dB compared with conventional ones. Experiments are also carried out on gearbox test rigs with chipped tooth and eccentricity gear, respectively. It is shown that the FTDA can identify the direction and severity of the eccentricity gear, and further enhances the amplitudes of impulses by 35%. The proposed technique not only solves the problem of PCE, but also provides a useful tool for the fault symptom extraction of rotating machinery.

  20. Host genetic susceptibility to severe dengue infection

    PubMed Central

    Lan, Nguyen Thi Phuong; Hirayama, Kenji

    2011-01-01

    Epidemiological evidence indicates that host genetic factors are relevant and predispose DHF/DSS development. Here, we review the host genetic studies concerning human leucocyte antigens, antibody receptors, immune/inflammatory mediators, attachment molecules, cytokines and other factors exerting an immunoregulatory effect as well as the current genome-wide association studies. We also discuss some viewpoints on future challenges related to the design of safe and effective prevention and treatment options. PMID:22500139

  1. Summary of laser speckle photogrammetry for HOST

    NASA Technical Reports Server (NTRS)

    Pollack, Frank G.

    1986-01-01

    High temperature static strain measurement capability is important for the success of the HOST program. As part of the NASA Lewis effort to develop the technology for improved hot-section durability, the HOST instrumentation program has, as a major goal, the development of methods for measuring strain at high temperature. Development work includes both improvements in resistance strain-gauge technology and, as an alternative approach, the development of optical techniques for high temperature strain measurement.

  2. DNA barcoding insect–host plant associations

    PubMed Central

    Jurado-Rivera, José A.; Vogler, Alfried P.; Reid, Chris A.M.; Petitpierre, Eduard; Gómez-Zurita, Jesús

    2008-01-01

    Short-sequence fragments (‘DNA barcodes’) used widely for plant identification and inventorying remain to be applied to complex biological problems. Host–herbivore interactions are fundamental to coevolutionary relationships of a large proportion of species on the Earth, but their study is frequently hampered by limited or unreliable host records. Here we demonstrate that DNA barcodes can greatly improve this situation as they (i) provide a secure identification of host plant species and (ii) establish the authenticity of the trophic association. Host plants of leaf beetles (subfamily Chrysomelinae) from Australia were identified using the chloroplast trnL(UAA) intron as barcode amplified from beetle DNA extracts. Sequence similarity and phylogenetic analyses provided precise identifications of each host species at tribal, generic and specific levels, depending on the available database coverage in various plant lineages. The 76 species of Chrysomelinae included—more than 10 per cent of the known Australian fauna—feed on 13 plant families, with preference for Australian radiations of Myrtaceae (eucalypts) and Fabaceae (acacias). Phylogenetic analysis of beetles shows general conservation of host association but with rare host shifts between distant plant lineages, including a few cases where barcodes supported two phylogenetically distant host plants. The study demonstrates that plant barcoding is already feasible with the current publicly available data. By sequencing plant barcodes directly from DNA extractions made from herbivorous beetles, strong physical evidence for the host association is provided. Thus, molecular identification using short DNA fragments brings together the detection of species and the analysis of their interactions. PMID:19004756

  3. Herpes simplex virus virion host shutoff function.

    PubMed Central

    Kwong, A D; Kruper, J A; Frenkel, N

    1988-01-01

    Herpes simplex virus (HSV) virions contain one or more functions which mediate the shutoff of host protein synthesis and the degradation of host mRNA. HSV type 1 (HSV-1) mutants deficient in the virion shutoff of host protein synthesis (vhs mutants) were isolated and were found to be defective in their ability to degrade host mRNA. Furthermore, it was found that viral mRNAs in cells infected with the vhs 1 mutant have a significantly longer functional half-life than viral mRNAs in wild-type virus-infected cells. In the present study we have mapped the vhs1 mutation affecting the virion shutoff of host protein synthesis to a 265-base-pair NruI-XmaIII fragment spanning map coordinates 0.604 to 0.606 of the HSV-1 genome. The mutation(s) affecting the functional half-lives of host mRNA as well as the alpha (immediate-early), beta (early), and gamma (late) viral mRNAs were also mapped within this 265-base-pair fragment. Thus, the shutoff of host protein synthesis is most likely mediated by the same function which decreases the half-life of viral mRNA. The shorter half-life of infected-cell mRNAs may allow a more rapid modulation of viral gene expression in response to changes in the transcription of viral genes. Interestingly, the vhs1 mutation of HSV-1 maps within a region which overlaps the Bg/II-N sequences of HSV-2 DNA shown previously to transform cells in culture. The possible relationship between the transformation and host shutoff functions are discussed. Images PMID:2828686

  4. Subharmonic Fourier domain mode locking.

    PubMed

    Eigenwillig, Christoph M; Wieser, Wolfgang; Biedermann, Benjamin R; Huber, Robert

    2009-03-15

    We demonstrate a subharmonically Fourier domain mode-locked wavelength-swept laser source with a substantially reduced cavity fiber length. In contrast to a standard Fourier domain mode-locked configuration, light is recirculated repetitively in the delay line with the optical bandpass filter used as switch. The laser has a fundamental optical round trip frequency of 285 kHz and can be operated at integer fractions thereof (subharmonics). Sweep ranges up to 95 nm full width centred at 1317 nm are achieved at the 1/5th subharmonic. A maximum sensitivity of 116 dB and an axial resolution of 12 microm in air are measured at an average sweep power of 12 mW. A sensitivity roll-off of 11 dB over 4 mm and 25 dB over 10 mm is observed and optical coherence tomography imaging is demonstrated. Besides the advantage of a reduced fiber length, subharmonic Fourier domain mode locking (shFDML) enables simple scaling of the sweep speed by extracting light from the delay part of the resonator. A sweep rate of 570 kHz is achieved. Characteristic features of shFDML operation, such as power leakage during fly-back and cw breakthrough, are investigated. PMID:19282912

  5. Mapping knowledge domains: Characterizing PNAS

    PubMed Central

    Boyack, Kevin W.

    2004-01-01

    A review of data mining and analysis techniques that can be used for the mapping of knowledge domains is given. Literature mapping techniques can be based on authors, documents, journals, words, and/or indicators. Most mapping questions are related to research assessment or to the structure and dynamics of disciplines or networks. Several mapping techniques are demonstrated on a data set comprising 20 years of papers published in PNAS. Data from a variety of sources are merged to provide unique indicators of the domain bounded by PNAS. By using funding source information and citation counts, it is shown that, on an aggregate basis, papers funded jointly by the U.S. Public Health Service (which includes the National Institutes of Health) and non-U.S. government sources outperform papers funded by other sources, including by the U.S. Public Health Service alone. Grant data from the National Institute on Aging show that, on average, papers from large grants are cited more than those from small grants, with performance increasing with grant amount. A map of the highest performing papers over the 20-year period was generated by using citation analysis. Changes and trends in the subjects of highest impact within the PNAS domain are described. Interactions between topics over the most recent 5-year period are also detailed. PMID:14963238

  6. Determinants of Host Society Acculturation and Its Relationship with Health Behaviors and Outcomes: A New Research and Intervention Framework.

    PubMed

    Andreeva, Valentina A; Unger, Jennifer B

    2015-10-01

    Host society acculturation (or reverse acculturation) is a complex, multifactorial process reflecting the attitude- and behavior-level impact of immigrants on the host society. However, this phenomenon has rarely been the subject of systematic research in the area of public health. Using qualitative and quantitative findings from different health behavior domains, we strove to identify potential individual- and environment-level determinants of host society acculturation. Next, we developed a context-driven multilevel public health research and intervention framework for the study of the relationship between host society acculturation and health practices and outcomes. The framework posits a number of associations to be evaluated by future multidisciplinary research nationally and internationally. PMID:25225079

  7. Allelic variation contributes to bacterial host specificity

    SciTech Connect

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

  8. Allelic variation contributes to bacterial host specificity

    DOE PAGESBeta

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; et al

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population andmore » functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.« less

  9. Allelic variation contributes to bacterial host specificity

    PubMed Central

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-01-01

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  10. Allelic variation contributes to bacterial host specificity.

    PubMed

    Yue, Min; Han, Xiangan; De Masi, Leon; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S; Fraser, George P; Zhao, Shaohua; McDermott, Patrick F; Weill, François-Xavier; Mainil, Jacques G; Arze, Cesar; Fricke, W Florian; Edwards, Robert A; Brisson, Dustin; Zhang, Nancy R; Rankin, Shelley C; Schifferli, Dieter M

    2015-01-01

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  11. A Complete Sample of Supernova Host Galaxies

    NASA Astrophysics Data System (ADS)

    Quimby, Robert

    2011-01-01

    Traditionally, supernova surveys have drawn their samples by monitoring pre-selected lists of host galaxies. More recently, some surveys have made efforts to ignore host properties when selecting candidates, but because of limited resources they must usually add additional selection criteria, such as the color or light curve shape of the transient, in order to select the best targets for a specific study. Since 2004, we have conducted a search for supernovae that is designed to select targets irrespective of their host environment, and we have spectroscopic classifications for all of the new transients detected. Here we report on the host galaxies of first 72 supernovae detected by ROTSE-IIIb as part of the Texas Supernova Search and the ROTSE Supernova Verification Project. The supernova sample includes everything from perfectly normal Type Ia and Type II, to spectroscopically peculiar events, to several of the most luminous supernovae ever found. We compare multi-band photometry and spectroscopy of the host galaxy sample to the larger galaxy population. We cannot securely identify host galaxies brighter than -10 mag absolute for four of our discoveries, which suggests that these may be hostless, "tramp supernovae."

  12. Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions

    SciTech Connect

    Krishnan, Vengadesan; Dwivedi, Prabhat; Kim, Brandon J.; Samal, Alexandra; Macon, Kevin; Ma, Xin; Mishra, Arunima; Doran, Kelly S.; Ton-That, Hung; Narayana, Sthanam V. L.

    2013-06-01

    The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. In addition, a homology model of the remaining two domains of GBS104 was built and a model of full-length GBS104 was generated by combining the homology model (the N1 and N4 domains) and the crystal structure of the 75 kDa fragment (the N2 and N3 domains). This rod-shaped GBS104 model is constructed of three IgG-like domains (the N1, N2 and N4 domains) and one vWFA-like domain (the N3 domain). The N1 and N2 domains of GBS104 are assembled with distinct and remote segments contributed by the N- and C-termini. The metal-binding site in the N3 domain of GBS104 is in the closed/low-affinity conformation. Interestingly, this domain hosts two long arms that project away from the metal-binding site. Using site-directed mutagenesis, two cysteine residues that lock the N3 domain of GBS104 into the open/high-affinity conformation were introduced. Both wild-type and disulfide-locked recombinant proteins were tested for binding to extracellular matrix proteins such as collagen, fibronectin, fibrinogen and laminin, and an increase in fibronectin binding affinity was identified for the disulfide-locked N3 domain, suggesting that induced conformational changes may play a possible role in receptor binding.

  13. Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions

    PubMed Central

    Krishnan, Vengadesan; Dwivedi, Prabhat; Kim, Brandon J.; Samal, Alexandra; Macon, Kevin; Ma, Xin; Mishra, Arunima; Doran, Kelly S.; Ton-That, Hung; Narayana, Sthanam V. L.

    2013-01-01

    The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. In addition, a homology model of the remaining two domains of GBS104 was built and a model of full-length GBS104 was generated by combining the homology model (the N1 and N4 domains) and the crystal structure of the 75 kDa fragment (the N2 and N3 domains). This rod-shaped GBS104 model is constructed of three IgG-like domains (the N1, N2 and N4 domains) and one vWFA-like domain (the N3 domain). The N1 and N2 domains of GBS104 are assembled with distinct and remote segments contributed by the N- and C-termini. The metal-binding site in the N3 domain of GBS104 is in the closed/low-affinity conformation. Interestingly, this domain hosts two long arms that project away from the metal-binding site. Using site-directed mutagenesis, two cysteine residues that lock the N3 domain of GBS104 into the open/high-affinity conformation were introduced. Both wild-type and disulfide-locked recombinant proteins were tested for binding to extracellular matrix proteins such as collagen, fibronectin, fibrinogen and laminin, and an increase in fibronectin binding affinity was identified for the disulfide-locked N3 domain, suggesting that induced conformational changes may play a possible role in receptor binding. PMID:23695252

  14. Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein

    PubMed Central

    Gruszka, Dominika T.; Whelan, Fiona; Farrance, Oliver E.; Fung, Herman K. H.; Paci, Emanuele; Jeffries, Cy M.; Svergun, Dmitri I.; Baldock, Clair; Baumann, Christoph G.; Brockwell, David J.; Potts, Jennifer R.; Clarke, Jane

    2015-01-01

    Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed ‘clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length. PMID:26027519

  15. An internal thioester in a pathogen surface protein mediates covalent host binding

    PubMed Central

    Walden, Miriam; Edwards, John M; Dziewulska, Aleksandra M; Bergmann, Rene; Saalbach, Gerhard; Kan, Su-Yin; Miller, Ona K; Weckener, Miriam; Jackson, Rosemary J; Shirran, Sally L; Botting, Catherine H; Florence, Gordon J; Rohde, Manfred; Banfield, Mark J; Schwarz-Linek, Ulrich

    2015-01-01

    To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a ‘chemical harpoon’. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. DOI: http://dx.doi.org/10.7554/eLife.06638.001 PMID:26032562

  16. Supramolecular Assembly of an Evolved Miniprotein Host and Fluorogenic Guest Pair.

    PubMed

    Xu, Bi; Zhou, Xinqi; Stains, Cliff I

    2015-11-18

    Small-molecule-induced assembly of defined protein structures could have broad implications for the fabrication of new materials as well as biological signaling pathways. However, the design of new host-guest pairs capable of small-molecule-induced assembly in a biologically relevant context remains a significant challenge. Herein, we report a series of miniprotein hosts, evolved from the tenth type III domain of fibronectin (Fn3), that display remarkable binding affinity toward a red-shifted environment-sensitive merocyanine derivative, termed sI-Pht. Importantly, the consensus binder isolated from directed evolution experiments (6.2.18) forms a higher order assembly in response to addition of sI-Pht, as assessed by analytical ultracentrifugation. sI-Pht-induced assembly of 6.2.18 results in a 570-fold increase in fluorescence compared to free dye. This property enables the direct visualization of host-guest assemblies by fluorescence microscopy. As a demonstration, we show that supramolecular assembly of the 6.2.18-sI-Pht system can be visualized on the surface of living yeast cells. This new host-guest pair provides a tool for the potential development of new materials as well as pathway engineering. In a broader context, this work details a new design paradigm for the discovery of host-guest systems that function in the context of living cells. PMID:26523606

  17. Species difference in ANP32A underlies influenza A virus polymerase host restriction

    PubMed Central

    Long, Jason S.; Giotis, Efstathios S.; Moncorgé, Olivier; Frise, Rebecca; Mistry, Bhakti; James, Joe; Morisson, Mireille; Iqbal, Munir; Vignal, Alain; Skinner, Michael A.; Barclay, Wendy S.

    2015-01-01

    Influenza pandemics occur unpredictably when zoonotic influenza viruses with novel antigenicity acquire the ability to transmit amongst humans 1. Incompatibilities between avian virus components and the human host limit host range breaches. Barriers include receptor preference, virion stability and poor activity of the avian virus RNA-dependent RNA polymerase in human cells 2. Mutants of the heterotrimeric viral polymerase components, particularly PB2 protein, are selected during mammalian adaptation, but their mode of action is unknown 3–6. We show that a species-specific difference in host protein ANP32A accounts for the suboptimal function of avian virus polymerase in mammalian cells. Avian ANP32A possesses an additional 33 amino acids between the LRR and LCAR domains. In mammalian cells, avian ANP32A rescued the suboptimal function of avian virus polymerase to levels similar to mammalian adapted polymerase. Deletion of the avian-specific sequence from chicken ANP32A abrogated this activity whereas its insertion into human ANP32A, or closely related ANP32B, supported avian virus polymerase function. Substitutions, such as PB2 E627K, rapidly selected upon infection of humans with avian H5N1 or H7N9 influenza viruses, adapt the viral polymerase for the shorter mammalian ANP32A. Thus ANP32A represents an essential host partner co-opted to support influenza virus replication and is a candidate host target for novel antivirals. PMID:26738596

  18. Interactions Between the Host Innate Immune System and Microbes in Inflammatory Bowel Disease

    PubMed Central

    Abraham, Clara; Medzhitov, Ruslan

    2013-01-01

    The intestinal immune system defends against pathogens and entry of excessive intestinal microbes; simultaneously, a state of immune tolerance to resident intestinal microbes must be maintained. Perturbation of this balance is associated with intestinal inflammation in various mouse models and is thought to predispose humans to inflammatory bowel disease (IBD). The innate immune system senses microbes; dendritic cells, macrophages, and epithelial cells produce an initial, rapid response. The immune system continuously monitors resident microbiota and utilizes constitutive antimicrobial mechanisms to maintain immune homeostasis. associations between IBD and genes that regulate microbial recognition and innate immune pathways, such as nucleotide oligomerization domain 2 (Nod2), genes that control autophagy (eg, ATG16L1, IRGM), and genes in the interleukin-23–T helper cell 17 pathway indicate the important roles of host-microbe interactions in regulating intestinal immune homeostasis. There is increasing evidence that intestinal microbes influence host immune development, immune responses, and susceptibility to human diseases such as IBD, diabetes mellitus, and obesity. Conversely, host factors can affect microbes, which in turn modulate disease susceptibility. We review the cell populations and mechanisms that mediate interactions between host defense and tolerance and how the dysregulation of host-microbe interactions leads to intestinal inflammation and IBD. PMID:21530739

  19. Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

    PubMed Central

    Rico, Patricia; Ivars, Pilar; Elena, Santiago F.; Hernández, Carmen

    2006-01-01

    The molecular diversity of Pelargonium flower break virus (PFBV) was assessed using a collection of isolates from different geographical origins, hosts, and collecting times. The genomic region examined was 1,828 nucleotides (nt) long and comprised the coding sequences for the movement (p7 and p12) and the coat (CP) proteins, as well as flanking segments including the entire 3′ untranslated region (3′ UTR). Some constraints limiting viral heterogeneity could be inferred from sequence analyses, such as the conservation of the amino acid sequences of p7 and of the shell domain of the CP, the maintenance of a leucine zipper motif in p12, and the preservation of a particular folding in the 3′ UTR. A remarkable covariation, involving five specific amino acid sites, was found in the CP of isolates largely propagated in the local lesion host Chenopodium quinoa and in the progeny of a PFBV variant subjected to serial passages in this host. Concomitant with this covariation, up to 30 nucleotide substitutions in a 1,428-nt region of the viral RNA could be attributable to C. quinoa-specific adaptation, representing one of the most outstanding cases of host-driven genome variation for a plant virus. Globally, the results indicate that the selective pressures exerted by the host play a critical role in shaping PFBV populations and that these populations are likely being selected for at both protein and RNA levels. PMID:16873268

  20. Species difference in ANP32A underlies influenza A virus polymerase host restriction.

    PubMed

    Long, Jason S; Giotis, Efstathios S; Moncorgé, Olivier; Frise, Rebecca; Mistry, Bhakti; James, Joe; Morisson, Mireille; Iqbal, Munir; Vignal, Alain; Skinner, Michael A; Barclay, Wendy S

    2016-01-01

    Influenza pandemics occur unpredictably when zoonotic influenza viruses with novel antigenicity acquire the ability to transmit amongst humans. Host range breaches are limited by incompatibilities between avian virus components and the human host. Barriers include receptor preference, virion stability and poor activity of the avian virus RNA-dependent RNA polymerase in human cells. Mutants of the heterotrimeric viral polymerase components, particularly PB2 protein, are selected during mammalian adaptation, but their mode of action is unknown. We show that a species-specific difference in host protein ANP32A accounts for the suboptimal function of avian virus polymerase in mammalian cells. Avian ANP32A possesses an additional 33 amino acids between the leucine-rich repeats and carboxy-terminal low-complexity acidic region domains. In mammalian cells, avian ANP32A rescued the suboptimal function of avian virus polymerase to levels similar to mammalian-adapted polymerase. Deletion of the avian-specific sequence from chicken ANP32A abrogated this activity, whereas its insertion into human ANP32A, or closely related ANP32B, supported avian virus polymerase function. Substitutions, such as PB2(E627K), were rapidly selected upon infection of humans with avian H5N1 or H7N9 influenza viruses, adapting the viral polymerase for the shorter mammalian ANP32A. Thus ANP32A represents an essential host partner co-opted to support influenza virus replication and is a candidate host target for novel antivirals. PMID:26738596

  1. Lipid composition and fluidity of the human immunodeficiency virus envelope and host cell plasma membranes.

    PubMed Central

    Aloia, R C; Tian, H; Jensen, F C

    1993-01-01

    Previous studies have indicated that human immunodeficiency virus (HIV) is enclosed with a lipid envelope similar in composition to cell plasma membranes and to other viruses. Further, the fluidity, as measured by spin resonance spectroscopy, is low and the viral envelope is among the most highly ordered membranes analyzed. However, the relationship between viral envelope lipids and those of the host cell is not known. Here we demonstrate that the phospholipids within the envelopes of HIV-1RF and HIV-2-L are similar to each other but significantly different from their respective host cell surface membranes. Further, we demonstrate that the cholesterol-to-phospholipid molar ratio of the viral envelope is approximately 2.5 times that of the host cell surface membranes. Consistent with the elevated cholesterol-to-phospholipid molar ratio, the viral envelopes of HIV-1RF and HIV-2-L were shown to be 7.5% and 10.5% more ordered than the plasma membranes of their respective host cells. These data demonstrate that HIV-1 and HIV-2-L select specific lipid domains within the surface membrane of their host cells through which to emerge during viral maturation. Images Fig. 1 PMID:8389472

  2. Magneto-mechanical resonance of a single superparamagnetic microbead trapped by a magnetic domain wall

    NASA Astrophysics Data System (ADS)

    Rapoport, Elizabeth; Beach, Geoffrey S. D.

    2012-04-01

    Magnetic domain walls in ferromagnetic tracks can be used to trap and transport superparamagnetic beads for lab-on-a-chip applications. Here it is shown that the magnetostatic binding between a domain wall and a superparamagnetic bead suspended in a host fluid leads to a distinct magneto-mechanical resonance under application of a sinusoidal driving field. The characteristic resonant frequency depends on the ratio of the magnetostatic binding force to the viscous drag on the bead. This resonance has been experimentally detected for a single trapped superparamagnetic bead using an optical detection technique.

  3. The Potential for Hosted Payloads at NASA

    NASA Technical Reports Server (NTRS)

    Andraschko, Mark; Antol, Jeffrey; Baize, Rosemary; Horan, Stephen; Neil, Doreen; Rinsland, Pamela; Zaiceva, Rita

    2012-01-01

    The 2010 National Space Policy encourages federal agencies to actively explore the use of inventive, nontraditional arrangements for acquiring commercial space goods and services to meet United States Government requirements, including...hosting government capabilities on commercial spacecraft. NASA's Science Mission Directorate has taken an important step towards this goal by adding an option for hosted payload responses to its recent Announcement of Opportunity (AO) for Earth Venture-2 missions. Since NASA selects a significant portion of its science missions through a competitive process, it is useful to understand the implications that this process has on the feasibility of successfully proposing a commercially hosted payload mission. This paper describes some of the impediments associated with proposing a hosted payload mission to NASA, and offers suggestions on how these impediments might be addressed. Commercially hosted payloads provide a novel way to serve the needs of the science and technology demonstration communities at a fraction of the cost of a traditional Geostationary Earth Orbit (GEO) mission. The commercial communications industry launches over 20 satellites to GEO each year. By exercising this repeatable commercial paradigm of privately financed access to space with proven vendors, NASA can achieve science goals at a significantly lower cost than the current dedicated spacecraft and launch vehicle approach affords. Commercial hosting could open up a new realm of opportunities for NASA science missions to make measurements from GEO. This paper also briefly describes two GEO missions recommended by the National Academies of Science Earth Science Decadal Survey, the Geostationary Coastal and Air Pollution Events (GEO-CAPE) mission and the Precipitation and All-weather Temperature and Humidity (PATH) mission. Hosted payload missions recently selected for implementation by the Office of the Chief Technologist are also discussed. Finally, there are

  4. Transcriptome dynamics of a broad host-range cyanophage and its hosts.

    PubMed

    Doron, Shany; Fedida, Ayalla; Hernández-Prieto, Miguel A; Sabehi, Gazalah; Karunker, Iris; Stazic, Damir; Feingersch, Roi; Steglich, Claudia; Futschik, Matthias; Lindell, Debbie; Sorek, Rotem

    2016-06-01

    Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host-ranges relative to other cyanophages. It is currently unknown whether broad host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH7803, WH8102 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early-gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage-cyanobacteria interactions. Our findings suggest that the ability of broad host-range phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage. PMID:26623542

  5. Inter-Domain Roaming Mechanism Transparent to Mobile Nodes among PMIPv6 Networks

    NASA Astrophysics Data System (ADS)

    Park, Soochang; Lee, Euisin; Jin, Min-Sook; Kim, Sang-Ha

    In Proxy Mobile IPv6 (PMIPv6), when a Mobile Node (MN) enters a PMIPv6 domain and attaches to an access link, the router on the access link detects attachment of the MN by the link-layer access. All elements of PMIPv6 including the router then provide network-based mobility management service for the MN. If the MN moves to another router in this PMIPv6 domain, the new router emulates attachment to the previous router by providing same network prefix to the MN. In other words, PMIPv6 provides rapid mobility management based on layer-2 attachment and transparent mobility support to the MN by emulating layer-3 attachment with respect to intra-domain roaming. However, when the MN moves to other PMIPv6 domains, although the domains also provide the network-based mobility management service, the MN should exploit the host-based mobility management protocol, i.e. Mobile IPv6 (MIPv6), for the inter-domain roaming. Hence, this letter proposes the rapid and transparent inter-domain roaming mechanism controlled by the networks adopting PMIPv6.

  6. Both LCCL-domains of human CRISPLD2 have high affinity for lipid A.

    PubMed

    Vásárhelyi, Viktor; Trexler, Mária; Patthy, László

    2014-02-01

    The LCCL-domain is a recently defined protein module present in diverse extracellular multidomain proteins. Practically nothing is known about the molecular function of these domains; based on functional features of proteins harboring LCCL-domains it has been suggested that these domains might function as lipopolysaccharide-binding domains. Here we show that the two LCCL-domains of human CRISPLD2 protein, a lipopolysaccharide-binding serum protein involved in defense against endotoxin shock, have higher affinity for the lipid A, the toxic moiety of lipopolysaccharides than for ipopolysaccharide. Our observation that the LCCL-domains of CRISPLD2 are specific for the toxic lipid A moiety of the endotoxin suggests that it may block the interaction between endotoxins and the host endotoxin receptors without interfering with the development of antibacterial immunity against the polysaccharide moiety of LPS. We suggest that the anti-inflammatory function of CRISPLD2 protein may account for its role in various pathological and developmental processes. PMID:24090571

  7. Transposable Prophage Mu Is Organized as a Stable Chromosomal Domain of E. coli

    PubMed Central

    Meng, Luke; Harshey, Rasika M.

    2013-01-01

    The E. coli chromosome is compacted by segregation into 400–500 supercoiled domains by both active and passive mechanisms, for example, transcription and DNA-protein association. We find that prophage Mu is organized as a stable domain bounded by the proximal location of Mu termini L and R, which are 37 kbp apart on the Mu genome. Formation/maintenance of the Mu ‘domain’ configuration, reported by Cre-loxP recombination and 3C (chromosome conformation capture), is dependent on a strong gyrase site (SGS) at the center of Mu, the Mu L end and MuB protein, and the E. coli nucleoid proteins IHF, Fis and HU. The Mu domain was observed at two different chromosomal locations tested. By contrast, prophage λ does not form an independent domain. The establishment/maintenance of the Mu domain was promoted by low-level transcription from two phage promoters, one of which was domain dependent. We propose that the domain confers transposition readiness to Mu by fostering topological requirements of the reaction and the proximity of Mu ends. The potential benefits to the host cell from a subset of proteins expressed by the prophage may in turn help its long-term stability. PMID:24244182

  8. HOST PLANT UTILIZATION, HOST RANGE OSCILLATIONS AND DIVERSIFICATION IN NYMPHALID BUTTERFLIES: A PHYLOGENETIC INVESTIGATION

    PubMed Central

    Nylin, Sören; Slove, Jessica; Janz, Niklas

    2014-01-01

    It has been suggested that phenotypic plasticity is a major factor in the diversification of life, and that variation in host range in phytophagous insects is a good model for investigating this claim. We explore the use of angiosperm plants as hosts for nymphalid butterflies, and in particular the evidence for past oscillations in host range and how they are linked to host shifts and to diversification. At the level of orders of plants, a relatively simple pattern of host use and host shifts emerges, despite the 100 million years of history of the family Nymphalidae. We review the evidence that these host shifts and the accompanying diversifications were associated with transient polyphagous stages, as suggested by the “oscillation hypothesis.” In addition, we investigate all currently polyphagous nymphalid species and demonstrate that the state of polyphagy is rare, has a weak phylogenetic signal, and a very apical distribution in the phylogeny; we argue that these are signs of its transient nature. We contrast our results with data from the bark beetles Dendroctonus, in which a more specialized host use is instead the apical state. We conclude that plasticity in host use is likely to have contributed to diversification in nymphalid butterflies. PMID:24372598

  9. Gingipains from Porphyromonas gingivalis – Complex domain structures confer diverse functions

    PubMed Central

    Li, N.

    2011-01-01

    Gingipains, a group of arginine or lysine specific cysteine proteinases (also known as RgpA, RgpB and Kgp), have been recognized as major virulence factors in Porphyromonas gingivalis. This bacterium is one of a handful of pathogens that cause chronic periodontitis. Gingipains are involved in adherence to and colonization of epithelial cells, haemagglutination and haemolysis of erythrocytes, disruption and manipulation of the inflammatory response, and the degradation of host proteins and tissues. RgpA and Kgp are multi-domain proteins composed of catalytic domains and haemagglutinin/adhesin (HA) regions. The structure of the HA regions have previously been defined by a gingipain domain structure hypothesis which is a set of putative domain boundaries derived from the sequences of fragments of these proteins extracted from the cell surface. However, multiple sequence alignments and hidden Markov models predict an alternative domain architecture for the HA regions of gingipains. In this alternate model, two or three repeats of the so-called “cleaved adhesin” domains (and one other undefined domain in some strains) are the modules which constitute the substructure of the HA regions. Recombinant forms of these putative cleaved adhesin domains are indeed stable folded protein modules and recently determined crystal structures support the hypothesis of a modular organisation of the HA region. Based on the observed K2 and K3 structures as well as multiple sequence alignments, it is proposed that all the cleaved adhesin domains in gingipains will share the same β-sandwich jelly roll fold. The new domain model of the structure for gingipains and the haemagglutinin (HagA) proteins of P. gingivalis will guide future functional studies of these virulence factors. PMID:24466435

  10. Elastic Domain Architectures in Constrained Layers

    NASA Astrophysics Data System (ADS)

    Slutsker, J.; Artemev, A.; Roytburd, A. L.

    2002-08-01

    The formation of elastic domains in transforming constrained films is a mechanism of relaxation of internal stresses caused by the misfit between a film and a substrate. The formation and evolution of polydomain microstructure as a result of the cubic-tetragonal transformation in a constrained layer are investigated by phase-field simulation. It has been shown that the three-domain hierarchical structure can be formed in the epitaxial films. With changing a fraction of out-of-plane domain there are two types of morphological transitions: from the three-domain structure to the two-domain one and from the hierarchical three-domain structure to the cellular three-domain structure. The results of the phase-field simulation are compared with available experimental data on 90deg domain structures in epitaxial ferroelectric films.

  11. Characterization of lipid domains in erythrocyte membranes.

    PubMed Central

    Rodgers, W; Glaser, M

    1991-01-01

    Fluorescence digital imaging microscopy was used to study the lateral distribution of the lipid components in erythrocyte membranes. Intact erythrocytes labeled with phospholipids containing a fluorophore attached to one fatty acid chain showed an uneven distribution of the phospholipids in the membrane thereby demonstrating the presence of membrane domains. The enrichment of the lipotropic compound chlor-promazine in domains in intact erythrocytes also suggested that the domains are lipid-enriched regions. Similar membrane domains were present in erythrocyte ghosts. The phospholipid enrichment was increased in the domains by inducing membrane protein aggregation. Double-labeling experiments were done to determine the relative distributions of different phospholipids in the membrane. Vesicles made from extracted lipids did not show the presence of domains consistent with the conclusion that membrane proteins were responsible for creating the domains. Overall, it was found that large domains exist in the red blood cell membrane with unequal enrichment of the different phospholipid species. Images PMID:1996337

  12. The Case for GEO Hosted SSA Payloads

    NASA Astrophysics Data System (ADS)

    Welsch, C.; Armand, B.; Repp, M.; Robinson, A.

    2014-09-01

    Space situational awareness (SSA) in the geosynchronous earth orbit (GEO) belt presents unique challenges, and given the national importance and high value of GEO satellites, is increasingly critical as space becomes more congested and contested. Space situational awareness capabilities can serve as an effective deterrent against potential adversaries if they provide accurate, timely, and persistent information and are resilient to the threat environment. This paper will demonstrate how simple optical SSA payloads hosted on GEO commercial and government satellites can complement the SSA mission and data provided by Space-Based Space Surveillance (SBSS) and the Geosynchronous Space Situational Awareness Program (GSSAP). GSSAP is built by Orbital Sciences Corporation and launched on July 28, 2014. Analysis performed for this paper will show how GEO hosted SSA payloads, working in combination with SBSS and GSSAP, can increase persistence and timely coverage of high value assets in the GEO belt. The potential to further increase GEO object identification and tracking accuracy by integrating SSA data from multiple sources across different viewing angles including GEO hosted SSA sources will be addressed. Hosting SSA payloads on GEO platforms also increases SSA mission architecture resiliency as the sensors are by distributed across multiple platforms including commercial platforms. This distributed architecture presents a challenging target for an adversary to attempt to degrade or disable. We will present a viable concept of operations to show how data from hosted SSA sensors could be integrated with SBSS and GSSAP data to present a comprehensive and more accurate data set to users. Lastly, we will present an acquisition approach using commercial practices and building on lessons learned from the Commercially Hosted Infra Red Payload CHIRP to demonstrate the affordability of GEO hosted SSA payloads.

  13. The Host RNAs in Retroviral Particles

    PubMed Central

    Telesnitsky, Alice; Wolin, Sandra L.

    2016-01-01

    As they assemble, retroviruses encapsidate both their genomic RNAs and several types of host RNA. Whereas limited amounts of messenger RNA (mRNA) are detectable within virion populations, the predominant classes of encapsidated host RNAs do not encode proteins, but instead include endogenous retroelements and several classes of non-coding RNA (ncRNA), some of which are packaged in significant molar excess to the viral genome. Surprisingly, although the most abundant host RNAs in retroviruses are also abundant in cells, unusual forms of these RNAs are packaged preferentially, suggesting that these RNAs are recruited early in their biogenesis: before associating with their cognate protein partners, and/or from transient or rare RNA populations. These RNAs’ packaging determinants differ from the viral genome’s, and several of the abundantly packaged host ncRNAs serve cells as the scaffolds of ribonucleoprotein particles. Because virion assembly is equally efficient whether or not genomic RNA is available, yet RNA appears critical to the structural integrity of retroviral particles, it seems possible that the selectively encapsidated host ncRNAs might play roles in assembly. Indeed, some host ncRNAs appear to act during replication, as some transfer RNA (tRNA) species may contribute to nuclear import of human immunodeficiency virus 1 (HIV-1) reverse transcription complexes, and other tRNA interactions with the viral Gag protein aid correct trafficking to plasma membrane assembly sites. However, despite high conservation of packaging for certain host RNAs, replication roles for most of these selectively encapsidated RNAs—if any—have remained elusive. PMID:27548206

  14. Spectroscopy of Kepler Candidate Exoplanet Host Stars

    NASA Astrophysics Data System (ADS)

    Everett, Mark E.; Howell, Steve B.; Silva, David R.; Szkody, Paula

    2014-02-01

    Currently the NASA Kepler Mission has identified 3449 exoplanet candidates, one third with estimated radii R_p<2.5R_oplus and orbiting faint (m_Kep>14.5) host stars. The NASA sponsored Kepler Follow-up Program is focusing on small exoplanet candidates (R_p<2.5R_oplus) and those in habitable zone orbits. Planet radii estimates depend on estimates of host star radii. Based on spectra previously obtained at the KPNO Mayall 4-m for 220 stars with candidate exoplanets, Everett et al. (2013) have shown that many host stars are larger than originally assumed (up to factor of 2). Therefore, the exoplanet candidates they host must be larger than originally assumed, which conversely reduces the number of known Earth- sized exoplanet candidates. Determination of the frequency of such Earth-sized planets is a cornerstone Kepler mission objective and of keen general interest. These Mayall spectra were also used to confirm the Buchhave et al. (2012) result that exoplanet candidates larger than 4R_oplus in short-period orbits are preferentially associated with host stars with solar or higher metallicity, using a fainter and larger sample of stars than Buchhave et al. In short, followup Mayall optical spectroscopy is critical to confirming the detection of Earth-sized exoplanets, a Kepler cornerstone goal, as well as characterizing the relationship between host star properties and planetary system properties. Here, we propose to continue our reconnaissance survey with a focus on the smallest (most rare) exoplanet candidates orbiting the faintest Kepler host stars.

  15. The Host RNAs in Retroviral Particles.

    PubMed

    Telesnitsky, Alice; Wolin, Sandra L

    2016-01-01

    As they assemble, retroviruses encapsidate both their genomic RNAs and several types of host RNA. Whereas limited amounts of messenger RNA (mRNA) are detectable within virion populations, the predominant classes of encapsidated host RNAs do not encode proteins, but instead include endogenous retroelements and several classes of non-coding RNA (ncRNA), some of which are packaged in significant molar excess to the viral genome. Surprisingly, although the most abundant host RNAs in retroviruses are also abundant in cells, unusual forms of these RNAs are packaged preferentially, suggesting that these RNAs are recruited early in their biogenesis: before associating with their cognate protein partners, and/or from transient or rare RNA populations. These RNAs' packaging determinants differ from the viral genome's, and several of the abundantly packaged host ncRNAs serve cells as the scaffolds of ribonucleoprotein particles. Because virion assembly is equally efficient whether or not genomic RNA is available, yet RNA appears critical to the structural integrity of retroviral particles, it seems possible that the selectively encapsidated host ncRNAs might play roles in assembly. Indeed, some host ncRNAs appear to act during replication, as some transfer RNA (tRNA) species may contribute to nuclear import of human immunodeficiency virus 1 (HIV-1) reverse transcription complexes, and other tRNA interactions with the viral Gag protein aid correct trafficking to plasma membrane assembly sites. However, despite high conservation of packaging for certain host RNAs, replication roles for most of these selectively encapsidated RNAs-if any-have remained elusive. PMID:27548206

  16. Tidal Disruption Events Prefer Unusual Host Galaxies

    NASA Astrophysics Data System (ADS)

    French, K. Decker; Arcavi, Iair; Zabludoff, Ann

    2016-02-01

    Tidal Disruption Events (TDEs) are transient events observed when a star passes close enough to a supermassive black hole to be tidally destroyed. Many TDE candidates have been discovered in host galaxies whose spectra have weak or no line emission yet strong Balmer line absorption, indicating a period of intense star formation that has recently ended. As such, TDE host galaxies fall into the rare class of quiescent Balmer-strong galaxies. Here, we quantify the fraction of galaxies in the Sloan Digital Sky Survey (SDSS) with spectral properties like those of TDE hosts, determining the extent to which TDEs are over-represented in such galaxies. Galaxies whose spectra have Balmer absorption {{H}}{δ }{{A}} - σ(H{δ }{{A}}) > 4 Å (where σ(H{δ }{{A}}) is the error in the Lick {{H}}{δ }{{A}} index) and Hα emission equivalent width (EW) < 3 Å have had a strong starburst in the last ˜Gyr. They represent 0.2% of the local galaxy population, yet host 3 of 8 (37.5%) optical/UV-selected TDE candidates. A broader cut, {{H}}{δ }{{A}}\\quad \\gt 1.31 Å and Hα EW < 3 Å, nets only 2.3% of SDSS galaxies, but 6 of 8 (75%) optical/UV TDE hosts. Thus, quiescent Balmer-strong galaxies are over-represented among the TDE hosts by a factor of 33-190. The high-energy-selected TDE Swift J1644 also lies in a galaxy with strong Balmer lines and weak Hα emission, implying a \\gt 80× enhancement in such hosts and providing an observational link between the γ/X-ray-bright and optical/UV-bright TDE classes.

  17. Interaction of Mycobacterium tuberculosis with Host Cell Death Pathways

    PubMed Central

    Srinivasan, Lalitha; Ahlbrand, Sarah; Briken, Volker

    2014-01-01

    Mycobacterium tuberculosis (Mtb) has coevolved with humans for tens of thousands of years. It is thus highly adapted to its human host and has evolved multiple mechanisms to manipulate host immune responses to its advantage. One central host pathogen interaction modality is host cell death pathways. Host cell apoptosis is associated with a protective response to Mtb infection, whereas a necrotic response favors the pathogen. Consistently, Mtb inhibits host cell apoptosis signaling but promotes induction of programmed necrosis. The molecular mechanisms involved in Mtb-mediated host cell death manipulation, the consequences for host immunity, and the potential for therapeutic and preventive approaches will be discussed. PMID:24968864

  18. Caspase recruitment domain-containing protein 9 signaling in innate immunity and inflammation.

    PubMed

    Roth, Susanne; Ruland, Jürgen

    2013-06-01

    Caspase recruitment domain-containing protein (Card)9 is a nonredundant adapter protein that functions in the innate immune system in the assembly of multifunctional signaling complexes. Together with B cell lymphoma (Bcl)10 and the paracaspase, mucosa-associated lymphoid tissue lymphoma translocation protein (Malt)1, Card9 links spleen-tyrosine kinase (Syk)-coupled C-type lectin receptors to inflammatory responses. Card9 signaling also responds to intracellular danger sensors, such as retinoic acid-inducible gene 1 (RIG-I)-like receptors (RLRs) and nucleotide-oligomerization domain (Nod)2. Card9 complexes are engaged upon fungal, bacterial, or viral recognition, and they are essential for host protection. Moreover, Card9 polymorphisms are commonly associated with human inflammatory diseases. Here, we discuss the molecular regulation and the physiological functions of Card9 in host defense and immune homeostasis, and provide a framework for the therapeutic targeting of Card9 signaling in immune-mediated diseases. PMID:23523010

  19. Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota

    PubMed Central

    Naito, Mizue; Morton, Joseph B.; Pawlowska, Teresa E.

    2015-01-01

    Arbuscular mycorrhizal fungi (AMF, Glomeromycota) colonize roots of the majority of terrestrial plants. They provide essential minerals to their plant hosts and receive photosynthates in return. All major lineages of AMF harbor endobacteria classified as Mollicutes, and known as mycoplasma-related endobacteria (MRE). Except for their substantial intrahost genetic diversity and ability to transmit vertically, virtually nothing is known about the life history of these endobacteria. To understand MRE biology, we sequenced metagenomes of three MRE populations, each associated with divergent AMF hosts. We found that each AMF species harbored a genetically distinct group of MRE. Despite vertical transmission, all MRE populations showed extensive chromosomal rearrangements, which we attributed to genetic recombination, activity of mobile elements, and a history of plectroviral invasion. The MRE genomes are characterized by a highly reduced gene content, indicating metabolic dependence on the fungal host, with the mechanism of energy production remaining unclear. Several MRE genes encode proteins with domains involved in protein–protein interactions with eukaryotic hosts. In addition, the MRE genomes harbor genes horizontally acquired from AMF. Some of these genes encode small ubiquitin-like modifier (SUMO) proteases specific to the SUMOylation systems of eukaryotes, which MRE likely use to manipulate their fungal host. The extent of MRE genome plasticity and reduction, along with the large number of horizontally acquired host genes, suggests a high degree of adaptation to the fungal host. These features, together with the ubiquity of the MRE–Glomeromycota associations, emphasize the significance of MRE in the biology of Glomeromycota. PMID:25964324

  20. Identification of host proteins, Spata3 and Dkk2, interacting with Toxoplasma gondii micronemal protein MIC3.

    PubMed

    Wang, Yifan; Fang, Rui; Yuan, Yuan; Pan, Ming; Hu, Min; Zhou, Yanqin; Shen, Bang; Zhao, Junlong

    2016-07-01

    As an obligate intracellular protozoan, Toxoplasma gondii is a successful pathogen infecting a variety of animals, including humans. As an adhesin involving in host invasion, the micronemal protein MIC3 plays important roles in host cell attachment, as well as modulation of host EGFR signaling cascade. However, the specific host proteins that interact with MIC3 are unknown and the identification of such proteins will increase our understanding of how MIC3 exerts its functions. This study was designed to identify host proteins interacting with MIC3 by yeast two-hybrid screens. Using MIC3 as bait, a library expressing mouse proteins was screened, uncovering eight mouse proteins that showed positive interactions with MIC3. Two of which, spermatogenesis-associated protein 3 (Spata3) and dickkopf-related protein 2 (Dkk2), were further confirmed to interact with MIC3 by additional protein-protein interaction tests. The results also revealed that the tandem repeat EGF domains of MIC3 were critical in mediating the interactions with the identified host proteins. This is the first study to show that MIC3 interacts with host proteins that are involved in reproduction, growth, and development. The results will provide a clearer understanding of the functions of adhesion-associated micronemal proteins in T. gondii. PMID:27053129

  1. Large scale identification of Legionella pneumophila Dot/Icm substrates that modulate host cell vesicle trafficking pathways

    PubMed Central

    Heidtman, Matthew; Chen, Emy J.; Moy, Man-Yu; Isberg, Ralph R.

    2009-01-01

    The bacterial pathogen Legionella pneumophila replicates in a specialized vacuole within host cells. Establishment of the replication vacuole depends on the Dot/Icm translocation system that delivers a large number of protein substrates into the host cell. The functions of most substrates are unknown. Here, we analyzed a defined set of 127 confirmed or candidate Dot/Icm substrates for their effect on host cell processes using yeast as a model system. Expression of 79 candidates caused significant yeast growth defects, indicating these proteins impact essential host cell pathways. Notably, a group of 21 candidates interfered with the trafficking of secretory proteins to the yeast vacuole. Three candidates that caused yeast secretory defects (SetA, Ceg19 and Ceg9) were investigated further. These proteins impinged upon vesicle trafficking at distinct stages and had signals that allowed translocation into host cells by the Dot/Icm system. Ectopically produced SetA, Ceg19 and Ceg9 localized to secretory organelles in mammalian cells, consistent with a role for these proteins in modulating host cell vesicle trafficking. Interestingly, the ability of SetA to cause yeast phenotypes was dependent upon a functional glycosyltransferase domain. We hypothesize that SetA may glycosylate a component of the host cell vesicle trafficking machinery during L. pneumophila infection. PMID:19016775

  2. Host-Parasitoid Dynamics and the Success of Biological Control When Parasitoids Are Prone to Allee Effects

    PubMed Central

    Bompard, Anaïs; Amat, Isabelle; Fauvergue, Xavier; Spataro, Thierry

    2013-01-01

    In sexual organisms, low population density can result in mating failures and subsequently yields a low population growth rate and high chance of extinction. For species that are in tight interaction, as in host-parasitoid systems, population dynamics are primarily constrained by demographic interdependences, so that mating failures may have much more intricate consequences. Our main objective is to study the demographic consequences of parasitoid mating failures at low density and its consequences on the success of biological control. For this, we developed a deterministic host-parasitoid model with a mate-finding Allee effect, allowing to tackle interactions between the Allee effect and key determinants of host-parasitoid demography such as the distribution of parasitoid attacks and host competition. Our study shows that parasitoid mating failures at low density result in an extinction threshold and increase the domain of parasitoid deterministic extinction. When proned to mate finding difficulties, parasitoids with cyclic dynamics or low searching efficiency go extinct; parasitoids with high searching efficiency may either persist or go extinct, depending on host intraspecific competition. We show that parasitoids suitable as biocontrol agents for their ability to reduce host populations are particularly likely to suffer from mate-finding Allee effects. This study highlights novel perspectives for understanding of the dynamics observed in natural host-parasitoid systems and improving the success of parasitoid introductions. PMID:24116153

  3. Generic domain models in software engineering

    NASA Technical Reports Server (NTRS)

    Maiden, Neil

    1992-01-01

    This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

  4. Frequency domain photoacoustic and fluorescence microscopy

    PubMed Central

    Langer, Gregor; Buchegger, Bianca; Jacak, Jaroslaw; Klar, Thomas A.; Berer, Thomas

    2016-01-01

    We report on simultaneous frequency domain optical-resolution photoacoustic and fluorescence microscopy with sub-µm lateral resolution. With the help of a blood smear, we show that photoacoustic and fluorescence images provide complementary information. Furthermore, we compare theoretically predicted signal-to-noise ratios of sinusoidal modulation in frequency domain with pulsed excitation in time domain. PMID:27446698

  5. Frequency domain photoacoustic and fluorescence microscopy.

    PubMed

    Langer, Gregor; Buchegger, Bianca; Jacak, Jaroslaw; Klar, Thomas A; Berer, Thomas

    2016-07-01

    We report on simultaneous frequency domain optical-resolution photoacoustic and fluorescence microscopy with sub-µm lateral resolution. With the help of a blood smear, we show that photoacoustic and fluorescence images provide complementary information. Furthermore, we compare theoretically predicted signal-to-noise ratios of sinusoidal modulation in frequency domain with pulsed excitation in time domain. PMID:27446698

  6. Pectin Homogalacturonans: Nanostructural Characterization of Methylesterified Domains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functionality of pectic hydrocolloids is largely dependent on the two major domains commonly found in their homogalacturonan (HG) regions, i.e., methylester protected domains (MPDs)and non methylesterified domains (NMDs). MPDs can participate in hydrogen bonding and hydrophobic interactions but unli...

  7. 22 CFR 120.11 - Public domain.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Public domain. 120.11 Section 120.11 Foreign... Public domain. (a) Public domain means information which is published and which is generally accessible or available to the public: (1) Through sales at newsstands and bookstores; (2) Through...

  8. The Promise of Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mahabal, Ashish A.; Li, Jingling; Vaijanapurkar, Samarth; Bue, Brian; Miller, Adam; Donalek, Ciro; Djorgovski, Stanislav G.; Drake, Andrew J.; Graham, Matthew; CRTS, iPTF

    2016-01-01

    Most new surveys spend an appreciable time in collecting data on which to train classifiers before they can be used on future observations from the same dataset. The result generating phase can start much earlier if the training could incorporate data accumulated from older surveys enhanced with a small set from the new survey. This is exactly what Domain Adaptation (DA) allows us to do. The main idea behind DAs can be summarized thus: if we have two classes of separable objects in some feature space of a Source survey (S), we can define a hyperplane to separate the two types. In a second Target survey (T), for the same features the hyperplane would be inclined differently. DA methods get the mapping between the two hyperplanes using a small fraction of data from the Target (T) survey and can then be used to predict the classes of the remaining majority of data in T. We discuss the parameters that need to be tuned, the difficulties involved, and ways to improve the results. As we move towards bigger, and deeper surveys, being able to use existing labelled information to conduct classification in future surveys will be more cost-effective and promote time efficiency as well. Starting with the light curve data of 50,000 periodic objects from Catalina Real-Time Transient Survey (CRTS), we have applied domain adaptation techniques such as Geodesic Flow Kernel (GFK) with Random forest classifier and Co-training for domain adaptation (CODA) to the CRTS data which has 35,000 points overlapping with Palomar Transient Factory (PTF), and 12,000 with Lincoln Near-Earth Asteroid Research (LINEAR). The results suggest that domain adaptation is an area worth exploring as the knowledge between these surveys is transferable and the approaches to find the mappings between these surveys can be applied to the remaining data as well as for near future surveys such as CRTS-II, Zwicky Transient Facility (ZTF) and the Large Synoptic Survey Telescope (LSST) to name a few at the optical

  9. Early-Season Host Switching in Adelphocoris spp. (Hemiptera: Miridae) of Differing Host Breadth

    PubMed Central

    Pan, Hongsheng; Lu, Yanhui; Wyckhuys, Kris A. G.

    2013-01-01

    The mirid bugs Adelphocoris suturalis (Jakovlev), Adelphocoris lineolatus (Goeze) and Adelphocoris fasciaticollis (Reuter) (Hemiptera: Miridae) are common pests of several agricultural crops. These three species have vastly different geographical distributions, phenologies and abundances, all of which are linked to their reliance on local plants. Previous work has shown notable differences in Adelphocoris spp. host use for overwintering. In this study, we assessed the extent to which each of the Adelphocoris spp. relies on some of its major overwinter hosts for spring development. Over the course of four consecutive years (2009–2012), we conducted population surveys on 77 different plant species from 39 families. During the spring, A. fasciaticollis used the broadest range of hosts, as it was found on 35 plant species, followed by A. suturalis (15 species) and A. lineolatus (7 species). Abundances of the species greatly differed between host plants, with A. fasciaticollis reaching the highest abundance on Chinese date (Ziziphus jujuba Mill.), whereas both A. suturalis and A. lineolatus preferred alfalfa (Medicago sativa L.). The host breadths of the three Adelphocoris spp. differed greatly between subsequent spring and winter seasons. The generalist species exhibited the least host fidelity, with A. suturalis and A. lineolatus using 8 of 22 and 4 of 12 overwinter host species for spring development, respectively. By contrast, the comparative specialist A. fasciaticollis relied on 9 of its 11 overwinter plants as early-season hosts. We highlight important seasonal changes in host breadth and interspecific differences in the extent of host switching behavior between the winter and spring seasons. These findings benefit our understanding of the evolutionary interactions between mirid bugs and their host plants and can be used to guide early-season population management. PMID:23527069

  10. Parasitism and phenotypic change in colonial hosts.

    PubMed

    Hartikainen, Hanna; Fontes, Inês; Okamura, Beth

    2013-09-01

    Changes in host phenotype are often attributed to manipulation that enables parasites to complete trophic transmission cycles. We characterized changes in host phenotype in a colonial host–endoparasite system that lacks trophic transmission (the freshwater bryozoan Fredericella sultana and myxozoan parasite Tetracapsuloides bryosalmonae). We show that parasitism exerts opposing phenotypic effects at the colony and module levels. Thus, overt infection (the development of infectious spores in the host body cavity) was linked to a reduction in colony size and growth rate, while colony modules exhibited a form of gigantism. Larger modules may support larger parasite sacs and increase metabolite availability to the parasite. Host metabolic rates were lower in overtly infected relative to uninfected hosts that were not investing in propagule production. This suggests a role for direct resource competition and active parasite manipulation (castration) in driving the expression of the infected phenotype. The malformed offspring (statoblasts) of infected colonies had greatly reduced hatching success. Coupled with the severe reduction in statoblast production this suggests that vertical transmission is rare in overtly infected modules. We show that although the parasite can occasionally infect statoblasts during overt infections, no infections were detected in the surviving mature offspring, suggesting that during overt infections, horizontal transmission incurs a trade-off with vertical transmission. PMID:23965820

  11. Nocardia species: host-parasite relationships.

    PubMed Central

    Beaman, B L; Beaman, L

    1994-01-01

    The nocardiae are bacteria belonging to the aerobic actinomycetes. They are an important part of the normal soil microflora worldwide. The type species, Nocardia asteroides, and N. brasiliensis, N. farcinica, N. otitidiscaviarum, N. nova, and N. transvalensis cause a variety of diseases in both normal and immunocompromised humans and animals. The mechanisms of pathogenesis are complex, not fully understood, and include the capacity to evade or neutralize the myriad microbicidal activities of the host. The relative virulence of N. asteroides correlates with the ability to inhibit phagosome-lysosome fusion in phagocytes; to neutralize phagosomal acidification; to detoxify the microbicidal products of oxidative metabolism; to modify phagocyte function; to grow within phagocytic cells; and to attach to, penetrate, and grow within host cells. Both activated macrophages and immunologically specific T lymphocytes constitute the major mechanisms for host resistance to nocardial infection, whereas B lymphocytes and humoral immunity do not appear to be as important in protecting the host. Thus, the nocardiae are facultative intracellular pathogens that can persist within the host, probably in a cryptic form (L-form), for life. Silent invasion of brain cells by some Nocardia strains can induce neurodegeneration in experimental animals; however, the role of nocardiae in neurodegenerative diseases in humans needs to be investigated. Images PMID:8055469

  12. Insects as alternative hosts for phytopathogenic bacteria.

    PubMed

    Nadarasah, Geetanchaly; Stavrinides, John

    2011-05-01

    Phytopathogens have evolved specialized pathogenicity determinants that enable them to colonize their specific plant hosts and cause disease, but their intimate associations with plants also predispose them to frequent encounters with herbivorous insects, providing these phytopathogens with ample opportunity to colonize and eventually evolve alternative associations with insects. Decades of research have revealed that these associations have resulted in the formation of bacterial-vector relationships, in which the insect mediates dissemination of the plant pathogen. Emerging research, however, has highlighted the ability of plant pathogenic bacteria to use insects as alternative hosts, exploiting them as they would their primary plant host. The identification of specific bacterial genetic determinants that mediate the interaction between bacterium and insect suggests that these interactions are not incidental, but have likely arisen following the repeated association of microorganisms with particular insects over evolutionary time. This review will address the biology and ecology of phytopathogenic bacteria that interact with insects, including the traditional role of insects as vectors, as well as the newly emerging paradigm of insects serving as alternative primary hosts. Also discussed is one case where an insect serves as both host and vector, which may represent a transitionary stage in the evolution of insect-phytopathogen associations. PMID:21251027

  13. Visualizing viral transport and host infection

    NASA Astrophysics Data System (ADS)

    Son, Kwangmin; Guasto, Jeffrey; Cubillos-Ruiz, Andres; Sullivan, Matthew; Stocker, Roman; MIT Team

    2013-11-01

    A virus is a non-motile infectious agent that can only replicate inside a living host. They consist of a <100 nm diameter capsid which houses their DNA, and a <20 nm diameter tail used to inject DNA to the host, which are classified into three different morphologies by the tail type: short tail (~ 10 nm, podovirus), rigid contractile tail (~ 100 nm, myovirus), or flexible noncontractile tail (~ 300 nm, siphovirus). Combining microfluidics with epifluorescent microscopy, we studied the simultaneous diffusive transport governing the initial encounter and ultimately the infection of a non-motile cyanobacteria host (~ 1 μm prochlorococcus) and their viral (phage) counterparts in real time. This methodology allows us to quantify the virus-host encounter/adsorption dynamics and subsequently the effectiveness of various tail morphologies for viral infection. Viral transport and the role of viral morphology in host-virus interactions are critical to our understanding of both ecosystem dynamics and human health, as well as to the evolution of virus morphology.

  14. Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions.

    PubMed

    Ruiz, Lorena; Delgado, Susana; Ruas-Madiedo, Patricia; Margolles, Abelardo; Sánchez, Borja

    2016-01-01

    Bifidobacteria are commensal microoganisms found in the gastrointestinal tract. Several strains have been attributed beneficial traits at local and systemic levels, through pathogen exclusion or immune modulation, among other benefits. This has promoted a growing industrial and scientific interest in bifidobacteria as probiotic supplements. However, the molecular mechanisms mediating this cross-talk with the human host remain unknown. High-throughput technologies, from functional genomics to transcriptomics, proteomics, and interactomics coupled to the development of both in vitro and in vivo models to study the dynamics of the intestinal microbiota and their effects on host cells, have eased the identification of key molecules in these interactions. Numerous secreted or surface-associated proteins or peptides have been identified as potential mediators of bifidobacteria-host interactions and molecular cross-talk, directly participating in sensing environmental factors, promoting intestinal colonization, or mediating a dialogue with mucosa-associated immune cells. On the other hand, bifidobacteria induce the production of proteins in the intestine, by epithelial or immune cells, and other gut bacteria, which are key elements in orchestrating interactions among bifidobacteria, gut microbiota, and host cells. This review aims to give a comprehensive overview on proteinaceous molecules described and characterized to date, as mediators of the dynamic interplay between bifidobacteria and the human host, providing a framework to identify knowledge gaps and future research needs. PMID:27536282

  15. Viral antibody dynamics in a chiropteran host.

    PubMed

    Baker, Kate S; Suu-Ire, Richard; Barr, Jennifer; Hayman, David T S; Broder, Christopher C; Horton, Daniel L; Durrant, Christopher; Murcia, Pablo R; Cunningham, Andrew A; Wood, James L N

    2014-03-01

    Bats host many viruses that are significant for human and domestic animal health, but the dynamics of these infections in their natural reservoir hosts remain poorly elucidated. In these, and other, systems, there is evidence that seasonal life-cycle events drive infection dynamics, directly impacting the risk of exposure to spillover hosts. Understanding these dynamics improves our ability to predict zoonotic spillover from the reservoir hosts. To this end, we followed henipavirus antibody levels of >100 individual E. helvum in a closed, captive, breeding population over a 30-month period, using a powerful novel antibody quantitation method. We demonstrate the presence of maternal antibodies in this system and accurately determine their longevity. We also present evidence of population-level persistence of viral infection and demonstrate periods of increased horizontal virus transmission associated with the pregnancy/lactation period. The novel findings of infection persistence and the effect of pregnancy on viral transmission, as well as an accurate quantitation of chiropteran maternal antiviral antibody half-life, provide fundamental baseline data for the continued study of viral infections in these important reservoir hosts. PMID:24111634

  16. Pathogen evolution under host avoidance plasticity.

    PubMed

    McLeod, David V; Day, Troy

    2015-09-01

    Host resistance consists of defences that limit pathogen burden, and can be classified as either adaptations targeting recovery from infection or those focused upon infection avoidance. Conventional theory treats avoidance as a fixed strategy which does not vary from one interaction to the next. However, there is increasing empirical evidence that many avoidance strategies are triggered by external stimuli, and thus should be treated as phenotypically plastic responses. Here, we consider the implications of avoidance plasticity for host-pathogen coevolution. We uncover a number of predictions challenging current theory. First, in the absence of pathogen trade-offs, plasticity can restrain pathogen evolution; moreover, the pathogen exploits conditions in which the host would otherwise invest less in resistance, causing resistance escalation. Second, when transmission trades off with pathogen-induced mortality, plasticity encourages avirulence, resulting in a superior fitness outcome for both host and pathogen. Third, plasticity ensures the sterilizing effect of pathogens has consequences for pathogen evolution. When pathogens castrate hosts, selection forces them to minimize mortality virulence; moreover, when transmission trades off with sterility alone, resistance plasticity is sufficient to prevent pathogens from evolving to fully castrate. PMID:26336170

  17. Broomrape can acquire viruses from its hosts.

    PubMed

    Gal-On, Amit; Naglis, Anna; Leibman, Diana; Ziadna, Hammam; Kathiravan, Kathir; Papayiannis, Lambros; Holdengreber, Vered; Guenoune-Gelbert, Dana; Lapidot, Moshe; Aly, Radi

    2009-11-01

    Broomrapes (Phelipanche, formerly Orobanche) are parasitic plants that physically connect with the vascular systems of their hosts through haustorial structures. In this study, we found that Cucumber mosaic virus (CMV), Tomato mosaic virus (ToMV), Potato virus Y (PVY), and Tomato yellow leaf curl virus (TYLCV) translocate from infected host plants to Phelipanche aegyptiaca. In order to examine whether these viruses, and specifically CMV, replicate in the parasite, we tested several replication parameters. We detected accumulation of both plus and minus strands of CMV genomic RNA and CMV-derived siRNAs in the shoots of Phelipanche grown on CMV-infected tobacco and tomato plants. We purified CMV particles from Phelipanche grown on CMV-infected plants. These particles were present in amounts comparable to those found in the hosts' leaves. These data indicate that CMV replicates in Phelipanche tissues. In addition, viable ToMV and PVY were observed, and the plus and minus strand RNAs of ToMV were detected in Phelipanche shoots grown on infected hosts. However, we found only low levels of ToMV coat protein and did not detect any PVY coat protein. We also detected genomic TYLCV DNA in shoots of Phelipanche grown on TYLCV-infected tomato. Thus, for the first time, we demonstrate that broomrape is a host for at least one plant virus CMV, and possibly various other viruses. PMID:19821737

  18. Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions

    PubMed Central

    Ruiz, Lorena; Delgado, Susana; Ruas-Madiedo, Patricia; Margolles, Abelardo; Sánchez, Borja

    2016-01-01

    Bifidobacteria are commensal microoganisms found in the gastrointestinal tract. Several strains have been attributed beneficial traits at local and systemic levels, through pathogen exclusion or immune modulation, among other benefits. This has promoted a growing industrial and scientific interest in bifidobacteria as probiotic supplements. However, the molecular mechanisms mediating this cross-talk with the human host remain unknown. High-throughput technologies, from functional genomics to transcriptomics, proteomics, and interactomics coupled to the development of both in vitro and in vivo models to study the dynamics of the intestinal microbiota and their effects on host cells, have eased the identification of key molecules in these interactions. Numerous secreted or surface-associated proteins or peptides have been identified as potential mediators of bifidobacteria-host interactions and molecular cross-talk, directly participating in sensing environmental factors, promoting intestinal colonization, or mediating a dialogue with mucosa-associated immune cells. On the other hand, bifidobacteria induce the production of proteins in the intestine, by epithelial or immune cells, and other gut bacteria, which are key elements in orchestrating interactions among bifidobacteria, gut microbiota, and host cells. This review aims to give a comprehensive overview on proteinaceous molecules described and characterized to date, as mediators of the dynamic interplay between bifidobacteria and the human host, providing a framework to identify knowledge gaps and future research needs. PMID:27536282

  19. AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

    PubMed Central

    Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

    2015-01-01

    Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

  20. The Hypervariable Amino-Terminus of P1 Protease Modulates Potyviral Replication and Host Defense Responses

    PubMed Central

    Pasin, Fabio; Simón-Mateo, Carmen; García, Juan Antonio

    2014-01-01

    The replication of many RNA viruses involves the translation of polyproteins, whose processing by endopeptidases is a critical step for the release of functional subunits. P1 is the first protease encoded in plant potyvirus genomes; once activated by an as-yet-unknown host factor, it acts in cis on its own C-terminal end, hydrolyzing the P1-HCPro junction. Earlier research suggests that P1 cooperates with HCPro to inhibit host RNA silencing defenses. Using Plum pox virus as a model, we show that although P1 does not have a major direct role in RNA silencing suppression, it can indeed modulate HCPro function by its self-cleavage activity. To study P1 protease regulation, we used bioinformatic analysis and in vitro activity experiments to map the core C-terminal catalytic domain. We present evidence that the hypervariable region that precedes the protease domain is predicted as intrinsically disordered, and that it behaves as a negative regulator of P1 proteolytic activity in in vitro cleavage assays. In viral infections, removal of the P1 protease antagonistic regulator is associated with greater symptom severity, induction of salicylate-dependent pathogenesis-related proteins, and reduced viral loads. We suggest that fine modulation of a viral protease activity has evolved to keep viral amplification below host-detrimental levels, and thus to maintain higher long-term replicative capacity. PMID:24603811

  1. Domain wall fermion quenched spectroscopy

    NASA Astrophysics Data System (ADS)

    Malureanu, Catalin Ionut

    We measure y and the hadron spectrum on quenched ensembles using the domain wall fermion formulation. For the first time a 1/mf behavior of y for small valence masses has been observed. Our measurements of y on two different volumes of 83 x 32 and 163 x 32 at β = 5.85 suggest the behavior goes away on large enough volumes. Extensive spectrum calculations were done on 8 3 x 32 lattices at β = 5.7 and 5.85 corresponding roughly to a box size of 1.6 fm and 1.0 fm respectively. We have investigated five values of the extent of the fifth dimension Ls = 10, 16, 24, 32 and 48 with valence masses in the range 0.02 to 0.2 for the β = 5.7 ensemble and two values of Ls = 10 and 16 with valence masses in the range 0.02 to 0.08 for the β = 5.85 ensemble. Our pion remains massive in the infinite Ls extrapolation. This may be a finite volume effect. The nucleon to rho mass ratio stays constant at 1.4(1). Scaling violations for domain wall fermions are smaller roughly by a factor of four compared to the scaling violations in similar calculations done with staggered fermions.

  2. Frequency-domain Hadamard spectroscopy

    NASA Astrophysics Data System (ADS)

    Kupče, Ēriks; Freeman, Ray

    2003-05-01

    A new technique is proposed for multichannel excitation and detection of NMR signals in the frequency domain, an alternative to the widely used pulse-excited Fourier transform method. An extensive array of N radiofrequency irradiation channels covers the spectrum of interest. A selective radiofrequency pulse sequence is applied to each channel, generating a steady-state NMR response acquired one-point-at-a-time in the intervals between pulses. The excitation pattern is repeated N times, phase-encoded according to a Hadamard matrix, and the corresponding N composite responses are decoded by reference to the same matrix. This multiplex technique offers the same sensitivity advantage as conventional Fourier transform spectroscopy. The irradiation pattern may be tailored to concentrate on interesting spectral regions, to facilitate homonuclear double resonance, or to avoid exciting strong solvent peaks. As no free induction decay is involved, the new method avoids problems of pulse breakthrough or lineshape distortion by premature termination of the time-domain signal.

  3. Interfaces between Block Copolymer Domains

    NASA Astrophysics Data System (ADS)

    Kim, Jaeup; Jeong, Seong-Jun; Kim, Sang Ouk

    2011-03-01

    Block copolymers naturally form nanometer scale structures which repeat their geometry on a larger scale. Such a small scale periodic pattern can be used for various applications such as storage media, nano-circuits and optical filters. However, perfect alignment of block copolymer domains in the macroscopic scale is still a distant dream. The nanostructure formation usually occurs with spontaneously broken symmetry; hence it is easily infected by topological defects which sneak in due to entropic fluctuation and incomplete annealing. Careful annealing can gradually reduce the number of defects, but once kinetically trapped, it is extremely difficult to remove all the defects. One of the main reasons is that the defect finds a locally metastable morphology whose potential depth is large enough to prohibit further morphology evolution. In this work, the domain boundaries between differently oriented lamellar structures in thin film are studied. For the first time, it became possible to quantitatively study the block copolymer morphology in the transitional region, and it was shown that the twisted grain boundary is energetically favorable compared to the T-junction grain boundary. [Nano Letters, 9, 2300 (2010)]. This theoretical method successfully explained the experimental results.

  4. Viral pathogen production in a wild grass host driven by host growth and soil nitrogen.

    PubMed

    Whitaker, Briana K; Rúa, Megan A; Mitchell, Charles E

    2015-08-01

    Nutrient limitation is a basic ecological constraint that has received little attention in studies on virus production and disease dynamics. Nutrient availability could directly limit the production of viral nucleic acids and proteins, or alternatively limit host growth and thus indirectly limit metabolic pathways necessary for viral replication. In order to compare direct and indirect effects of nutrient limitation on virus production within hosts, we manipulated soil nitrogen (N) and phosphorus (P) availability in a glasshouse for the wild grass host Bromus hordeaceus and the viral pathogen Barley yellow dwarf virus-PAV. We found that soil N additions increased viral concentrations within host tissues, and the effect was mediated by host growth. Specifically, in statistical models evaluating the roles of host biomass production, leaf N and leaf P, viral production depended most strongly on host biomass, rather than the concentration of either nutrient. Furthermore, at low soil N, larger plants supported greater viral concentrations than smaller ones, whereas at high N, smaller plants supported greater viral concentrations. Our results suggest that enhanced viral productivity under N enrichment is an indirect consequence of nutrient stimulation to host growth rate. Heightened pathogen production in plants has important implications for a world facing increasing rates of nutrient deposition. PMID:25782030

  5. Host Chemical Footprints Induce Host Sex Discrimination Ability in Egg Parasitoids

    PubMed Central

    Peri, Ezio; Frati, Francesca; Salerno, Gianandrea; Conti, Eric; Colazza, Stefano

    2013-01-01

    Trissolcus egg parasitoids, when perceiving the chemical footprints left on a substrate by pentatomid host bugs, adopt a motivated searching behaviour characterized by longer searching time on patches were signals are present. Once in contact with host chemical footprints, Trissolcus wasps search longer on traces left by associated hosts rather than non-associated species, and, in the former case, they search longer on traces left by females than males. Based on these evidences, we hypothesized that only associated hosts induce the ability to discriminate host sex in wasps. To test this hypothesis we investigated the ability of Trissolcus basalis, T. brochymenae, and Trissolcus sp. to distinguish female from male Nezara viridula, Murgantia histrionica, and Graphosoma semipunctatum footprints. These three pentatomid bugs were selected according to variable association levels. Bioassays were conducted on filter paper sheets, and on Brassica oleracea (broccoli) leaves. The results confirmed our hypothesis showing that wasps spent significantly more time on female rather than male traces left by associated hosts on both substrates. No differences were observed in the presence of traces left by non-associated hosts. The ecological consequences for parasitoid host location behaviour are discussed. PMID:24244417

  6. Wolbachia-Host Interactions: Host Mating Patterns Affect Wolbachia Density Dynamics

    PubMed Central

    Zhao, Dong-Xiao; Zhang, Xiang-Fei; Chen, Da-Song; Zhang, Yan-Kai; Hong, Xiao-Yue

    2013-01-01

    Wolbachia are maternally inherited intracellular bacteria that infect a wide range of arthropods and cause an array of effects on host reproduction, fitness and mating behavior. Although our understanding of the Wolbachia-associated effects on hosts is rapidly expanding, our knowledge of the host factors that mediate Wolbachia dynamics is rudimentary. Here, we explore the interactions between Wolbachia and its host, the two-spotted spider mite Tetranychus urticae Koch. Our results indicate that Wolbachia induces strong cytoplasmic incompatibility (CI), increases host fecundity, but has no effects on the longevity of females and the mating competitiveness of males in T. urticae. Most importantly, host mating pattern was found to affect Wolbachia density dynamics during host aging. Mating of an uninfected mite of either sex with an infected mite attenuates the Wolbachia density in the infected mite. According to the results of Wolbachia localization, this finding may be associated with the tropism of Wolbachia for the reproductive tissue in adult spider mites. Our findings describe a new interaction between Wolbachia and their hosts. PMID:23823081

  7. Host innate immune responses to sepsis

    PubMed Central

    Wiersinga, Willem Joost; Leopold, Stije J; Cranendonk, Duncan R; van der Poll, Tom

    2014-01-01

    The immune response to sepsis can be seen as a pattern recognition receptor-mediated dysregulation of the immune system following pathogen invasion in which a careful balance between inflammatory and anti-inflammatory responses is vital. Invasive infection triggers both pro-inflammatory and anti-inflammatory host responses, the magnitude of which depends on multiple factors, including pathogen virulence, site of infection, host genetics, and comorbidities. Toll-like receptors, the inflammasomes, and other pattern recognition receptors initiate the immune response after recognition of danger signals derived from microorganisms, so-called pathogen-associated molecular patterns or derived from the host, so-called danger-associated molecular patterns. Further dissection of the role of host–pathogen interactions, the cytokine response, the coagulation cascade, and their multidirectional interactions in sepsis should lead toward the development of new therapeutic strategies in sepsis. PMID:23774844

  8. Gut microbiota, metabolites and host immunity.

    PubMed

    Rooks, Michelle G; Garrett, Wendy S

    2016-05-27

    The microbiota - the collection of microorganisms that live within and on all mammals - provides crucial signals for the development and function of the immune system. Increased availability of technologies that profile microbial communities is facilitating the entry of many immunologists into the evolving field of host-microbiota studies. The microbial communities, their metabolites and components are not only necessary for immune homeostasis, they also influence the susceptibility of the host to many immune-mediated diseases and disorders. In this Review, we discuss technological and computational approaches for investigating the microbiome, as well as recent advances in our understanding of host immunity and microbial mutualism with a focus on specific microbial metabolites, bacterial components and the immune system. PMID:27231050

  9. New Hosts of The Lassa Virus.

    PubMed

    Olayemi, Ayodeji; Cadar, Daniel; Magassouba, N'Faly; Obadare, Adeoba; Kourouma, Fode; Oyeyiola, Akinlabi; Fasogbon, Samuel; Igbokwe, Joseph; Rieger, Toni; Bockholt, Sabrina; Jérôme, Hanna; Schmidt-Chanasit, Jonas; Garigliany, Mutien; Lorenzen, Stephan; Igbahenah, Felix; Fichet, Jean-Nicolas; Ortsega, Daniel; Omilabu, Sunday; Günther, Stephan; Fichet-Calvet, Elisabeth

    2016-01-01

    Lassa virus (LASV) causes a deadly haemorrhagic fever in humans, killing several thousand people in West Africa annually. For 40 years, the Natal multimammate rat, Mastomys natalensis, has been assumed to be the sole host of LASV. We found evidence that LASV is also hosted by other rodent species: the African wood mouse Hylomyscus pamfi in Nigeria, and the Guinea multimammate mouse Mastomys erythroleucus in both Nigeria and Guinea. Virus strains from these animals were isolated in the BSL-4 laboratory and fully sequenced. Phylogenetic analyses of viral genes coding for glycoprotein, nucleoprotein, polymerase and matrix protein show that Lassa strains detected in M. erythroleucus belong to lineages III and IV. The strain from H. pamfi clusters close to lineage I (for S gene) and between II &III (for L gene). Discovery of new rodent hosts has implications for LASV evolution and its spread into new areas within West Africa. PMID:27140942

  10. Salt, chloride, bleach, and innate host defense

    PubMed Central

    Wang, Guoshun; Nauseef, William M.

    2015-01-01

    Salt provides 2 life-essential elements: sodium and chlorine. Chloride, the ionic form of chlorine, derived exclusively from dietary absorption and constituting the most abundant anion in the human body, plays critical roles in many vital physiologic functions, from fluid retention and secretion to osmotic maintenance and pH balance. However, an often overlooked role of chloride is its function in innate host defense against infection. Chloride serves as a substrate for the generation of the potent microbicide chlorine bleach by stimulated neutrophils and also contributes to regulation of ionic homeostasis for optimal antimicrobial activity within phagosomes. An inadequate supply of chloride to phagocytes and their phagosomes, such as in CF disease and other chloride channel disorders, severely compromises host defense against infection. We provide an overview of the roles that chloride plays in normal innate immunity, highlighting specific links between defective chloride channel function and failures in host defense. PMID:26048979

  11. Rhizobial gibberellin negatively regulates host nodule number.

    PubMed

    Tatsukami, Yohei; Ueda, Mitsuyoshi

    2016-01-01

    In legume-rhizobia symbiosis, the nodule number is controlled to ensure optimal growth of the host. In Lotus japonicus, the nodule number has been considered to be tightly regulated by host-derived phytohormones and glycopeptides. However, we have discovered a symbiont-derived phytohormonal regulation of nodule number in Mesorhizobium loti. In this study, we found that M. loti synthesized gibberellic acid (GA) under symbiosis. Hosts inoculated with a GA-synthesis-deficient M. loti mutant formed more nodules than those inoculated with the wild-type form at four weeks post inoculation, indicating that GA from already-incorporated rhizobia prevents new nodule formation. Interestingly, the genes for GA synthesis are only found in rhizobial species that inhabit determinate nodules. Our findings suggest that the already-incorporated rhizobia perform GA-associated negative regulation of nodule number to prevent delayed infection by other rhizobia. PMID:27307029

  12. Salt, chloride, bleach, and innate host defense.

    PubMed

    Wang, Guoshun; Nauseef, William M

    2015-08-01

    Salt provides 2 life-essential elements: sodium and chlorine. Chloride, the ionic form of chlorine, derived exclusively from dietary absorption and constituting the most abundant anion in the human body, plays critical roles in many vital physiologic functions, from fluid retention and secretion to osmotic maintenance and pH balance. However, an often overlooked role of chloride is its function in innate host defense against infection. Chloride serves as a substrate for the generation of the potent microbicide chlorine bleach by stimulated neutrophils and also contributes to regulation of ionic homeostasis for optimal antimicrobial activity within phagosomes. An inadequate supply of chloride to phagocytes and their phagosomes, such as in CF disease and other chloride channel disorders, severely compromises host defense against infection. We provide an overview of the roles that chloride plays in normal innate immunity, highlighting specific links between defective chloride channel function and failures in host defense. PMID:26048979

  13. New Hosts of The Lassa Virus

    PubMed Central

    Olayemi, Ayodeji; Cadar, Daniel; Magassouba, N’Faly; Obadare, Adeoba; Kourouma, Fode; Oyeyiola, Akinlabi; Fasogbon, Samuel; Igbokwe, Joseph; Rieger, Toni; Bockholt, Sabrina; Jérôme, Hanna; Schmidt-Chanasit, Jonas; Garigliany, Mutien; Lorenzen, Stephan; Igbahenah, Felix; Fichet, Jean-Nicolas; Ortsega, Daniel; Omilabu, Sunday; Günther, Stephan; Fichet-Calvet, Elisabeth

    2016-01-01

    Lassa virus (LASV) causes a deadly haemorrhagic fever in humans, killing several thousand people in West Africa annually. For 40 years, the Natal multimammate rat, Mastomys natalensis, has been assumed to be the sole host of LASV. We found evidence that LASV is also hosted by other rodent species: the African wood mouse Hylomyscus pamfi in Nigeria, and the Guinea multimammate mouse Mastomys erythroleucus in both Nigeria and Guinea. Virus strains from these animals were isolated in the BSL-4 laboratory and fully sequenced. Phylogenetic analyses of viral genes coding for glycoprotein, nucleoprotein, polymerase and matrix protein show that Lassa strains detected in M. erythroleucus belong to lineages III and IV. The strain from H. pamfi clusters close to lineage I (for S gene) and between II & III (for L gene). Discovery of new rodent hosts has implications for LASV evolution and its spread into new areas within West Africa. PMID:27140942

  14. Rhizobial gibberellin negatively regulates host nodule number

    PubMed Central

    Tatsukami, Yohei; Ueda, Mitsuyoshi

    2016-01-01

    In legume–rhizobia symbiosis, the nodule number is controlled to ensure optimal growth of the host. In Lotus japonicus, the nodule number has been considered to be tightly regulated by host-derived phytohormones and glycopeptides. However, we have discovered a symbiont-derived phytohormonal regulation of nodule number in Mesorhizobium loti. In this study, we found that M. loti synthesized gibberellic acid (GA) under symbiosis. Hosts inoculated with a GA-synthesis-deficient M. loti mutant formed more nodules than those inoculated with the wild-type form at four weeks post inoculation, indicating that GA from already-incorporated rhizobia prevents new nodule formation. Interestingly, the genes for GA synthesis are only found in rhizobial species that inhabit determinate nodules. Our findings suggest that the already-incorporated rhizobia perform GA-associated negative regulation of nodule number to prevent delayed infection by other rhizobia. PMID:27307029

  15. Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor

    SciTech Connect

    Peng, Guiqing; Sun, Dawei; Rajashankar, Kanagalaghatta R.; Qian, Zhaohui; Holmes, Kathryn V.; Li, Fang

    2011-09-28

    Coronaviruses have evolved diverse mechanisms to recognize different receptors for their cross-species transmission and host-range expansion. Mouse hepatitis coronavirus (MHV) uses the N-terminal domain (NTD) of its spike protein as its receptor-binding domain. Here we present the crystal structure of MHV NTD complexed with its receptor murine carcinoembryonic antigen-related cell adhesion molecule 1a (mCEACAM1a). Unexpectedly, MHV NTD contains a core structure that has the same {beta}-sandwich fold as human galectins (S-lectins) and additional structural motifs that bind to the N-terminal Ig-like domain of mCEACAM1a. Despite its galectin fold, MHV NTD does not bind sugars, but instead binds mCEACAM1a through exclusive protein-protein interactions. Critical contacts at the interface have been confirmed by mutagenesis, providing a structural basis for viral and host specificities of coronavirus/CEACAM1 interactions. Sugar-binding assays reveal that galectin-like NTDs of some coronaviruses such as human coronavirus OC43 and bovine coronavirus bind sugars. Structural analysis and mutagenesis localize the sugar-binding site in coronavirus NTDs to be above the {beta}-sandwich core. We propose that coronavirus NTDs originated from a host galectin and retained sugar-binding functions in some contemporary coronaviruses, but evolved new structural features in MHV for mCEACAM1a binding.

  16. Word Domain Disambiguation via Word Sense Disambiguation

    SciTech Connect

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-04

    Word subject domains have been widely used to improve the perform-ance of word sense disambiguation al-gorithms. However, comparatively little effort has been devoted so far to the disambiguation of word subject do-mains. The few existing approaches have focused on the development of al-gorithms specific to word domain dis-ambiguation. In this paper we explore an alternative approach where word domain disambiguation is achieved via word sense disambiguation. Our study shows that this approach yields very strong results, suggesting that word domain disambiguation can be ad-dressed in terms of word sense disam-biguation with no need for special purpose algorithms.

  17. Single-domain antibodies for biomedical applications.

    PubMed

    Krah, Simon; Schröter, Christian; Zielonka, Stefan; Empting, Martin; Valldorf, Bernhard; Kolmar, Harald

    2016-01-01

    Single-domain antibodies are the smallest antigen-binding units of antibodies, consisting either only of one variable domain or one engineered constant domain that solely facilitates target binding. This class of antibody derivatives comprises naturally occurring variable domains derived from camelids and sharks as well as engineered human variable or constant antibody domains of the heavy or light chain. Because of their high affinity and specificity as well as stability, small size and benefit of multiple re-formatting opportunities, those molecules emerged as promising candidates for biomedical applications and some of these entities have already proven to be successful in clinical development. PMID:26551147

  18. FETI Prime Domain Decomposition base Parallel Iterative Solver Library Ver.1.0

    Energy Science and Technology Software Center (ESTSC)

    2003-09-15

    FETI Prime is a library for the iterative solution of linear equations in solid and structural mechanics. The algorithm employs preconditioned conjugate gradients, with a domain decomposition-based preconditioner. The software is written in C++ and is designed for use with massively parallel computers, using MPI. The algorithm is based on the FETI-DP method, with additional capabilities for handling constraint equations, as well as interfacing with the Salinas structural dynamics code and the Finite Element Interfacemore » (FEI) library. Practical Application: FETI Prime is designed for use with finite element-based simulation codes for solid and structural mechanics. The solver uses element matrices, connectivity information, nodal information, and force vectors computed by the host code and provides back the solution to the linear system of equations, to the user specified level of accuracy, The library is compiled with the host code and becomes an integral part of the host code executable.« less

  19. Host Range Specificity in Verticillium dahliae.

    PubMed

    Bhat, R G; Subbarao, K V

    1999-12-01

    ABSTRACT Verticillium dahliae isolates from artichoke, bell pepper, cabbage, cauliflower, chili pepper, cotton, eggplant, lettuce, mint, potato, strawberry, tomato, and watermelon and V. albo-atrum from alfalfa were evaluated for their pathogenicity on all 14 hosts. One-month-old seedlings were inoculated with a spore suspension of about 10(7) conidia per ml using a root-dip technique and incubated in the greenhouse. Disease incidence and severity, plant height, and root and shoot dry weights were recorded 6 weeks after inoculation. Bell pepper, cabbage, cauliflower, cotton, eggplant, and mint isolates exhibited host specificity and differential pathogenicity on other hosts, whereas isolates from artichoke, lettuce, potato, strawberry, tomato, and watermelon did not. Bell pepper was resistant to all Verticillium isolates except isolates from bell pepper and eggplant. Thus, host specificity exists in some isolates of V. dahliae. The same isolates were characterized for vegetative compatibility groups (VCGs) through complementation of nitrate nonutilizing (nit) mutants. Cabbage and cauliflower isolates did not produce nit mutants. The isolate from cotton belonged to VCG 1; isolates from bell pepper, eggplant, potato, and tomato, to VCG 4; and the remaining isolates, to VCG 2. These isolates were also analyzed using the random amplified polymorphic DNA (RAPD) method. Forty random primers were screened, and eighteen of them amplified DNA from Verticillium. Based on RAPD banding patterns, cabbage and cauliflower isolates formed a unique group, distinct from other V. dahliae and V. albo-atrum groups. Minor genetic variations were observed among V. dahliae isolates from other hosts, regardless of whether they were host specific or not. There was no correlation among pathogenicity, VCGs, and RAPD banding patterns. Even though the isolates belonged to different VCGs, they shared similar RAPD profiles. These results suggest that management of Verticillium wilt in some crops

  20. Opportunistic Pulmonary Infections in Immunocompromised Hosts.

    PubMed

    Rali, Parth; Veer, Manik; Gupta, Nupur; Singh, Anil C; Bhanot, Nitin

    2016-01-01

    Infections that are typically innocuous in immunocompetent persons may cause significant disease states in immunocompromised hosts. These individuals may be immunosuppressed secondary to many different causes such as drugs, malignancy, solid-organ or hematopoietic stem cell transplantation, HIV/AIDS, or anatomic reasons (asplenia). These immunocompromised hosts are at high risk for developing opportunistic infections. Here, we discuss some of these infections caused by bacteria, fungi, viruses, and parasites. Clinicians should be aware of the risk factors, common clinical presentations, diagnostic modalities, and treatment options for these potentially fatal illnesses. PMID:26919677

  1. Protective host immune responses to Salmonella infection

    PubMed Central

    Pham, Oanh H; McSorley, Stephen J.

    2015-01-01

    Salmonella enterica serovars Typhi and Paratyphi are the causative agents of human typhoid fever. Current typhoid vaccines are ineffective and are not widely used in endemic areas. Greater understanding of host–pathogen interactions during Salmonella infection should facilitate the development of improved vaccines to combat typhoid and nontyphoidal Salmonellosis. This review will focus on our current understanding of Salmonella pathogenesis and the major host immune components that participate in immunity to Salmonella infection. In addition, recent findings regarding host immune mechanisms in response to Salmonella infection will be also discussed, providing a new perspective on the utility of improved tools to study the immune response to Salmonella infections. PMID:25598340

  2. Bacterial Stress Responses during Host Infection.

    PubMed

    Fang, Ferric C; Frawley, Elaine R; Tapscott, Timothy; Vázquez-Torres, Andrés

    2016-08-10

    Pathogenic bacteria must withstand diverse host environments during infection. Environmental signals, such as pH, temperature, nutrient limitation, etc., not only trigger adaptive responses within bacteria to these specific stress conditions but also direct the expression of virulence genes at an appropriate time and place. An appreciation of stress responses and their regulation is therefore essential for an understanding of bacterial pathogenesis. This review considers specific stresses in the host environment and their relevance to pathogenesis, with a particular focus on the enteric pathogen Salmonella. PMID:27512901

  3. Interactions between hemiparasitic plants and their hosts

    PubMed Central

    Plavcová, Lenka; Cameron, Duncan D

    2010-01-01

    Hemiparasitic plants display a unique strategy of resource acquisition combining parasitism of other species and own photosynthetic activity. Despite the active photoassimilation and green habit, they acquire substantial amount of carbon from their hosts. The organic carbon transfer has a crucial influence on the nature of the interaction between hemiparasites and their hosts which can oscillate between parasitism and competition for light. In this minireview, we summarize methodical approaches and results of various studies dealing with carbon budget of hemiparasites and the ecological implications of carbon heterotrophy in hemiparasites. PMID:20729638

  4. (New hosts and vectors for genome cloning)

    SciTech Connect

    Not Available

    1991-01-01

    The main goal of our project remains the development of new bacterial hosts and vectors for the stable propagation of human DNA clones in E. coli. During the past six months of our current budget period, we have (1) continued to develop new hosts that permit the stable maintenance of unstable features of human DNA, and (2) developed a series of vectors for (a) cloning large DNA inserts, (b) assessing the frequency of human sequences that are lethal to the growth of E. coli, and (c) assessing the stability of human sequences cloned in M13 for large-scale sequencing projects.

  5. Glycoconjugates in Host-Helminth Interactions

    PubMed Central

    Prasanphanich, Nina Salinger; Mickum, Megan L.; Heimburg-Molinaro, Jamie; Cummings, Richard D.

    2013-01-01

    Helminths are multicellular parasitic worms that comprise a major class of human pathogens and cause an immense amount of suffering worldwide. Helminths possess an abundance of complex and unique glycoconjugates that interact with both the innate and adaptive arms of immunity in definitive and intermediate hosts. These glycoconjugates represent a major untapped reservoir of immunomodulatory compounds, which have the potential to treat autoimmune and inflammatory disorders, and antigenic glycans, which could be exploited as vaccines and diagnostics. This review will survey current knowledge of the interactions between helminth glycans and host immunity and highlight the gaps in our understanding which are relevant to advancing therapeutics, vaccine development, and diagnostics. PMID:24009607

  6. Recombinant vector and eukaryotic host transformed thereby

    SciTech Connect

    Sugden, W.M.

    1987-08-11

    A recombinant plasmid is described comprising: a segment from a first plasmid which is not a lymphotrophic herpes virus segment and which facilitates the replication of the recombinant plasmid in a prokaryotic host; a segment from a lymphotrophic herpes virus which is linked to the first plasmid segment such that is a capable of assisting in maintaining the recombinant plasmid as a plasmid if the recombinant plasmid is inserted into a eukaryotic host that has been transformed by the lymphotrophic herpes virus; and a foreign eukaryotic gene component linked as part of the recombinant plasmid.

  7. Cell-host, LINE and environment

    PubMed Central

    Del Re, Brunella; Giorgi, Gianfranco

    2013-01-01

    Long interspersed nuclear elements -1 (LINEs, L1s) are retroelements occupying almost 17% of the human genome. L1 retrotransposition can cause deleterious effects on the host-cell and it is generally inhibited by suppressive mechanisms, but it can occur in some specific cells during early development as well as in some tumor cells and in the presence of several environmental factors. In a recent publication we reported that extremely low frequency pulsed magnetic field can affect L1 retrotransposition in neuroblastoma cells. In this commentary we discuss the interaction between environment and L1 activity in the light of the new emerging paradigm of host-LINE relationship. PMID:23734298

  8. Morphology of methane hydrate host sediments

    USGS Publications Warehouse

    Jones, K.W.; Feng, H.; Tomov, S.; Winters, W.J.; Eaton, M.; Mahajan, D.

    2005-01-01

    The morphological features including porosity and grains of methane hydrate host sediments were investigated using synchrotron computed microtomography (CMT) technique. The sediment sample was obtained during Ocean Drilling Program Leg 164 on the Blake Ridge at water depth of 2278.5 m. The CMT experiment was performed at the Brookhaven National Synchrotron Light Source facility. The analysis gave ample porosity, specific surface area, mean particle size, and tortuosity. The method was found to be highly effective for the study of methane hydrate host sediments.

  9. Domain swapping: entangling alliances between proteins.

    PubMed Central

    Bennett, M J; Choe, S; Eisenberg, D

    1994-01-01

    The comparison of monomeric and dimeric diphtheria toxin (DT) reveals a mode for protein association which we call domain swapping. The structure of dimeric DT has been extensively refined against data to 2.0-A resolution and a three-residue loop has been corrected as compared with our published 2.5-A-resolution structure. The monomeric DT structure has also been determined, at 2.3-A resolution. Monomeric DT is a Y-shaped molecule with three domains: catalytic (C), transmembrane (T), and receptor binding (R). Upon freezing in phosphate buffer, DT forms a long-lived, metastable dimer. The protein chain tracing discloses that upon dimerization an unprecedented conformational rearrangement occurs: the entire R domain from each molecule of the dimer is exchanged for the R domain from the other. This involves breaking the noncovalent interactions between the R domain and the C and T domains, rotating the R domain by 180 degrees with atomic movements up to 65 A, and re-forming the same noncovalent interactions between the R domain and the C and T domains of the other chain of the dimer. This conformational transition explains the long life and metastability of the DT dimer. Several other intertwined, dimeric protein structures satisfy our definition of domain swapping and suggest that domain swapping may be the molecular mechanism for evolution of these oligomers and possibly of oligomeric proteins in general. Images PMID:8159715

  10. Enhanced protein domain discovery using taxonomy

    PubMed Central

    Coin, Lachlan; Bateman, Alex; Durbin, Richard

    2004-01-01

    Background It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical methods for finding domains in sequences of amino acids. Results We show that by incorporating our understanding of the taxonomic distribution of specific protein domains, we can enhance domain recognition in protein sequences. We identify 4447 new instances of Pfam domains in the SP-TREMBL database using this technique, equivalent to the coverage increase given by the last 8.3% of Pfam families and to a 0.7% increase in the number of domain predictions. We use PSI-BLAST to cross-validate our new predictions. We also benchmark our approach using a SCOP test set of proteins of known structure, and demonstrate improvements relative to standard Hidden Markov model techniques. Conclusions Explicitly including knowledge about the taxonomic distribution of protein domains can enhance protein domain recognition. Our method can also incorporate other context-specific domain distributions – such as domain co-occurrence and protein localisation. PMID:15137915

  11. Domain adaptive boosting method and its applications

    NASA Astrophysics Data System (ADS)

    Geng, Jie; Miao, Zhenjiang

    2015-03-01

    Differences of data distributions widely exist among datasets, i.e., domains. For many pattern recognition, nature language processing, and content-based analysis systems, a decrease in performance caused by the domain differences between the training and testing datasets is still a notable problem. We propose a domain adaptation method called domain adaptive boosting (DAB). It is based on the AdaBoost approach with extensions to cover the domain differences between the source and target domains. Two main stages are contained in this approach: source-domain clustering and source-domain sample selection. By iteratively adding the selected training samples from the source domain, the discrimination model is able to achieve better domain adaptation performance based on a small validation set. The DAB algorithm is suitable for the domains with large scale samples and easy to extend for multisource adaptation. We implement this method on three computer vision systems: the skin detection model in single images, the video concept detection model, and the object classification model. In the experiments, we compare the performances of several commonly used methods and the proposed DAB. Under most situations, the DAB is superior.

  12. Domain wall conduction in multiaxial ferroelectrics

    SciTech Connect

    Eliseev, E. A.; Morozovska, A. N.; Svechnikov, S. V.; Maksymovych, Petro; Kalinin, Sergei V

    2012-01-01

    The conductance of domain wall structures consisting of either stripes or cylindrical domains in multiaxial ferroelectric-semiconductors is analyzed. The effects of the flexoelectric coupling, domain size, wall tilt, and curvature on charge accumulation are analyzed using the Landau-Ginsburg Devonshire theory for polarization vector combined with the Poisson equation for charge distributions. The proximity and size effect of the electron and donor accumulation/depletion by thin stripe domains and cylindrical nanodomains are revealed. In contrast to thick domain stripes and wider cylindrical domains, in which the carrier accumulation (and so the static conductivity) sharply increases at the domain walls only, small nanodomains of radii less than 5-10 correlation lengths appeared conducting across the entire cross-section. Implications of such conductive nanosized channels may be promising for nanoelectronics.

  13. Host plant genotype influences survival of hybrids between Eurosta solidaginis host races.

    PubMed

    Craig, Timothy P; Itami, Joanne K; Craig, James V

    2007-11-01

    Extrinsic, host-associated environmental factors may influence postmating isolation between herbivorous insect populations and represent a fundamentally ecological cause of speciation. We investigated this issue in experiments on hybrids between the host races of Eurosta solidaginis, a fly that induces galls on the goldenrods Solidago altissima and S. gigantea. To do so, we measured the performance of parental host races and their hybrids on five genotypes of S. gigantea and nine genotypes of S. altissima to test hypotheses about how variation in plant genotype affects performance (i.e., fitness) and potentially influences gene flow between these host races. We found that rates of gall induction and of survival to adult emergence by hybrid larvae were significantly lower than those of both parental host races on both host species, adding support to the hypothesis that there is partial postmating isolation between the host races. Hybrid flies significantly varied in their performance across plant genotypes of both host species. A significant interaction between the effects of plant genotype and mating treatment (parental vs. hybrid crosses) on larval performance indicated that the relative suitability of particular plant genotypes differed between the parental host races and their hybrids. These patterns illustrate a poor correspondence between optimal parental and hybrid environments, consistent with the hypothesis that these host races are partially isolated due to extrinsic (ecological) factors. Based on these findings, we discuss the possibility that plant genotypes in which hybrid performance is high can facilitate hybridization and gene flow between partially reproductively isolated populations of herbivorous insects, thus affecting the dynamics of ecological speciation. PMID:17725623

  14. Functional innovation from changes in protein domains and their combinations.

    PubMed

    Lees, Jonathan G; Dawson, Natalie L; Sillitoe, Ian; Orengo, Christine A

    2016-06-01

    Domains are the functional building blocks of proteins. In this work we discuss how domains can contribute to the evolution of new functions. Domains themselves can evolve through various mechanisms, altering their intrinsic function. Domains can also facilitate functional innovations by combining with other domains to make novel proteins. We discuss the mechanisms by which domain and domain combinations support functional innovations. We highlight interesting examples where changes in domain combination promote changes at the domain level. PMID:27309309

  15. Structure of Yellow Fever Virus Envelope Protein Domain III

    PubMed Central

    Volk, David E.; May, Fiona J.; Gandham, Sai H. A.; Anderson, Anjenique; Von Lindern, Jana J.; Beasley, David W. C.; Barrett, Alan D. T.; Gorenstein, David G.

    2009-01-01

    The structure of recombinant domain III of the envelope protein (rED3) of yellow fever virus (YFV), containing the major neutralization site, was determined using NMR spectroscopy. The amino acid sequence and structure of the YFV-rED3 shows differences from ED3s of other mosquito-borne flaviviruses; in particular, the partially surface-exposed BC loop where methionine-304 and valine-324 were identified as being critical for the structure of the loop. Variations in the structure and surface chemistry of ED3 between flaviviruses affect neutralization sites and may affect host cell receptor interactions and play a role in the observed variations in viral pathogenesis and tissue tropism. PMID:19818466

  16. Structure and Function of KH Domains

    SciTech Connect

    Valverde, R.; Regan, E

    2008-01-01

    The hnRNP K homology (KH) domain was first identified in the protein human heterogeneous nuclear ribonucleoprotein K (hnRNP K) 14 years ago. Since then, KH domains have been identified as nucleic acid recognition motifs in proteins that perform a wide range of cellular functions. KH domains bind RNA or ssDNA, and are found in proteins associated with transcriptional and translational regulation, along with other cellular processes. Several diseases, e.g. fragile X mental retardation syndrome and paraneoplastic disease, are associated with the loss of function of a particular KH domain. Here we discuss the progress made towards understanding both general and specific features of the molecular recognition of nucleic acids by KH domains. The typical binding surface of KH domains is a cleft that is versatile but that can typically accommodate only four unpaired bases. Van der Waals forces and hydrophobic interactions and, to a lesser extent, electrostatic interactions, contribute to the nucleic acid binding affinity. 'Augmented' KH domains or multiple copies of KH domains within a protein are two strategies that are used to achieve greater affinity and specificity of nucleic acid binding. Isolated KH domains have been seen to crystallize as monomers, dimers and tetramers, but no published data support the formation of noncovalent higher-order oligomers by KH domains in solution. Much attention has been given in the literature to a conserved hydrophobic residue (typically Ile or Leu) that is present in most KH domains. The interest derives from the observation that an individual with this Ile mutated to Asn, in the KH2 domain of fragile X mental retardation protein, exhibits a particularly severe form of the syndrome. The structural effects of this mutation in the fragile X mental retardation protein KH2 domain have recently been reported. We discuss the use of analogous point mutations at this position in other KH domains to dissect both structure and function.

  17. Host specificity in bat ectoparasites: a natural experiment.

    PubMed

    Seneviratne, Sampath S; Fernando, H Chandrika; Udagama-Randeniya, Preethi V

    2009-07-15

    We undertook a field study to determine patterns of specialisation of ectoparasites in cave-dwelling bats in Sri Lanka. The hypothesis tested was that strict host specificity (monoxeny) could evolve through the development of differential species preferences through association with the different host groups. Three species of cave-dwelling bats were chosen to represent a wide range of host-parasite associations (monoxeny to polyxeny), and both sympatric and allopatric roosting assemblages. Of the eight caves selected, six caves were "allopatric" roosts where two of each housed only one of the three host species examined: Rousettus leschenaulti (Pteropodidae), Rhinolophus rouxi and Hipposideros speoris (Rhinolophidae). The remaining two caves were "sympatric" roosts and housed all three host species. Thirty bats of each species were examined for ectoparasites in each cave, which resulted in a collection of nycteribiid and streblid flies, an ischnopsyllid bat flea, argasid and ixodid ticks, and mites belonging to three families. The host specificity of bat parasites showed a trend to monoxeny in which 70% of the 30 species reported were monoxenous. Odds ratios derived from chi(2)-tests revealed two levels of host preferences in less-specific parasites (i) the parasite was found on two host species under conditions of both host sympatry and host allopatry, with a preference for a single host in the case of host sympatry and (ii) the preference for a single host was very high, hence under conditions of host sympatry, it was confined to the preferred host only. However, under conditions of host allopatry, it utilized both hosts. There appears to be an increasing prevalence in host preferences of the parasites toward confinement to a single host species. The ecological isolation of the bat hosts and a long history of host-parasite co-existence could have contributed to an overall tendency of bat ectoparasites to become specialists, here reflected in the high percentage

  18. Feeding guild of non-host community members affects host-foraging efficiency of a parasitic wasp.

    PubMed

    De Rijk, Marjolein; Yang, Daowei; Engel, Bas; Dicke, Marcel; Poelman, Erik H

    2016-06-01

    Interactions between predator and prey, or parasitoid and host, are shaped by trait- and density-mediated processes involving other community members. Parasitoids that lay their eggs in herbivorous insects locate their hosts through infochemicals such as herbivore-induced plant volatiles (HIPVs) and host-produced kairomones. Hosts are frequently accompanied by non-host herbivores that are unsuitable for the parasitoid. These non-hosts may interfere with host location primarily through trait-mediated processes, by their own infochemicals, and their induction of the emission of plant volatiles. Although it is known that single non-hosts can interfere with parasitoid host location, it is still unknown whether the observed effects are due to species specific characteristics or to the feeding habits of the non-host herbivores. Here we addressed whether the feeding guild of non-host herbivores differentially affects foraging of the parasitoid Cotesia glomerata for its common host, caterpillars of Pieris brassicae feeding on Brassica oleracea plants. We used different phloem-feeding and leaf-chewing non-hosts to study their effects on host location by the parasitoid when searching for host-infested plants based on HIPVs and when searching for hosts on the plant using infochemicals. To evaluate the ultimate effect of these two phases in host location, we studied parasitism efficiency of parasitoids in small plant communities under field-tent conditions. We show that leaf-chewing non-hosts primarily affected host location through trait-mediated effects via plant volatiles, whereas phloem-feeding non-hosts exerted trait-mediated effects by affecting foraging efficiency of the parasitoid on the plant. These trait-mediated effects resulted in associational susceptibility of hosts in environments with phloem feeders and associational resistance in environments with non-host leaf chewers. PMID:27459770

  19. Ceramic Hosts for Fission Products Immobilization

    SciTech Connect

    Peter C Kong

    2010-07-01

    Natural spinel, perovskite and zirconolite rank among the most leach resistant of mineral forms. They also have a strong affinity for a large number of other elements and including actinides. Specimens of natural perovskite and zirconolite were radioisotope dated and found to have survived at least 2 billion years of natural process while still remain their loading of uranium and thorium . Developers of the Synroc waste form recognized and exploited the capability of these minerals to securely immobilize TRU elements in high-level waste . However, the Synroc process requires a relatively uniform input and hot pressing equipment to produce the waste form. It is desirable to develop alternative approaches to fabricate these durable waste forms to immobilize the radioactive elements. One approach is using a high temperature process to synthesize these mineral host phases to incorporate the fission products in their crystalline structures. These mineral assemblages with immobilized fission products are then isolated in a durable high temperature glass for periods measured on a geologic time scale. This is a long term research concept and will begin with the laboratory synthesis of the pure spinel (MgAl2O4), perovskite (CaTiO3) and zirconolite (CaZrTi2O7) from their constituent oxides. High temperature furnace and/or thermal plasma will be used for the synthesis of these ceramic host phases. Nonradioactive strontium oxide will be doped into these ceramic phases to investigate the development of substitutional phases such as Mg1-xSrxAl2O4, Ca1-xSrxTiO3 and Ca1-xSrxZrTi2O7. X-ray diffraction will be used to establish the crystalline structures of the pure ceramic hosts and the substitution phases. Scanning electron microscopy and energy dispersive X-ray analysis (SEM-EDX) will be performed for product morphology and fission product surrogates distribution in the crystalline hosts. The range of strontium doping is planned to reach the full substitution of the divalent

  20. Moraxella catarrhalis Binds Plasminogen To Evade Host Innate Immunity.

    PubMed

    Singh, Birendra; Al-Jubair, Tamim; Voraganti, Chandrashekar; Andersson, Tobias; Mukherjee, Oindrilla; Su, Yu-Ching; Zipfel, Peter; Riesbeck, Kristian

    2015-09-01

    Several bacterial species recruit the complement regulators C4b-binding protein, factor H, and vitronectin, resulting in resistance against the bactericidal activity of human serum. It was recently demonstrated that bacteria also bind plasminogen, which is converted to plasmin that degrades C3b and C5. In this study, we found that a series of clinical isolates (n = 58) of the respiratory pathogen Moraxella catarrhalis, which is commonly isolated from preschool children and adults with chronic obstructive pulmonary disease (COPD), significantly binds human plasminogen. Ubiquitous surface protein A2 (UspA2) and hybrid UspA2 (UspA2H) were identified as the plasminogen-binding factors in the outer membrane proteome of Moraxella. Furthermore, expression of a series of truncated recombinant UspA2 and UspA2H proteins followed by a detailed analysis of protein-protein interactions suggested that the N-terminal head domains bound to the kringle domains of plasminogen. The binding affinity constant (KD) values of full-length UspA2(30-539) (amino acids 30 to 539 of UspA2) and full-length UspA2H(50-720) for immobilized plasminogen were 4.8 × 10(-8) M and 3.13 × 10(-8) M, respectively, as measured by biolayer interferometry. Plasminogen bound to intact M. catarrhalis or to recombinant UspA2/UspA2H was readily accessible for a urokinase plasminogen activator that converted the zymogen into active plasmin, as verified by the specific substrate S-2251 and a degradation assay with fibrinogen. Importantly, plasmin bound at the bacterial surface also degraded C3b and C5, which consequently may contribute to reduced bacterial killing. Our findings suggest that binding of plasminogen to M. catarrhalis may lead to increased virulence and, hence, more efficient colonization of the host. PMID:26099590

  1. Moraxella catarrhalis Binds Plasminogen To Evade Host Innate Immunity

    PubMed Central

    Singh, Birendra; Al-Jubair, Tamim; Voraganti, Chandrashekar; Andersson, Tobias; Mukherjee, Oindrilla; Su, Yu-Ching; Zipfel, Peter

    2015-01-01

    Several bacterial species recruit the complement regulators C4b-binding protein, factor H, and vitronectin, resulting in resistance against the bactericidal activity of human serum. It was recently demonstrated that bacteria also bind plasminogen, which is converted to plasmin that degrades C3b and C5. In this study, we found that a series of clinical isolates (n = 58) of the respiratory pathogen Moraxella catarrhalis, which is commonly isolated from preschool children and adults with chronic obstructive pulmonary disease (COPD), significantly binds human plasminogen. Ubiquitous surface protein A2 (UspA2) and hybrid UspA2 (UspA2H) were identified as the plasminogen-binding factors in the outer membrane proteome of Moraxella. Furthermore, expression of a series of truncated recombinant UspA2 and UspA2H proteins followed by a detailed analysis of protein-protein interactions suggested that the N-terminal head domains bound to the kringle domains of plasminogen. The binding affinity constant (KD) values of full-length UspA230–539 (amino acids 30 to 539 of UspA2) and full-length UspA2H50–720 for immobilized plasminogen were 4.8 × 10−8 M and 3.13 × 10−8 M, respectively, as measured by biolayer interferometry. Plasminogen bound to intact M. catarrhalis or to recombinant UspA2/UspA2H was readily accessible for a urokinase plasminogen activator that converted the zymogen into active plasmin, as verified by the specific substrate S-2251 and a degradation assay with fibrinogen. Importantly, plasmin bound at the bacterial surface also degraded C3b and C5, which consequently may contribute to reduced bacterial killing. Our findings suggest that binding of plasminogen to M. catarrhalis may lead to increased virulence and, hence, more efficient colonization of the host. PMID:26099590

  2. For Host's Sake: The Pluses of Parasite Preservation.

    PubMed

    Spencer, Hamish G; Zuk, Marlene

    2016-05-01

    Conservation biologists now realize that parasites of endangered hosts should be conserved for their own sake and as part of their host's natural environment. But parasites should also be conserved because parasitic exposure might be crucial to the host's development of a fully functional immune system and hence to the survival of the host. PMID:27020732

  3. Multifaceted determinants of host specificity in an aphid parasitoid

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The host specificity of insect parasitoids and herbivores is thought to be shaped by a suite of behavioral and physiological factors that mediate host acceptance and host suitability. We conducted laboratory experiments to identify mechanisms shaping the host specificity of the aphid parasitoid Bin...

  4. A Study Focusing on American Expatriates' Learning in Host Countries.

    ERIC Educational Resources Information Center

    Shim, In-Sun; Paprock, Kenneth C.

    2002-01-01

    A survey of 70 U.S. expatriate workers found that most learned the culture of their host country through reflective learning. Factors helping their adjustment included previous cross-cultural experience, language competence, long-term relationship with hosts, and information about the host country from both home and host sources. (Contains 29…

  5. Effect of Interdomain Linker Length on an Antagonistic Folding-Unfolding Equilibrium between Two Protein Domains

    PubMed Central

    Cutler, Thomas A.; Mills, Brandon M.; Lubin, David J.; Chong, Lillian T.; Loh, Stewart N.

    2009-01-01

    Fusion of one protein domain with another is a common event in both evolution and protein engineering experiments. When insertion is at an internal site (e.g., a surface loop or turn), as opposed to one of the termini, conformational strain can be introduced into both domains. Strain is manifested by an antagonistic folding-unfolding equilibrium between the two domains, which we previously showed can be parameterized by a coupling free-energy term (ΔGX). The extent of strain is predicted to depend primarily on the ratio of the N-to-C distance of the guest protein to the distance between ends of the surface loop in the host protein. Here, we test that hypothesis by inserting ubiquitin (Ub) into the bacterial ribonuclease barnase (Bn), using peptide linkers from zero to 10 amino acids each. ΔGX values are determined by measuring the extent to which Co2+ binding to an engineered site on the Ub domain destabilizes the Bn domain. All-atom, unforced Langevin dynamics simulations are employed to gain structural insight into the mechanism of mechanically induced unfolding. Experimental and computational results find that the two domains are structurally and energetically uncoupled when linkers are long and that ΔGX increases with decreasing linker length. When the linkers are fewer than two amino acids, strain is so great that one domain unfolds the other. However, the protein is able to refold as dimers and higher-order oligomers. The likely mechanism is a three-dimensional domain swap of the Bn domain, which relieves conformational strain. The simulations suggest that an effective route to mechanical unfolding begins with disruption of the hydrophobic core of Bn near the Ub insertion site. PMID:19038264

  6. Staphylococcal superantigen super-domains in immune evasion.

    PubMed

    Langley, Ries; Patel, Deepa; Jackson, Nicola; Clow, Fiona; Fraser, John D

    2010-01-01

    Staphylococcus aureus is a robust pathogen that is capable of growing in virtually any part of the human body, and can also survive and grow in many other species. S. aureus remains the most frequent cause of hospital-acquired infection and, with the emergence and spread of drug-resistant, hypervirulent, community-acquired strains, the specter looms of the ultimate superbug. S. aureus produces an array of immune evasion factors that target various components of host immune defense. Among them are the powerful superantigen (SAg) and SAg-like (SSL) molecules, which are coded for by genes scattered across several genomic and pathogenicity islands. The SAgs universally bind MHC (major histocompatibility complex) class II and T-cell receptors to induce profound T-cell activation, while the SSLs target a range of molecules regulating opsonophagocytosis and neutrophil function. Despite functional differences, the SAgs and SSLs have clearly evolved from a single ancestral gene that now codes for a stable, two-domain protein, with each domain responsible for binding a different target molecule. This superstructure tolerates extensive surface variation, enabling a wide assortment of virulence factors targeting multiple steps in innate immunity. Notably, both the SAgs and the SSLs exhibit optimal activity for humans and non-human primates, clearly indicating that primates have been the preferred host for S. aureus evolution. This restricted function makes it difficult to assess their role in staphylococcal virulence using animal models of infection. This brief review focuses on the structural features of SAgs and SSLs and their individual functions as we currently understand them. PMID:20370627

  7. Solution structure of the NEAT (NEAr Transporter) domain from IsdH/HarA: the human hemoglobin receptor in Staphylococcus aureus.

    PubMed

    Pilpa, Rosemarie M; Fadeev, Evgeny A; Villareal, Valerie A; Wong, Melissa L; Phillips, Martin; Clubb, Robert T

    2006-07-01

    During infections the pathogen Staphylococcus aureus procures the essential nutrient iron from its host using iron-regulated surface determinant (Isd) proteins, which scavenge heme bound iron from host hemoproteins. Four Isd proteins are displayed in the cell wall, where they function as receptors for host proteins and heme. Each of the receptors contains one or more copies of a recently discovered domain called NEAT (NEAr Transporter) that has been shown to mediate protein binding. Here we report the three-dimensional solution structure of the NEAT domain from the IsdH/HarA protein, which is the hemoglobin receptor in the Isd system. This is the first structure of a NEAT domain and reveals that they adopt a beta sandwich fold that consists of two five-stranded antiparallel beta sheets. Although unrelated at the primary sequence level, our results indicate that NEAT domains belong to the immunoglobulin superfamily. Binding studies indicate that two IsdH/HarA NEAT domains bind a single molecule of methemoglobin, while the distantly related NEAT domain from the S. aureus IsdC protein binds only heme. A comparison of their primary sequences in light of the new structure is used to predict the hemoglobin and heme binding surfaces on NEAT domains. PMID:16762363

  8. Parasite calcineurin regulates host cell recognition and attachment by apicomplexans

    PubMed Central

    Paul, Aditya S.; Saha, Sudeshna; Engelberg, Klemens; Jiang, Rays H.Y.; Coleman, Bradley I.; Kosber, Aziz L.; Chen, Chun-Ti; Ganter, Markus; Espy, Nicole; Gilberger, Tim W.; Gubbels, Marc-Jan; Duraisingh, Manoj T.

    2015-01-01

    SUMMARY Apicomplexans invade a variety of metazoan host cells through mechanisms involving host cell receptor engagement and secretion of parasite factors to facilitate cellular attachment. We find that the parasite homolog of calcineurin, a calcium-regulated phosphatase complex central to signal transduction in eukaryotes, also contributes to host cell invasion by the malaria parasite Plasmodium falciparum and related Toxoplasma gondii. Using reverse genetic and chemical-genetic approaches, we determine that calcineurin critically regulates and stabilizes attachment of extracellular P. falciparum to host erythrocytes before intracellular entry and has similar functions in host cell engagement by T. gondii. Calcineurin-mediated Plasmodium invasion is strongly associated with host receptors required for host cell recognition and calcineurin function distinguishes this form of receptor-mediated attachment from a second mode of host-parasite adhesion independent of host receptors. This specific role of calcineurin in coordinating physical interactions with host cells highlights an ancestral mechanism for parasitism used by apicomplexans. PMID:26118996

  9. Listening natively across perceptual domains?

    PubMed

    Langus, Alan; Seyed-Allaei, Shima; Uysal, Ertuğrul; Pirmoradian, Sahar; Marino, Caterina; Asaadi, Sina; Eren, Ömer; Toro, Juan M; Peña, Marcela; Bion, Ricardo A H; Nespor, Marina

    2016-07-01

    Our native tongue influences the way we perceive other languages. But does it also determine the way we perceive nonlinguistic sounds? The authors investigated how speakers of Italian, Turkish, and Persian group sequences of syllables, tones, or visual shapes alternating in either frequency or duration. We found strong native listening effects with linguistic stimuli. Speakers of Italian grouped the linguistic stimuli differently from speakers of Turkish and Persian. However, speakers of all languages showed the same perceptual biases when grouping the nonlinguistic auditory and the visual stimuli. The shared perceptual biases appear to be determined by universal grouping principles, and the linguistic differences caused by prosodic differences between the languages. Although previous findings suggest that acquired linguistic knowledge can either enhance or diminish the perception of both linguistic and nonlinguistic auditory stimuli, we found no transfer of native listening effects across auditory domains or perceptual modalities. (PsycINFO Database Record PMID:26820498

  10. Analysis of DCC domain structure

    SciTech Connect

    Randrup, J.; Thews, R.L.

    1997-10-01

    Wavelet-type methods are employed for the analysis of pion field configurations that have been obtained by dynamical simulations in idealized scenarios relevant to the formation of disoriented chiral condensates. It is illustrated how the measurement of the isospin domain structure depends on the ability to zoom in on limited parts of the phase space, due to the interplay between the pion correlation length and the effective source geometry. The need for advanced analysis methods is underscored by the fact that the extracted neutral-fraction distribution would differ significantly from the ideal form, even under perfect experimental conditions, and, moreover, by the circumstance that thermal sources with suitably adjusted temperatures can lead to distributions that may be practically indistinguishable from those arising from DCC-type nonequilibrium evolutions. {copyright} {ital 1997} {ital The American Physical Society}

  11. Analysis of DCC domain structure

    SciTech Connect

    Randrup, J.; Thews, R.L.

    1997-05-07

    Wavelet-type methods are employed for the analysis of pion field configurations that have been obtained by dynamical simulations in idealized scenarios relevant to the formation of disoriented chiral condensates. It is illustrated how the measurement of the isospin domain structure depends on the ability to zoom in on limited parts of the phase space, due to the interplay between the pion correlation length and the effective source geometry. The need for advanced analysis methods is underscored by the fact that the extracted neutral-fraction distribution would differ significantly from the ideal form, even under perfect experimental conditions, and, moreover, by the circumstance that thermal sources with suitably adjusted temperatures can lead to distributions that may be practically indistinguishable from those arising from DCC-type nonequilibrium evolutions.

  12. Time domain electromagnetic metal detectors

    SciTech Connect

    Hoekstra, P.

    1996-04-01

    This presentation focuses on illustrating by case histories the range of applications and limitations of time domain electromagnetic (TDEM) systems for buried metal detection. Advantages claimed for TDEM metal detectors are: independent of instrument response (Geonics EM61) to surrounding soil and rock type; simple anomaly shape; mitigation of interference by ambient electromagnetic noise; and responsive to both ferrous and non-ferrous metallic targets. The data in all case histories to be presented were acquired with the Geonics EM61 TDEM system. Case histories are a test bed site on Molokai, Hawaii; Fort Monroe, Virginia; and USDOE, Rocky Flats Plant. The present limitations of this technology are: discrimination capabilities in terms of type of ordnance, and depth of burial is limited, and ability of resolving targets with small metallic ambient needs to be improved.

  13. Comparative analysis of Leishmania exoproteomes: implication for host-pathogen interactions.

    PubMed

    Peysselon, Franck; Launay, Guillaume; Lisacek, Frédérique; Duclos, Bertrand; Ricard-Blum, Sylvie

    2013-12-01

    Leishmaniasis is a vector-borne disease caused by the protozoa Leishmania. We have analyzed and compared the sequences of three experimental exoproteomes of Leishmania promastigotes from different species to determine their specific features and to identify new candidate proteins involved in interactions of Leishmania with the host. The exoproteomes differ from the proteomes by a decrease in the average molecular weight per protein, in disordered amino acid residues and in basic proteins. The exoproteome of the visceral species is significantly enriched in sites predicted to be phosphorylated as well as in features frequently associated with molecular interactions (intrinsic disorder, number of disordered binding regions per protein, interaction and/or trafficking motifs) compared to the other species. The visceral species might thus have a larger interaction repertoire with the host than the other species. Less than 10% of the exoproteomes contain heparin-binding and RGD sequences, and ~30% the host targeting signal RXLXE/D/Q. These latter proteins might thus be exported inside the host cell during the intracellular stage of the infection. Furthermore we have identified nine protein families conserved in the three exoproteomes with specific combinations of Pfam domains and selected eleven proteins containing at least three interaction and/or trafficking motifs including two splicing factors, phosphomannomutase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, the paraflagellar rod protein-1D and a putative helicase. Their role in host-Leishmania interactions warrants further investigation but the putative ATP-dependent DEAD/H RNA helicase, which contains numerous interaction motifs, a host targeting signal and two disordered regions, is a very promising candidate. PMID:24096101

  14. Bacterial SET domain proteins and their role in eukaryotic chromatin modification

    PubMed Central

    Alvarez-Venegas, Raúl

    2014-01-01

    It has been shown by many researchers that SET-domain containing proteins modify chromatin structure and, as expected, genes coding for SET-domain containing proteins have been found in all eukaryotic genomes sequenced to date. However, during the last years, a great number of bacterial genomes have been sequenced and an important number of putative genes involved in histone post-translational modifications (histone PTMs) have been identified in many bacterial genomes. Here, I aim at presenting an overview of SET domain genes that have been identified in numbers of bacterial genomes based on similarity to SET domains of eukaryotic histone methyltransferases. I will argue in favor of the hypothesis that SET domain genes found in extant bacteria are of bacterial origin. Then, I will focus on the available information on pathogen and symbiont SET-domain containing proteins and their targets in eukaryotic organisms, and how such histone methyltransferases allow a pathogen to inhibit transcriptional activation of host defense genes. PMID:24765100

  15. LINCS Authentication Domain Interface (ADI) Logon protocol. (Preliminary specification and implementation guide)

    SciTech Connect

    Nessett, D.M.; Fletcher, J.G.

    1984-10-11

    With the development of computer networking a need has arisen for users to interact with various computers and distributed operating systems from terminals remotely located from those systems. By remotely located terminals we mean those connected to networks using a different protocol family than the computer or distributed operating system being logged onto. Each terminal is said to belong to an authentication domain (NESD84). We express the above requirement as the desirability to provide inter-authentication-domain interactive services. The problems and attendant requirements of accomplishing inter-authentication-domain interactive services are discussed in (NESD84). Readers are assumed to be familiar with the concepts and protocol defined in that document. This specification defines the Authentication Domain Interface (ADI) Logon protocol for the LINCS distributed operating system that in conjunction with the Inter-Authentication-Domain Logon protocol gives users of LINCS terminals the ability to logon to hosts that do not support LINCS. Hereafter, the Inter-Authentication-Domain Logon Protocol is called the IAD Logon protocol for the sake of brevity. In addition, it gives users of terminals connected to networks that do not directly support LINCS the ability to logon and use LINCS distributed resources.

  16. Reversible Conformational Change in the Plasmodium falciparum Circumsporozoite Protein Masks Its Adhesion Domains

    PubMed Central

    Herrera, Raul; Anderson, Charles; Kumar, Krishan; Molina-Cruz, Alvaro; Nguyen, Vu; Burkhardt, Martin; Reiter, Karine; Shimp, Richard; Howard, Randall F.; Srinivasan, Prakash; Nold, Michael J.; Ragheb, Daniel; Shi, Lirong; DeCotiis, Mark; Aebig, Joan; Lambert, Lynn; Rausch, Kelly M.; Muratova, Olga; Jin, Albert; Reed, Steven G.; Sinnis, Photini; Barillas-Mury, Carolina; Duffy, Patrick E.; MacDonald, Nicholas J.

    2015-01-01

    The extended rod-like Plasmodium falciparum circumsporozoite protein (CSP) is comprised of three primary domains: a charged N terminus that binds heparan sulfate proteoglycans, a central NANP repeat domain, and a C terminus containing a thrombospondin-like type I repeat (TSR) domain. Only the last two domains are incorporated in RTS,S, the leading malaria vaccine in phase 3 trials that, to date, protects about 50% of vaccinated children against clinical disease. A seroepidemiological study indicated that the N-terminal domain might improve the efficacy of a new CSP vaccine. Using a panel of CSP-specific monoclonal antibodies, well-characterized recombinant CSPs, label-free quantitative proteomics, and in vitro inhibition of sporozoite invasion, we show that native CSP is N-terminally processed in the mosquito host and undergoes a reversible conformational change to mask some epitopes in the N- and C-terminal domains until the sporozoite interacts with the liver hepatocyte. Our findings show the importance of understanding processing and the biophysical change in conformation, possibly due to a mechanical or molecular signal, and may aid in the development of a new CSP vaccine. PMID:26169272

  17. Reversible Conformational Change in the Plasmodium falciparum Circumsporozoite Protein Masks Its Adhesion Domains.

    PubMed

    Herrera, Raul; Anderson, Charles; Kumar, Krishan; Molina-Cruz, Alvaro; Nguyen, Vu; Burkhardt, Martin; Reiter, Karine; Shimp, Richard; Howard, Randall F; Srinivasan, Prakash; Nold, Michael J; Ragheb, Daniel; Shi, Lirong; DeCotiis, Mark; Aebig, Joan; Lambert, Lynn; Rausch, Kelly M; Muratova, Olga; Jin, Albert; Reed, Steven G; Sinnis, Photini; Barillas-Mury, Carolina; Duffy, Patrick E; MacDonald, Nicholas J; Narum, David L

    2015-10-01

    The extended rod-like Plasmodium falciparum circumsporozoite protein (CSP) is comprised of three primary domains: a charged N terminus that binds heparan sulfate proteoglycans, a central NANP repeat domain, and a C terminus containing a thrombospondin-like type I repeat (TSR) domain. Only the last two domains are incorporated in RTS,S, the leading malaria vaccine in phase 3 trials that, to date, protects about 50% of vaccinated children against clinical disease. A seroepidemiological study indicated that the N-terminal domain might improve the efficacy of a new CSP vaccine. Using a panel of CSP-specific monoclonal antibodies, well-characterized recombinant CSPs, label-free quantitative proteomics, and in vitro inhibition of sporozoite invasion, we show that native CSP is N-terminally processed in the mosquito host and undergoes a reversible conformational change to mask some epitopes in the N- and C-terminal domains until the sporozoite interacts with the liver hepatocyte. Our findings show the importance of understanding processing and the biophysical change in conformation, possibly due to a mechanical or molecular signal, and may aid in the development of a new CSP vaccine. PMID:26169272

  18. Host-Salmonella interaction: human trials.

    PubMed

    Levine, M M; Tacket, C O; Sztein, M B

    2001-01-01

    Human clinical trials, including experimental challenges of volunteers with pathogenic Salmonella enterica serovar Typhi, small phase I and II trials that monitor the immune responses to vaccines, and large-scale controlled field trials that assess vaccine efficacy under conditions of natural challenge, have helped elucidate the interactions between Salmonella typhi and human hosts. PMID:11755415

  19. Detecting Intermediary Hosts by TCP Latency Measurements

    NASA Astrophysics Data System (ADS)

    Singh, Gurvinder; Eian, Martin; Willassen, Svein Y.; Mjølsnes, Stig Fr.

    Use of intermediary hosts as stepping stones to conceal tracks is common in Internet misuse. It is therefore desirable to find a method to detect whether the originating party is using an intermediary host. Such a detection technique would allow the activation of a number of countermeasures that would neutralize the effects of misuse, and make it easier to trace a perpetrator. This work explores a new approach in determining if a host communicating via TCP is the data originator or if it is acting as a mere TCP proxy. The approach is based on measuring the inter packet arrival time at the receiving end of the connection only, and correlating the observed results with the network latency between the receiver and the proxy. The results presented here indicate that determining the use of a proxy host is possible, if the network latency between the originator and proxy is larger than the network latency between the proxy and the receiver. We show that this technique has potential to be used to detect connections were data is sent through a TCP proxy, such as remote login through TCP proxies, or rejecting spam sent through a bot network.

  20. How to Host a School Visit

    ERIC Educational Resources Information Center

    Eboch, Chris

    2006-01-01

    Bringing a "real live" author into the school can be a great fun for both kids and staff. However, it can also be a disaster. In this article, the author offers ideas on how to host a school visit. Library media specialists can help ensure a successful visit by preparing in advance: define the goals, communicate the expectations, provide…

  1. Citrus tristeza virus-host interactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrus tristeza virus (CTV) is a phloem-limited virus whose natural host range is restricted to citrus and related species. Although the virus has killed millions of trees, almost destroying whole industries, and continually limits production in many citrus growing areas, most isolates are mild or s...

  2. Host genomic influences on HIV/AIDS

    PubMed Central

    2013-01-01

    The AIDS era has seen multiple advances in the power of genetics research; scores of host genetic protective factors have been nominated and several have translated to the bedside. We discuss how genomics may inform HIV/AIDS prevention, treatment and eradication. PMID:23369251

  3. Gut microbiota, host gene expression, and aging.

    PubMed

    Patrignani, Paola; Tacconelli, Stefania; Bruno, Annalisa

    2014-01-01

    Novel concepts of disease susceptibility and development suggest an important role of gastrointestinal microbiota and microbial pathogens. They can contribute to physiological systems and disease processes, even outside of the gastrointestinal tract. There is increasing evidence that genetics of the host influence and interact with gut microbiota. Moreover, aging-associated oxidative stress may cause morphologic alterations of bacterial cells, thus influencing the aggressive potential and virulence markers of an anaerobic bacterium and finally the type of interaction with the host. At the same time, microbiota may influence host gene expression and it is becoming apparent that it may occur through the regulation of microRNAs. They are short single-stranded noncoding RNAs that regulate posttranscriptional gene expression by affecting mRNA stability and/or translational repression of their target mRNAs. The introduction of -omics approaches (such as metagenomics, metaproteomics, and metatranscriptomics) in microbiota research will certainly advance our knowledge of this area. This will lead to greatly deepen our understanding of the molecular targets in the homeostatic interaction between the gut microbiota and the host and, thereby, promises to reveal new ways to treat diseases and maintain health. PMID:25291121

  4. Host plants of psyllids in south Texas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Psyllids typically breed on a narrow range of usually related host plants. However, adult psyllids often feed on a wider array of plants, a strategy which undoubtedly enhances survival and perhaps even reproduction. For example, although the Asian citrus psyllid is the most common species on comme...

  5. Host selection by a kleptobiotic spider

    NASA Astrophysics Data System (ADS)

    Hénaut, Yann; Delme, Juliette; Legal, Luc; Williams, Trevor

    2005-02-01

    Why do kleptobiotic spiders of the genus Argyrodes seem to be associated with spiders of the genus Nephila worldwide? Observations following introduction of experimental insect prey of different sizes and weights on to host webs revealed that: (1) small prey are more effectively retained on the web of Nephila clavipes than on the web of another common host, Leucauge venusta. (2) N. clavipes did not consume small prey that accumulated on the web whereas larger, heavier prey were enveloped and stored. (3) We observed clear partitioning of prey items between N. clavipes and Argyrodes spp.; diet selection by Argyrodes did not overlap with that of N. clavipes but closely overlapped with that of L. venusta. (4) L. venusta responds very quickly to prey impact whereas N. clavipes is slower, offering a temporal window of opportunity for Argyrodes foraging. (5) The ability of L. venusta to detect and respond to small items also means that it acts aggressively to Argyrodes spp., whereas N. clavipes does not. Consequently, food-acquisition behaviours of Argyrodes were clearly less risky with N. clavipes compared with L. venusta. We conclude that when a kleptobiotic organism has a choice of various host species, it will opt for the least risky host that presents the highest rate of availability of food items. The fact that Nephila species present such characteristics explains the worldwide association with Argyrodes kleptobiotic spiders.

  6. GENETICS OF HOST RANGE IN LEPIDOPTERA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic basis of complex, ecologically relevant traits is not well known for any organism. The question is particularly compelling where closely-related species have diverged radically in their adaptation to the environment. Differences in host plant use among moths and butterflies often provi...

  7. Probing Pseudomonas syringae host interactions using metatranscriptomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transcriptome analyses during the interaction of plants and pathogens can be used to provide insights into molecular mechanisms of plant resistance as well as the mechanisms used by bacteria to adapt to hosts and cause disease. We performed a dual in planta RNA-Seq experiment to profile RNA expressi...

  8. New Hosts for Equine Herpesvirus 9

    PubMed Central

    Tucker, Tammy A.; Donovan, Taryn A.; Busch, Martin D.M.; Wise, Annabel G.; Maes, Roger K.; Kiupel, Matti

    2008-01-01

    Equine herpesvirus 9 was detected in a polar bear with progressive encephalitis; the source was traced to 2 members of a potential equid reservoir species, Grevy’s zebras. The virus was also found in an aborted Persian onager. Thus, the natural host range is extended to 6 species in 3 mammalian orders. PMID:18826828

  9. HOST INNATE IMMUNITY AGAINST INTESTINAL PARASITES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the poultry industry, there are mounting concerns over the ability of current vaccines to adequately protect against emerging hyper-virulent strains of pathogens and a lack of suitable, cost effective adjuvants. Thorough investigation of the immunogenetic responses involved in host-pathogen inte...

  10. The Swift GRB Host Galaxy Legacy Survey

    NASA Astrophysics Data System (ADS)

    Perley, Daniel

    2015-08-01

    I will describe the Swift Host Galaxy Legacy Survey (SHOALS), a comprehensive multiwavelength program to characterize the demographics of the GRB host population and its redshift evolution from z=0 to z=7. Using unbiased selection criteria we have designated a subset of 119 Swift gamma-ray bursts which are now being targeted with intensive observational follow-up. Deep Spitzer imaging of every field has already been obtained and analyzed, with major programs ongoing at Keck, GTC, Gemini, VLT, and Magellan to obtain complementary optical/NIR photometry and spectroscopy to enable full SED modeling and derivation of fundamental physical parameters such as mass, extinction, and star-formation rate. Using these data I will present an unbiased measurement of the GRB host-galaxy luminosity and mass distributions and their evolution with redshift, compare GRB hosts to other star-forming galaxy populations, and discuss implications for the nature of the GRB progenitor and the ability of GRBs to serve as tools for measuring and studying cosmic star-formation in the distant universe.

  11. Host factors governing resistance to Rhizoctonia solani

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the state of Washington, USA, annual losses of wheat attributed to soilborne necrotrophic fungal pathogens, such as Rhizoctonia solani, are estimated to be over US$100 million, and global estimates exceed US$1 billion. Host genetic resistance is a sustainable means of disease control that can be ...

  12. How Do Wireworms Find Their Host Plants?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wireworms are important pests of potatoes throughout North America. The means by which wireworms locate the potato host plant are briefly reviewed, and shown to include chemical cues that act to prompt long-distance orientation, and other chemicals that act as feeding stimulants. The possibility o...

  13. Viral Takeover of the Host Ubiquitin System

    PubMed Central

    Gustin, Jean K.; Moses, Ashlee V.; Früh, Klaus; Douglas, Janet L.

    2011-01-01

    Like the other more well-characterized post-translational modifications (phosphorylation, methylation, acetylation, acylation, etc.), the attachment of the 76 amino acid ubiquitin (Ub) protein to substrates has been shown to govern countless cellular processes. As obligate intracellular parasites, viruses have evolved the capability to commandeer many host processes in order to maximize their own survival, whether it be to increase viral production or to ensure the long-term survival of latently infected host cells. The first evidence that viruses could usurp the Ub system came from the DNA tumor viruses and Adenoviruses, each of which use Ub to dysregulate the host cell cycle (Scheffner et al., 1990; Querido et al., 2001). Today, the list of viruses that utilize Ub includes members from almost every viral class, encompassing both RNA and DNA viruses. Among these, there are examples of Ub usage at every stage of the viral life cycle, involving both ubiquitination and de-ubiquitination. In addition to viruses that merely modify the host Ub system, many of the large DNA viruses encode their own Ub modifying machinery. In this review, we highlight the latest discoveries regarding the myriad ways that viruses utilize Ub to their advantage. PMID:21847386

  14. A Guide to Hosting a Theatre Festival.

    ERIC Educational Resources Information Center

    Texas Education Agency, Austin. Div. of Curriculum Development.

    Based on the premise that a multischool theatre festival can provide educational interaction on a noncompetitive basis, this guide has been prepared as an aid for schools and theatre arts departments wishing to host such a festival. The guide discusses a variety of theatre festival components, including (1) the purpose and types of festivals; (2)…

  15. Mycobacterium bovis: characteristics of wildlife reservoir hosts.

    PubMed

    Palmer, M V

    2013-11-01

    Mycobacterium bovis is the cause of tuberculosis in animals and sometimes humans. Many developed nations have long-standing programmes to eradicate tuberculosis in livestock, principally cattle. As disease prevalence in cattle decreases these efforts are sometimes impeded by passage of M. bovis from wildlife to cattle. In epidemiological terms, disease can persist in some wildlife species, creating disease reservoirs, if the basic reproduction rate (R0) and critical community size (CCS) thresholds are achieved. Recognized wildlife reservoir hosts of M. bovis include the brushtail possum (Trichosurus vulpecula) in New Zealand, European badger (Meles meles) in Great Britain and Ireland, African buffalo (Syncerus caffer) in South Africa, wild boar (Sus scrofa) in the Iberian Peninsula and white-tailed deer (Odocoileus virginianus) in Michigan, USA. The epidemiological concepts of R0 and CCS are related to more tangible disease/pathogen characteristics such as prevalence, pathogen-induced pathology, host behaviour and ecology. An understanding of both epidemiological and disease/pathogen characteristics is necessary to identify wildlife reservoirs of M. bovis. In some cases, there is a single wildlife reservoir host involved in transmission of M. bovis to cattle. Complexity increases, however, in multihost systems where multiple potential reservoir hosts exist. Bovine tuberculosis eradication efforts require elimination of M. bovis transmission between wildlife reservoirs and cattle. For successful eradication identification of true wildlife reservoirs is critical, as disease control efforts are most effective when directed towards true reservoirs. PMID:24171844

  16. Host-dependent genetic structure of parasite populations: differential dispersal of seabird tick host races.

    PubMed

    McCoy, Karen D; Boulinier, Thierry; Tirard, Claire; Michalakis, Yannis

    2003-02-01

    Despite the fact that parasite dispersal is likely to be one of the most important processes influencing the dynamics and coevolution of host-parasite interactions, little information is available on the factors that affect it. In most cases, opportunities for parasite dispersal should be closely linked to host biology. Here we use microsatellite genetic markers to compare the population structure and dispersal of two host races of the seabird tick Ixodes uriae at the scale of the North Atlantic. Interestingly, tick populations showed high within-population genetic variation and relatively low population differentiation. However, gene flow at different spatial scales seemed to depend on the host species exploited. The black-legged kittiwake (Rissa tridactyla) had structured tick populations showing patterns of isolation by distance, whereas tick populations of the Atlantic puffin (Fratercula arctica) were only weakly structured at the largest scale considered. Host-dependent rates of tick dispersal between colonies will alter infestation probabilities and local dynamics and may thus modify the adaptation potential of ticks to local hosts. Moreover, as I. uriae is a vector of the Lyme disease agent Borrelia burgdorferi sensu lato in both hemispheres, the large-scale movements of birds and the subsequent dispersal of ticks will have important consequences for the dynamics and coevolutionary interactions of this microparasite with its different vertebrate and invertebrate hosts. PMID:12683525

  17. Host-Directed Therapeutics for Tuberculosis: Can We Harness the Host?

    PubMed Central

    Matheson, Alastair I.; Maley, Stephen N.; Vandal, Omar

    2013-01-01

    SUMMARY Treatment of tuberculosis (TB) remains challenging, with lengthy treatment durations and complex drug regimens that are toxic and difficult to administer. Similar to the vast majority of antibiotics, drugs for Mycobacterium tuberculosis are directed against microbial targets. Although more effective drugs that target the bacterium may lead to faster cure of patients, it is possible that a biological limit will be reached that can be overcome only by adopting a fundamentally new treatment approach. TB regimens might be improved by including agents that target host pathways. Recent work on host-pathogen interactions, host immunity, and host-directed interventions suggests that supplementing anti-TB therapy with host modulators may lead to shorter treatment times, a reduction in lung damage caused by the disease, and a lower risk of relapse or reinfection. We undertook this review to identify molecular pathways of the host that may be amenable to modulation by small molecules for the treatment of TB. Although several approaches to augmenting standard TB treatment have been proposed, only a few have been explored in detail or advanced to preclinical and clinical studies. Our review focuses on molecular targets and inhibitory small molecules that function within the macrophage or other myeloid cells, on host inflammatory pathways, or at the level of TB-induced lung pathology. PMID:24296574

  18. Ancient host shifts followed by host conservatism in a group of ant parasitoids

    PubMed Central

    Murray, Elizabeth A.; Carmichael, Andrew E.; Heraty, John M.

    2013-01-01

    While ant colonies serve as host to a diverse array of myrmecophiles, few parasitoids are able to exploit this vast resource. A notable exception is the wasp family Eucharitidae, which is the only family of insects known to exclusively parasitize ants. Worldwide, approximately 700 Eucharitidae species attack five subfamilies across the ant phylogeny. Our goal is to uncover the pattern of eucharitid diversification, including timing of key evolutionary events, biogeographic patterns and potential cophylogeny with ant hosts. We present the most comprehensive molecular phylogeny of Eucharitidae to date, including 44 of the 53 genera and fossil-calibrated estimates of divergence dates. Eucharitidae arose approximately 50 Ma after their hosts, during the time when the major ant lineages were already established and diversifying. We incorporate host association data to test for congruence between eucharitid and ant phylogenies and find that their evolutionary histories are more similar than expected at random. After a series of initial host shifts, clades within Eucharitidae maintained their host affinity. Even after multiple dispersal events to the New World and extensive speciation within biogeographic regions, eucharitids remain parasitic on the same ant subfamilies as their Old World relatives, suggesting host conservatism despite access to a diverse novel ant fauna. PMID:23554396

  19. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.

    PubMed

    Normand, Philippe; Lapierre, Pascal; Tisa, Louis S; Gogarten, Johann Peter; Alloisio, Nicole; Bagnarol, Emilie; Bassi, Carla A; Berry, Alison M; Bickhart, Derek M; Choisne, Nathalie; Couloux, Arnaud; Cournoyer, Benoit; Cruveiller, Stephane; Daubin, Vincent; Demange, Nadia; Francino, Maria Pilar; Goltsman, Eugene; Huang, Ying; Kopp, Olga R; Labarre, Laurent; Lapidus, Alla; Lavire, Celine; Marechal, Joelle; Martinez, Michele; Mastronunzio, Juliana E; Mullin, Beth C; Niemann, James; Pujic, Pierre; Rawnsley, Tania; Rouy, Zoe; Schenowitz, Chantal; Sellstedt, Anita; Tavares, Fernando; Tomkins, Jeffrey P; Vallenet, David; Valverde, Claudio; Wall, Luis G; Wang, Ying; Medigue, Claudine; Benson, David R

    2007-01-01

    Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N(2)-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%-98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses. PMID:17151343

  20. Novel Mechanism of Regulation of Tomato Bushy Stunt Virus Replication by Cellular WW-Domain Proteins

    PubMed Central

    Barajas, Daniel; Kovalev, Nikolay; Qin, Jun

    2014-01-01

    ABSTRACT Replication of (+)RNA viruses depends on several co-opted host proteins but is also under the control of cell-intrinsic restriction factors (CIRFs). By using tombusviruses, small model viruses of plants, we dissect the mechanism of inhibition of viral replication by cellular WW-domain-containing proteins, which act as CIRFs. By using fusion proteins between the WW domain and the p33 replication protein, we show that the WW domain inhibits the ability of p33 to bind to the viral RNA and to other p33 and p92 replication proteins leading to inhibition of viral replication in yeast and in a cell extract. Overexpression of WW-domain protein in yeast also leads to reduction of several co-opted host factors in the viral replicase complex (VRC). These host proteins, such as eEF1A, Cdc34 E2 ubiquitin-conjugating enzyme, and ESCRT proteins (Bro1p and Vps4p), are known to be involved in VRC assembly. Simultaneous coexpression of proviral cellular factors with WW-domain protein partly neutralizes the inhibitory effect of the WW-domain protein. We propose that cellular WW-domain proteins act as CIRFs and also as regulators of tombusvirus replication by inhibiting the assembly of new membrane-bound VRCs at the late stage of infection. We suggest that tombusviruses could sense the status of the infected cells via the availability of cellular susceptibility factors versus WW-domain proteins for binding to p33 replication protein that ultimately controls the formation of new VRCs. This regulatory mechanism might explain how tombusviruses could adjust the efficiency of RNA replication to the limiting resources of the host cells during infections. IMPORTANCE Replication of positive-stranded RNA viruses, which are major pathogens of plants, animals, and humans, is inhibited by several cell-intrinsic restriction factors (CIRFs) in infected cells. We define here the inhibitory roles of the cellular Rsp5 ubiquitin ligase and its WW domain in plant-infecting tombusvirus

  1. CPDadh: A new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins

    PubMed Central

    Pei, Jimin; Lupardus, Patrick J; Garcia, K Christopher; Grishin, Nick V

    2009-01-01

    A cysteine protease domain (CPD) has been recently discovered in a group of multifunctional, autoprocessing RTX toxins (MARTX) and Clostridium difficile toxins A and B. These CPDs (referred to as CPDmartx) autocleave the toxins to release domains with toxic effects inside host cells. We report identification and computational analysis of CPDadh, a new cysteine peptidase family homologous to CPDmartx. CPDadh and CPDmartx share a Rossmann-like structural core and conserved catalytic residues. In bacteria, domains of the CPDadh family are present at the N-termini of a diverse group of putative cell-cell interaction proteins and at the C-termini of some RHS (recombination hot spot) proteins. In eukaryotes, catalytically inactive members of the CPDadh family are found in cell surface protein NELF (nasal embryonic LHRH factor) and some putative signaling proteins. PMID:19309740

  2. Crystal Structure of the Protease-Resistant Core Domain of Yersinia Pestis Virulence Factor Yopr

    SciTech Connect

    Schubot,F.; Cherry, S.; Austin, B.; Tropea, J.; Waugh, D.

    2005-01-01

    Yersinia pestis, the causative agent of the plague, employs a type III secretion system (T3SS) to secrete and translocate virulence factors into the cytoplasm of mammalian host cells. One of the secreted virulence factors is YopR. Little is known about the function of YopR other than that it is secreted into the extracellular milieu during the early stages of infection and that it contributes to virulence. Hoping to gain some insight into the function of YopR, we determined the crystal structure of its protease-resistant core domain, which consists of residues 38--149 out of 165 amino acids. The core domain is composed of five {alpha}-helices that display unexpected structural similarity with one domain of YopN, a central regulator of type III secretion in Y. pestis. This finding raises the possibility that YopR may play a role in the regulation of type III secretion.

  3. TOPOLOGICAL MATTER. Observation of chiral currents at the magnetic domain boundary of a topological insulator.

    PubMed

    Wang, Y H; Kirtley, J R; Katmis, F; Jarillo-Herrero, P; Moodera, J S; Moler, K A

    2015-08-28

    A magnetic domain boundary on the surface of a three-dimensional topological insulator is predicted to host a chiral edge state, but direct demonstration is challenging. We used a scanning superconducting quantum interference device to show that current in a magnetized topological insulator heterostructure (EuS/Bi2Se3) flows at the edge when the Fermi level is gate-tuned to the surface band gap. We further induced micrometer-scale magnetic structures on the heterostructure and detected a chiral edge current at the magnetic domain boundary. The chirality of the current was determined by magnetization of the surrounding domain, and its magnitude by the local chemical potential rather than the applied current. Such magnetic structures provide a platform for detecting topological magnetoelectric effects and may enable progress in quantum information processing and spintronics. PMID:26272905

  4. Frequency domain modelling of wind turbine structures

    SciTech Connect

    Soerensen, P.; Larsen, G.C.; Christensen, C.J.

    1995-09-01

    The present paper describes a frequency domain model of the structure of an operating horizontal axis wind turbine. The frequency domain model is implemented along with an analogous time domain modeling the Risoe PC code Design Basis 2, and a more detailed description of the model is offered in a Risoe report by Soerensen (1994). The structure of an operating wind turbine is affected by essential non-linearities between structural variables on blades and tower respectively. These non-linearities are caused by the rotation of the blades. The transformations between the blade coordinate systems and the tower coordinate system will depend on the instantaneous azimuth positions of the blades as they rotate. Frequency domain analysis are much faster than time simulations and in some respects they give more insight into the dynamics of the structure. However, the non-linear terms in the dynamic equations for a complex wind turbine structure are usually thought to preclude the use of frequency domain methods. Design Basis 2 is used to verify the frequency domain model comparing loads on the structure calculated with the frequency domain model both to loads calculated with the time domain model and to measured loads. Examples show that frequency and time domain calculations of typical PSD`s of loads are in very good agreement. Also the agreement between the calculated and measured PSD`s is good. Moreover, Design Basis 2 has shown that the frequency domain model results in an extremely fast calculation method.

  5. No adaptation of a herbivore to a novel host but loss of adaptation to its native host.

    PubMed

    Grosman, Amir H; Molina-Rugama, Adrián J; Mendes-Dias, Rondinelli; Sabelis, Maurice W; Menken, Steph B J; Pallini, Angelo; Breeuwer, Johannes A J; Janssen, Arne

    2015-01-01

    Most herbivorous arthropods are host specialists and the question is which mechanisms drive the evolution of such specialization. The theory of antagonistic pleiotropy suggests that there is a trade-off between adaptation of herbivores to a novel host and their native host. The mutation accumulation hypothesis proposes that herbivores on a novel host lose their adaptation to the native host through the accumulation of mutations with negligible effects on performance on the novel host. Experimental evidence for either of the two hypotheses is scarce. We compared the fitness of two sympatric moth strains from an introduced host and a native host. The strain from the novel host did not perform better on this host than the strain from the native host. The strain from the novel host performed less well on the native host than did the strain from the native host. Hence, selection on the novel host did not result in noticeable gain in performance, but adaptation to the native host was lost. These results are more readily explained by the mutation-accumulation hypothesis than by the trade-off hypothesis. PMID:26577696

  6. No adaptation of a herbivore to a novel host but loss of adaptation to its native host

    PubMed Central

    Grosman, Amir H.; Molina-Rugama, Adrián J.; Mendes-Dias, Rondinelli; Sabelis, Maurice W.; Menken, Steph B.J.; Pallini, Angelo; Breeuwer, Johannes A.J.; Janssen, Arne

    2015-01-01

    Most herbivorous arthropods are host specialists and the question is which mechanisms drive the evolution of such specialization. The theory of antagonistic pleiotropy suggests that there is a trade-off between adaptation of herbivores to a novel host and their native host. The mutation accumulation hypothesis proposes that herbivores on a novel host lose their adaptation to the native host through the accumulation of mutations with negligible effects on performance on the novel host. Experimental evidence for either of the two hypotheses is scarce. We compared the fitness of two sympatric moth strains from an introduced host and a native host. The strain from the novel host did not perform better on this host than the strain from the native host. The strain from the novel host performed less well on the native host than did the strain from the native host. Hence, selection on the novel host did not result in noticeable gain in performance, but adaptation to the native host was lost. These results are more readily explained by the mutation-accumulation hypothesis than by the trade-off hypothesis. PMID:26577696

  7. Escherichia coli lipoprotein binds human plasminogen via an intramolecular domain

    PubMed Central

    Gonzalez, Tammy; Gaultney, Robert A.; Floden, Angela M.; Brissette, Catherine A.

    2015-01-01

    Escherichia coli lipoprotein (Lpp) is a major cellular component that exists in two distinct states, bound-form and free-form. Bound-form Lpp is known to interact with the periplasmic bacterial cell wall, while free-form Lpp is localized to the bacterial cell surface. A function for surface-exposed Lpp has yet to be determined. We hypothesized that the presence of C-terminal lysinses in the surface-exposed region of Lpp would facilitate binding to the host zymogen plasminogen (Plg), a protease commandeered by a number of clinically important bacteria. Recombinant Lpp was synthesized and the binding of Lpp to Plg, the effect of various inhibitors on this binding, and the effects of various mutations of Lpp on Lpp–Plg interactions were examined. Additionally, the ability of Lpp-bound Plg to be converted to active plasmin was analyzed. We determined that Lpp binds Plg via an atypical domain located near the center of mature Lpp that may not be exposed on the surface of intact E. coli according to the current localization model. Finally, we found that Plg bound by Lpp can be converted to active plasmin. While the consequences of Lpp binding Plg are unclear, these results prompt further investigation of the ability of surface exposed Lpp to interact with host molecules such as extracellular matrix components and complement regulators, and the role of these interactions in infections caused by E. coli and other bacteria. PMID:26500634

  8. Trophic Relationships between the Parasitic Plant Species Phelipanche ramosa (L.) and Different Hosts Depending on Host Phenological Stage and Host Growth Rate.

    PubMed

    Moreau, Delphine; Gibot-Leclerc, Stéphanie; Girardin, Annette; Pointurier, Olivia; Reibel, Carole; Strbik, Florence; Fernández-Aparicio, Mónica; Colbach, Nathalie

    2016-01-01

    Phelipanche ramosa (L.) Pomel (branched broomrape) is a holoparasitic plant that reproduces on crops and also on weeds, which contributes to increase the parasite seed bank in fields. This parasite extracts all its nutrients at the host's expense so that host-parasite trophic relationships are crucial to determine host and parasite growth. This study quantified the intensity with which P. ramosa draws assimilates from its host and analyzed whether it varied with host species, host phenological stage and host growth rate. A greenhouse experiment was conducted on three host species: the crop species Brassica napus (L.) (oilseed rape) and two weed species, Capsella bursa-pastoris (L.) Medik. and Geranium dissectum (L.). Plants were grown with or without P. ramosa and under three light levels to modulate host growth rate. The proportion of host biomass loss due to parasitism by P. ramosa differed between host species (at host fructification, biomass loss ranged from 34 to 84%). B. napus and C. bursa-pastoris displayed a similar response to P. ramosa, probably because they belong to the same botanical family. The sensitivity to P. ramosa in each host species could be related to the precocity of P. ramosa development on them. Host compartments could be ranked as a function of their sensitivity to parasitism, with the reproductive compartment being the most severely affected, followed by stems and roots. The proportion of biomass allocated to leaves was not reduced by parasitism. The proportion of pathosystem biomass allocated to the parasite depended on host species. It generally increased with host stage progression but was constant across light induced-host growth rate, showing that P. ramosa adapts its growth to host biomass production. The rank order of host species in terms of sink strength differed from that in terms of host sensitivity. Finally, for B. napus, the biomass of individual parasite shoots decreased with increasing their number per host plant

  9. [Up-to-date findings in the host defence mechanism to cryptococcus infection].

    PubMed

    Ishii, Keiko; Kawakami, Kazuyoshi

    2014-01-01

    Cryptococcus neoformans is a medically important opportunistic fungal pathogen with a polysaccharide capsule surrounding the yeast-like cells. In hosts with impaired cell-mediated immunity such as AIDS, uncontrolled infection causes life-threatening meningoencephalitis. In immunocompetent individuals, the host immune response usually limits the growth of the fungal pathogen at the primary infected site, where it may persist, without completely eradicated, in a latent state because of its ability to escape from killing by macrophages. Th1 response in adaptive immunity is essential for the host defense to cryptococcal infection, in which interferon (IFN)-γ polarizes innate macrophages into fungicidal M1 macrophages. Recently, we found that caspase recruitment domain family member (CARD9), an adaptor protein in a signal transduction triggered by C-type lectin receptors, plays a key role in the early production of IFN-γ at the site of infection by recruiting NK cells and CD4(+) and CD8(+) memory-phenotype T cells. We also found that IL-4 produced by Th2 cells stimulates broncoepithelial cells to secrete mucin, which may lead to promotion in the mucociliary clearance of C. neoformans. Here, we summarize the up-to-date findings in the host defense mechanism to this infection with focusing on our recent data. PMID:25231225

  10. The virA promoter is a host-range determinant in Agrobacterium tumefaciens.

    PubMed

    Turk, S C; Nester, E W; Hooykaas, P J

    1993-03-01

    The limited host range (LHR) Agrobacterium tumefaciens strain Ag162 is an isolate with a narrow host range. Introduction of the wide host range (WHR) virA gene is essential for extending the host range to Kalanchoë daigremontiana. In this report we show that the region upstream of the ATG start codon is responsible for the LHR phenomenon and that this is probably due to the non-inducibility of the LHRvirA promoter. By comparing the characteristics of the LHR and WHR VirA receptor proteins, it was found that the LHR VirA protein is able to activate the WHR VirG protein in the presence of acetosyringone and that this acetosyringone-dependent vir-induction is enhanced by the presence of D-glucose, as in the case of WHR VirA proteins. These results indicate that the domains, acting as receptors for sugars and phenolic signals, must be conserved between the LHR and WHR VirA receptor proteins. PMID:8469115

  11. Natural History of Innate Host Defense Peptides.

    PubMed

    Linde, A; Wachter, B; Höner, O P; Dib, L; Ross, C; Tamayo, A R; Blecha, F; Melgarejo, T

    2009-12-01

    Host defense peptides act on the forefront of innate immunity, thus playing a central role in the survival of animals and plants. Despite vast morphological changes in species through evolutionary history, all animals examined to date share common features in their innate immune defense strategies, hereunder expression of host defense peptides (HDPs). Most studies on HDPs have focused on humans, domestic and laboratory animals. More than a thousand different sequences have been identified, yet data on HDPs in wild-living animals are sparse. The biological functions of HDPs include broad-spectrum antimicrobial activity and immunomodulation. Natural selection and coevolutionary host-pathogen arms race theory suggest that the extent and specificity of the microbial load influences the spectrum and potency of HDPs in different species. Individuals of extant species-that have lived for an extended period in evolutionary history amid populations with intact processes of natural selection-likely possess the most powerful and well-adapted "natural antibiotics". Research on the evolutionary history of the innate defense system and the host in context of the consequences of challenges as well as the efficacy of the innate immune system under natural conditions is therefore of immediate interest. This review focuses on evolutionary aspects of immunophysiology, with emphasis on innate effector molecules. Studies on host defense in wild-living animals may significantly enhance our understanding of inborn immune mechanisms, and help identify molecules that may assist us to cope better with the increasing microbial challenges that likely follow from the continuous amplification of biodiversity levels on Earth. PMID:26783164

  12. NOD2, an Intracellular Innate Immune Sensor Involved in Host Defense and Crohn's Disease

    PubMed Central

    Strober, Warren; Watanabe, Tomohiro

    2013-01-01

    Nucleotide binding oligomerization domain 2 (NOD2) is an intracellular sensor for small peptides derived from the bacterial cell wall component, peptidoglycan. Recent studies have uncovered unexpected functions of NOD2 in innate immune responses such as induction of type I IFN and facilitation of autophagy; moreover, they have disclosed extensive cross-talk between NOD2 and Toll-like receptors which plays an indispensable role both in host defense against microbial infection and in the development of autoimmunity. Of particular interest, polymorphisms of CARD15 encoding NOD2 are associated with Crohn's disease and other autoimmune states such as graft versus host disease. In this review, we summarize recent findings regarding normal functions of NOD2 and discuss the mechanisms by which NOD2 polymorphisms associated with Crohn's disease lead to intestinal inflammation. PMID:21750585

  13. Host life history and host-parasite syntopy predict behavioural resistance and tolerance of parasites.

    PubMed

    Sears, Brittany F; Snyder, Paul W; Rohr, Jason R

    2015-05-01

    There is growing interest in the role that life-history traits of hosts, such as their 'pace-of-life', play in the evolution of resistance and tolerance to parasites. Theory suggests that, relative to host species that have high syntopy (local spatial and temporal overlap) with parasites, host species with low syntopy should have lower selection pressures for more constitutive (always present) and costly defences, such as tolerance, and greater reliance on more inducible and cheaper defences, such as behaviour. Consequently, we postulated that the degree of host-parasite syntopy, which is negatively correlated with host pace-of-life (an axis reflecting the developmental rate of tadpoles and the inverse of their size at metamorphosis) in our tadpole-parasitic cercarial (trematode) system, would be a negative and positive predictor of behavioural resistance and tolerance, respectively. To test these hypotheses, we exposed seven tadpole species to a range of parasite (cercarial) doses crossed with anaesthesia treatments that controlled for anti-parasite behaviour. We quantified host behaviour, successful and unsuccessful infections, and each species' reaction norm for behavioural resistance and tolerance, defined as the slope between cercarial exposure (or attempted infections) and anti-cercarial behaviours and mass change, respectively. Hence, tolerance is capturing any cost of parasite exposure. As hypothesized, tadpole pace-of-life was a significant positive predictor of behavioural resistance and negative predictor of tolerance, a result that is consistent with a trade-off between behavioural resistance and tolerance across species that warrants further investigation. Moreover, these results were robust to considerations of phylogeny, all possible re-orderings of the three fastest or slowest paced species, and various measurements of tolerance. These results suggest that host pace-of-life and host-parasite syntopy are powerful drivers of both the strength and type

  14. Structural Basis for Host Membrane Remodeling Induced by Protein 2B of Hepatitis A Virus

    PubMed Central

    Vives-Adrián, Laia; Garriga, Damià; Buxaderas, Mònica; Fraga, Joana; Pereira, Pedro José Barbosa

    2015-01-01

    ABSTRACT The complexity of viral RNA synthesis and the numerous participating factors require a mechanism to topologically coordinate and concentrate these multiple viral and cellular components, ensuring a concerted function. Similarly to all other positive-strand RNA viruses, picornaviruses induce rearrangements of host intracellular membranes to create structures that act as functional scaffolds for genome replication. The membrane-targeting proteins 2B and 2C, their precursor 2BC, and protein 3A appear to be primarily involved in membrane remodeling. Little is known about the structure of these proteins and the mechanisms by which they induce massive membrane remodeling. Here we report the crystal structure of the soluble region of hepatitis A virus (HAV) protein 2B, consisting of two domains: a C-terminal helical bundle preceded by an N-terminally curved five-stranded antiparallel β-sheet that displays striking structural similarity to the β-barrel domain of enteroviral 2A proteins. Moreover, the helicoidal arrangement of the protein molecules in the crystal provides a model for 2B-induced host membrane remodeling during HAV infection. IMPORTANCE No structural information is currently available for the 2B protein of any picornavirus despite it being involved in a critical process in viral factory formation: the rearrangement of host intracellular membranes. Here we present the structure of the soluble domain of the 2B protein of hepatitis A virus (HAV). Its arrangement, both in crystals and in solution under physiological conditions, can help to understand its function and sheds some light on the membrane rearrangement process, a putative target of future antiviral drugs. Moreover, this first structure of a picornaviral 2B protein also unveils a closer evolutionary relationship between the hepatovirus and enterovirus genera within the Picornaviridae family. PMID:25589659

  15. Characterization of Prohibitin 1 as a Host Partner of Vibrio vulnificus RtxA1 Toxin.

    PubMed

    Kim, Bo A; Lim, Ju Young; Rhee, Joon Haeng; Kim, Young Ran

    2016-01-01

    RtxA1 toxin, which results in cytoskeletal rearrangement, contact cytotoxicity, hemolysis, tissue invasion, and lethality in mice, is the most potent cytotoxic virulence factor of Vibrio vulnificus. Bioinformatics analysis of rtxA1 predicted 4 functional domains that presumably performed discrete functions during host cell killing. V. vulnificus RtxA1 has a unique domain designated as RtxA1-D2, corresponding to amino acids 1951-2574, which is absent in Vibrio cholerae multifunctional-autoprocessing repeats-in-toxin, suggesting that this domain confers specific biological functions to V. vulnificus RtxA1. HeLa cells expressing green fluorescent protein-RtxA1-D2 became round and lost their viability. A yeast 2-hybrid system identified prohibitin (PHB) 1 as the host partner of RtxA1-D2. The specific interaction of RtxA1-D2 with PHB1 was confirmed by performing immunoprecipitation. Interestingly, V. vulnificus RtxA1 up-regulated PHB1 expression on the cytoplasmic membrane of host cells. Extracellular signal-regulated kinase and p38 mitogen-activated protein kinase pathways were confirmed as being important in the up-regulation of PHB1 by using inhibitors. Down-regulation of PHB1 by small interfering RNAs decreased the cytotoxicity of RtxA1-D2 against HeLa cells. The pretreatment of an anti-PHB1 antibody impaired the cytotoxicity of V. vulnificus RtxA1. These results suggest that the involvement PHB1 in the RtxA1 cytotoxicity has significant implications for the pathogenesis of V. vulnificus infections. PMID:26136468

  16. Two-Dimensional Confinement of Nanorods in Block Copolymer Domains

    NASA Astrophysics Data System (ADS)

    Liu, Yu; Deshmukh, Ranjan; Composto, Russell

    2008-03-01

    To control their unique electrical and optical properties, one-dimensional metallic/semiconductor nanoparticles need to be aligned and assembled within a host material. In our research, we investigated the assembly of gold nanorods (NRs) in films of a symmetric diblock copolymer, poly(styrene-b-methyl methacrylate), PS-b-PMMA (211kg/mol). The NR length and diameter was 42nm and 13nm, respectively. The NRs were grafted with a short PEG-brush (5kg/mol). During solvent annealing, the NRs become oriented as the PS-b-PMMA chains assemble into a parallel lamellar morphology. The NRs are selectively sequestered and confined in the PMMA domains, which are narrower than the NR length, due to the favorable interaction between the PEG brush and PMMA block. This confinement orients 71% of NRs within ± 5^o of the lamella plane. This route to produce alternating layers containing conducting NRs separated by dielectric domains has the potential for fabricating self-assembled nanodevices. The thermal stability of the NRs in PS-b-PMMA and homo PMMA films will also be discussed.

  17. Domain-Specific Languages for Composing Signature Discovery Workflows

    SciTech Connect

    Jacob, Ferosh; Gray, Jeff; Wynne, Adam S.; Liu, Yan; Baker, Nathan A.

    2012-10-23

    Domain-agnostic signature discovery entails investigation across multiple scientific disciplines. The breadth and cross-disciplinary nature of this work requires that existing executables be integrated with new capabilities into workflows, representing a wide range of user tasks. An algorithm may be written in multiple programming languages for various hardware platforms, and so workflow composition requires integrating executables from any number of remote hosts. This raises an engineering issue on how to generate web service wrappers for these heterogeneous executables and to compose them into a scientific workflow environment (e.g., Taverna). In this paper, we introduce two simple Domain-Specific Languages (DSLs) to automate these processes. Our Service Description Language (SDL) describes key elements of a signature discovery service and automatically generates its implementation code. The Workflow Description Language (WDL) describes the pipeline of services and generates deployable artifacts for the Taverna workflow management system. We demonstrate our approach with a real-world workflow composed of services wrapping remote executables.

  18. Imaging Ferroelectric Domains and Domain Walls Using Charge Gradient Microscopy: Role of Screening Charges.

    PubMed

    Tong, Sheng; Jung, Il Woong; Choi, Yoon-Young; Hong, Seungbum; Roelofs, Andreas

    2016-02-23

    Advanced scanning probe microscopies (SPMs) open up the possibilities of the next-generation ferroic devices that utilize both domains and domain walls as active elements. However, current SPMs lack the capability of dynamically monitoring the motion of domains and domain walls in conjunction with the transport of the screening charges that lower the total electrostatic energy of both domains and domain walls. Charge gradient microscopy (CGM) is a strong candidate to overcome these shortcomings because it can map domains and domain walls at high speed and mechanically remove the screening charges. Yet the underlying mechanism of the CGM signals is not fully understood due to the complexity of the electrostatic interactions. Here, we designed a semiconductor-metal CGM tip, which can separate and quantify the ferroelectric domain and domain wall signals by simply changing its scanning direction. Our investigation reveals that the domain wall signals are due to the spatial change of polarization charges, while the domain signals are due to continuous removal and supply of screening charges at the CGM tip. In addition, we observed asymmetric CGM domain currents from the up and down domains, which are originated from the different debonding energies and the amount of the screening charges on positive and negative bound charges. We believe that our findings can help design CGM with high spatial resolution and lead to breakthroughs in information storage and energy-harvesting devices. PMID:26751281

  19. Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells.

    PubMed

    Day, Christopher J; Tran, Elizabeth N; Semchenko, Evgeny A; Tram, Greg; Hartley-Tassell, Lauren E; Ng, Preston S K; King, Rebecca M; Ulanovsky, Rachel; McAtamney, Sarah; Apicella, Michael A; Tiralongo, Joe; Morona, Renato; Korolik, Victoria; Jennings, Michael P

    2015-12-29

    Cells from all domains of life express glycan structures attached to lipids and proteins on their surface, called glycoconjugates. Cell-to-cell contact mediated by glycan:glycan interactions have been considered to be low-affinity interactions that precede high-affinity protein-glycan or protein-protein interactions. In several pathogenic bacteria, truncation of surface glycans, lipooligosaccharide (LOS), or lipopolysaccharide (LPS) have been reported to significantly reduce bacterial adherence to host cells. Here, we show that the saccharide component of LOS/LPS have direct, high-affinity interactions with host glycans. Glycan microarrays reveal that LOS/LPS of four distinct bacterial pathogens bind to numerous host glycan structures. Surface plasmon resonance was used to determine the affinity of these interactions and revealed 66 high-affinity host-glycan:bacterial-glycan pairs with equilibrium dissociation constants (K(D)) ranging between 100 nM and 50 µM. These glycan:glycan affinity values are similar to those reported for lectins or antibodies with glycans. Cell assays demonstrated that glycan:glycan interaction-mediated bacterial adherence could be competitively inhibited by either host cell or bacterial glycans. This is the first report to our knowledge of high affinity glycan:glycan interactions between bacterial pathogens and the host. The discovery of large numbers of glycan:glycan interactions between a diverse range of structures suggests that these interactions may be important in all biological systems. PMID:26676578

  20. Is the myonuclear domain size fixed?

    PubMed

    Van der Meer, S F T; Jaspers, R T; Degens, H

    2011-12-01

    It has been suggested that the number of myonuclei in a muscle fibre changes in proportion to the change in fibre size, resulting in a constant myonuclear domain size, defined as the cytoplasmic volume per myonucleus. The myonuclear domain size varies, however, between fibre types and is inversely related with the oxidative capacity of a fibre. Overall, the observations of an increase in myonuclear domain size during both maturational growth and overload-induced hypertrophy, and the decrease in myonuclear domain size during disuse- and ageing-associated muscle atrophy suggest that the concept of a constant myonuclear domain size needs to be treated cautiously. It also suggests that only when the myonuclear domain size exceeds a certain threshold during growth or overload-induced hypertrophy acquisition of new myonuclei is required for further fibre hypertrophy. PMID:22130137

  1. Dissecting the Role of E2 Protein Domains in Alphavirus Pathogenicity

    PubMed Central

    Weger-Lucarelli, James; Aliota, Matthew T.; Wlodarchak, Nathan; Kamlangdee, Attapon; Swanson, Ryan

    2015-01-01

    ABSTRACT Alphaviruses represent a diverse set of arboviruses, many of which are important pathogens. Chikungunya virus (CHIKV), an arthritis-inducing alphavirus, is the cause of a massive ongoing outbreak in the Caribbean and South America. In contrast to CHIKV, other related alphaviruses, such as Venezuelan equine encephalitis virus (VEEV) and Semliki Forest virus (SFV), can cause encephalitic disease. E2, the receptor binding protein, has been implicated as a determinant in cell tropism, host range, pathogenicity, and immunogenicity. Previous reports also have demonstrated that E2 contains residues important for host range expansions and monoclonal antibody binding; however, little is known about what role each protein domain (e.g., A, B, and C) of E2 plays on these factors. Therefore, we constructed chimeric cDNA clones between CHIKV and VEEV or SFV to probe the effect of each domain on pathogenicity in vitro and in vivo. CHIKV chimeras containing each of the domains of the E2 (ΔDomA, ΔDomB, and ΔDomC) from SFV, but not VEEV, were successfully rescued. Interestingly, while all chimeric viruses were attenuated compared to CHIKV in mice, ΔDomB virus showed similar rates of infection and dissemination in Aedes aegypti mosquitoes, suggesting differing roles for the E2 protein in different hosts. In contrast to CHIKV; ΔDomB, and to a lesser extent ΔDomA, caused neuron degeneration and demyelination in mice infected intracranially, suggesting a shift toward a phenotype similar to SFV. Thus, chimeric CHIKV/SFV provide insights on the role the alphavirus E2 protein plays on pathogenesis. IMPORTANCE Chikungunya virus (CHIKV) has caused large outbreaks of acute and chronic arthritis throughout Africa and Southeast Asia and has now become a massive public health threat in the Americas, causing an estimated 1.2 million human cases in just over a year. No approved vaccines or antivirals exist for human use against CHIKV or any other alphavirus. Despite the threat

  2. Protein Domain Decomposition Using a Graph-Theoretic Approach

    SciTech Connect

    Xu, Y.; Xu, D.; Gabow, H.N.

    2000-08-20

    This paper presents a new algorithm for the decomposition of a multi-domain protein into individual structural domains. The underlying principle used is that residue-residue contacts are denser within a domain than between domains.

  3. Domain Transfer Learning for MCI Conversion Prediction

    PubMed Central

    Cheng, Bo; Liu, Mingxia; Zhang, Daoqiang; Munsell, Brent C.; Shen, Dinggang

    2015-01-01

    Machine learning methods have been increasingly used to predict the conversion of mild cognitive impairment (MCI) to Alzheimer's disease (AD), by classifying MCI converters (MCI-C) from MCI non-converters (MCI-NC). However, most of existing methods construct classifiers using only data from one particular target domain (e.g., MCI), and ignore data in the other related domains (e.g., AD and normal control (NC)) that could provide valuable information to promote the performance of MCI conversion prediction. To this end, we develop a novel domain transfer learning method for MCI conversion prediction, which can use data from both the target domain (i.e., MCI) and the auxiliary domains (i.e., AD and NC). Specifically, the proposed method consists of three key components: 1) a domain transfer feature selection (DTFS) component that selects the most informative feature-subset from both target domain and auxiliary domains with different imaging modalities, 2) a domain transfer sample selection (DTSS) component that selects the most informative sample-subset from the same target and auxiliary domains with different data modalities, and 3) a domain transfer support vector machine (DTSVM) classification component that fuses the selected features and samples to separate MCI-C and MCI-NC patients. We evaluate our method on 202 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) with MRI, FDG-PET and CSF data. The experimental results show that the proposed method can classify MCI-C patients from MCI-NC patients with an accuracy of 79.4%, with the aid of additional domain knowledge learned from AD and NC. PMID:25751861

  4. Domain decomposition for the SPN solver MINOS

    SciTech Connect

    Jamelot, Erell; Baudron, Anne-Marie; Lautard, Jean-Jacques

    2012-07-01

    In this article we present a domain decomposition method for the mixed SPN equations, discretized with Raviart-Thomas-Nedelec finite elements. This domain decomposition is based on the iterative Schwarz algorithm with Robin interface conditions to handle communications. After having described this method, we give details on how to optimize the convergence. Finally, we give some numerical results computed in a realistic 3D domain. The computations are done with the MINOS solver of the APOLLO3 (R) code. (authors)

  5. Domain Transfer Learning for MCI Conversion Prediction.

    PubMed

    Cheng, Bo; Liu, Mingxia; Zhang, Daoqiang; Munsell, Brent C; Shen, Dinggang

    2015-07-01

    Machine learning methods have successfully been used to predict the conversion of mild cognitive impairment (MCI) to Alzheimer's disease (AD), by classifying MCI converters (MCI-C) from MCI nonconverters (MCI-NC). However, most existing methods construct classifiers using data from one particular target domain (e.g., MCI), and ignore data in other related domains (e.g., AD and normal control (NC)) that may provide valuable information to improve MCI conversion prediction performance. To address is limitation, we develop a novel domain transfer learning method for MCI conversion prediction, which can use data from both the target domain (i.e., MCI) and auxiliary domains (i.e., AD and NC). Specifically, the proposed method consists of three key components: 1) a domain transfer feature selection component that selects the most informative feature-subset from both target domain and auxiliary domains from different imaging modalities; 2) a domain transfer sample selection component that selects the most informative sample-subset from the same target and auxiliary domains from different data modalities; and 3) a domain transfer support vector machine classification component that fuses the selected features and samples to separate MCI-C and MCI-NC patients. We evaluate our method on 202 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) that have MRI, FDG-PET, and CSF data. The experimental results show the proposed method can classify MCI-C patients from MCI-NC patients with an accuracy of 79.4%, with the aid of additional domain knowledge learned from AD and NC. PMID:25751861

  6. Domain wall dynamics in cylindrical nanomagnet

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Soumik; Singh, Amrita; Ghosh, Arindam

    2011-06-01

    The stochasticity associated with domain wall nucleation and propagation in a cylinderical nanowire has been studied using time resolved resistance measurement in presence of magnetic field. We have shown that the propagation stochasticity of domain wall in a cylindrical nanowire is reflected in the magnetic field dependent velocity distribution whereas the stochasticity involved in the domain wall nucleation can be effectively tuned by varying the angle between the direction of applied magnetic field and the long axis of the cylinder.

  7. Spread spectrum time domain reflectometry

    NASA Astrophysics Data System (ADS)

    Smith, Paul Samuel

    For many years, wiring has been treated as a system that could be installed and expected to work for the life of the aircraft. As aircraft age far beyond their original expected life span, this attitude is rapidly changing. Wiring problems have recently been identified as the cause of several tragic mishaps and hundreds of thousands of lost mission hours. Intermittent wiring faults have been and continue to be difficult to resolve. Test methods that pinpoint faults on the ground can miss intermittent failures. New test methods involving spread spectrum signals are investigated that could be used in flight to locate intermittent failures, including open circuits, short circuits, and arcs. Spread spectrum time domain reflectometry (SSTDR) and sequence time domain reflectometry (STDR) are analyzed in light of the signals commonly present on aircraft wiring. Pseudo noise codes used for the generation of STDR and SSTDR signals are analyzed for application in a STDR/SSTDR test system in the presence of noise. The effects of Mil-Std 1553 and white noise on the STDR and SSTDR signals are discussed analytically, through simulations, and with the use of test hardware. A test system using STDR and SSTDR is designed, built, and used to collect STDR and SSTDR test data. The data collected with the STDR/SSTDR test hardware is analyzed and compared to the theoretical results. Experimental data for open and short circuits collected using SSTDR and a curve fitting algorithm shows a maximum range estimation error of +/-0.2 ft for 75O coaxial cable up to 100ft, and +/-0.6ft for a sample 32.5ft non-controlled impedance aircraft cable. Mil-Std 1553 is specified to operate reliably with a signal-to-noise ratio of 17.5dB, and the SSTDR test system was able to locate an open circuit on a cable also carrying simulated Mil-Std 1553 data where the SSTDR signal was 50dB below the Mil-Std 1553 signal. STDR and SSTDR are shown to be effective in detecting and locating dry and wet arcs on wires.

  8. Divergence in Olfactory Host Plant Preference in D. mojavensis in Response to Cactus Host Use

    PubMed Central

    Stensmyr, Marcus C.; Shann, Jodi; Hansson, Bill S.; Rollmann, Stephanie M.

    2013-01-01

    Divergence in host adaptive traits has been well studied from an ecological and evolutionary perspective, but identification of the proximate mechanisms underlying such divergence is less well understood. Behavioral preferences for host plants are often mediated by olfaction and shifts in preference may be accompanied by changes in the olfactory system. In this study, we examine the evolution of host plant preferences in cactophilic Drosophila mojavensis that feeds and breeds on different cacti throughout its range. We show divergence in electrophysiological responses and olfactory behavior among populations with host plant shifts. Specifically, significant divergence was observed in the Mojave Desert population that specializes on barrel cactus. Differences were observed in electrophysiological responses of the olfactory organs and in behavioral responses to barrel cactus volatiles. Together our results suggest that the peripheral nervous system has changed in response to different ecological environments and that these changes likely contribute to divergence among D. mojavensis populations. PMID:23936137

  9. The role of host genetic factors and host immunity in necrotic enteritis.

    PubMed

    Oh, Sung T; Lillehoj, Hyun S

    2016-06-01

    The increasing number of legislative restrictions and the voluntary withdrawal of antibiotic growth promoters worldwide will continue to impact poultry health and production. The rising incidence of Clostridium infections and development of necrotic enteritis (NE) in commercial chickens has been associated with the withdrawal of antibiotics. High-throughput genomic analysis of intestinal tissues from NE-afflicted chickens showed alterations in the local immunity and gut microbiota. Therefore, a better understanding of host- and environmentally related factors on Clostridium perfringens infections will be necessary for the development of effective sustainable strategies aimed to reduce the negative consequences of NE. In this short review, we summarize the current knowledge on the role of host genomics and immunity in NE. The limited progress in understanding the complexity of host-pathogen interactions in NE underscores the urgent need for more fundamental research in host immunity against Clostridium pathogens in order to develop effective control strategies against NE. PMID:26957203

  10. Geographic host use variabiliy and host range evolutionary dynamics in the phytophagous insect Apagomerella versicolor (Cerambycidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The high diversity of phytophagous insects has been explained by the tendency of the group towards specialization; however, generalism may be advantageous in some environments. The cerambycid Apagomerella versicolor exhibits intraspecific geographical variation in host use. In northern Argentina it ...

  11. Divergence in olfactory host plant preference in D. mojavensis in response to cactus host use.

    PubMed

    Date, Priya; Dweck, Hany K M; Stensmyr, Marcus C; Shann, Jodi; Hansson, Bill S; Rollmann, Stephanie M

    2013-01-01

    Divergence in host adaptive traits has been well studied from an ecological and evolutionary perspective, but identification of the proximate mechanisms underlying such divergence is less well understood. Behavioral preferences for host plants are often mediated by olfaction and shifts in preference may be accompanied by changes in the olfactory system. In this study, we examine the evolution of host plant preferences in cactophilic Drosophila mojavensis that feeds and breeds on different cacti throughout its range. We show divergence in electrophysiological responses and olfactory behavior among populations with host plant shifts. Specifically, significant divergence was observed in the Mojave Desert population that specializes on barrel cactus. Differences were observed in electrophysiological responses of the olfactory organs and in behavioral responses to barrel cactus volatiles. Together our results suggest that the peripheral nervous system has changed in response to different ecological environments and that these changes likely contribute to divergence among D. mojavensis populations. PMID:23936137

  12. The Baculovirus Uses a Captured Host Phosphatase to Induce Enhanced Locomotory Activity in Host Caterpillars

    PubMed Central

    Katsuma, Susumu; Koyano, Yasue; Kang, WonKyung; Kokusho, Ryuhei; Kamita, Shizuo George; Shimada, Toru

    2012-01-01

    The baculovirus is a classic example of a parasite that alters the behavior or physiology of its host so that progeny transmission is maximized. Baculoviruses do this by inducing enhanced locomotory activity (ELA) that causes the host caterpillars to climb to the upper foliage of plants. We previously reported that this behavior is not induced in silkworms that are infected with a mutant baculovirus lacking its protein tyrosine phosphatase (ptp) gene, a gene likely captured from an ancestral host. Here we show that the product of the ptp gene, PTP, associates with baculovirus ORF1629 as a virion structural protein, but surprisingly phosphatase activity associated with PTP was not required for the induction of ELA. Interestingly, the ptp knockout baculovirus showed significantly reduced infectivity of larval brain tissues. Collectively, we show that the modern baculovirus uses the host-derived phosphatase to establish adequate infection for ELA as a virion-associated structural protein rather than as an enzyme. PMID:22496662

  13. Adaptation to resistant hosts increases fitness on susceptible hosts in the plant parasitic nematode Globodera pallida.

    PubMed

    Fournet, Sylvain; Eoche-Bosy, Delphine; Renault, Lionel; Hamelin, Frédéric M; Montarry, Josselin

    2016-04-01

    Trade-offs between virulence (defined as the ability to infect a resistant host) and life-history traits are of particular interest in plant pathogens for durable management of plant resistances. Adaptation to plant resistances (i.e., virulence acquisition) is indeed expected to be associated with a fitness cost on susceptible hosts. Here, we investigated whether life-history traits involved in the fitness of the potato cyst nematode Globodera pallida are affected in a virulent lineage compared to an avirulent one. Both lineages were obtained from the same natural population through experimental evolution on resistant and susceptible hosts, respectively. Unexpectedly, we found that virulent lineages were more fit than avirulent lineages on susceptible hosts: they produced bigger cysts, containing more larvae and hatching faster. We thus discuss possible reasons explaining why virulence did not spread into natural G. pallida populations. PMID:27066239

  14. Water loss from olivine hosted melt inclusions

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Provost, A.; Schiano, P.; Cluzel, N.

    2009-12-01

    Water content in melt inclusions has long been used as an important index for the water content of the hosting magma. However, many studies have shown that post-entrapment diffusive re-equilibration can affect the water content of melt inclusions. This process must be considered when using melt inclusions to infer water content of the hosting magma. Theoretical model on the diffusive re-equilibration between melt inclusions and external melts showed that the re-equilibration rate depends on the diffusivity of the re-equilibrating species in the host mineral, the partition coefficient of this species between the host mineral and melt, and the geometry of the melt inclusion and host mineral. The water diffusivity in olivine and water partition coefficient between melt and olivine have been measured by recent studies, therefore the diffusive re-equilibration model can be tested by experiments. In this study, we carried out in-situ Fourier transform infrared spectroscopy (FTIR) measurements on the water content of olivine hosted melt inclusions at high temperatures. Initial water content of the melt inclusions is about 4 wt%. A heating stage system is combined with a microscope FTIR and the absorption spectrum through the olivine and melt inclusion is repeatedly measured. Although the absorption band at around 3540 cm-1 has not be calibrated at high temperatures, it is assumed that the absorbance is linearly related to the total water concentration in the melt inclusion, and the relative water content can be inferred. Cautions have been exercised to maintain a consistent measurement spot such that the thickness of the melt inclusion within the beam path did not change significantly during each experiment. Oxygen fugacity in the heating stage is controlled by Zr purified Ar gas to be about 7 logarithm units below the QFM buffer and about 1 logarithm unit above the QIF buffer at 1473 K. Preliminary results showed that at 1430 and 1581 K, the total water content of the

  15. Cross-domain human action recognition.

    PubMed

    Bian, Wei; Tao, Dacheng; Rui, Yong

    2012-04-01

    Conventional human action recognition algorithms cannot work well when the amount of training videos is insufficient. We solve this problem by proposing a transfer topic model (TTM), which utilizes information extracted from videos in the auxiliary domain to assist recognition tasks in the target domain. The TTM is well characterized by two aspects: 1) it uses the bag-of-words model trained from the auxiliary domain to represent videos in the target domain; and 2) it assumes each human action is a mixture of a set of topics and uses the topics learned from the auxiliary domain to regularize the topic estimation in the target domain, wherein the regularization is the summation of Kullback-Leibler divergences between topic pairs of the two domains. The utilization of the auxiliary domain knowledge improves the generalization ability of the learned topic model. Experiments on Weizmann and KTH human action databases suggest the effectiveness of the proposed TTM for cross-domain human action recognition. PMID:21954214

  16. Transform domain steganography with blind source separation

    NASA Astrophysics Data System (ADS)

    Jouny, Ismail

    2015-05-01

    This paper applies blind source separation or independent component analysis for images that may contain mixtures of text, audio, or other images for steganography purposes. The paper focuses on separating mixtures in the transform domain such as Fourier domain or the Wavelet domain. The study addresses the effectiveness of steganography when using linear mixtures of multimedia components and the ability of standard blind sources separation techniques to discern hidden multimedia messages. Mixing in the space, frequency, and wavelet (scale) domains is compared. Effectiveness is measured using mean square error rate between original and recovered images.

  17. Cooperative interactions between paired domain and homeodomain.

    PubMed

    Jun, S; Desplan, C

    1996-09-01

    The Pax proteins are a family of transcriptional regulators involved in many developmental processes in all higher eukaryotes. They are characterized by the presence of a paired domain (PD), a bipartite DNA binding domain composed of two helix-turn-helix (HTH) motifs,the PAI and RED domains. The PD is also often associated with a homeodomain (HD) which is itself able to form homo- and hetero-dimers on DNA. Many of these proteins therefore contain three HTH motifs each able to recognize DNA. However, all PDs recognize highly related DNA sequences, and most HDs also recognize almost identical sites. We show here that different Pax proteins use multiple combinations of their HTHs to recognize several types of target sites. For instance, the Drosophila Paired protein can bind, in vitro, exclusively through its PAI domain, or through a dimer of its HD, or through cooperative interaction between PAI domain and HD. However, prd function in vivo requires the synergistic action of both the PAI domain and the HD. Pax proteins with only a PD appear to require both PAI and RED domains, while a Pax-6 isoform and a new Pax protein, Lune, may rely on the RED domain and HD. We propose a model by which Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expanding their recognition repertoire. PMID:8787739

  18. Frequency domain FIR and IIR adaptive filters

    NASA Technical Reports Server (NTRS)

    Lynn, D. W.

    1990-01-01

    A discussion of the LMS adaptive filter relating to its convergence characteristics and the problems associated with disparate eigenvalues is presented. This is used to introduce the concept of proportional convergence. An approach is used to analyze the convergence characteristics of block frequency-domain adaptive filters. This leads to a development showing how the frequency-domain FIR adaptive filter is easily modified to provide proportional convergence. These ideas are extended to a block frequency-domain IIR adaptive filter and the idea of proportional convergence is applied. Experimental results illustrating proportional convergence in both FIR and IIR frequency-domain block adaptive filters is presented.

  19. On the function of chitin synthase extracellular domains in biomineralization.

    PubMed

    Weiss, Ingrid M; Lüke, Florian; Eichner, Norbert; Guth, Christina; Clausen-Schaumann, Hauke

    2013-08-01

    Molluscs with various shell architectures evolved around 542-525 million years ago, as part of a larger phenomenon related to the diversification of metazoan phyla. Molluscs deposit minerals in a chitin matrix. The mollusc chitin is synthesized by transmembrane enzymes that contain several unique extracellular domains. Here we investigate the assembly mechanism of the chitin synthase Ar-CS1 via its extracellular domain ArCS1_E22. The corresponding transmembrane protein ArCS1_E22TM accumulates in membrane fractions of the expression host Dictyostelium discoideum. Soluble recombinant ArCS1_E22 proteins can be purified as monomers only at basic pH. According to confocal fluorescence microscopy experiments, immunolabeled ArCS1_E22 proteins adsorb preferably to aragonitic nacre platelets at pH 7.75. At pH 8.2 or pH 9.0 the fluorescence signal is less intense, indicating that protein-mineral interaction is reduced with increasing pH. Furthermore, ArCS1_E22 forms regular nanostructures on cationic substrates as revealed by atomic force microscopy (AFM) experiments on modified mica cleavage planes. These experiments suggest that the extracellular domain ArCS1_E22 is involved in regulating the multiple enzyme activities of Ar-CS1 such as chitin synthesis and myosin movements by interaction with mineral surfaces and eventually by protein assembly. The protein complexes could locally probe the status of mineralization according to pH unless ions and pCO2 are balanced with suitable buffer substances. Taking into account that the intact enzyme could act as a force sensor, the results presented here provide further evidence that shell formation is coordinated physiologically with precise adjustment of cellular activities to the structure, topography and stiffness at the mineralizing interface. PMID:23643908

  20. Environmentally transmitted parasites: Host-jumping in a heterogeneous environment.

    PubMed

    Caraco, Thomas; Cizauskas, Carrie A; Wang, Ing-Nang

    2016-05-21

    Groups of chronically infected reservoir-hosts contaminate resource patches by shedding a parasite׳s free-living stage. Novel-host groups visit the same patches, where they are exposed to infection. We treat arrival at patches, levels of parasite deposition, and infection of the novel host as stochastic processes, and derive the expected time elapsing until a host-jump (initial infection of a novel host) occurs. At stationarity, mean parasite densities are independent of reservoir-host group size. But within-patch parasite-density variances increase with reservoir group size. The probability of infecting a novel host declines with parasite-density variance; consequently larger reservoir groups extend the mean waiting time for host-jumping. Larger novel-host groups increase the probability of a host-jump during any single patch visit, but also reduce the total number of visits per unit time. Interaction of these effects implies that the waiting time for the first infection increases with the novel-host group size. If the reservoir-host uses resource patches in any non-uniform manner, reduced spatial overlap between host species increases the waiting time for host-jumping. PMID:26921466

  1. Trophic Relationships between the Parasitic Plant Species Phelipanche ramosa (L.) and Different Hosts Depending on Host Phenological Stage and Host Growth Rate

    PubMed Central

    Moreau, Delphine; Gibot-Leclerc, Stéphanie; Girardin, Annette; Pointurier, Olivia; Reibel, Carole; Strbik, Florence; Fernández-Aparicio, Mónica; Colbach, Nathalie

    2016-01-01

    Phelipanche ramosa (L.) Pomel (branched broomrape) is a holoparasitic plant that reproduces on crops and also on weeds, which contributes to increase the parasite seed bank in fields. This parasite extracts all its nutrients at the host’s expense so that host–parasite trophic relationships are crucial to determine host and parasite growth. This study quantified the intensity with which P. ramosa draws assimilates from its host and analyzed whether it varied with host species, host phenological stage and host growth rate. A greenhouse experiment was conducted on three host species: the crop species Brassica napus (L.) (oilseed rape) and two weed species, Capsella bursa-pastoris (L.) Medik. and Geranium dissectum (L.). Plants were grown with or without P. ramosa and under three light levels to modulate host growth rate. The proportion of host biomass loss due to parasitism by P. ramosa differed between host species (at host fructification, biomass loss ranged from 34 to 84%). B. napus and C. bursa-pastoris displayed a similar response to P. ramosa, probably because they belong to the same botanical family. The sensitivity to P. ramosa in each host species could be related to the precocity of P. ramosa development on them. Host compartments could be ranked as a function of their sensitivity to parasitism, with the reproductive compartment being the most severely affected, followed by stems and roots. The proportion of biomass allocated to leaves was not reduced by parasitism. The proportion of pathosystem biomass allocated to the parasite depended on host species. It generally increased with host stage progression but was constant across light induced-host growth rate, showing that P. ramosa adapts its growth to host biomass production. The rank order of host species in terms of sink strength differed from that in terms of host sensitivity. Finally, for B. napus, the biomass of individual parasite shoots decreased with increasing their number per host plant

  2. Discoidin domain receptors in disease.

    PubMed

    Borza, Corina M; Pozzi, Ambra

    2014-02-01

    Discoidin domain receptors, DDR1 and DDR2, lie at the intersection of two large receptor families, namely the extracellular matrix and tyrosine kinase receptors. As such, DDRs are uniquely positioned to function as sensors for extracellular matrix and to regulate a wide range of cell functions from migration and proliferation to cytokine secretion and extracellular matrix homeostasis/remodeling. While activation of DDRs by extracellular matrix collagens is required for normal development and tissue homeostasis, aberrant activation of these receptors following injury or in disease is detrimental. The availability of mice lacking DDRs has enabled us to identify key roles played by these receptors in disease initiation and progression. DDR1 promotes inflammation in atherosclerosis, lung fibrosis and kidney injury, while DDR2 contributes to osteoarthritis. Furthermore, both DDRs have been implicated in cancer progression. Yet the mechanisms whereby DDRs contribute to disease progression are poorly understood. In this review we highlight the mechanisms whereby DDRs regulate two important processes, namely inflammation and tissue fibrosis. In addition, we discuss the challenges of targeting DDRs in disease. Selective targeting of these receptors requires understanding of how they interact with and are activated by extracellular matrix, and whether their cellular function is dependent on or independent of receptor kinase activity. PMID:24361528

  3. Discoidin Domain Receptors in Disease

    PubMed Central

    Borza, Corina M; Pozzi, Ambra

    2014-01-01

    Discoidin domain receptors, DDR1 and DDR2, lie at the intersection of two large receptor families, namely the extracellular matrix and tyrosine kinase receptors. As such, DDRs are uniquely positioned to function as sensors for extracellular matrix and to regulate a wide range of cell functions from migration and proliferation to cytokine secretion and extracellular matrix homeostasis/remodeling. While activation of DDRs by extracellular matrix collagens is required for normal development and tissue homeostasis, aberrant activation of these receptors following injury or in disease is detrimental. The availability of mice lacking DDRs has enabled us to identify key roles played by these receptors in disease initiation and progression. DDR1 promotes inflammation in atherosclerosis, lung fibrosis and kidney injury, while DDR2 contributes to osteoarthritis. Furthermore, both DDRs have been implicated in cancer progression. Yet the mechanisms whereby DDRs contribute to diseases progression are poorly understood. In this review we highlight the mechanisms whereby DDRs regulate two important processes, namely inflammation and tissue fibrosis. In addition, we discuss the challenges of targeting DDRs in disease. Selective targeting of these receptors requires understanding of how they interact with and are activated by extracellular matrix, and whether their cellular function is dependent on or independent of receptor kinase activity. PMID:24361528

  4. Charged domain walls in ferroelectrics

    NASA Astrophysics Data System (ADS)

    Sluka, Tomas

    2014-03-01

    Solid interfaces including compositionally homogeneous ferroic domain walls (DWs) display uniquely distorted electronic structures and ionic displacements. Their intrinsic properties may therefore be fundamentally different from those of their parent matrices. Indeed, phenomena like semiconductor-metal transition, the quantum Hall effect, magnetoresistance and superconductivity were discovered at hetero-interfaces between transition metal oxides and elevated photoactivity and conductivity were reported at (multi-) ferroic DWs. Unlike hetero-interfaces, the DWs provide ``perfect'' structure by nature and can be written, displaced, and erased inside a material monolith of functioning devices. Theory predicts the existence of charged DWs which seemingly violate electrostatic compatibility due to head-to-head and tail-to-tail polarization discontinuity, but are stable because bound polarization charge is compensated by mobile charge carriers including quasi-two-dimensional electron gas. This talk will introduce current theory, engineering, control and characteristics of charged DWs, which are mobile, extremely wide and exhibit steady metallic-like conductivity up to 109 times that of the insulating bulk.

  5. Bioconvection in spatially extended domains

    NASA Astrophysics Data System (ADS)

    Karimi, A.; Paul, M. R.

    2013-05-01

    We numerically explore gyrotactic bioconvection in large spatially extended domains of finite depth using parameter values from available experiments with the unicellular alga Chlamydomonas nivalis. We numerically integrate the three-dimensional, time-dependent continuum model of Pedley [J. Fluid Mech.10.1017/S0022112088002393 195, 223 (1988)] using a high-order, parallel, spectral-element approach. We explore the long-time nonlinear patterns and dynamics found for layers with an aspect ratio of 10 over a range of Rayleigh numbers. Our results yield the pattern wavelength and pattern dynamics which we compare with available theory and experimental measurement. There is good agreement for the pattern wavelength at short times between numerics, experiment, and a linear stability analysis. At long times we find that the general sequence of patterns given by the nonlinear evolution of the governing equations correspond qualitatively to what has been described experimentally. However, at long times the patterns in numerics grow to larger wavelengths, in contrast to what is observed in experiment where the wavelength is found to decrease with time.

  6. Optical coherence domain reflectometry guidewire

    DOEpatents

    Colston, Billy W.; Everett, Matthew; Da Silva, Luiz B.; Matthews, Dennis

    2001-01-01

    A guidewire with optical sensing capabilities is based on a multiplexed optical coherence domain reflectometer (OCDR), which allows it to sense location, thickness, and structure of the arterial walls or other intra-cavity regions as it travels through the body during minimally invasive medical procedures. This information will be used both to direct the guidewire through the body by detecting vascular junctions and to evaluate the nearby tissue. The guidewire contains multiple optical fibers which couple light from the proximal to distal end. Light from the fibers at the distal end of the guidewire is directed onto interior cavity walls via small diameter optics such as gradient index lenses and mirrored corner cubes. Both forward viewing and side viewing fibers can be included. The light reflected or scattered from the cavity walls is then collected by the fibers, which are multiplexed at the proximal end to the sample arm of an optical low coherence reflectometer. The guidewire can also be used in nonmedical applications.

  7. Domain adaptation for microscopy imaging.

    PubMed

    Becker, Carlos; Christoudias, C Mario; Fua, Pascal

    2015-05-01

    Electron and light microscopy imaging can now deliver high-quality image stacks of neural structures. However, the amount of human annotation effort required to analyze them remains a major bottleneck. While machine learning algorithms can be used to help automate this process, they require training data, which is time-consuming to obtain manually, especially in image stacks. Furthermore, due to changing experimental conditions, successive stacks often exhibit differences that are severe enough to make it difficult to use a classifier trained for a specific one on another. This means that this tedious annotation process has to be repeated for each new stack. In this paper, we present a domain adaptation algorithm that addresses this issue by effectively leveraging labeled examples across different acquisitions and significantly reducing the annotation requirements. Our approach can handle complex, nonlinear image feature transformations and scales to large microscopy datasets that often involve high-dimensional feature spaces and large 3D data volumes. We evaluate our approach on four challenging electron and light microscopy applications that exhibit very different image modalities and where annotation is very costly. Across all applications we achieve a significant improvement over the state-of-the-art machine learning methods and demonstrate our ability to greatly reduce human annotation effort. PMID:25474809

  8. A host-parasitoid system with predation-driven component Allee effects in host population.

    PubMed

    Kang, Yun; Sasmal, Sourav Kumar; Bhowmick, Amiya Ranjan; Chattopadhyay, Joydev

    2015-01-01

    Allee effects and parasitism are common biological phenomena observed in nature, which are believed to have significant impacts in ecological conservation programmes. In this article, we investigate population dynamics of a discrete-time host-parasitoid system with component Allee effects induced by predation satiation in host to study the synergy effects of Allee effects and parasitism. Our model assumes that parasitism attacks the host after the density dependence of the host. The interactions of component Allee effects and parasitism can lead to extremely rich dynamics that include but are not limited to extinction of both species due to Allee effects at their low population density, multiple attractors, strange interior attractors and even crisis of strange attractor due to high parasitism. We perform local and global analysis to study the number of equilibria and their stability; and study the extinction and permanence of our host-parasitoid system. One of the most interesting results shows that the combination of strong Allee effects and parasitism may promote the coexistence of both host and parasite at their high population density. In addition, component Allee effects may destroy interior equilibrium under different values of parameters' ranges. PMID:25340591

  9. Hepcidin and Host Defense against Infectious Diseases

    PubMed Central

    Michels, Kathryn; Nemeth, Elizabeta; Ganz, Tomas; Mehrad, Borna

    2015-01-01

    Hepcidin is the master regulator of iron homeostasis in vertebrates. The synthesis of hepcidin is induced by systemic iron levels and by inflammatory stimuli. While the role of hepcidin in iron regulation is well established, its contribution to host defense is emerging as complex and multifaceted. In this review, we summarize the literature on the role of hepcidin as a mediator of antimicrobial immunity. Hepcidin induction during infection causes depletion of extracellular iron, which is thought to be a general defense mechanism against many infections by withholding iron from invading pathogens. Conversely, by promoting iron sequestration in macrophages, hepcidin may be detrimental to cellular defense against certain intracellular infections, although critical in vivo studies are needed to confirm this concept. It is not yet clear whether hepcidin exerts any iron-independent effects on host defenses. PMID:26291319

  10. Exploiting host immunity: the Salmonella paradigm

    PubMed Central

    Behnsen, Judith; Perez-Lopez, Araceli; Nuccio, Sean-Paul; Raffatellu, Manuela

    2014-01-01

    Pathogens have evolved clever strategies to evade and in some cases exploit the attacks of an activated immune system. Salmonella enterica is one such pathogen, exploiting multiple aspects of host defense to promote its replication in the host. Here we review recent findings on the mechanisms by which Salmonella establishes systemic and chronic infection, including strategies involving manipulation of innate immune signaling and inflammatory forms of cell death, as well as immune evasion by establishing residency in M2 macrophages. We also examine recent evidence showing that the oxidative environment and the high levels of antimicrobial proteins produced in response to localized Salmonella gastrointestinal infection enable the pathogen to successfully outcompete the resident gut microbiota. PMID:25582038

  11. Measles virus neurovirulence and host immunity

    PubMed Central

    Oglesbee, Michael; Niewiesk, Stefan

    2011-01-01

    Measles virus is highly neuroinvasive, yet host immune responses are highly effective at limiting neurovirulence in humans. We know that neurons are an important target of infection and that both IFN-γ and -β expression are observed in the measles virus-infected human brain. Rodent models can be used to understand how this response is orchestrated. Constitutive expression of the major inducible 70-kDa heat-shock protein is a feature of primate tissues that is lacking in mice. This article examines the importance of addressing this difference when modeling outcomes of brain infection in mice, particularly in terms of understanding how infected neurons may activate uninfected brain macrophages to produce IFN-β and support T-cell production of IFN-γ, a mediator of noncytolytic viral clearance. New and historical data suggest that the virus heat-shock protein 70 relationship is key to a protective host immune response and has potential broad relevance. PMID:21461314

  12. HOST turbine heat transfer program summary

    NASA Technical Reports Server (NTRS)

    Gladden, Herbert J.; Simoneau, Robert J.

    1988-01-01

    The objectives of the HOST Turbine Heat Transfer subproject were to obtain a better understanding of the physics of the aerothermodynamic phenomena and to assess and improve the analytical methods used to predict the flow and heat transfer in high temperature gas turbines. At the time the HOST project was initiated, an across-the-board improvement in turbine design technology was needed. A building-block approach was utilized and the research ranged from the study of fundamental phenomena and modeling to experiments in simulated real engine environments. Experimental research accounted for approximately 75 percent of the funding with the remainder going to analytical efforts. A healthy government/industry/university partnership, with industry providing almost half of the research, was created to advance the turbine heat transfer design technology base.

  13. Giardia duodenalis genetic assemblages and hosts

    PubMed Central

    Heyworth, Martin F.

    2016-01-01

    Techniques for sub-classifying morphologically identical Giardia duodenalis trophozoites have included comparisons of the electrophoretic mobility of enzymes and of chromosomes, and sequencing of genes encoding β-giardin, triose phosphate isomerase, the small subunit of ribosomal RNA and glutamate dehydrogenase. To date, G. duodenalis organisms have been sub-classified into eight genetic assemblages (designated A–H). Genotyping of G. duodenalis organisms isolated from various hosts has shown that assemblages A and B infect the largest range of host species, and appear to be the main (or possibly only) G. duodenalis assemblages that undeniably infect human subjects. In at least some cases of assemblage A or B infection in wild mammals, there is suggestive evidence that the infection had resulted from environmental contamination by G. duodenalis cysts of human origin. PMID:26984116

  14. All ecosystems potentially host electrogenic bacteria.

    PubMed

    Chabert, Nicolas; Amin Ali, Oulfat; Achouak, Wafa

    2015-12-01

    Instead of requiring metal catalysts, MFCs utilize bacteria that oxidize organic matter and either transfer electrons to the anode or take electrons from the cathode. These devices are thus based on a wide microbial diversity that can convert a large array of organic matter components into sustainable and renewable energy. A wide variety of explored environments were found to host electrogenic bacteria, including extreme environments. In the present review, we describe how different ecosystems host electrogenic bacteria, as well as the physicochemical, electrochemical and biological parameters that control the currents from MFCs. We also report how using new molecular techniques allowed characterization of electrochemical biofilms and identification of potentially new electrogenic species. Finally we discuss these findings in the context of future research directions. PMID:26298511

  15. Views on the impact of HOST

    NASA Technical Reports Server (NTRS)

    Esgar, J. B.; Sokolowski, Daniel E.

    1989-01-01

    The Hot Section Technology (HOST) Project, which was initiated by NASA Lewis Research Center in 1980 and concluded in 1987, was aimed at improving advanced aircraft engine hot section durability through better technical understanding and more accurate design analysis capability. The project was a multidisciplinary, multiorganizational, focused research effort that involved 21 organizations and 70 research and technology activities and generated approximately 250 research reports. No major hardware was developed. To evaluate whether HOST had a significant impact on the overall aircraft engine industry in the development of new engines, interviews were conducted with 41 participants in the project to obtain their views. The summarized results of these interviews are presented. Emphasis is placed on results relative to three-dimensional inelastic structural analysis, thermomechanical fatigue testing, constitutive modeling, combustor aerothermal modeling, turbine heat transfer, protective coatings, computer codes, improved engine design capability, reduced engine development costs, and the impacts on technology transfer and the industry-government partnership.

  16. Host genetic determinants of influenza pathogenicity

    PubMed Central

    Lin, Tsai-Yu; Brass, Abraham L.

    2014-01-01

    Despite effective vaccines, influenza remains a major global health threat due to the morbidity and mortality caused by seasonal epidemics, as well as the 2009 pandemic. Also of profound concern are the rare but potentially catastrophic transmissions of avian influenza to humans, highlighted by a recent H7N9 influenza outbreak. Murine and human studies reveal that the clinical course of influenza is the result of a combination of both host and viral genetic determinants. While viral pathogenicity has long been the subject of intensive efforts, research to elucidate host genetic determinants, particularly human, is now in the ascendant, and the goal of this review is to highlight these recent insights. PMID:23933004

  17. Magnetic activity of planet-hosting stars

    NASA Astrophysics Data System (ADS)

    Poppenhaeger, Katja

    2011-05-01

    Magnetic activity in cool stars is a widely observed phenomenon, however it is still far from being understood. How fundamental stellar parameters like mass and rotational period quantitatively cause a stellar magnetic field which manifests itself in features such as spots, flares and high-energy coronal emission is a lively area of research in solar and stellar astrophysics. Especially for planet-hosting stars, stellar activity profiles are very interesting as exoplanets are affected by high-energy radiation, both at the time of planet formation as well as during the further lifetime of a star-planet system. In extreme cases, the atmosphere of a planet very close to its host star can be strongly heated by the stellar X-ray and EUV emission and finally escape the planet's gravitational attraction, so that the atmosphere of the planet evaporates over time. Theoretically, planets can also affect their host star's magnetic activity. In analogy to processes in binary stars which lead to enhanced - both overall and periodically varying - activity levels, also giant planets might influence the stellar activity by tidal or magnetic interaction processes, however on a weaker level than in binaries. Some indications for such interactions exist from chromospheric measurements in stars with Hot Jupiters. In this thesis I investigate the magnetic activity of planet-hosting stars and especially possible effects from star-planet interactions with an emphasis on stellar coronae in X-rays. I tested a complete sample of all known planet-hosting stars within 30 pc distance from the Sun for correlations of stellar X-ray properties with planetary parameters. A significant correlation exists between the stellar X-ray luminosity and the product of planetary mass and inverse semimajor axis. However, this could be traced back to a selection effect introduced by planetary detection methods. For stars in the solar neighborhood, planets are mainly detected by radial velocity shifts in the

  18. Host Range and Emerging and Reemerging Pathogens

    PubMed Central

    Gowtage-Sequeria, Sonya

    2005-01-01

    An updated literature survey identified 1,407 recognized species of human pathogen, 58% of which are zoonotic. Of the total, 177 are regarded as emerging or reemerging. Zoonotic pathogens are twice as likely to be in this category as are nonzoonotic pathogens. Emerging and reemerging pathogens are not strongly associated with particular types of nonhuman hosts, but they are most likely to have the broadest host ranges. Emerging and reemerging zoonoses are associated with a wide range of drivers, but changes in land use and agriculture and demographic and societal changes are most commonly cited. However, although zoonotic pathogens do represent the most likely source of emerging and reemerging infectious disease, only a small minority have proved capable of causing major epidemics in the human population. PMID:16485468

  19. Standardised animal models of host microbial mutualism

    PubMed Central

    Macpherson, A J; McCoy, K D

    2015-01-01

    An appreciation of the importance of interactions between microbes and multicellular organisms is currently driving research in biology and biomedicine. Many human diseases involve interactions between the host and the microbiota, so investigating the mechanisms involved is important for human health. Although microbial ecology measurements capture considerable diversity of the communities between individuals, this diversity is highly problematic for reproducible experimental animal models that seek to establish the mechanistic basis for interactions within the overall host-microbial superorganism. Conflicting experimental results may be explained away through unknown differences in the microbiota composition between vivaria or between the microenvironment of different isolated cages. In this position paper, we propose standardised criteria for stabilised and defined experimental animal microbiotas to generate reproducible models of human disease that are suitable for systematic experimentation and are reproducible across different institutions. PMID:25492472

  20. Hepcidin and Host Defense against Infectious Diseases.

    PubMed

    Michels, Kathryn; Nemeth, Elizabeta; Ganz, Tomas; Mehrad, Borna

    2015-08-01

    Hepcidin is the master regulator of iron homeostasis in vertebrates. The synthesis of hepcidin is induced by systemic iron levels and by inflammatory stimuli. While the role of hepcidin in iron regulation is well established, its contribution to host defense is emerging as complex and multifaceted. In this review, we summarize the literature on the role of hepcidin as a mediator of antimicrobial immunity. Hepcidin induction during infection causes depletion of extracellular iron, which is thought to be a general defense mechanism against many infections by withholding iron from invading pathogens. Conversely, by promoting iron sequestration in macrophages, hepcidin may be detrimental to cellular defense against certain intracellular infections, although critical in vivo studies are needed to confirm this concept. It is not yet clear whether hepcidin exerts any iron-independent effects on host defenses. PMID:26291319

  1. Blood Groups in Infection and Host Susceptibility

    PubMed Central

    2015-01-01

    SUMMARY Blood group antigens represent polymorphic traits inherited among individuals and populations. At present, there are 34 recognized human blood groups and hundreds of individual blood group antigens and alleles. Differences in blood group antigen expression can increase or decrease host susceptibility to many infections. Blood groups can play a direct role in infection by serving as receptors and/or coreceptors for microorganisms, parasites, and viruses. In addition, many blood group antigens facilitate intracellular uptake, signal transduction, or adhesion through the organization of membrane microdomains. Several blood groups can modify the innate immune response to infection. Several distinct phenotypes associated with increased host resistance to malaria are overrepresented in populations living in areas where malaria is endemic, as a result of evolutionary pressures. Microorganisms can also stimulate antibodies against blood group antigens, including ABO, T, and Kell. Finally, there is a symbiotic relationship between blood group expression and maturation of the gastrointestinal microbiome. PMID:26085552

  2. Bromeliad treefrogs as phoretic hosts of ostracods

    NASA Astrophysics Data System (ADS)

    Sabagh, Leandro T.; Rocha, Carlos F. D.

    2014-06-01

    Aquatic organisms can use many methods of dispersal among discrete freshwater habitats, and phoresy is an important but poorly understood mechanism. Tank bromeliads are small and unconnected habitats used by many animals, and some of them use phoresy for dispersal. Ostracods living in bromeliads used treefrogs as phoretic hosts for dispersal. We investigated the distribution of phoretic ostracods among body parts of treefrogs ( Scinax littoreus and Scinax perpusillus), the prevalence and intensity of ostracods ( Elpidium sp.) between Scinax species, and the prevalence and mean intensity of ostracods among the frogs in wet vs. dry seasons in two inselbergs areas at Rio de Janeiro State (Brazil). There were significant differences among the body parts occupied by ostracods and between the Scinax species. Seasonal differences were found only for S. littoreus showing greater abundance during the wet season. Additionally, we record Scinax cuspidatus and Thoropa miliaris as new phoretic hosts for Elpidium sp. to use phoresy.

  3. Bromeliad treefrogs as phoretic hosts of ostracods.

    PubMed

    Sabagh, Leandro T; Rocha, Carlos F D

    2014-06-01

    Aquatic organisms can use many methods of dispersal among discrete freshwater habitats, and phoresy is an important but poorly understood mechanism. Tank bromeliads are small and unconnected habitats used by many animals, and some of them use phoresy for dispersal. Ostracods living in bromeliads used treefrogs as phoretic hosts for dispersal. We investigated the distribution of phoretic ostracods among body parts of treefrogs (Scinax littoreus and Scinax perpusillus), the prevalence and intensity of ostracods (Elpidium sp.) between Scinax species, and the prevalence and mean intensity of ostracods among the frogs in wet vs. dry seasons in two inselbergs areas at Rio de Janeiro State (Brazil). There were significant differences among the body parts occupied by ostracods and between the Scinax species. Seasonal differences were found only for S. littoreus showing greater abundance during the wet season. Additionally, we record Scinax cuspidatus and Thoropa miliaris as new phoretic hosts for Elpidium sp. to use phoresy. PMID:24796544

  4. Prokaryotes Versus Eukaryotes: Who is Hosting Whom?

    PubMed

    Tellez, Guillermo

    2014-01-01

    Microorganisms represent the largest component of biodiversity in our world. For millions of years, prokaryotic microorganisms have functioned as a major selective force shaping eukaryotic evolution. Microbes that live inside and on animals outnumber the animals' actual somatic and germ cells by an estimated 10-fold. Collectively, the intestinal microbiome represents a "forgotten organ," functioning as an organ inside another that can execute many physiological responsibilities. The nature of primitive eukaryotes was drastically changed due to the association with symbiotic prokaryotes facilitating mutual coevolution of host and microbe. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. From termites and honey bees to ruminants and mammals, depending on novel biochemistries provided by the prokaryotic microbiome, the association helps to metabolize several nutrients that the host cannot digest and converting these into useful end products (such as short-chain fatty acids), a process, which has huge impact on the biology and homeostasis of metazoans. More importantly, in a direct and/or indirect way, the intestinal microbiota influences the assembly of gut-associated lymphoid tissue, helps to educate immune system, affects the integrity of the intestinal mucosal barrier, modulates proliferation and differentiation of its epithelial lineages, regulates angiogenesis, and modifies the activity of enteric as well as the central nervous system. Despite these important effects, the mechanisms by which the gut microbial community influences the host's biology remain almost entirely unknown. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification between prokaryotes and eukaryotes, which encourage us to postulate: who is hosting whom? PMID:26664911

  5. PAK in pathogen-host interactions

    PubMed Central

    Semblat, Jean-Philippe; Doerig, Christian

    2012-01-01

    Eukaryotic, prokaryotic and viral pathogens are known to interfere with signaling pathways of their host to promote their own survival and proliferation. Here, we present selected examples of modulation of PAK activity in human cells by both intracellular and extracellular pathogens, focusing on one eukaryotic pathogen, the human malaria parasite Plasmodium falciparum, two Gram-negative bacteria (Helicobacter pylori and Pseudomonas aeruginosa), and two viruses belonging to distinct groups, the lentivirus HIV and the orthomyxovirus Influenza virus A. PMID:23125952

  6. Identification of host response signatures of infection.

    SciTech Connect

    Branda, Steven S.; Sinha, Anupama; Bent, Zachary

    2013-02-01

    Biological weapons of mass destruction and emerging infectious diseases represent a serious and growing threat to our national security. Effective response to a bioattack or disease outbreak critically depends upon efficient and reliable distinguishing between infected vs healthy individuals, to enable rational use of scarce, invasive, and/or costly countermeasures (diagnostics, therapies, quarantine). Screening based on direct detection of the causative pathogen can be problematic, because culture- and probe-based assays are confounded by unanticipated pathogens (e.g., deeply diverged, engineered), and readily-accessible specimens (e.g., blood) often contain little or no pathogen, particularly at pre-symptomatic stages of disease. Thus, in addition to the pathogen itself, one would like to detect infection-specific host response signatures in the specimen, preferably ones comprised of nucleic acids (NA), which can be recovered and amplified from tiny specimens (e.g., fingerstick draws). Proof-of-concept studies have not been definitive, however, largely due to use of sub-optimal sample preparation and detection technologies. For purposes of pathogen detection, Sandia has developed novel molecular biology methods that enable selective isolation of NA unique to, or shared between, complex samples, followed by identification and quantitation via Second Generation Sequencing (SGS). The central hypothesis of the current study is that variations on this approach will support efficient identification and verification of NA-based host response signatures of infectious disease. To test this hypothesis, we re-engineered Sandia's sophisticated sample preparation pipelines, and developed new SGS data analysis tools and strategies, in order to pioneer use of SGS for identification of host NA correlating with infection. Proof-of-concept studies were carried out using specimens drawn from pathogen-infected non-human primates (NHP). This work provides a strong foundation for

  7. Host Plants of Xylosandrus mutilatus in Mississippi

    SciTech Connect

    Stone, W.D.; Nebeker, T.E.; Gerard, P.D.

    2007-03-15

    Host range of Xylosandrus mutilatus (Blandford) in North America is reported here for the first time. Descriptive data such as number of attacks per host, size of stems at point of attacks, and height of attacks above ground are presented. Hosts observed in Mississippi were Acer rubrum L., Acer saccharum Marsh., Acer palmatum Thunb., Ostrya virginiana (Mill.) K. Koch., Cornus florida L., Fagus grandifolia Ehrh., Liquidamber styraciflua L., Carya spp., Liriodendron tulipifera L., Melia azedarach L., Pinus taeda L., Prunus serotina Ehrh., Prunus americana Marsh., Ulmus alata Michaux, and Vitus rotundifolia Michaux. Liquidamber styraciflua had significantly more successful attacks, significantly higher probability of attacks, and significantly higher number of adult beetles per host tree than did Carya spp., A. rubrum, and L. tulipifera. This information is relevant in determining the impact this exotic beetle may have in nurseries, urban areas, and other forestry systems where this beetle becomes established. (author) [Spanish] El rango de hospederos de Xylosandrus mutilatus (Blandford) en America del Norte esta reportado aqui por la primera vez. Se presentan datos descriptivos como el numero de ataques por hospederos, el tamano de los tallos en el punto de ataque y la altura por encima del nivel de tierra de los ataques. Los hospederos observados en el estado de Mississippi fueron Acer rubrum L., Acer saccharum Marsh., Acer palmatum Thunb., Ostrya virginiana (Mill.) K. Koch., Cornus florida L., Fagus grandifolia Ehrh., Liquidamber styraciflua L., Carya spp., Liriodendron tulipifera L., Melia azedarach L., Pinus taeda L., Prunus serotina Ehrh., Prunus americana Marsh., Ulmus alata Michaux y Vitus rotundifolia Michaux. Liquidamber styraciflua tuvo ataques significativamente mas exitosos, una probabilidad significativamente mas alta de ataques y un numero significativamente mayor de adultos de escarabajos por arbol hospedero que Carya spp., A. rubrum y L. tulipifera

  8. Linking Virus Genomes with Host Taxonomy.

    PubMed

    Mihara, Tomoko; Nishimura, Yosuke; Shimizu, Yugo; Nishiyama, Hiroki; Yoshikawa, Genki; Uehara, Hideya; Hingamp, Pascal; Goto, Susumu; Ogata, Hiroyuki

    2016-03-01

    Environmental genomics can describe all forms of organisms--cellular and viral--present in a community. The analysis of such eco-systems biology data relies heavily on reference databases, e.g., taxonomy or gene function databases. Reference databases of symbiosis sensu lato, although essential for the analysis of organism interaction networks, are lacking. By mining existing databases and literature, we here provide a comprehensive and manually curated database of taxonomic links between viruses and their cellular hosts. PMID:26938550

  9. Trichinella inflammatory myopathy: host or parasite strategy?

    PubMed Central

    2011-01-01

    The parasitic nematode Trichinella has a special relation with muscle, because of its unique intracellular localization in the skeletal muscle cell, completely devoted in morphology and biochemistry to become the parasite protective niche, otherwise called the nurse cell. The long-lasting muscle infection of Trichinella exhibits a strong interplay with the host immune response, mainly characterized by a Th2 phenotype. The aim of this review is to illustrate the role of the Th2 host immune response at the muscle level during trichinellosis in different experimental models, such as knock-out or immuno-modulated mice. In particular, in knock-out mice a crucial role of IL-10 is evident for the regulation of inflammation intensity. The muscular host immune response to Trichinella is partially regulated by the intestinal phase of the parasite which emphasizes the intensity of the following muscle inflammation compared with animals infected by synchronized injections of newborn larvae. In eosinophil-ablated mice such as PHIL and GATA-- animals it was observed that there was an increased NOS2 expression in macrophages, driven by higher IFN-γ release, thus responsible for muscle larva damage. Besides modulation of the intestinal stage of the infection, using recombinant IL-12, increases the muscular parasite burden delaying adult worm expulsion from the intestine. Furthermore, a Th1 adjuvant of bacterial origin called Helicobacter pylori neutrophil activating protein (HP-NAP), administered during the intestinal phase of trichinellosis, alters the Th2 dependent response at muscle level. All these data from the literature delineate then a mutual adaptation between parasite and host immune response in order to achieve a strategic compromise between two evolutionary forces pointed towards the survival of both species. PMID:21429196

  10. Turbine Engine Hot Section Technology (HOST) Project

    NASA Technical Reports Server (NTRS)

    Sokolowski, Daniel E.; Ensign, C. Robert

    1986-01-01

    The Hot Section Technology (HOST) Project is a NASA-sponsored endeavor to improve the durability of advanced gas turbine engines for commercial and military aircraft. Through improvements in the analytical models and life prediction systems, designs for future hot section components, the combustor and turbine, will be more accurately analyzed and will incorporate features required for longer life in the more hostile operating environment of high performance engines.

  11. Linking Virus Genomes with Host Taxonomy

    PubMed Central

    Mihara, Tomoko; Nishimura, Yosuke; Shimizu, Yugo; Nishiyama, Hiroki; Yoshikawa, Genki; Uehara, Hideya; Hingamp, Pascal; Goto, Susumu; Ogata, Hiroyuki

    2016-01-01

    Environmental genomics can describe all forms of organisms—cellular and viral—present in a community. The analysis of such eco-systems biology data relies heavily on reference databases, e.g., taxonomy or gene function databases. Reference databases of symbiosis sensu lato, although essential for the analysis of organism interaction networks, are lacking. By mining existing databases and literature, we here provide a comprehensive and manually curated database of taxonomic links between viruses and their cellular hosts. PMID:26938550

  12. Revisiting the host as a growth medium

    PubMed Central

    Brown, Stacie A.; Palmer, Kelli L.; Whiteley, Marvin

    2011-01-01

    The ability of the human body to play host to bacterial pathogens has been studied for more than 200 years. Successful pathogenesis relies on the ability to acquire the nutrients that are necessary for growth and survival, yet relatively little is understood about the in vivo physiology and metabolism of most human pathogens. This Review discusses how in vivo carbon sources can affect disease and highlights the concept that carbon metabolic pathways provide viable targets for antibiotic development. PMID:18679171

  13. Functionality of host proteins in Cucumber mosaic virus replication: GAPDH is obligatory to promote interaction between replication-associated proteins.

    PubMed

    Chaturvedi, Sonali; Seo, Jang-Kyun; Rao, A L N

    2016-07-01

    Here, we evaluated the role of two host proteins, a Bromo domain containing RNA binding protein (BRP1) and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), in the replication of Cucumber mosaic virus (CMV). LC-MS/MS analysis of host/viral proteins pull down against BRP1 from CMV-infected plants co-infiltrated with BRP1-FLAG agroconstruct identified that BRP1 specifically interacts with a ten amino acid motif (843-SPQDVVPLVR-852) encompassing the helicase domain of replicase protein p1a. The interaction between BRP1 and p1a was subsequently confirmed using a BiFC assay. Among fourteen other host proteins identified to interact with BRP1 during CMV infection, six were found to block accumulation of viral progeny in Arabidopsis thaliana lines defective in each of these host proteins. Additional BiFC assays followed by trans-complementation assays identified that plant lines defective in the expression of GAPDH blocked CMV replication by interfering with p1a:p2a interaction. Distinct roles of BRP1 and GAPDH in the replication of CMV are discussed. PMID:27077230

  14. Amoebal Endosymbiont Neochlamydia Genome Sequence Illuminates the Bacterial Role in the Defense of the Host Amoebae against Legionella pneumophila

    PubMed Central

    Ishida, Kasumi; Sekizuka, Tsuyoshi; Hayashida, Kyoko; Matsuo, Junji; Takeuchi, Fumihiko; Kuroda, Makoto; Nakamura, Shinji; Yamazaki, Tomohiro; Yoshida, Mitsutaka; Takahashi, Kaori; Nagai, Hiroki; Sugimoto, Chihiro; Yamaguchi, Hiroyuki

    2014-01-01

    Previous work has shown that the obligate intracellular amoebal endosymbiont Neochlamydia S13, an environmental chlamydia strain, has an amoebal infection rate of 100%, but does not cause amoebal lysis and lacks transferability to other host amoebae. The underlying mechanism for these observations remains unknown. In this study, we found that the host amoeba could completely evade Legionella infection. The draft genome sequence of Neochlamydia S13 revealed several defects in essential metabolic pathways, as well as unique molecules with leucine-rich repeats (LRRs) and ankyrin domains, responsible for protein-protein interaction. Neochlamydia S13 lacked an intact tricarboxylic acid cycle and had an incomplete respiratory chain. ADP/ATP translocases, ATP-binding cassette transporters, and secretion systems (types II and III) were well conserved, but no type IV secretion system was found. The number of outer membrane proteins (OmcB, PomS, 76-kDa protein, and OmpW) was limited. Interestingly, genes predicting unique proteins with LRRs (30 genes) or ankyrin domains (one gene) were identified. Furthermore, 33 transposases were found, possibly explaining the drastic genome modification. Taken together, the genomic features of Neochlamydia S13 explain the intimate interaction with the host amoeba to compensate for bacterial metabolic defects, and illuminate the role of the endosymbiont in the defense of the host amoebae against Legionella infection. PMID:24747986

  15. Fungal effector Ecp6 outcompetes host immune receptor for chitin binding through intrachain LysM dimerization

    PubMed Central

    Kombrink, Anja; Hansen, Guido; Valkenburg, Dirk-Jan

    2013-01-01

    While host immune receptors detect pathogen-associated molecular patterns to activate immunity, pathogens attempt to deregulate host immunity through secreted effectors. Fungi employ LysM effectors to prevent recognition of cell wall-derived chitin by host immune receptors, although the mechanism to compete for chitin binding remained unclear. Structural analysis of the LysM effector Ecp6 of the fungal tomato pathogen Cladosporium fulvum reveals a novel mechanism for chitin binding, mediated by intrachain LysM dimerization, leading to a chitin-binding groove that is deeply buried in the effector protein. This composite binding site involves two of the three LysMs of Ecp6 and mediates chitin binding with ultra-high (pM) affinity. Intriguingly, the remaining singular LysM domain of Ecp6 binds chitin with low micromolar affinity but can nevertheless still perturb chitin-triggered immunity. Conceivably, the perturbation by this LysM domain is not established through chitin sequestration but possibly through interference with the host immune receptor complex. DOI: http://dx.doi.org/10.7554/eLife.00790.001 PMID:23840930

  16. Progress in computational studies of host-pathogen interactions.

    PubMed

    Zhou, Hufeng; Jin, Jingjing; Wong, Limsoon

    2013-04-01

    Host-pathogen interactions are important for understanding infection mechanism and developing better treatment and prevention of infectious diseases. Many computational studies on host-pathogen interactions have been published. Here, we review recent progress and results in this field and provide a systematic summary, comparison and discussion of computational studies on host-pathogen interactions, including prediction and analysis of host-pathogen protein-protein interactions; basic principles revealed from host-pathogen interactions; and database and software tools for host-pathogen interaction data collection, integration and analysis. PMID:23600809

  17. Host range of poliovirus is restricted to simians because of a rapid sequence change of the poliovirus receptor gene during evolution.

    PubMed

    Ida-Hosonuma, M; Sasaki, Y; Toyoda, H; Nomoto, A; Gotoh, O; Yonekawa, H; Koike, S

    2003-01-01

    The host range of most poliovirus (PV) strains is restricted to simians. This host range specificity is believed to be determined by the interaction between PV and its receptor molecule. To elucidate the molecular basis of this species-specific infection of PV, we cloned orthologs of the PV receptor (PVR) gene ( pvr) as well as those of PV receptor-related genes 1 and 2 ( prr1 and prr2) from various mammalian species. These three genes are widely present in mammalian genomes including those of non-susceptible species. Comparison of the deduced amino acid sequences of PVR orthologs revealed that the NH(2)-terminal immunoglobulin-like domain (domain 1), which is the virus binding site in the human PVR, is highly variable among species, whereas that of PRR1 is highly conserved. Domain 1 of the PVR orthologs for the ring-tailed lemur and rabbit, which are not susceptible to PV, show only 51 and 61% amino acid sequence identity to that of human PVR, respectively. Chimeric PVR proteins that have the domain 1 of the ring-tailed lemur and rabbit PVRs failed to serve as receptors for PV. These results suggest that rapid changes in the domain 1 sequence during mammalian evolution determined the host range restriction of PV. PMID:12536294

  18. Comparative phylogenies and host specialization in the alder ectomycorrhizal fungi Alnicola, Alpova and Lactarius (Basidiomycota) in Europe

    PubMed Central

    2011-01-01

    Background Mycorrhizal fungi form intimate associations with their host plants that constitute their carbon resource and habitat. Alnus spp. (Betulaceae) are known to host an exceptional species-poor and specialized ectomycorrhizal (ECM) fungal community compared to other tree species, but the host-specificity pattern and its significance in terms of fungal diversification and speciation remain poorly documented. The degree of parallel speciation, host switching, and patterns of biogeography were explored in the historical associations between alders and three ECM taxa of Basidiomycetes: Alnicola (Agaricales), Alpova (Boletales), and Lactarius (Russulales). The aim was to develop an evolutionary framework on host specificity and diversification of Basidiomycetes in this highly specialized plant-fungus symbiosis. Results Sporocarps of Alnicola (220), Lactarius (61) and Alpova (29) were collected from stands of the four European alder species (A. alnobetula including the endemic subsp. suaveolens in Corsica, A. cordata, A. glutinosa, A. incana) in Western Europe (mainly in France and Austria), from 1995 to 2009. Specimens were morphologically identified to the species level. From these, 402 sequences of four DNA regions (ITS, rpb2, gpd, and the V9 domain of the mit-SSU rDNA) were successfully obtained and analyzed in addition with 89 sequences available in GenBank and UNITE databases. Phylogenetic analyses were conducted on all sequence data sets (individual and combined) using maximum likelihood reconstruction and Bayesian inference. Fungal phylogenies are compared and discussed in relation to the host, with a focus on species boundaries by associating taxonomic, systematic and molecular information. Conclusions Patterns of host specificity and phylogenies of Alnicola and Lactarius suggest coevolution as a basal factor of speciation in relation with the subgeneric diversification of Alnus, possibly due to the very selective pressure of the host. A second element of

  19. Characterization of Kepler Exoplanet Host Stars

    NASA Astrophysics Data System (ADS)

    Howell, Steve B.; Everett, M.; Ciardi, D. R.; Silva, D.; Szkody, P.

    2014-01-01

    Using a sample of 220 Exoplanet host stars in the Kepler field for which spectroscopic properties have been determined, we examine their spatial, physical, and time variable properties. Covering effective temperatures from 4670K to 6400K (K4 to F4) and masses from 0.7 to 1.4 M-sun, this sample represents host stars covering the entire Kepler field of view. The majority of the host stars contain one or more Earth-sized exoplanet and range in log g from 4.0 to 4.7 and [Fe/H] from -02.4 to +0.3. Using Yale-Yonsei isochrone fits and photometric information form the Howell-Everett UBV survey of the Kepler field, we examine a complete set of parameters for these stars including their likely residence in the thin or thick disk of the Galaxy. the variability of this sample, in terms of time sale and amplitude, is examined as well.

  20. THE MASS DISTRIBUTION OF SUBGIANT PLANET HOSTS

    SciTech Connect

    Lloyd, James P.

    2013-09-01

    High mass stars are hostile to Doppler measurements due to rotation and activity on the main-sequence, so RV searches for planets around massive stars have relied on evolved stars. A large number of planets have been found around evolved stars with M > 1.5 M{sub Sun }. To test the robustness of mass determinations, Lloyd compared mass distributions of planet hosting subgiants with distributions from integrating isochrones and concluded that it is unlikely the subgiant planet hosts are this massive, but rather that the mass inferences are systematically in error. The conclusions of Lloyd have been called in to question by Johnson et al., who show TRILEGAL-based mass distributions that disagree with the mass distributions in Lloyd, which they attribute to Malmquist bias. Johnson et al. argue that the very small spectroscopic observational uncertainties favor high masses, and there are a large number of high mass sub giants in RV surveys. However, in this Letter, it is shown that Malmquist bias does not impact the mass distributions, but the mass distribution is sensitive to Galaxy model. The relationship needed to reconcile the subgiant planet host masses with any model of the Galactic stellar population is implausible, and the conclusion of Lloyd that spectroscopic mass determinations of subgiants are likely to have been overestimated is robust.