Ligand Binding to WW Tandem Domains of YAP2 Transcriptional Regulator Is Under Negative Cooperativity

PubMed Central

Schuchardt, Brett J.; Mikles, David C.; Hoang, Lawrence M.; Bhat, Vikas; McDonald, Caleb B.; Sudol, Marius; Farooq, Amjad

2014-01-01

YAP2 transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well-documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules. PMID:25283809

Ligand binding to WW tandem domains of YAP2 transcriptional regulator is under negative cooperativity.

PubMed

Schuchardt, Brett J; Mikles, David C; Hoang, Lawrence M; Bhat, Vikas; McDonald, Caleb B; Sudol, Marius; Farooq, Amjad

2014-12-01

YES-associated protein 2 (YAP2) transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of the WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules. © 2014 FEBS.

Changes at the KinA PAS-A Dimerization Interface Influence Histidine Kinase Function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, James; Tomchick, Diana R.; Brautigam, Chad A.

2008-11-12

The Bacillus subtilis KinA protein is a histidine protein kinase that controls the commitment of this organism to sporulate in response to nutrient deprivation and several other conditions. Prior studies indicated that the N-terminal Per-ARNT-Sim domain (PAS-A) plays a critical role in the catalytic activity of this enzyme, as demonstrated by the significant decrease of the autophosphorylation rate of a KinA protein lacking this domain. On the basis of the environmental sensing role played by PAS domains in a wide range of proteins, including other bacterial sensor kinases, it has been suggested that the PAS-A domain plays an important regulatorymore » role in KinA function. We have investigated this potential by using a combination of biophysical and biochemical methods to examine PAS-A structure and function, both in isolation and within the intact protein. Here, we present the X-ray crystal structure of the KinA PAS-A domain, showing that it crystallizes as a homodimer using {beta}-sheet/{beta}-sheet packing interactions as observed for several other PAS domain complexes. Notably, we observed two dimers with tertiary and quaternary structure differences in the crystalline lattice, indicating significant structural flexibility in these domains. To confirm that KinA PAS-A also forms dimers in solution, we used a combination of NMR spectroscopy, gel filtration chromatography, and analytical ultracentrifugation, the results of which are all consistent with the crystallographic results. We experimentally tested the importance of several residues at the dimer interface using site-directed mutagenesis, finding changes in the PAS-A domain that significantly alter KinA enzymatic activity in vitro and in vivo. These results support the importance of PAS domains within KinA and other histidine kinases and suggest possible routes for natural or artificial regulation of kinase activity.« less

The PAS domains of the major sporulation kinase in Bacillus subtilis play a role in tetramer formation that is essential for the autokinase activity.

PubMed

Kiehler, Brittany; Haggett, Lindsey; Fujita, Masaya

2017-08-01

Sporulation in Bacillus subtilis is induced upon starvation. In a widely accepted model, an N-terminal "sensor" domain of the major sporulation kinase KinA recognizes a hypothetical starvation signal(s) and autophosphorylates a histidine residue to activate the master regulator Spo0A via a multicomponent phosphorelay. However, to date no confirmed signal has been found. Here, we demonstrated that PAS-A, the most N-terminal of the three PAS domains (PAS-ABC), is dispensable for the activity, contrary to a previous report. Our data indicated that the autokinase activity is dependent on the formation of a functional tetramer, which is mediated by, at least, PAS-B and PAS-C. Additionally, we ruled out the previously proposed notion that NAD + /NADH ratio controls KinA activity through the PAS-A domain by demonstrating that the cofactors show no effects on the kinase activity in vitro. In support of these data, we found that the cofactors exist in approximately 1000-fold excess of KinA in the cell and the cofactors' ratio does not change significantly during growth and sporulation, suggesting that changes in the cofactor ratio might not play a role in controlling KinA activity. These data may refute the widely-held belief that the activity of KinA is regulated in response to an unknown starvation signal(s). © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Specificity and autoregulation of Notch binding by tandem WW domains in suppressor of Deltex.

PubMed

Jennings, Martin D; Blankley, Richard T; Baron, Martin; Golovanov, Alexander P; Avis, Johanna M

2007-09-28

WW domains target proline-tyrosine (PY) motifs and frequently function as tandem pairs. When studied in isolation, single WW domains are notably promiscuous and regulatory mechanisms are undoubtedly required to ensure selective interactions. Here, we show that the fourth WW domain (WW4) of Suppressor of Deltex, a modular Nedd4-like protein that down-regulates the Notch receptor, is the primary mediator of a direct interaction with a Notch-PY motif. A natural Trp to Phe substitution in WW4 reduces its affinity for general PY sequences and enhances selective interaction with the Notch-PY motif via compensatory specificity-determining interactions with PY-flanking residues. When WW4 is paired with WW3, domain-domain association, impeding proper folding, competes with Notch-PY binding to WW4. This novel mode of autoinhibition is relieved by binding of another ligand to WW3. Such cooperativity may facilitate the transient regulatory interactions observed in vivo between Su(dx) and Notch in the endocytic pathway. The highly conserved tandem arrangement of WW domains in Nedd4 proteins, and similar arrangements in more diverse proteins, suggests domain-domain communication may be integral to regulation of their associated cellular activities.

Structure and Function of the Two Tandem WW Domains of the Pre-mRNA Splicing Factor FBP21 (Formin-binding Protein 21)*

PubMed Central

Huang, Xiaojuan; Beullens, Monique; Zhang, Jiahai; Zhou, Yi; Nicolaescu, Emilia; Lesage, Bart; Hu, Qi; Wu, Jihui; Bollen, Mathieu; Shi, Yunyu

2009-01-01

Human FBP21 (formin-binding protein 21) contains a matrin-type zinc finger and two tandem WW domains. It is a component of the spliceosomes and interacts with several established splicing factors. Here we demonstrate for the first time that FBP21 is an activator of pre-mRNA splicing in vivo and that its splicing activation function and interaction with the splicing factor SIPP1 (splicing factor that interacts with PQBP1 and PP1) are both mediated by the two tandem WW domains of group III. We determined the solution structure of the tandem WW domains of FBP21 and found that the WW domains recognize peptide ligands containing either group II (PPLP) or group III (PPR) motifs. The binding interfaces involve both the XP and XP2 grooves of the two WW domains. Significantly, the tandem WW domains of FBP21 are connected by a highly flexible region, enabling their simultaneous interaction with two proline-rich motifs of SIPP1. The strong interaction between SIPP1 and FBP21 can be explained by the conjugation of two low affinity interactions with the tandem WW domains. Our study provides a structural basis for understanding the molecular mechanism underlying the functional implication of FBP21 and the biological specificity of tandem WW domains. PMID:19592703

Solution structure of the tandem acyl carrier protein domains from a polyunsaturated fatty acid synthase reveals beads-on-a-string configuration.

PubMed

Trujillo, Uldaeliz; Vázquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J; Vassallo, David A; Vega, Irving E; Arold, Stefan T; Baerga-Ortiz, Abel

2013-01-01

The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

PubMed Central

Trujillo, Uldaeliz; Vázquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J.; Vassallo, David A.; Vega, Irving E.; Arold, Stefan T.; Baerga-Ortiz, Abel

2013-01-01

The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

The PAS domain-containing histidine kinase RpfS is a second sensor for the diffusible signal factor of Xanthomonas campestris.

PubMed

An, Shi-Qi; Allan, John H; McCarthy, Yvonne; Febrer, Melanie; Dow, J Maxwell; Ryan, Robert P

2014-05-01

A cell-cell signalling system mediated by the fatty acid signal DSF controls the virulence of Xanthomonas campestris pv. campestris (Xcc) to plants. The synthesis and recognition of the DSF signal depends upon different Rpf proteins. DSF signal generation requires RpfF whereas signal perception and transduction depends upon the sensor RpfC and regulator RpfG. Detailed analyses of the regulatory roles of different Rpf proteins have suggested the occurrence of further sensors for DSF. Here we have used a mutagenesis approach coupled with high-resolution transcriptional analysis to identify XC_2579 (RpfS) as a second sensor for DSF in Xcc. RpfS is a complex sensor kinase predicted to have multiple Per/Arnt/Sim (PAS) domains, a histidine kinase domain and a C-terminal receiver (REC) domain. Isothermal calorimetry showed that DSF bound to the isolated N-terminal PAS domain with a Kd of 1.4 μM. RpfS controlled expression of a sub-set of genes distinct from those controlled by RpfC to include genes involved in type IV secretion and chemotaxis. Mutation of XC_2579 was associated with a reduction in virulence of Xcc to Chinese Radish when assayed by leaf spraying but not by leaf inoculation, suggesting a role for RpfS-controlled factors in the epiphytic phase of the disease cycle. © 2014 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.

Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation

PubMed Central

Corrada, Dario; Soshilov, Anatoly A.; Denison, Michael S.

2016-01-01

The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the

Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation.

PubMed

Corrada, Dario; Soshilov, Anatoly A; Denison, Michael S; Bonati, Laura

2016-06-01

The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the

Spanish validation of the Premorbid Adjustment Scale (PAS-S).

PubMed

Barajas, Ana; Ochoa, Susana; Baños, Iris; Dolz, Montse; Villalta-Gil, Victoria; Vilaplana, Miriam; Autonell, Jaume; Sánchez, Bernardo; Cervilla, Jorge A; Foix, Alexandrina; Obiols, Jordi E; Haro, Josep Maria; Usall, Judith

2013-02-01

The Premorbid Adjustment Scale (PAS) has been the most widely used scale to quantify premorbid status in schizophrenia, coming to be regarded as the gold standard of retrospective assessment instruments. To examine the psychometric properties of the Spanish version of the PAS (PAS-S). Retrospective study of 140 individuals experiencing a first episode of psychosis (n=77) and individuals who have schizophrenia (n=63), both adult and adolescent patients. Data were collected through a socio-demographic questionnaire and a battery of instruments which includes the following scales: PAS-S, PANSS, LSP, GAF and DAS-sv. The Cronbach's alpha was performed to assess the internal consistency of PAS-S. Pearson's correlations were performed to assess the convergent and discriminant validity. The Cronbach's alpha of the PAS-S scale was 0.85. The correlation between social PAS-S and total PAS-S was 0.85 (p<0.001); while for academic PAS-S and total PAS-S it was 0.53 (p<0.001). Significant correlations were observed between all the scores of each age period evaluated across the PAS-S scale, with a significance value less than 0.001. There was a relationship between negative symptoms and social PAS-S (0.20, p<0.05) and total PAS-S (0.22, p<0.05), but not with academic PAS-S. However, there was a correlation between academic PAS-S and general subscale of the PANSS (0.19, p<0.05). Social PAS-S was related to disability measures (DAS-sv); and academic PAS-S showed discriminant validity with most of the variables of social functioning. PAS-S did not show association with the total LSP scale (discriminant validity). The Spanish version of the Premorbid Adjustment Scale showed appropriate psychometric properties in patients experiencing a first episode of psychosis and who have a chronic evolution of the illness. Moreover, each domain of the PAS-S (social and academic premorbid functioning) showed a differential relationship to other characteristics such as psychotic symptoms, disability

Structure of the tandem PX-PH domains of Bem3 from Saccharomyces cerevisiae.

PubMed

Ali, Imtiaz; Eu, Sungmin; Koch, Daniel; Bleimling, Nathalie; Goody, Roger S; Müller, Matthias P

2018-05-01

The structure of the tandem lipid-binding PX and pleckstrin-homology (PH) domains of the Cdc42 GTPase-activating protein Bem3 from Saccharomyces cerevisiae (strain S288c) has been determined to a resolution of 2.2 Å (R work = 21.1%, R free = 23.4%). It shows that the domains adopt a relative orientation that enables them to simultaneously bind to a membrane and suggests possible cooperativity in membrane binding. open access.

Structure of the tandem PX-PH domains of Bem3 from Saccharomyces cerevisiae

PubMed Central

Ali, Imtiaz; Eu, Sungmin; Bleimling, Nathalie

2018-01-01

The structure of the tandem lipid-binding PX and pleckstrin-homology (PH) domains of the Cdc42 GTPase-activating protein Bem3 from Saccharomyces cerevisiae (strain S288c) has been determined to a resolution of 2.2 Å (R work = 21.1%, R free = 23.4%). It shows that the domains adopt a relative orientation that enables them to simultaneously bind to a membrane and suggests possible cooperativity in membrane binding. PMID:29718000

H2O2 production rate in Lactobacillus johnsonii is modulated via the interplay of a heterodimeric flavin oxidoreductase with a soluble 28 Kd PAS domain containing protein

PubMed Central

Valladares, Ricardo B.; Graves, Christina; Wright, Kaitlyn; Gardner, Christopher L.; Lorca, Graciela L.; Gonzalez, Claudio F.

2015-01-01

Host and commensals crosstalk, mediated by reactive oxygen species (ROS), has triggered a growing scientific interest to understand the mechanisms governing such interaction. However, the majority of the scientific studies published do not evaluate the ROS production by commensals bacteria. In this context we recently showed that Lactobacillus johnsonii N6.2, a strain of probiotic value, modulates the activity of the critical enzymes 2,3-indoleamine dioxygenase via H2O2 production. L. johnsonii N6.2 by decreasing IDO activity, is able to modify the tryptophan/kynurenine ratio in the host blood with further systemic consequences. Understanding the mechanisms of H2O2 production is critical to predict the probiotic value of these strains and to optimize bacterial biomass production in industrial processes. We performed a transcriptome analysis to identify genes differentially expressed in L. johnsonii N6.2 cells collected from cultures grown under different aeration conditions. Herein we described the biochemical characteristics of a heterodimeric FMN reductase (FRedA/B) whose in vitro activity is controlled by LjPAS protein with a typical Per-Arnst-Sim (PAS) sensor domain. Interestingly, LjPAS is fused to the FMN reductase domains in other lactobacillaceae. In L. johnsonii, LjPAS is encoded by an independent gene which expression is repressed under anaerobic conditions (>3 fold). Purified LjPAS was able to slow down the FRedA/B initial activity rate when the holoenzyme precursors (FredA, FredB, and FMN) were mixed in vitro. Altogether the results obtained suggest that LjPAS module regulates the H2O2 production helping the cells to minimize oxidative stress in response to environmental conditions. PMID:26236298

H2O2 production rate in Lactobacillus johnsonii is modulated via the interplay of a heterodimeric flavin oxidoreductase with a soluble 28 Kd PAS domain containing protein.

PubMed

Valladares, Ricardo B; Graves, Christina; Wright, Kaitlyn; Gardner, Christopher L; Lorca, Graciela L; Gonzalez, Claudio F

2015-01-01

Host and commensals crosstalk, mediated by reactive oxygen species (ROS), has triggered a growing scientific interest to understand the mechanisms governing such interaction. However, the majority of the scientific studies published do not evaluate the ROS production by commensals bacteria. In this context we recently showed that Lactobacillus johnsonii N6.2, a strain of probiotic value, modulates the activity of the critical enzymes 2,3-indoleamine dioxygenase via H2O2 production. L. johnsonii N6.2 by decreasing IDO activity, is able to modify the tryptophan/kynurenine ratio in the host blood with further systemic consequences. Understanding the mechanisms of H2O2 production is critical to predict the probiotic value of these strains and to optimize bacterial biomass production in industrial processes. We performed a transcriptome analysis to identify genes differentially expressed in L. johnsonii N6.2 cells collected from cultures grown under different aeration conditions. Herein we described the biochemical characteristics of a heterodimeric FMN reductase (FRedA/B) whose in vitro activity is controlled by LjPAS protein with a typical Per-Arnst-Sim (PAS) sensor domain. Interestingly, LjPAS is fused to the FMN reductase domains in other lactobacillaceae. In L. johnsonii, LjPAS is encoded by an independent gene which expression is repressed under anaerobic conditions (>3 fold). Purified LjPAS was able to slow down the FRedA/B initial activity rate when the holoenzyme precursors (FredA, FredB, and FMN) were mixed in vitro. Altogether the results obtained suggest that LjPAS module regulates the H2O2 production helping the cells to minimize oxidative stress in response to environmental conditions.

Multivalent binding of formin-binding protein 21 (FBP21)-tandem-WW domains fosters protein recognition in the pre-spliceosome.

PubMed

Klippel, Stefan; Wieczorek, Marek; Schümann, Michael; Krause, Eberhard; Marg, Berenice; Seidel, Thorsten; Meyer, Tim; Knapp, Ernst-Walter; Freund, Christian

2011-11-04

The high abundance of repetitive but nonidentical proline-rich sequences in spliceosomal proteins raises the question of how these known interaction motifs recruit their interacting protein domains. Whereas complex formation of these adaptors with individual motifs has been studied in great detail, little is known about the binding mode of domains arranged in tandem repeats and long proline-rich sequences including multiple motifs. Here we studied the interaction of the two adjacent WW domains of spliceosomal protein FBP21 with several ligands of different lengths and composition to elucidate the hallmarks of multivalent binding for this class of recognition domains. First, we show that many of the proteins that define the cellular proteome interacting with FBP21-WW1-WW2 contain multiple proline-rich motifs. Among these is the newly identified binding partner SF3B4. Fluorescence resonance energy transfer (FRET) analysis reveals the tandem-WW domains of FBP21 to interact with splicing factor 3B4 (SF3B4) in nuclear speckles where splicing takes place. Isothermal titration calorimetry and NMR shows that the tandem arrangement of WW domains and the multivalency of the proline-rich ligands both contribute to affinity enhancement. However, ligand exchange remains fast compared with the NMR time scale. Surprisingly, a N-terminal spin label attached to a bivalent ligand induces NMR line broadening of signals corresponding to both WW domains of the FBP21-WW1-WW2 protein. This suggests that distinct orientations of the ligand contribute to a delocalized and semispecific binding mode that should facilitate search processes within the spliceosome.

Mechanism of Mediator recruitment by tandem Gcn4 activation domains and three Gal11 activator-binding domains.

PubMed

Herbig, Eric; Warfield, Linda; Fish, Lisa; Fishburn, James; Knutson, Bruce A; Moorefield, Beth; Pacheco, Derek; Hahn, Steven

2010-05-01

Targets of the tandem Gcn4 acidic activation domains in transcription preinitiation complexes were identified by site-specific cross-linking. The individual Gcn4 activation domains cross-link to three common targets, Gal11/Med15, Taf12, and Tra1, which are subunits of four conserved coactivator complexes, Mediator, SAGA, TFIID, and NuA4. The Gcn4 N-terminal activation domain also cross-links to the Mediator subunit Sin4/Med16. The contribution of the two Gcn4 activation domains to transcription was gene specific and varied from synergistic to less than additive. Gcn4-dependent genes had a requirement for Gal11 ranging from 10-fold dependence to complete Gal11 independence, while the Gcn4-Taf12 interaction did not significantly contribute to the expression of any gene studied. Complementary methods identified three conserved Gal11 activator-binding domains that bind each Gcn4 activation domain with micromolar affinity. These Gal11 activator-binding domains contribute additively to transcription activation and Mediator recruitment at Gcn4- and Gal11-dependent genes. Although we found that the conserved Gal11 KIX domain contributes to Gal11 function, we found no evidence of specific Gcn4-KIX interaction and conclude that the Gal11 KIX domain does not function by specific interaction with Gcn4. Our combined results show gene-specific coactivator requirements, a surprising redundancy in activator-target interactions, and an activator-coactivator interaction mediated by multiple low-affinity protein-protein interactions.

The structure and dynamics of tandem WW domains in a negative regulator of notch signaling, Suppressor of deltex.

PubMed

Fedoroff, Oleg Y; Townson, Sharon A; Golovanov, Alexander P; Baron, Martin; Avis, Johanna M

2004-08-13

WW domains mediate protein recognition, usually though binding to proline-rich sequences. In many proteins, WW domains occur in tandem arrays. Whether or how individual domains within such arrays cooperate to recognize biological partners is, as yet, poorly characterized. An important question is whether functional diversity of different WW domain proteins is reflected in the structural organization and ligand interaction mechanisms of their multiple domains. We have determined the solution structure and dynamics of a pair of WW domains (WW3-4) from a Drosophila Nedd4 family protein called Suppressor of deltex (Su(dx)), a regulator of Notch receptor signaling. We find that the binding of a type 1 PPPY ligand to WW3 stabilizes the structure with effects propagating to the WW4 domain, a domain that is not active for ligand binding. Both WW domains adopt the characteristic triple-stranded beta-sheet structure, and significantly, this is the first example of a WW domain structure to include a domain (WW4) lacking the second conserved Trp (replaced by Phe). The domains are connected by a flexible linker, which allows a hinge-like motion of domains that may be important for the recognition of functionally relevant targets. Our results contrast markedly with those of the only previously determined three-dimensional structure of tandem WW domains, that of the rigidly oriented WW domain pair from the RNA-splicing factor Prp40. Our data illustrate that arrays of WW domains can exhibit a variety of higher order structures and ligand interaction mechanisms.

Multivalent Binding of Formin-binding Protein 21 (FBP21)-Tandem-WW Domains Fosters Protein Recognition in the Pre-spliceosome*

PubMed Central

Klippel, Stefan; Wieczorek, Marek; Schümann, Michael; Krause, Eberhard; Marg, Berenice; Seidel, Thorsten; Meyer, Tim; Knapp, Ernst-Walter; Freund, Christian

2011-01-01

The high abundance of repetitive but nonidentical proline-rich sequences in spliceosomal proteins raises the question of how these known interaction motifs recruit their interacting protein domains. Whereas complex formation of these adaptors with individual motifs has been studied in great detail, little is known about the binding mode of domains arranged in tandem repeats and long proline-rich sequences including multiple motifs. Here we studied the interaction of the two adjacent WW domains of spliceosomal protein FBP21 with several ligands of different lengths and composition to elucidate the hallmarks of multivalent binding for this class of recognition domains. First, we show that many of the proteins that define the cellular proteome interacting with FBP21-WW1-WW2 contain multiple proline-rich motifs. Among these is the newly identified binding partner SF3B4. Fluorescence resonance energy transfer (FRET) analysis reveals the tandem-WW domains of FBP21 to interact with splicing factor 3B4 (SF3B4) in nuclear speckles where splicing takes place. Isothermal titration calorimetry and NMR shows that the tandem arrangement of WW domains and the multivalency of the proline-rich ligands both contribute to affinity enhancement. However, ligand exchange remains fast compared with the NMR time scale. Surprisingly, a N-terminal spin label attached to a bivalent ligand induces NMR line broadening of signals corresponding to both WW domains of the FBP21-WW1-WW2 protein. This suggests that distinct orientations of the ligand contribute to a delocalized and semispecific binding mode that should facilitate search processes within the spliceosome. PMID:21917930

Structural features and ligand binding properties of tandem WW domains from YAP and TAZ, nuclear effectors of the Hippo pathway.

PubMed

Webb, Claire; Upadhyay, Abhishek; Giuntini, Francesca; Eggleston, Ian; Furutani-Seiki, Makoto; Ishima, Rieko; Bagby, Stefan

2011-04-26

The paralogous multifunctional adaptor proteins YAP and TAZ are the nuclear effectors of the Hippo pathway, a central mechanism of organ size control and stem cell self-renewal. WW domains, mediators of protein-protein interactions, are essential for YAP and TAZ function, enabling interactions with PPxY motifs of numerous partner proteins. YAP has single and double WW domain isoforms (YAP1 and YAP2) whereas only a single WW domain isoform of TAZ has been described to date. Here we identify the first example of a double WW domain isoform of TAZ. Using NMR, we have characterized conformational features and peptide binding of YAP and TAZ tandem WW domains (WW1-WW2). The solution structure of YAP WW2 confirms that it has a canonical three-stranded antiparallel β-sheet WW domain fold. While chemical shift-based analysis indicates that the WW domains in the tandem WW pairs retain the characteristic WW domain fold, 15N relaxation data show that, within the respective WW pairs, YAP WW1 and both WW1 and WW2 of TAZ undergo conformational exchange. 15N relaxation data also indicate that the linker between the WW domains is flexible in both YAP and TAZ. Within both YAP and TAZ tandem WW pairs, WW1 and WW2 bind single PPxY-containing peptide ligand concurrently and noncooperatively with sub-mM affinity. YAP and TAZ WW1-WW2 bind a dual PPxY-containing peptide with approximately 6-fold higher affinity. Our results indicate that both WW domains in YAP and TAZ are functional and capable of enhanced affinity binding to multi-PPxY partner proteins such as LATS1, ErbB4, and AMOT.

Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain - A fragment based approach.

PubMed

Upadhyay, Anup K; Judge, Russell A; Li, Leiming; Pithawalla, Ron; Simanis, Justin; Bodelle, Pierre M; Marin, Violeta L; Henry, Rodger F; Petros, Andrew M; Sun, Chaohong

2018-06-01

The tandem TUDOR domains present in the non-catalytic C-terminal half of the KDM4A, 4B and 4C enzymes play important roles in regulating their chromatin localizations and substrate specificities. They achieve this regulatory role by binding to different tri-methylated lysine residues on histone H3 (H3-K4me3, H3-K23me3) and histone H4 (H4-K20me3) depending upon the specific chromatin environment. In this work, we have used a 2D-NMR based fragment screening approach to identify a novel fragment (1a), which binds to the KDM4A-TUDOR domain and shows modest competition with H3-K4me3 binding in biochemical as well as in vitro cell based assays. A co-crystal structure of KDM4A TUDOR domain in complex with 1a shows that the fragment binds stereo-specifically to the methyl lysine binding pocket forming a network of strong hydrogen bonds and hydrophobic interactions. We anticipate that the fragment 1a can be further developed into a novel allosteric inhibitor of the KDM4 family of enzymes through targeting their C-terminal tandem TUDOR domain. Copyright © 2018 Elsevier Ltd. All rights reserved.

Production of novel recombinant single-domain antibodies against tandem repeat region of MUC1 mucin.

PubMed

Rahbarizadeh, F; Rasaee, M J; Forouzandeh Moghadam, M; Allameh, A A; Sadroddiny, E

2004-06-01

Recently, the existence of "heavy-chain" antibody in Camelidae has been described. However, as yet there is no data on the binding of this type of antibody to peptides. In addition, there was not any report of production of single-domain antibodies in two-humped camels (Camelus bactrianus). In the present study, these questions are addressed. We showed the feasibility of immunizing old world camels, cloning the repertoire of the variable domain of their heavy-chain antibodies, panning and selection, leading to the successful identification of minimum-sized antigen binders. Antigen-specific fragments of the heavy-chain IgGs (V(HH)) are of great interest in biotechnology because they are very stable, highly soluble, and react specifically and with high affinity to the antigens. In this study, we immunized two camels (Camelus dromedarius and Camelus bactrianus) with homogenized cancerous tissues, synthetic peptide, and human milk fat globule membrane (HMFG), and generated two V(HH) libraries displayed on phage particles. Some single-domain antibody fragments have been isolated that specifically recognize the tandem repeat region of MUC1. The camels' single-domain V(HH) harbor the original, intact antigen binding site and reacted specifically and with high affinity to the tandem repeat region of MUC1. Indeed soluble, specific antigen binders and good affinities (in the range of 0.2 x 10(9) M(-1) to 0.6 x 10(9) M(-1)) were identified from these libraries. This is the first example of the isolation of camel anti-peptide V(HH) domains.

Lateral diffusion of proteins on supported lipid bilayers: additive friction of synaptotagmin 7 C2A-C2B tandem domains.

PubMed

Vasquez, Joseph K; Chantranuvatana, Kan; Giardina, Daniel T; Coffman, Matthew D; Knight, Jefferson D

2014-12-23

The synaptotagmin (Syt) family of proteins contains tandem C2 domains, C2A and C2B, which bind membranes in the presence of Ca(2+) to trigger vesicle fusion during exocytosis. Despite recent progress, the role and extent of interdomain interactions between C2A and C2B in membrane binding remain unclear. To test whether the two domains interact on a planar lipid bilayer (i.e., experience thermodynamic interdomain contacts), diffusion of fluorescent-tagged C2A, C2B, and C2AB domains from human Syt7 was measured using total internal reflection fluorescence microscopy with single-particle tracking. The C2AB tandem exhibits a lateral diffusion constant approximately half the value of the isolated single domains and does not change when additional residues are engineered into the C2A-C2B linker. This is the expected result if C2A and C2B are separated when membrane-bound; theory predicts that C2AB diffusion would be faster if the two domains were close enough together to have interdomain contact. Stopped-flow measurements of membrane dissociation kinetics further support an absence of interdomain interactions, as dissociation kinetics of the C2AB tandem remain unchanged when rigid or flexible linker extensions are included. Together, the results suggest that the two C2 domains of Syt7 bind independently to planar membranes, in contrast to reported interdomain cooperativity in Syt1.

Crystal structure of tandem type III fibronectin domains from Drosophila neuroglian at 2.0 A.

PubMed

Huber, A H; Wang, Y M; Bieber, A J; Bjorkman, P J

1994-04-01

We report the crystal structure of two adjacent fibronectin type III repeats from the Drosophila neural cell adhesion molecule neuroglian. Each domain consists of two antiparallel beta sheets and is folded topologically identically to single fibronectin type III domains from the extracellular matrix proteins tenascin and fibronectin. beta bulges and left-handed polyproline II helices disrupt the regular beta sheet structure of both neuroglian domains. The hydrophobic interdomain interface includes a metal-binding site, presumably involved in stabilizing the relative orientation between domains and predicted by sequence comparision to be present in the vertebrate homolog molecule L1. The neuroglian domains are related by a near perfect 2-fold screw axis along the longest molecular dimension. Using this relationship, a model for arrays of tandem fibronectin type III repeats in neuroglian and other molecules is proposed.

Tandem SAM Domain Structure of Human Caskin1: A Presynaptic, Self-Assembling Scaffold for CASK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stafford, Ryan L.; Hinde, Elizabeth; Knight, Mary Jane

2012-02-07

The synaptic scaffolding proteins CASK and Caskin1 are part of the fibrous mesh of proteins that organize the active zones of neural synapses. CASK binds to a region of Caskin1 called the CASK interaction domain (CID). Adjacent to the CID, Caskin1 contains two tandem sterile a motif (SAM) domains. Many SAM domains form polymers so they are good candidates for forming the fibrous structures seen in the active zone. We show here that the SAM domains of Caskin1 form a new type of SAM helical polymer. The Caskin1 polymer interface exhibits a remarkable segregation of charged residues, resulting in amore » high sensitivity to ionic strength in vitro. The Caskin1 polymers can be decorated with CASK proteins, illustrating how these proteins may work together to organize the cytomatrix in active zones.« less

ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae.

PubMed

Albornos, Lucía; Martín, Ignacio; Iglesias, Rebeca; Jiménez, Teresa; Labrador, Emilia; Dopico, Berta

2012-11-07

Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40

ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae

PubMed Central

2012-01-01

Background Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. Results ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. Conclusions We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the

An ice-binding and tandem beta-sandwich domain-containing protein in Shewanella frigidimarina is a potential new type of ice adhesin.

PubMed

Vance, Tyler D R; Graham, Laurie A; Davies, Peter L

2018-04-01

Out of the dozen different ice-binding protein (IBP) structures known, the DUF3494 domain is the most widespread, having been passed many times between prokaryotic and eukaryotic microorganisms by horizontal gene transfer. This ~25-kDa β-solenoid domain with an adjacent parallel α-helix is most commonly associated with an N-terminal secretory signal peptide. However, examples of the DUF3494 domain preceded by tandem Bacterial Immunoglobulin-like (BIg) domains are sometimes found, though uncharacterized. Here, we present one such protein (SfIBP_1) from the Antarctic bacterium Shewanella frigidimarina. We have confirmed and characterized the ice-binding activity of its ice-binding domain using thermal hysteresis measurements, fluorescent ice plane affinity analysis, and ice recrystallization inhibition assays. X-ray crystallography was used to solve the structure of the SfIBP_1 ice-binding domain, to further characterize its ice-binding surface and unique method of stabilizing or 'capping' the ends of the solenoid structure. The latter is formed from the interaction of two loops mediated by a combination of tandem prolines and electrostatic interactions. Furthermore, given their domain architecture and membrane association, we propose that these BIg-containing DUF3494 IBPs serve as ice-binding adhesion proteins that are capable of adsorbing their host bacterium onto ice. Submitted new structure to the Protein Data Bank (PDB: 6BG8). © 2018 Federation of European Biochemical Societies.

A history of US Army PAs.

PubMed

Chalupa, Robyn L; Marble, W Sanders

2017-11-01

The US military has a long tradition of using physician assistants (PAs). The Army began using PAs in 1971 in an effort to supplement the physicians and surgeons in the medical corps. As their numbers grew, PAs gradually replaced general medical officers assigned to battalions. Later, specialty positions developed in aviation medicine, orthopedics, and emergency medicine. The need for a PA serving as an adviser in the major commands slowly developed at all levels of leadership. In 2015, the Army removed limitations on female PAs assigned to combat units. PAs lead in tactical and clinical settings, filling command roles, senior clinical positions, and administrative leadership roles.

Histopathological examination of nail clippings using PAS staining (HPE-PAS): gold standard in diagnosis of Onychomycosis.

PubMed

Jeelani, Shazia; Ahmed, Qazi Masood; Lanker, Audil Mohmad; Hassan, Iffat; Jeelani, Nasir; Fazili, Tawheeda

2015-01-01

Onychomycosis is fungal infection of one or more of the nail units. However, because fungi cause only about half of all nail dystrophies, the use of appropriate diagnostic techniques is important to ensure correct diagnosis and treatment. Aim of the present study was to compare direct microscopy, culture and HPE-PAS for diagnosis of onychomycosis by evaluating their sensitivity and various other relevant statistical parameters. A prospective, hospital-based, cross-sectional study was conducted on 216 patients with a high degree of clinical suspicion of onychomycosis. Nail specimens were evaluated using three diagnostic methods, i.e. direct microscopy using 20% Potassium hydroxide (KOH) & 40% Di-methyl-suphoxide (DMSO), culture and histopathological examination using PAS stain (HPE-PAS). Of 216 patients direct microscopy was positive in 138 (63.9%), culture in 147 (68%) and HPE-PAS in 164 patients (76%). One hundred and seventy-nine patients fitted into the criteria set for confirmed diagnosis of onychomycosis. Using this as a denominator; direct microscopy, culture and HPE-PAS had sensitivities of 77.1%, 70% and 91.6% respectively. Also, HPE-PAS showed the highest sensitivity of 94.7% in 19 cases with prediagnostic antimycotic treatment compared to direct microscopy (42.1%) or culture (57.9%). HPE-PAS shows high sensitivity for diagnosis of onychomycosis and can be considered as a gold standard in the diagnosis of onychomycosis. © 2014 Blackwell Verlag GmbH.

The central domain of bovine submaxillary mucin consists of over 50 tandem repeats of 329 amino acids. Chromosomal localization of the BSM1 gene and relations to ovine and porcine counterparts.

PubMed

Jiang, W; Gupta, D; Gallagher, D; Davis, S; Bhavanandan, V P

2000-04-01

We previously elucidated five distinct protein domains (I-V) for bovine submaxillary mucin, which is encoded by two genes, BSM1 and BSM2. Using Southern blot analysis, genomic cloning and sequencing of the BSM1 gene, we now show that the central domain (V) consists of approximately 55 tandem repeats of 329 amino acids and that domains III-V are encoded by a 58.4-kb exon, the largest exon known for all genes to date. The BSM1 gene was mapped by fluorescence in situ hybridization to the proximal half of chromosome 5 at bands q2. 2-q2.3. The amino-acid sequence of six tandem repeats (two full and four partial) were found to have only 92-94% identities. We propose that the variability in the amino-acid sequences of the mucin tandem repeat is important for generating the combinatorial library of saccharides that are necessary for the protective function of mucins. The deduced peptide sequences of the central domain match those determined from the purified bovine submaxillary mucin and also show 68-94% identity to published peptide sequences of ovine submaxillary mucin. This indicates that the core protein of ovine submaxillary mucin is closely related to that of bovine submaxillary mucin and contains similar tandem repeats in the central domain. In contrast, the central domain of porcine submaxillary mucin is reported to consist of 81-amino-acid tandem repeats. However, both bovine submaxillary mucin and porcine submaxillary mucin contain similar N-terminal and C-terminal domains and the corresponding genes are in the conserved linkage regions of the respective genomes.

Structural Basis of Actin Filament Nucleation by Tandem W Domains

PubMed Central

Chen, Xiaorui; Ni, Fengyun; Tian, Xia; Kondrashkina, Elena; Wang, Qinghua; Ma, Jianpeng

2013-01-01

SUMMARY Spontaneous nucleation of actin is very inefficient in cells. To overcome this barrier, cells have evolved a set of actin filament nucleators to promote rapid nucleation and polymerization in response to specific stimuli. However, the molecular mechanism of actin nucleation remains poorly understood. This is hindered largely by the fact that actin nucleus, once formed, rapidly polymerizes into filament, thus making it impossible to capture stable multisubunit actin nucleus. Here, we report an effective double-mutant strategy to stabilize actin nucleus by preventing further polymerization. Employing this strategy, we solved the crystal structure of AMPPNP-actin in complex with the first two tandem W domains of Cordon-bleu (Cobl), a potent actin filament nucleator. Further sequence comparison and functional studies suggest that the nucleation mechanism of Cobl is probably shared by the p53 cofactor JMY, but not Spire. Moreover, the double-mutant strategy opens the way for atomic mechanistic study of actin nucleation and polymerization. PMID:23727244

Partners in crime: The role of tandem modules in gene transcription.

PubMed

Sharma, Rajal; Zhou, Ming-Ming

2015-09-01

Histones and their modifications play an important role in the regulation of gene transcription. Numerous modifications, such as acetylation, phosphorylation, methylation, ubiquitination, and SUMOylation, have been described. These modifications almost always co-occur and thereby increase the combinatorial complexity of post-translational modification detection. The domains that recognize these histone modifications often occur in tandem in the context of larger proteins and complexes. The presence of multiple modifications can positively or negatively regulate the binding of these tandem domains, influencing downstream cellular function. Alternatively, these tandem domains can have novel functions from their independent parts. Here we summarize structural and functional information known about major tandem domains and their histone binding properties. An understanding of these interactions is key for the development of epigenetic therapy. © 2015 The Protein Society.

Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Jun; Wu, Ruiying; Adkins, Joshua N.

2014-09-16

In the F-family of conjugative plasmids, TraJ is an essential transcriptional activator of the tra operon that encodes most of the proteins required for conjugation. Here we report for the first time the X-ray crystal structures of the TraJ N-terminal regions from the prototypic F plasmid (TraJF11-130) and from the Salmonella virulence plasmid pSLT (TraJpSLT 1-128). Both proteins form similar homodimeric Per-ARNT-Sim (PAS) fold structures. Mutational analysis reveals that the observed dimeric interface is critical for TraJF transcriptional activation, indicating that dimerization of TraJ is required for its in vivo function. An artificial ligand (oxidized dithiothreitol) occupies a cavity inmore » the TraJF dimer interface, while a smaller cavity in corresponding region of the TraJpSLT structure lacks a ligand. Gas chromatography/mass spectrometry-electron ionization analysis of dithiothreitol-free TraJF suggests indole may be the natural TraJ ligand; however, disruption of the indole biosynthetic pathway does not affect TraJF function. Heterologous PAS domains from pSLT and R100 TraJ can functionally replace the TraJF PAS domain, suggesting that TraJ allelic specificity is mediated by the region C-terminal to the PAS domain.« less

Ford Partnership for Advanced Studies (Ford PAS)

ERIC Educational Resources Information Center

Carrier, Cheryl

2006-01-01

This article features the Ford Partnership for Advanced Studies (Ford PAS) program that helps students gain knowledge about real-life business issues. Ford PAS is an educational program that combines college-prep academics with the critical 21st century skills students will need to succeed in college and in the workplace. The Ford PAS program uses…

Multiple Interactions between Cytoplasmic Domains Regulate Slow Deactivation of Kv11.1 Channels*

PubMed Central

Ng, Chai Ann; Phan, Kevin; Hill, Adam P.; Vandenberg, Jamie I.; Perry, Matthew D.

2014-01-01

The intracellular domains of many ion channels are important for fine-tuning their gating kinetics. In Kv11.1 channels, the slow kinetics of channel deactivation, which are critical for their function in the heart, are largely regulated by the N-terminal N-Cap and Per-Arnt-Sim (PAS) domains, as well as the C-terminal cyclic nucleotide-binding homology (cNBH) domain. Here, we use mutant cycle analysis to probe for functional interactions between the N-Cap/PAS domains and the cNBH domain. We identified a specific and stable charge-charge interaction between Arg56 of the PAS domain and Asp803 of the cNBH domain, as well an additional interaction between the cNBH domain and the N-Cap, both of which are critical for maintaining slow deactivation kinetics. Furthermore, we found that positively charged arginine residues within the disordered region of the N-Cap interact with negatively charged residues of the C-linker domain. Although this interaction is likely more transient than the PAS-cNBD interaction, it is strong enough to stabilize the open conformation of the channel and thus slow deactivation. These findings provide novel insights into the slow deactivation mechanism of Kv11.1 channels. PMID:25074935

Structural Studies of the Tandem Tudor Domains of Fragile X Mental Retardation Related Proteins FXR1 and FXR2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams-Cioaba, Melanie A.; Guo, Yahong; Bian, ChuanBing

Expansion of the CGG trinucleotide repeat in the 5'-untranslated region of the FMR1, fragile X mental retardation 1, gene results in suppression of protein expression for this gene and is the underlying cause of Fragile X syndrome. In unaffected individuals, the FMRP protein, together with two additional paralogues (Fragile X Mental Retardation Syndrome-related Protein 1 and 2), associates with mRNA to form a ribonucleoprotein complex in the nucleus that is transported to dendrites and spines of neuronal cells. It is thought that the fragile X family of proteins contributes to the regulation of protein synthesis at sites where mRNAs aremore » locally translated in response to stimuli. Here, we report the X-ray crystal structures of the non-canonical nuclear localization signals of the FXR1 and FXR2 autosomal paralogues of FMRP, which were determined at 2.50 and 1.92 {angstrom}, respectively. The nuclear localization signals of the FXR1 and FXR2 comprise tandem Tudor domain architectures, closely resembling that of UHRF1, which is proposed to bind methylated histone H3K9. The FMRP, FXR1 and FXR2 proteins comprise a small family of highly conserved proteins that appear to be important in translational regulation, particularly in neuronal cells. The crystal structures of the N-terminal tandem Tudor domains of FXR1 and FXR2 revealed a conserved architecture with that of FMRP. Biochemical analysis of the tandem Tudor doamins reveals their ability to preferentially recognize trimethylated peptides in a sequence-specific manner.« less

NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Dalei; Su, Xiaoyu; Potluri, Nalini

Here, the neuronal PAS domain proteins NPAS1 and NPAS3 are members of the basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) family, and their genetic deficiencies are linked to a variety of human psychiatric disorders including schizophrenia, autism spectrum disorders and bipolar disease. NPAS1 and NPAS3 must each heterodimerize with the aryl hydrocarbon receptor nuclear translocator (ARNT), to form functional transcription complexes capable of DNA binding and gene regulation. Here we examined the crystal structures of multi-domain NPAS1-ARNT and NPAS3-ARNT-DNA complexes, discovering each to contain four putative ligand-binding pockets. Through expanded architectural comparisons between these complexes and HIF-1α-ARNT, HIF-2α-ARNT and CLOCK-BMAL1, we show the widermore » mammalian bHLH-PAS family is capable of multi-ligand-binding and presents as an ideal class of transcription factors for direct targeting by small-molecule drugs.« less

NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors

DOE PAGES

Wu, Dalei; Su, Xiaoyu; Potluri, Nalini; ...

2016-10-26

Here, the neuronal PAS domain proteins NPAS1 and NPAS3 are members of the basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) family, and their genetic deficiencies are linked to a variety of human psychiatric disorders including schizophrenia, autism spectrum disorders and bipolar disease. NPAS1 and NPAS3 must each heterodimerize with the aryl hydrocarbon receptor nuclear translocator (ARNT), to form functional transcription complexes capable of DNA binding and gene regulation. Here we examined the crystal structures of multi-domain NPAS1-ARNT and NPAS3-ARNT-DNA complexes, discovering each to contain four putative ligand-binding pockets. Through expanded architectural comparisons between these complexes and HIF-1α-ARNT, HIF-2α-ARNT and CLOCK-BMAL1, we show the widermore » mammalian bHLH-PAS family is capable of multi-ligand-binding and presents as an ideal class of transcription factors for direct targeting by small-molecule drugs.« less

Coiled-Coil Antagonism Regulates Activity of Venus Flytrap-Domain-Containing Sensor Kinases of the BvgS Family

PubMed Central

Lesne, Elodie; Dupré, Elian; Lensink, Marc F.; Locht, Camille

2018-01-01

ABSTRACT Bordetella pertussis controls the expression of its virulence regulon through the two-component system BvgAS. BvgS is a prototype for a family of multidomain sensor kinases. In BvgS, helical linkers connect periplasmic Venus flytrap (VFT) perception domains to a cytoplasmic Per-Arnt-Sim (PAS) domain and the PAS domain to the dimerization/histidine phosphotransfer (DHp) domain of the kinase. The two linkers can adopt coiled-coil structures but cannot do so simultaneously. The first linker forms a coiled coil in the kinase mode and the second in the phosphatase mode, with the other linker in both cases showing an increase in dynamic behavior. The intervening PAS domain changes its quaternary structure between the two modes. In BvgS homologues without a PAS domain, a helical “X” linker directly connects the VFT and DHp domains. Here, we used BvgS as a platform to characterize regulation in members of the PAS-less subfamily. BvgS chimeras of homologues with natural X linkers displayed various regulation phenotypes. We identified two distinct coiled-coil registers in the N- and C-terminal portions of the X linkers. Stable coil formation in the C-terminal moiety determines the phosphatase mode, similarly to BvgS; in contrast, coil formation in the N-terminal moiety along the other register leads to the kinase mode. Thus, antagonism between two registers in the VFT-DHp linker forms the basis for activity regulation in the absence of the PAS domain. The N and C moieties of the X linker play roles similar to those played by the two independent linkers in sensor kinases with a PAS domain, providing a unified mechanism of regulation for the entire family. PMID:29487240

Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant

NASA Astrophysics Data System (ADS)

Yuchi, Zhiguang; Yuen, Siobhan M. Wong King; Lau, Kelvin; Underhill, Ainsley Q.; Cornea, Razvan L.; Fessenden, James D.; van Petegem, Filip

2015-08-01

Ryanodine receptors (RyRs) form calcium release channels located in the membranes of the sarcoplasmic and endoplasmic reticulum. RyRs play a major role in excitation-contraction coupling and other Ca2+-dependent signalling events, and consist of several globular domains that together form a large assembly. Here we describe the crystal structures of the SPRY1 and tandem-repeat domains at 1.2-1.5 Å resolution, which reveal several structural elements not detected in recent cryo-EM reconstructions of RyRs. The cryo-EM studies disagree on the position of SPRY domains, which had been proposed based on homology modelling. Computational docking of the crystal structures, combined with FRET studies, show that the SPRY1 domain is located next to FK506-binding protein (FKBP). Molecular dynamics flexible fitting and mutagenesis experiments suggest a hydrophobic cluster within SPRY1 that is crucial for FKBP binding. A RyR1 disease mutation, N760D, appears to directly impact FKBP binding through interfering with SPRY1 folding.

Mutations in the LRRK2 Roc-COR tandem domain link Parkinson's disease to Wnt signalling pathways.

PubMed

Sancho, Rosa M; Law, Bernard M H; Harvey, Kirsten

2009-10-15

Mutations in PARK8, encoding LRRK2, are the most common known cause of Parkinson's disease. The LRRK2 Roc-COR tandem domain exhibits GTPase activity controlling LRRK2 kinase activity via an intramolecular process. We report the interaction of LRRK2 with the dishevelled family of phosphoproteins (DVL1-3), key regulators of Wnt (Wingless/Int) signalling pathways important for axon guidance, synapse formation and neuronal maintenance. Interestingly, DVLs can interact with and mediate the activation of small GTPases with structural similarity to the LRRK2 Roc domain. The LRRK2 Roc-COR domain and the DVL1 DEP domain were necessary and sufficient for LRRK2-DVL1 interaction. Co-expression of DVL1 increased LRRK2 steady-state protein levels, an effect that was dependent on the DEP domain. Strikingly, LRRK2-DVL1-3 interactions were disrupted by the familial PARK8 mutation Y1699C, whereas pathogenic mutations at residues R1441 and R1728 strengthened LRRK2-DVL1 interactions. Co-expression of DVL1 with LRRK2 in mammalian cells resulted in the redistribution of LRRK2 to typical cytoplasmic DVL1 aggregates in HEK293 and SH-SY5Y cells and co-localization in neurites and growth cones of differentiated dopaminergic SH-SY5Y cells. This is the first report of the modulation of a key LRRK2-accessory protein interaction by PARK8 Roc-COR domain mutations segregating with Parkinson's disease. Since the DVL1 DEP domain is known to be involved in the regulation of small GTPases, we propose that: (i) DVLs may influence LRRK2 GTPase activity, and (ii) Roc-COR domain mutations modulating LRRK2-DVL interactions indirectly influence kinase activity. Our findings also link LRRK2 to Wnt signalling pathways, suggesting novel pathogenic mechanisms and new targets for genetic analysis in Parkinson's disease.

Female PAs-Where are we today?

PubMed

Curtis, L Gail; Dobbs, Lauren; Hildebrandt, Carol A

2017-09-01

As the physician assistant (PA) profession celebrates its 50th birthday, we can be proud of the gains our profession has accomplished. However, despite the positive reports of job satisfaction, a marked increase in female PA leaders, and overall gains in PA compensation, a significant wage gap remains between male and female PAs. The PA profession is flourishing but it is time female PAs are paid equitably.

Solution structure and function of the "tandem inactivation domain" of the neuronal A-type potassium channel Kv1.4.

PubMed

Wissmann, Ralph; Bildl, Wolfgang; Oliver, Dominik; Beyermann, Michael; Kalbitzer, Hans-Robert; Bentrop, Detlef; Fakler, Bernd

2003-05-02

Cumulative inactivation of voltage-gated (Kv) K(+) channels shapes the presynaptic action potential and determines timing and strength of synaptic transmission. Kv1.4 channels exhibit rapid "ball-and-chain"-type inactivation gating. Different from all other Kvalpha subunits, Kv1.4 harbors two inactivation domains at its N terminus. Here we report the solution structure and function of this "tandem inactivation domain" using NMR spectroscopy and patch clamp recordings. Inactivation domain 1 (ID1, residues 1-38) consists of a flexible N terminus anchored at a 5-turn helix, whereas ID2 (residues 40-50) is a 2.5-turn helix made up of small hydrophobic amino acids. Functional analysis suggests that only ID1 may work as a pore-occluding ball domain, whereas ID2 most likely acts as a "docking domain" that attaches ID1 to the cytoplasmic face of the channel. Deletion of ID2 slows inactivation considerably and largely impairs cumulative inactivation. Together, the concerted action of ID1 and ID2 may promote rapid inactivation of Kv1.4 that is crucial for the channel function in short term plasticity.

Modification by covalent reaction or oxidation of cysteine residues in the tandem-SH2 domains of ZAP-70 and Syk can block phosphopeptide binding.

PubMed

Visperas, Patrick R; Winger, Jonathan A; Horton, Timothy M; Shah, Neel H; Aum, Diane J; Tao, Alyssa; Barros, Tiago; Yan, Qingrong; Wilson, Christopher G; Arkin, Michelle R; Weiss, Arthur; Kuriyan, John

2015-01-01

Zeta-chain associated protein of 70 kDa (ZAP-70) and spleen tyrosine kinase (Syk) are non-receptor tyrosine kinases that are essential for T-cell and B-cell antigen receptor signalling respectively. They are recruited, via their tandem-SH2 (Src-homology domain 2) domains, to doubly phosphorylated immunoreceptor tyrosine-based activation motifs (ITAMs) on invariant chains of immune antigen receptors. Because of their critical roles in immune signalling, ZAP-70 and Syk are targets for the development of drugs for autoimmune diseases. We show that three thiol-reactive small molecules can prevent the tandem-SH2 domains of ZAP-70 and Syk from binding to phosphorylated ITAMs. We identify a specific cysteine residue in the phosphotyrosine-binding pocket of each protein (Cys39 in ZAP-70, Cys206 in Syk) that is necessary for inhibition by two of these compounds. We also find that ITAM binding to ZAP-70 and Syk is sensitive to the presence of H2O2 and these two cysteine residues are also necessary for inhibition by H2O2. Our findings suggest a mechanism by which the reactive oxygen species generated during responses to antigen could attenuate signalling through these kinases and may also inform the development of ZAP-70 and Syk inhibitors that bind covalently to their SH2 domains.

Rapid qualitative and quantitative analysis of proanthocyanidin oligomers and polymers by ultra-performance liquid chromatography – tandem mass spectrometry (UPLC-MS/MS)

USDA-ARS?s Scientific Manuscript database

We developed a rapid method with ultra-performance liquid chromatography – tandem mass spectrometry (UPLC-MS/MS) for the qualitative and quantitative analysis of plant proanthocyanidins (PAs) directly from crude plant extracts. The method utilizes a range of cone voltages to achieve the depolymeriza...

Structure and Specificity of a Binary Tandem Domain F-Lectin from Striped Bass (Morone saxatilis)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bianchet, M.; Odom, E; Vasta, J

2010-01-01

The plasma of the striped bass Morone saxatilis contains a fucose-specific lectin (MsaFBP32) that consists of two F-type carbohydrate recognition domains (CRDs) in tandem. The crystal structure of the complex of MsaFBP32 with l-fucose reported here shows a cylindrical 81-A-long and 60-A-wide trimer divided into two globular halves: one containing N-terminal CRDs (N-CRDs) and the other containing C-terminal CRDs (C-CRDs). The resulting binding surfaces at the opposite ends of the cylindrical trimer have the potential to cross-link cell surface or humoral carbohydrate ligands. The N-CRDs and C-CRDs of MsaFBP32 exhibit significant structural differences, suggesting that they recognize different glycans. Analysismore » of the carbohydrate binding sites provides the structural basis for the observed specificity of MsaFBP32 for simple carbohydrates and suggests that the N-CRD recognizes more complex fucosylated oligosaccharides and with a relatively higher avidity than the C-CRD. Modeling of MsaFBP32 complexed with fucosylated glycans that are widely distributed in prokaryotes and eukaryotes rationalizes the observation that binary tandem CRD F-type lectins function as opsonins by cross-linking 'non-self' carbohydrate ligands and 'self' carbohydrate ligands, such as sugar structures displayed by microbial pathogens and glycans on the surface of phagocytic cells from the host.« less

Games network and application to PAs system.

PubMed

Chettaoui, C; Delaplace, F; Manceny, M; Malo, M

2007-02-01

In this article, we present a game theory based framework, named games network, for modeling biological interactions. After introducing the theory, we more precisely describe the methodology to model biological interactions. Then we apply it to the plasminogen activator system (PAs) which is a signal transduction pathway involved in cancer cell migration. The games network theory extends game theory by including the locality of interactions. Each game in a games network represents local interactions between biological agents. The PAs system is implicated in cytoskeleton modifications via regulation of actin and microtubules, which in turn favors cell migration. The games network model has enabled us a better understanding of the regulation involved in the PAs system.

Structure and function of Per-ARNT-Sim domains and their possible role in the life-cycle biology of Trypanosoma cruzi.

PubMed

Rojas-Pirela, Maura; Rigden, Daniel J; Michels, Paul A; Cáceres, Ana J; Concepción, Juan Luis; Quiñones, Wilfredo

2018-01-01

Per-ARNT-Sim (PAS) domains of proteins play important roles as modules for signalling and cellular regulation processes in widely diverse organisms such as Archaea, Bacteria, protists, plants, yeasts, insects and vertebrates. These domains are present in many proteins where they are used as sensors of stimuli and modules for protein interactions. Characteristically, they can bind a broad spectrum of molecules. Such binding causes the domain to trigger a specific cellular response or to make the protein containing the domain susceptible to responding to additional physical or chemical signals. Different PAS proteins have the ability to sense redox potential, light, oxygen, energy levels, carboxylic acids, fatty acids and several other stimuli. Such proteins have been found to be involved in cellular processes such as development, virulence, sporulation, adaptation to hypoxia, circadian cycle, metabolism and gene regulation and expression. Our analysis of the genome of different kinetoplastid species revealed the presence of PAS domains also in different predicted kinases from these protists. Open-reading frames coding for these PAS-kinases are unusually large. In addition, the products of these genes appear to contain in their structure combinations of domains uncommon in other eukaryotes. The physiological significance of PAS domains in these parasites, specifically in Trypanosoma cruzi, is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Mutations in the LRRK2 Roc-COR tandem domain link Parkinson's disease to Wnt signalling pathways

PubMed Central

Sancho, Rosa M.; Law, Bernard M.H.; Harvey, Kirsten

2009-01-01

Mutations in PARK8, encoding LRRK2, are the most common known cause of Parkinson's disease. The LRRK2 Roc-COR tandem domain exhibits GTPase activity controlling LRRK2 kinase activity via an intramolecular process. We report the interaction of LRRK2 with the dishevelled family of phosphoproteins (DVL1-3), key regulators of Wnt (Wingless/Int) signalling pathways important for axon guidance, synapse formation and neuronal maintenance. Interestingly, DVLs can interact with and mediate the activation of small GTPases with structural similarity to the LRRK2 Roc domain. The LRRK2 Roc-COR domain and the DVL1 DEP domain were necessary and sufficient for LRRK2–DVL1 interaction. Co-expression of DVL1 increased LRRK2 steady-state protein levels, an effect that was dependent on the DEP domain. Strikingly, LRRK2–DVL1-3 interactions were disrupted by the familial PARK8 mutation Y1699C, whereas pathogenic mutations at residues R1441 and R1728 strengthened LRRK2–DVL1 interactions. Co-expression of DVL1 with LRRK2 in mammalian cells resulted in the redistribution of LRRK2 to typical cytoplasmic DVL1 aggregates in HEK293 and SH-SY5Y cells and co-localization in neurites and growth cones of differentiated dopaminergic SH-SY5Y cells. This is the first report of the modulation of a key LRRK2-accessory protein interaction by PARK8 Roc-COR domain mutations segregating with Parkinson's disease. Since the DVL1 DEP domain is known to be involved in the regulation of small GTPases, we propose that: (i) DVLs may influence LRRK2 GTPase activity, and (ii) Roc-COR domain mutations modulating LRRK2–DVL interactions indirectly influence kinase activity. Our findings also link LRRK2 to Wnt signalling pathways, suggesting novel pathogenic mechanisms and new targets for genetic analysis in Parkinson's disease. PMID:19625296

Tandem duplications of a degenerated GTP-binding domain at the origin of GTPase receptors Toc159 and thylakoidal SRP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez Torres, Jorge; Maldonado, Monica Alexandra Arias; Chomilier, Jacques

2007-12-14

The evolutionary origin of some nuclear encoded proteins that translocate proteins across the chloroplast envelope remains unknown. Therefore, sequences of GTPase proteins constituting the Arabidopsis thaliana translocon at the outer membrane of chloroplast (atToc) complexes were analyzed by means of HCA. In particular, atToc159 and related proteins (atToc132, atToc120, and atToc90) do not have proven homologues of prokaryotic or eukaryotic ancestry. We established that the three domains commonly referred to as A, G, and M originate from the GTPase G domain, tandemly repeated, and probably evolving toward an unstructured conformation in the case of the A domain. It resulted frommore » this study a putative common ancestor for these proteins and a new domain definition, in particular the splitting of A into three domains (A1, A2, and A3), has been proposed. The family of Toc159, previously containing A. thaliana and Pisum sativum, has been extended to Medicago truncatula and Populus trichocarpa and it has been revised for Oryza sativa. They have also been compared to GTPase subunits involved in the cpSRP system. A distant homology has been revealed among Toc and cpSRP GTP-hydrolyzing proteins of A. thaliana, and repetitions of a GTPase domain were also found in cpSRP protein receptors, by means of HCA analysis.« less

The evolution of filamin-a protein domain repeat perspective.

PubMed

Light, Sara; Sagit, Rauan; Ithychanda, Sujay S; Qin, Jun; Elofsson, Arne

2012-09-01

Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin β3, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates. Copyright © 2012 Elsevier Inc. All rights reserved.

The productivity of PAs, APRNs, and physicians in Utah.

PubMed

Pedersen, Donald M; Chappell, Boyd; Elison, Gar; Bunnell, Robert

2008-01-01

The physician assistant workforce in Utah is experiencing remarkable growth, with a 9% net annual rate of increase since 1998. An additional 84 PAs provided patient care in Utah in the 4-year period of 1998 through 2001, an average increase of 21 per year. The Utah Medical Education Council believes that the demand for PAs will be high over the next 10 to 15 years, with several factors fueling this growth. Productivity is one of these factors. Even though Utah PAs make up only approximately 6.3% of the state's combined clinician (physician, PA, advanced practice registered nurse [APRN]) workforce; the PAs contribute approximately 7.2% of the patient care full-time equivalents (FTE) in the state. This is in contrast to the 10% FTE contribution made by the state's APRN workforce, which has nearly triple the number of clinicians providing patient care in the state. The majority (73%) of Utah PAs work at least 36 hours per week. Utah PAs also spend a greater percentage of the total hours worked in patient care, when compared to the physician workforce. The rural PA workforce reported working a greater number of total hours and patient care hours when compared to the overall PA workforce.

Modification by covalent reaction or oxidation of cysteine residues in the Tandem-SH2 Domains of ZAP-70 and Syk Can Block Phosphopeptide Binding

PubMed Central

Visperas, Patrick R.; Winger, Jonathan A.; Horton, Timothy M.; Shah, Neel H.; Aum, Diane J.; Tao, Alyssa; Barros, Tiago; Yan, Qingrong; Wilson, Christopher G.; Arkin, Michelle R.; Weiss, Arthur; Kuriyan, John

2015-01-01

Zeta-chain Associated Protein of 70kDa (ZAP-70) and Spleen tyrosine kinase (Syk) are non-receptor tyrosine kinases that are essential for T-cell and B-cell antigen receptor signaling, respectively. They are recruited, via their tandem-SH2 domains, to doubly-phosphorylated Immunoreceptor Tyrosine-based Activation Motifs (ITAMs) on invariant chains of immune antigen receptors. Because of their critical roles in immune signaling, ZAP-70 and Syk are targets for the development of drugs for autoimmune diseases. We show that three thiol-reactive small molecules can prevent the tandem-SH2 domains of ZAP-70 and Syk from binding to phosphorylated ITAMs. We identify a specific cysteine residue in the phosphotyrosine-binding pocket of each protein (Cys 39 in ZAP-70, Cys 206 in Syk) that is necessary for inhibition by two of these compounds. We also find that ITAM binding to ZAP-70 and Syk is sensitive to the presence of hydrogen peroxide, and these two cysteine residues are also necessary for inhibition by hydrogen peroxide. Our findings suggest a mechanism by which the generation of reactive oxygen species generated during responses to antigen could attenuate signaling through these kinases, and may also inform the development of ZAP-70 and Syk inhibitors that bind covalently to their SH2 domains. PMID:25287889

The evolution of filamin – A protein domain repeat perspective

PubMed Central

Light, Sara; Sagit, Rauan; Ithychanda, Sujay S.; Qin, Jun; Elofsson, Arne

2013-01-01

Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin β3, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates. PMID:22414427

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, R.; Wilton, R.; Cuff, M. E.

The tandem Per-Arnt-Sim (PAS) like sensors are commonly found in signal transduction proteins. The periplasmic solute binding protein (SBP) domains are found ubiquitously and are generally involved in solute transport. These domains are widely observed as parts of separate proteins but not within the same polypeptide chain. We report the structural and biochemical characterization of the extracellular ligand-binding receptor, Dret_0059 from Desulfohalobium retbaense DSM 5692, an organism isolated from the Retba salt lake in Senegal. The structure of Dret_0059 consists of a novel combination of SBP and TPAS sensor domains. The N-terminal region forms an SBP domain and the C-terminalmore » region folds into a tandem PAS-like domain structure. A ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS domain of the TPAS. The differential scanning flourimetry studies in solution support the ligands observed in the crystal structure. There are only two other proteins with this structural architecture in the non-redundant sequence data base and we predict that they too bind the same substrates. There is significant interaction between the SBP and TPAS domains, and it is quite conceivable that the binding of one ligand will have an effect on the binding of the other. Our attempts to remove the ligands bound to the protein during expression were not successful, therefore, it is not clear what the relative affects are. The genomic context of this receptor does not contain any protein components expected for transport function, hence, we suggest that Dret_0059 is likely involved in signal transduction and not in solute transport.« less

Personal Assistance Services (PAS) for individuals with disabilities: self-care at the workplace.

PubMed

Solovieva, Tatiana I; Walls, Richard T; Dowler, Denetta L

2010-01-01

The intent of this investigation was to identify current definitions, issues, and strategies related to the use of Personal Assistance Services (PAS) in the workplace. The participants were employees with disabilities who used PAS in the workplace as well as employers who participated in research studies over the past 20 years. More than 30 articles were reviewed to determine PAS definitions, use, policies, and outcomes. A comprehensive search of bibliographic resources (e.g., EBSCOhost) was conducted to identify appropriate articles. The articles revealed current definitions of workplace PAS, demonstrated an increasing need for PAS, and highlighted fiscal and societal barriers to the full implementation of PAS at work. The outcomes clarify the historical components, but also identify questions that remain. These questions concern the effectiveness of PAS, best practices for funding PAS, and the need for national and local policies to support the use of PAS for workers with disabilities.

Analysis of periplasmic sensor domains from Anaeromyxobacter dehalogenans 2CP-C: Structure of one sensor domain from a histidine kinase and another from a chemotaxis protein

PubMed Central

Pokkuluri, P Raj; Dwulit-Smith, Jeff; Duke, Norma E; Wilton, Rosemarie; Mack, Jamey C; Bearden, Jessica; Rakowski, Ella; Babnigg, Gyorgy; Szurmant, Hendrik; Joachimiak, Andrzej; Schiffer, Marianne

2013-01-01

Anaeromyxobacter dehalogenans is a δ-proteobacterium found in diverse soils and sediments. It is of interest in bioremediation efforts due to its dechlorination and metal-reducing capabilities. To gain an understanding on A. dehalogenans' abilities to adapt to diverse environments we analyzed its signal transduction proteins. The A. dehalogenans genome codes for a large number of sensor histidine kinases (HK) and methyl-accepting chemotaxis proteins (MCP); among these 23 HK and 11 MCP proteins have a sensor domain in the periplasm. These proteins most likely contribute to adaptation to the organism's surroundings. We predicted their three-dimensional folds and determined the structures of two of the periplasmic sensor domains by X-ray diffraction. Most of the domains are predicted to have either PAS-like or helical bundle structures, with two predicted to have solute-binding protein fold, and another predicted to have a 6-phosphogluconolactonase like fold. Atomic structures of two sensor domains confirmed the respective fold predictions. The Adeh_2942 sensor (HK) was found to have a helical bundle structure, and the Adeh_3718 sensor (MCP) has a PAS-like structure. Interestingly, the Adeh_3718 sensor has an acetate moiety bound in a binding site typical for PAS-like domains. Future work is needed to determine whether Adeh_3718 is involved in acetate sensing by A. dehalogenans. PMID:23897711

Basic Fibroblast Growth Factor Fused with Tandem Collagen-Binding Domains from Clostridium histolyticum Collagenase ColG Increases Bone Formation.

PubMed

Sekiguchi, Hiroyuki; Uchida, Kentaro; Matsushita, Osamu; Inoue, Gen; Nishi, Nozomu; Masuda, Ryo; Hamamoto, Nana; Koide, Takaki; Shoji, Shintaro; Takaso, Masashi

2018-01-01

Basic fibroblast growth factor 2 (bFGF) accelerates bone formation during fracture healing. Because the efficacy of bFGF decreases rapidly following its diffusion from fracture sites, however, repeated dosing is required to ensure a sustained therapeutic effect. We previously developed a fusion protein comprising bFGF, a polycystic kidney disease domain (PKD; s2b), and collagen-binding domain (CBD; s3) sourced from the Clostridium histolyticum class II collagenase, ColH, and reported that the combination of this fusion protein with a collagen-like peptide, poly(Pro-Hyp-Gly) 10 , induced mesenchymal cell proliferation and callus formation at fracture sites. In addition, C. histolyticum produces class I collagenase (ColG) with tandem CBDs (s3a and s3b) at the C-terminus. We therefore hypothesized that a bFGF fusion protein containing ColG-derived tandem CBDs (s3a and s3b) would show enhanced collagen-binding activity, leading to improved bone formation. Here, we examined the binding affinity of four collagen anchors derived from the two clostridial collagenases to H-Gly-Pro-Arg-Gly-(Pro-Hyp-Gly) 12 -NH 2 , a collagenous peptide, by surface plasmon resonance and found that tandem CBDs (s3a-s3b) have the highest affinity for the collagenous peptide. We also constructed four fusion proteins consisting of bFGF and s3 (bFGF-s3), s2b-s3b (bFGF-s2b-s3), s3b (bFGF-s3b), and s3a-s3b (bFGF-s3a-s3b) and compared their biological activities to those of a previous fusion construct (bFGF-s2b-s3) using a cell proliferation assay in vitro and a mouse femoral fracture model in vivo. Among these CB-bFGFs, bFGF-s3a-s3b showed the highest capacity to induce mesenchymal cell proliferation and callus formation in the mice fracture model. The poly(Pro-Hyp-Gly) 10 /bFGF-s3a-s3b construct may therefore have the potential to promote bone formation in clinical settings.

PAS-cal: a Generic Recombinant Peptide Calibration Standard for Mass Spectrometry

NASA Astrophysics Data System (ADS)

Breibeck, Joscha; Serafin, Adam; Reichert, Andreas; Maier, Stefan; Küster, Bernhard; Skerra, Arne

2014-08-01

We describe the design, preparation, and mass-spectrometric characterization of a new recombinant peptide calibration standard with uniform biophysical and ionization characteristics for mass spectrometry. "PAS-cal" is an artificial polypeptide concatamer of peptide cassettes with varying lengths, each composed of the three small, chemically stable amino acids Pro, Ala, and Ser, which are interspersed by Arg residues to allow site-specific cleavage with trypsin. PAS-cal is expressed at high yields in Escherichia coli as a Small Ubiquitin-like MOdifier (SUMO) fusion protein, which is easily purified and allows isolation of the PAS-cal moiety after SUMO protease cleavage. Upon subsequent in situ treatment with trypsin, the PAS-cal polypeptide yields a set of four defined homogeneous peptides in the range from 2 to 8 kDa with equal mass spacing. ESI-MS analysis revealed a conveniently interpretable raw spectrum, which after deconvolution resulted in a very simple pattern of four peaks with similar ionization signals. MALDI-MS analysis of a PAS-cal peptide mixture comprising both the intact polypeptide and its tryptic fragments revealed not only the four standard peptides but also the singly and doubly charged states of the intact concatamer as well as di- and trimeric adduct ion species between the peptides, thus augmenting the observable m/z range. The advantageous properties of PAS-cal are most likely a result of the strongly hydrophilic and conformationally disordered PEG-like properties of the PAS sequences. Therefore, PAS-cal offers an inexpensive and versatile recombinant peptide calibration standard for mass spectrometry in protein/peptide bioanalytics and proteomics research, the composition of which may be further adapted to fit individual needs.

Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-cap.

PubMed

Corbi-Verge, Carles; Marinelli, Fabrizio; Zafra-Ruano, Ana; Ruiz-Sanz, Javier; Luque, Irene; Faraldo-Gómez, José D

2013-09-03

The regulation and localization of signaling enzymes is often mediated by accessory modular domains, which frequently function in tandems. The ability of these tandems to adopt multiple conformations is as important for proper regulation as the individual domain specificity. A paradigmatic example is Abl, a ubiquitous tyrosine kinase of significant pharmacological interest. SH3 and SH2 domains inhibit Abl by assembling onto the catalytic domain, allosterically clamping it in an inactive state. We investigate the dynamics of this SH3-SH2 tandem, using microsecond all-atom simulations and differential scanning calorimetry. Our results indicate that the Abl tandem is a two-state switch, alternating between the conformation observed in the structure of the autoinhibited enzyme and another configuration that is consistent with existing scattering data for an activated form. Intriguingly, we find that the latter is the most probable when the tandem is disengaged from the catalytic domain. Nevertheless, an amino acid stretch preceding the SH3 domain, the so-called N-cap, reshapes the free-energy landscape of the tandem and favors the interaction of this domain with the SH2-kinase linker, an intermediate step necessary for assembly of the autoinhibited complex. This allosteric effect arises from interactions between N-cap and the SH2 domain and SH3-SH2 connector, which involve a phosphorylation site. We also show that the SH3-SH2 connector plays a determinant role in the assembly equilibrium of Abl, because mutations thereof hinder the engagement of the SH2-kinase linker. These results provide a thermodynamic rationale for the involvement of N-cap and SH3-SH2 connector in Abl regulation and expand our understanding of the principles of modular domain organization.

Communication between Tandem cAMP Binding Domains in the Regulatory Subunit of Protein Kinase A-Iα as Revealed by Domain-silencing Mutations*

PubMed Central

McNicholl, E. Tyler; Das, Rahul; SilDas, Soumita; Taylor, Susan S.; Melacini, Giuseppe

2010-01-01

Protein kinase A (PKA) is the main receptor for the universal cAMP second messenger. PKA is a tetramer with two catalytic (C) and two regulatory (R) subunits, each including two tandem cAMP binding domains, i.e. CBD-A and -B. Structural investigations of RIα have revealed that although CBD-A plays a pivotal role in the cAMP-dependent inhibition of C, the main function of CBD-B is to regulate the access of cAMP to site A. To further understand the mechanism underlying the cross-talk between CBD-A and -B, we report here the NMR investigation of a construct of R, RIα-(119–379), which unlike previous fragments characterized by NMR, spans in full both CBDs. Our NMR studies were also extended to two mutants, R209K and the corresponding R333K, which severely reduce the affinity of cAMP for CBD-A and -B, respectively. The comparative NMR analysis of wild-type RIα-(119–379) and of the two domain silencing mutations has led to the definition at an unprecedented level of detail of both intra- and interdomain allosteric networks, revealing several striking differences between the two CBDs. First, the two domains, although homologous in sequence and structure, exhibit remarkably different responses to the R/K mutations especially at the β2-3 allosteric “hot spot.” Second, although the two CBDs are reciprocally coupled at the level of local unfolding of the hinge, the A-to-B and B-to-A pathways are dramatically asymmetrical at the level of global unfolding. Such an asymmetric interdomain cross-talk ensures efficiency and robustness in both the activation and de-activation of PKA. PMID:20202931

How electronic health records can unmask the hidden value of PAs.

PubMed

Ogunfiditimi, Folusho; Sherry, Scott P; Foote, Monica; Christie, Sarah L; Shock, Lisa P; Cawley, James; Browne, Aaron

2017-06-01

The Fee for Value (FFV) Task Force, a subgroup of the American Academy of PAs' Research and Strategic Initiatives Commission, has examined tools and mechanisms aimed at better clarifying the volume and value of PA work and how that work contributes to improving access to high-quality care. Establishing the value of PAs has been a challenging task for many healthcare providers. Often, PA value has been defined by their clinical productivity, without any clear direction as to what constitutes value versus productivity. The objective of this article is to unmask the value of PAs through the role of electronic health records and highlight PAs' ability to produce services that are value-oriented and quantifiably productive.

PAs in orthopedics in the VHA's community-based outpatient clinics.

PubMed

Reed, Daniel O; Hooker, Roderick S

2017-04-01

In the Veterans Health Administration (VHA) system, most orthopedic care takes place in the VA medical centers (VAMCs). Because most patients receiving orthopedic care were referred by adult medicine providers, more widely deploying physician assistants (PAs) in orthopedic medicine might help offset this workload. An orthopedic medicine demonstration project recruited, trained, and positioned PAs in community-based outpatient clinics (CBOCs) to improve access to care. The project involved surgeons at the Houston VAMC instructing five newly employed PAs in a wide range of orthopedic evaluation and management strategies before their assignment to a CBOC. An administrative assessment compared encounter data pre- and postproject (2012 and 2014) to determine if this strategy modified orthopedic workload and improved patient access to care. By 2014, orthopedic patient visit volume had increased 31%-10% at the VAMC and 21% at the five CBOCs. Overall, the five deployed PAs managed 28% of all orthopedic encounters spread over 1 year and only 3.2% of visits required VAMC referral for further evaluation or treatment. During the project, the total volume of patient visits increased throughout the Houston VAMC region but access to care for this specialty service also increased, with more veteran musculoskeletal care being met at the five CBOCs, off-loading visit demand centrally. The adaptability and flexibility of new roles has been identified as one of the defining characteristics of PAs. That the VHA can take advantage of this role malleability suggests that employing PAs is useful in meeting medical service needs of veterans.

Two-state dynamics of the SH3–SH2 tandem of Abl kinase and the allosteric role of the N-cap

PubMed Central

Corbi-Verge, Carles; Marinelli, Fabrizio; Zafra-Ruano, Ana; Ruiz-Sanz, Javier; Luque, Irene; Faraldo-Gómez, José D.

2013-01-01

The regulation and localization of signaling enzymes is often mediated by accessory modular domains, which frequently function in tandems. The ability of these tandems to adopt multiple conformations is as important for proper regulation as the individual domain specificity. A paradigmatic example is Abl, a ubiquitous tyrosine kinase of significant pharmacological interest. SH3 and SH2 domains inhibit Abl by assembling onto the catalytic domain, allosterically clamping it in an inactive state. We investigate the dynamics of this SH3–SH2 tandem, using microsecond all-atom simulations and differential scanning calorimetry. Our results indicate that the Abl tandem is a two-state switch, alternating between the conformation observed in the structure of the autoinhibited enzyme and another configuration that is consistent with existing scattering data for an activated form. Intriguingly, we find that the latter is the most probable when the tandem is disengaged from the catalytic domain. Nevertheless, an amino acid stretch preceding the SH3 domain, the so-called N-cap, reshapes the free-energy landscape of the tandem and favors the interaction of this domain with the SH2-kinase linker, an intermediate step necessary for assembly of the autoinhibited complex. This allosteric effect arises from interactions between N-cap and the SH2 domain and SH3–SH2 connector, which involve a phosphorylation site. We also show that the SH3–SH2 connector plays a determinant role in the assembly equilibrium of Abl, because mutations thereof hinder the engagement of the SH2-kinase linker. These results provide a thermodynamic rationale for the involvement of N-cap and SH3–SH2 connector in Abl regulation and expand our understanding of the principles of modular domain organization. PMID:23959873

2-Phenylacetylenesulfonamide (PAS) induces p53-independent apoptotic killing of B-chronic lymphocytic leukemia (CLL) cells.

PubMed

Steele, Andrew J; Prentice, Archibald G; Hoffbrand, A Victor; Yogashangary, Birunthini C; Hart, Stephen M; Lowdell, Mark W; Samuel, Edward R; North, Janet M; Nacheva, Elisabeth P; Chanalaris, Anastasios; Kottaridis, Panagiotis; Cwynarski, Kate; Wickremasinghe, R Gitendra

2009-08-06

We studied the actions of 2-phenylacetylenesulfonamide (PAS) on B-chronic lymphocytic leukemia (CLL) cells. PAS (5-20 microM) initiated apoptosis within 24 hours, with maximal death at 48 hours asassessed by morphology, cleavage of poly(ADP-ribose) polymerase (PARP), caspase 3 activation, and annexin V staining. PAS treatment induced Bax proapoptotic conformational change, Bax movement from the cytosol to the mitochondria, and cytochrome c release, indicating that PAS induced apoptosis via the mitochondrial pathway. PAS induced approximately 3-fold up-regulation of proapoptotic Noxa protein and mRNA levels. In addition, Noxa was found unexpectedly to be bound to Bcl-2 in PAS-treated cells. PAS treatment of CLL cells failed to up-regulate p53, suggesting that PAS induced apoptosis independently of p53. Furthermore, PAS induced apoptosis in CLL isolates with p53 gene deletion in more than 97% of cells. Normal B lymphocytes were as sensitive to PAS-induced Noxa up-regulation and apoptosis as were CLL cells. However, both T lymphocytes and bone marrow hematopoietic progenitor cells were relatively resistant to PAS. Our data suggest that PAS may represent a novel class of drug that induces apoptosis in CLL cells independently of p53 status by a mechanism involving Noxa up-regulation.

Personal Assistance Services (PAS): Toward Universal Access to Support. Annotated Bibliography.

ERIC Educational Resources Information Center

Racino, Julie Ann

This annotated bibliography provides approximately 100 summaries and evaluations of documents, published from 1979 to 1995, on personal assistance services (PAS) for individuals with disabilities. Studies and articles were selected for inclusion based upon their capacity to inform the development of PAS models, including conceptual, policy, and…

PAs: Fifty years young.

PubMed

Mandel, Ellen D; North, Shannon

2017-10-01

The PA profession is 50 years young. Practicing PAs and current students hail from several generational categories ranging from Builders to Generation Z. This article reviews how different generations may have experienced PA program expansion, professional identity, state licensing, and prescription delegation. The authors sampled a cohort of PA program applicants about their views on what evokes optimism and concern for the PA profession. These themes mirror the recently paved professional road, while posing the all-important question: What construction lies on the horizon?

Digital radiography using amorphous selenium: photoconductively activated switch (PAS) readout system.

PubMed

Reznik, Nikita; Komljenovic, Philip T; Germann, Stephen; Rowlands, John A

2008-03-01

A new amorphous selenium (a-Se) digital radiography detector is introduced. The proposed detector generates a charge image in the a-Se layer in a conventional manner, which is stored on electrode pixels at the surface of the a-Se layer. A novel method, called photoconductively activated switch (PAS), is used to read out the latent x-ray charge image. The PAS readout method uses lateral photoconduction at the a-Se surface which is a revolutionary modification of the bulk photoinduced discharge (PID) methods. The PAS method addresses and eliminates the fundamental weaknesses of the PID methods--long readout times and high readout noise--while maintaining the structural simplicity and high resolution for which PID optical readout systems are noted. The photoconduction properties of the a-Se surface were investigated and the geometrical design for the electrode pixels for a PAS radiography system was determined. This design was implemented in a single pixel PAS evaluation system. The results show that the PAS x-ray induced output charge signal was reproducible and depended linearly on the x-ray exposure in the diagnostic exposure range. Furthermore, the readout was reasonably rapid (10 ms for pixel discharge). The proposed detector allows readout of half a pixel row at a time (odd pixels followed by even pixels), thus permitting the readout of a complete image in 30 s for a 40 cm x 40 cm detector with the potential of reducing that time by using greater readout light intensity. This demonstrates that a-Se based x-ray detectors using photoconductively activated switches could form a basis for a practical integrated digital radiography system.

Switching Cyclic Nucleotide-Selective Activation of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Holoenzyme Reveals Distinct Roles of Tandem Cyclic Nucleotide-Binding Domains.

PubMed

He, Daniel; Lorenz, Robin; Kim, Choel; Herberg, Friedrich W; Lim, Chinten James

2017-12-15

The cyclic adenosine monophosphate (cAMP)- and cyclic guanosine monophosphate (cGMP)-dependent protein kinases (PKA and PKG) are key effectors of cyclic nucleotide signaling. Both share structural features that include tandem cyclic nucleotide-binding (CNB) domains, CNB-A and CNB-B, yet their functions are separated through preferential activation by either cAMP or cGMP. Based on structural studies and modeling, key CNB contact residues have been identified for both kinases. In this study, we explored the requirements for conversion of PKA activation from cAMP-dependent to cGMP-dependent. The consequences of the residue substitutions T192R/A212T within CNB-A or G316R/A336T within CNB-B of PKA-RIα on cyclic nucleotide binding and holoenzyme activation were assessed in vitro using purified recombinant proteins, and ex vivo using RIα-deficient mouse embryonic fibroblasts genetically reconstituted with wild-type or mutant PKA-RIα. In vitro, a loss of binding and activation selectivity was observed when residues in either one of the CNB domains were mutated, while mutations in both CNB domains resulted in a complete switch of selectivity from cAMP to cGMP. The switch in selectivity was also recapitulated ex vivo, confirming their functional roles in cells. Our results highlight the importance of key cyclic nucleotide contacts within each CNB domain and suggest that these domains may have evolved from an ancestral gene product to yield two distinct cyclic nucleotide-dependent protein kinases.

Structural insights into the functional versatility of WW domain-containing oxidoreductase tumor suppressor

PubMed Central

2015-01-01

Recent work on WW domain-containing oxidoreductase (WWOX) tumor suppressor is beginning to shed new light on both the molecular mechanism of action of its WW domains as well as the contiguous catalytic domain. Herein, the structural basis underlying the ability of WW1 domain to bind to various physiological ligands and how the orphan WW2 tandem partner synergizes its ligand binding in the context of WW1–WW2 tandem module of WWOX is discussed. Notably, the WW domains within the WW1–WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. In this manner, the association of WW2 domain with WW1 hinders ligand binding to the latter. Consequently, ligand binding to WW1 domain not only results in the displacement of WW2 lid but also disrupts the fixed orientation of WW domains in the liganded conformation. Equally importantly, structure-guided functional approach suggests that the catalytic domain of WWOX likely serves as a retinal oxidoreductase that catalyzes the reversible oxidation and reduction of all-trans-retinal. Collectively, this review provides structural insights into the functional versatility of a key signaling protein with important implications on its biology. PMID:25662954

Structural insights into the functional versatility of WW domain-containing oxidoreductase tumor suppressor.

PubMed

Farooq, Amjad

2015-03-01

Recent work on WW domain-containing oxidoreductase (WWOX) tumor suppressor is beginning to shed new light on both the molecular mechanism of action of its WW domains as well as the contiguous catalytic domain. Herein, the structural basis underlying the ability of WW1 domain to bind to various physiological ligands and how the orphan WW2 tandem partner synergizes its ligand binding in the context of WW1-WW2 tandem module of WWOX is discussed. Notably, the WW domains within the WW1-WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. In this manner, the association of WW2 domain with WW1 hinders ligand binding to the latter. Consequently, ligand binding to WW1 domain not only results in the displacement of WW2 lid but also disrupts the fixed orientation of WW domains in the liganded conformation. Equally importantly, structure-guided functional approach suggests that the catalytic domain of WWOX likely serves as a retinal oxidoreductase that catalyzes the reversible oxidation and reduction of all-trans-retinal. Collectively, this review provides structural insights into the functional versatility of a key signaling protein with important implications on its biology. © 2015 by the Society for Experimental Biology and Medicine.

Extravehicular Activity (EVA) Power, Avionics, and Software (PAS) 101

NASA Technical Reports Server (NTRS)

Irimies, David

2011-01-01

EVA systems consist of a spacesuit or garment, a PLSS, a PAS system, and spacesuit interface hardware. The PAS system is responsible for providing power for the suit, communication of several types of data between the suit and other mission assets, avionics hardware to perform numerous data display and processing functions, and information systems that provide crewmembers data to perform their tasks with more autonomy and efficiency. Irimies discussed how technology development efforts have advanced the state-of-the-art in these areas and shared technology development challenges.

47 CFR 69.111 - Tandem-switched transport and tandem charge.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Tandem-switched transport and tandem charge. 69... SERVICES (CONTINUED) ACCESS CHARGES Computation of Charges § 69.111 Tandem-switched transport and tandem...-switched transport shall consist of two rate elements, a transmission charge and a tandem switching charge...

Identification and characterization of tandem repeats in exon III of dopamine receptor D4 (DRD4) genes from different mammalian species.

PubMed

Larsen, Svend Arild; Mogensen, Line; Dietz, Rune; Baagøe, Hans Jørgen; Andersen, Mogens; Werge, Thomas; Rasmussen, Henrik Berg

2005-12-01

In this study we have identified and characterized dopamine receptor D4 (DRD4) exon III tandem repeats in 33 public available nucleotide sequences from different mammalian species. We found that the tandem repeat in canids could be described in a novel and simple way, namely, as a structure composed of 15- and 12- bp modules. Tandem repeats composed of 18-bp modules were found in sequences from the horse, zebra, onager, and donkey, Asiatic bear, polar bear, common raccoon, dolphin, harbor porpoise, and domestic cat. Several of these sequences have been analyzed previously without a tandem repeat being found. In the domestic cow and gray seal we identified tandem repeats composed of 36-bp modules, each consisting of two closely related 18-bp basic units. A tandem repeat consisting of 9-bp modules was identified in sequences from mink and ferret. In the European otter we detected an 18-bp tandem repeat, while a tandem repeat consisting of 27-bp modules was identified in a sequence from European badger. Both these tandem repeats were composed of 9-bp basic units, which were closely related with the 9-bp repeat modules identified in the mink and ferret. Tandem repeats could not be identified in sequences from rodents. All tandem repeats possessed a high GC content with a strong bias for C. On phylogenetic analysis of the tandem repeats evolutionary related species were clustered into the same groups. The degree of conservation of the tandem repeats varied significantly between species. The deduced amino acid sequences of most of the tandem repeats exhibited a high propensity for disorder. This was also the case with an amino acid sequence of the human DRD4 exon III tandem repeat, which was included in the study for comparative purposes. We identified proline-containing motifs for SH3 and WW domain binding proteins, potential phosphorylation sites, PDZ domain binding motifs, and FHA domain binding motifs in the amino acid sequences of the tandem repeats. The numbers of

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

PubMed Central

Shepard, Peter J.; Choi, Eun-A; Lu, Jente; Flanagan, Lisa A.; Hertel, Klemens J.; Shi, Yongsheng

2011-01-01

Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs. PAS-Seq analyses of human and mouse transcriptomes showed that 40%–50% of all expressed genes produce alternatively polyadenylated mRNAs. Furthermore, our study detected evolutionarily conserved polyadenylation of histone mRNAs and revealed novel features of mitochondrial RNA polyadenylation. Finally, PAS-Seq analyses of mouse embryonic stem (ES) cells, neural stem/progenitor (NSP) cells, and neurons not only identified more poly(A) sites than what was found in the entire mouse EST database, but also detected significant changes in the global APA profile that lead to lengthening of 3′ untranslated regions (UTR) in many mRNAs during stem cell differentiation. Together, our PAS-Seq analyses revealed a complex landscape of RNA polyadenylation in mammalian cells and the dynamic regulation of APA during stem cell differentiation. PMID:21343387

The dynamic Atg13-free conformation of the Atg1 EAT domain is required for phagophore expansion.

PubMed

Lin, Mary G; Schöneberg, Johannes; Davies, Christopher W; Ren, Xuefeng; Hurley, James H

2018-05-15

Yeast macroautophagy begins with the de novo formation of a double-membrane phagophore at the preautophagosomal structure/phagophore assembly site (PAS), followed by its expansion into the autophagosome responsible for cargo engulfment. The kinase Atg1 is recruited to the PAS by Atg13 through interactions between the EAT domain of the former and the tMIM motif of the latter. Mass-spectrometry data have shown that, in the absence of Atg13, the EAT domain structure is strikingly dynamic, but the function of this Atg13-free dynamic state has been unclear. We used structure-based mutational analysis and quantitative and superresolution microscopy to show that Atg1 is present on autophagic puncta at, on average, twice the stoichiometry of Atg13. Moreover, Atg1 colocalizes with the expanding autophagosome in a manner dependent on Atg8 but not Atg13. We used isothermal titration calorimetry and crystal structure information to design an EAT domain mutant allele ATG1 DD that selectively perturbs the function of the Atg13-free state. Atg1 DD shows reduced PAS formation and does not support phagophore expansion, showing that the EAT domain has an essential function that is separate from its Atg13-dependent role in autophagy initiation.

Bacterial growth kinetics in ACD-A apheresis platelets: comparison of plasma and PAS III storage.

PubMed

Dumont, Larry J; Wood, Tammara A; Housman, Molly; Herschel, Louise; Brantigan, Barbara; Heber, Cheryl; Houghton, Jaime

2011-05-01

Our objective was to determine the growth kinetics of bacteria in leukoreduced apheresis platelets (LR-AP) in a platelet (PLT) additive solution (PAS; InterSol, Fenwal, Inc.) compared to LR-AP stored in plasma. Hyperconcentrated, double-dose LR-AP were collected from healthy donors with a separator (AMICUS, Fenwal, Inc.). LR-AP were evenly divided, InterSol was added to half (65% InterSol:35% plasma [PAS]), and PLTs in autologous plasma were used for a paired control (PL). Bacteria were inoculated into each LR-AP PAS/PL pair (0.5-1.6 colony-forming units [CFUs]/mL), and bacterial growth was followed for up to 7 days. Time to the end of the lag phase, doubling times, maximum concentration (conc-max), and time to maximum concentration (time-max) were estimated. Streptococcus viridans did not grow to detectable levels in either PAS or PL units. The other bacteria had no significant overall difference in the conc-max (p = 0.47) or time-max (p = 0.7) between PL and PAS LR-AP; PL had a 0.14 hours faster doubling rate (p = 0.023); and PAS had a 4.7 hours shorter lag time (p = 0.016). We observed that five index organisms will grow in LR-AP stored in a 35%:65% ratio of plasma to InterSol where initial bacterial concentrations are 0.5 to 1.6 CFUs/mL. The more rapid initiation of log-phase growth for bacteria within a PAS storage environment resulted in a bacterial concentration up to 4 logs higher in the PAS units compared to the plasma units at 24 hours, but with no difference in the conc-max. This may present an early bacterial detection advantage for PAS-stored PLTs. © 2010 American Association of Blood Banks.

Does DSM-IV Have Equivalents for the Parental Alienation Syndrome (PAS) Diagnosis?

ERIC Educational Resources Information Center

Gardner, Richard A.

2003-01-01

Child custody evaluators commonly find themselves confronted with resistance when they attempt to use the term parental alienation syndrome (PAS) in courts of law. The purpose of this article is to elucidate the reasons for the reluctance to use the PAS diagnosis and the applicability of parental alienation, as well as current DSM-IV substitute…

Evidence that the tandem-pleckstrin-homology-domain-containing protein TAPP1 interacts with Ptd(3,4)P2 and the multi-PDZ-domain-containing protein MUPP1 in vivo.

PubMed Central

Kimber, Wendy A; Trinkle-Mulcahy, Laura; Cheung, Peter C F; Deak, Maria; Marsden, Louisa J; Kieloch, Agnieszka; Watt, Stephen; Javier, Ronald T; Gray, Alex; Downes, C Peter; Lucocq, John M; Alessi, Dario R

2002-01-01

PtdIns(3,4,5)P3 is an established second messenger of growth-factor and insulin-induced signalling pathways. There is increasing evidence that one of the immediate breakdown products of PtdIns(3,4,5)P3, namely PtdIns(3,4)P2, whose levels are elevated by numerous extracellular agonists, might also function as a signalling molecule. Recently, we identified two related pleckstrin-homology (PH)-domain-containing proteins, termed 'tandem-PH-domain-containing protein-1' (TAPP1) and TAPP2, which interacted in vitro with high affinity with PtdIns(3,4)P2, but did not bind PtdIns(3,4,5)P3 or other phosphoinositides. In the present study we demonstrate that stimulation of Swiss 3T3 or 293 cells with agonists that stimulate PtdIns(3,4)P2 production results in the marked translocation of TAPP1 to the plasma membrane. This recruitment is dependent on a functional PtdIns(3,4)P2-binding PH domain and is inhibited by wortmannin, a phosphoinositide 3-kinase inhibitor that prevents PtdIns(3,4)P2 generation. A search for proteins that interact with TAPP1 identified the multi-PDZ-containing protein termed 'MUPP1', a protein possessing 13 PDZ domains and no other known modular or catalytic domains [PDZ is postsynaptic density protein (PSD-95)/Drosophila disc large tumour suppressor (dlg)/tight junction protein (ZO1)]. We demonstrate that immunoprecipitation of endogenously expressed TAPP1 from 293-cell lysates results in the co-immunoprecipitation of endogenous MUPP1, indicating that these proteins are likely to interact with each other physiologically. We show that TAPP1 and TAPP2 interact with the 10th and 13th PDZ domain of MUPP1 through their C-terminal amino acids. The results of the present study suggest that TAPP1 and TAPP2 could function in cells as adapter proteins to recruit MUPP1, or other proteins that they may interact with, to the plasma membrane in response to signals that elevate PtdIns(3,4)P2. PMID:11802782

Epitaxial nanowire formation in metamorphic GaAs/GaPAs short-period superlattices

NASA Astrophysics Data System (ADS)

Zheng, Nan; Ahrenkiel, S. Phillip

2017-07-01

Metamorphic growth presents routes to novel nanomaterials with unique properties that may be suitable for a range of applications. We discuss self-assembled, epitaxial nanowires formed during metalorganic chemical vapor deposition of metamorphic GaAs/GaPAs short-period superlattices. The heterostructures incorporate strain-engineered GaPAs compositional grades on 6°-<111>B miscut GaAs substrates. Lateral diffusion within the SPS into vertically aligned, three-dimensional columns results in nanowires extending along <110>A directions with a lateral period of 70-90 nm. The microstructure is probed by transmission electron microscopy to confirm the presence of coherent GaAs nanowires within GaPAs barriers. The compositional profile is inferred from analysis of {200} dark-field image contrast and <210> lattice images.

Phylogenetic and specificity studies of two-domain GNA-related lectins: generation of multispecificity through domain duplication and divergent evolution

PubMed Central

Van Damme, Els J. M.; Nakamura-Tsuruta, Sachiko; Smith, David F.; Ongenaert, Maté; Winter, Harry C.; Rougé, Pierre; Goldstein, Irwin J.; Mo, Hanqing; Kominami, Junko; Culerrier, Raphaël; Barre, Annick; Hirabayashi, Jun; Peumans, Willy J.

2007-01-01

A re-investigation of the occurrence and taxonomic distribution of proteins built up of protomers consisting of two tandem arrayed domains equivalent to the GNA [Galanthus nivalis (snowdrop) agglutinin] revealed that these are widespread among monotyledonous plants. Phylogenetic analysis of the available sequences indicated that these proteins do not represent a monophylogenetic group but most probably result from multiple independent domain duplication/in tandem insertion events. To corroborate the relationship between inter-domain sequence divergence and the widening of specificity range, a detailed comparative analysis was made of the sequences and specificity of a set of two-domain GNA-related lectins. Glycan microarray analyses, frontal affinity chromatography and surface plasmon resonance measurements demonstrated that the two-domain GNA-related lectins acquired a marked diversity in carbohydrate-binding specificity that strikingly contrasts the canonical exclusive specificity of their single domain counterparts towards mannose. Moreover, it appears that most two-domain GNA-related lectins interact with both high mannose and complex N-glycans and that this dual specificity relies on the simultaneous presence of at least two different independently acting binding sites. The combined phylogenetic, specificity and structural data strongly suggest that plants used domain duplication followed by divergent evolution as a mechanism to generate multispecific lectins from a single mannose-binding domain. Taking into account that the shift in specificity of some binding sites from high mannose to complex type N-glycans implies that the two-domain GNA-related lectins are primarily directed against typical animal glycans, it is tempting to speculate that plants developed two-domain GNA-related lectins for defence purposes. PMID:17288538

The elastic free energy of a tandem modular protein under force.

PubMed

Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

2015-05-01

Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins. Copyright © 2015. Published by Elsevier Inc.

MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services.

PubMed

Pratt, Brian; Howbert, J Jeffry; Tasman, Natalie I; Nilsson, Erik J

2012-01-01

MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows. MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL. brian.pratt@insilicos.com

[Parental alienation syndrome (PAS): unknown in medical settings, endemic in courts].

PubMed

Pignotti, Maria Serenella

2013-02-01

A purposed syndrome of so-called parental alienation (PAS), unsupported by any evidence-based data, unknown in medical settings, unquoted in medical books, absent in DSM and ICD, never demonstrated by controlled studies published in high scientific level journals, is rampant in Courts where it can lead to loose parental custody. During a divorce trial, almost always the mothers and the children, become joint in a sort of folie au deux, in a denigration campaign of ex-husband/father. From a review on this issue it seems evident its theoretical roots lie on a theory that justify gender violence and children sexual abuse. The bias that both of them are layers and that he children have not autonomy block their possibility of any defence in front of a Court. In severe cases, PAS becomes a new and efficient tool of intra-familiar violence. The treatment of severe cases is to stop any contact between mother and children. The resort to PAS in Courts must be strongly rejected.

PAS positivity of erythroid precursor cells is associated with a poor prognosis in newly diagnosed myelodysplastic syndrome patients.

PubMed

Masuda, Kenta; Shiga, Shuichi; Kawabata, Hiroshi; Takaori-Kondo, Akifumi; Ichiyama, Satoshi; Kamikubo, Yasuhiko

2018-07-01

Myelodysplastic syndrome (MDS) is a group of clonal stem cell disorders characterized by hematopoietic insufficiency. The accurate risk stratification of patients with MDS is essential for selection of appropriate therapies. We herein conducted a retrospective cohort study to examine the prognostic value of periodic acid-Schiff (PAS) reaction-positive erythroblasts in MDS patients. We examined the PAS positivity of the bone marrow erythroblasts of 144 patients newly diagnosed with MDS; 26 (18.1%) of them had PAS-positive erythroblasts, whereas 118 (81.9%) did not. The PAS-positive group showed significantly poorer karyotypes as defined in the revised International Prognostic Scoring System (IPSS-R) and higher scores in age-adjusted IPSS-R (IPSS-RA) than the PAS-negative group. Overall survival (OS) and leukemia-free survival (LFS) were also significantly shorter in the PAS-positive group than in the PAS-negative group. Similar results were obtained when only high- and very high risk groups were analyzed using IPSS-RA. This retrospective study suggested that the PAS positivity of erythroblasts is an additional prognostic factor combined with other risk scores for OS and LFS in MDS, and our results may contribute to improved clinical decision-making and rapid risk stratification.

MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services

PubMed Central

Pratt, Brian; Howbert, J. Jeffry; Tasman, Natalie I.; Nilsson, Erik J.

2012-01-01

Summary: MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows. Availability and implementation: MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL. Contact: brian.pratt@insilicos.com PMID:22072385

Return on investment of advanced practice medical degrees: NPs vs. PAs.

PubMed

Craig, Christopher K; Holmes, James H; Carter, Jeffery E

2017-06-01

As the United States faces a predicted physician shortage over the next 2 decades, physician assistants (PAs) and NPs are expected to fill the void. At the same time, because education is expensive, student loan and tuition increases have many potential applicants assessing differences in reimbursement and wondering about their return on investment (ROI). An analysis compared PA and NP salaries by incorporating national salary data, federal income tax, and student loans for a comparative analysis of each career pathway. Salaries were abstracted from the 2012 Bureau of Labor Statistics database. The net present value (NPV) of PA and NP salaries was calculated with a 5% discount rate. Principal and interest for student loans was calculated at a 6% interest fixed-rate loan over 30 years. NPVs were then compared with projected ROI at retirement age. Relative career values were also given to each career choice, based on a retirement age of 65 years, which translates to about 41 years of employment for both PAs and NPs. PAs' and NPs' educational loans both equalled $129,484 on total repayment. The median annual salary of a PA was $90,930 and $89,960 for an NP. PA data yielded a 5% NPV of $781,323 compared with $764,348 for NPs. Of note, the 5% NPV of a 4-year nursing degree is $728,436. PAs have a slightly higher ROI compared with NPs. These findings may change due to adjustments in nursing training models. Many PA programs allow matriculation immediately after obtaining a bachelor's degree. NP schools often require nursing experience before entering their program. Some schools are considering an accelerated NP program, allowing immediate matriculation after obtaining a bachelor's degree. Because many NP programs have become doctoral degrees, the increased duration of training, higher tuition, and fewer years worked before retirement lower the overall NP ROI. A similar reduction in ROI was considered marginal in PAs who attend residency programs-though these programs are

Developing Tools to Search for PNe in the J­PAS Survey

NASA Astrophysics Data System (ADS)

Gonçalves, D.; Villegas, T. A.; Marcolino, W.; Lorenz-Martins, S.; Borges Fernandes, M.; Kanaan, A.; Pereira, C. B.; Daflon, S.; Ederoclite, A.; Alfaro, E. J.; Ribeiro, T.; Vázquez Ramió, H.; Schmitz, T.; Martínez-Delgado, D.; JPAS Collaboration

2014-04-01

The Javalambre Physics of the Accelerating Universe Astrophysical Survey (J-PAS) is a new astronomical facility dedicated to mapping the observable Universe in 59 colors, and will produce high-quality images and an unique spectral resolution over the 8000 deg^2. It will consist of two telescopes. One of 2.5-m (J-PAS) and another of 0.8-m (J-PLUS, mainly for calibrations). The former will have a dedicated 1.2-G pixel survey camera (containing an array of 14 CCDs) with a FoV of 5 deg^2. It is planned to take 4-5 years and is expected to map the above area to a 5σ magnitude depth for point sources equivalent to i˜23.3 over an aperture of 2 arcsec^2. The J-PAS filter system consists of 54 contiguous narrow band filters of 100-Å FWHM, from 3,500 to 10,000Å. To those filters 2 broad-band ones will be at the extremes, UV and IR, plus 3 SDSS g, r, and i filters. J-PLUS, on the other hand, comprise 12 filters, including g, r, i and z SDSS ones. Though about 2,500 PNe (confirmed spectroscopically) are known in the Galaxy, only about 20 objects have been identified as halo PNe. They were found from their location, kinematics and chemistry. Halo PNe are able to reveal precious information for the study of low- and intermediate-mass star evolution and the early chemical conditions of the Galaxy. The characteristic low continuum and intense line emissions of PNe make them good objects to be searched for by J-PAS. For instance, the halo PNe BoBn 1, DdDm 1 and PS 1, located somewhere between 11 and 24 kpc from the Sun, have B magnitudes of 16, 14 and 13.4, respectively. Such values are easily encompassed by J-PAS, given the typical limit magnitude of the survey. Because of the low number of halo PNe detected so far, we are developing tools to find these objects by using J-PAS/J-PLUS, and planning a follow-up study for any possible candidate identified by the survey. Color magnitudes diagram able to separate PNe from other strong line emission objects are being explored by the

Controlled human malaria infection trials: How tandems of trust and control construct scientific knowledge.

PubMed

Bijker, Else M; Sauerwein, Robert W; Bijker, Wiebe E

2016-02-01

Controlled human malaria infections are clinical trials in which healthy volunteers are deliberately infected with malaria under controlled conditions. Controlled human malaria infections are complex clinical trials: many different groups and institutions are involved, and several complex technologies are required to function together. This functioning together of technologies, people, and institutions is under special pressure because of potential risks to the volunteers. In this article, the authors use controlled human malaria infections as a strategic research site to study the use of control, the role of trust, and the interactions between trust and control in the construction of scientific knowledge. The authors argue that tandems of trust and control play a central role in the successful execution of clinical trials and the construction of scientific knowledge. More specifically, two aspects of tandems of trust and control will be highlighted: tandems are sites where trust and control coproduce each other, and tandems link the personal, the technical, and the institutional domains. Understanding tandems of trust and control results in setting some agendas for both clinical trial research and science and technology studies.

Protective effects of ebselen (Ebs) and para-aminosalicylic acid (PAS) against manganese (Mn)-induced neurotoxicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marreilha dos Santos, A.P., E-mail: apsantos@ff.ul.pt; Lucas, Rui L.; Andrade, Vanda

2012-02-01

Chronic, excessive exposure to manganese (Mn) may induce neurotoxicity and cause an irreversible brain disease, referred to as manganism. Efficacious therapies for the treatment of Mn are lacking, mandating the development of new interventions. The purpose of the present study was to investigate the efficacy of ebselen (Ebs) and para-aminosalicylic acid (PAS) in attenuating the neurotoxic effects of Mn in an in vivo rat model. Exposure biomarkers, inflammatory and oxidative stress biomarkers, as well as behavioral parameters were evaluated. Co-treatment with Mn plus Ebs or Mn plus PAS caused a significant decrease in blood and brain Mn concentrations (compared tomore » rats treated with Mn alone), concomitant with reduced brain E{sub 2} prostaglandin (PGE{sub 2}) and enhanced brain glutathione (GSH) levels, decreased serum prolactin (PRL) levels, and increased ambulation and rearing activities. Taken together, these results establish that both PAS and Ebs are efficacious in reducing Mn body burden, neuroinflammation, oxidative stress and locomotor activity impairments in a rat model of Mn-induced toxicity. -- Highlights: ► The manuscript is unique in its approach to the neurotoxicity of Mn. ► The manuscript incorporates molecular, cellular and functional (behavioral) analyses. ► Both PAS and Ebs are effective in restoring Mn behavioral function. ► Both PAS and Ebs are effective in reducing Mn-induced oxidative stress. ► Both PAS and Ebs led to a decrease in Mn-induced neuro-inflammation.« less

Changes in pH and NADPH regulate the DNA binding activity of neuronal PAS domain protein 2, a mammalian circadian transcription factor.

PubMed

Yoshii, Katsuhiro; Tajima, Fumihisa; Ishijima, Sumio; Sagami, Ikuko

2015-01-20

Neuronal PAS domain protein 2 (NPAS2) is a core clock transcription factor that forms a heterodimer with BMAL1 to bind the E-box in the promoter of clock genes and is regulated by various environmental stimuli such as heme, carbon monoxide, and NAD(P)H. In this study, we investigated the effects of pH and NADPH on the DNA binding activity of NPAS2. In an electrophoretic mobility shift (EMS) assay, the pH of the reaction mixture affected the DNA binding activity of the NPAS2/BMAL1 heterodimer but not that of the BMAL1/BMAL1 homodimer. A change in pH from 7.0 to 7.5 resulted in a 1.7-fold increase in activity in the absence of NADPH, and NADPH additively enhanced the activity up to 2.7-fold at pH 7.5. The experiments using truncated mutants revealed that N-terminal amino acids 1-61 of NPAS2 were sufficient to sense the change in both pH and NADPH. We further analyzed the kinetics of formation and DNA binding of the NPAS2/BMAL1 heterodimer at various pH values. In the absence of NADPH, a change in pH from 6.5 to 8.0 decreased the KD(app) value of the E-box from 125 to 22 nM, with an 8-fold increase in the maximal level of DNA binding for the NPAS2/BMAL1 heterodimer. The addition of NADPH resulted in a further decrease in KD(app) to 9 nM at pH 8.0. Furthermore, NPAS2-dependent transcriptional activity in a luciferase assay using NIH3T3 cells also increased with the pH of the culture medium. These results suggest that NPAS2 has a role as a pH and metabolite sensor in regulating circadian rhythms.

Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis

PubMed Central

Pudasaini, Ashutosh; Shim, Jae Sung; Song, Young Hun; Shi, Hua; Kiba, Takatoshi; Somers, David E; Imaizumi, Takato; Zoltowski, Brian D

2017-01-01

A LOV (Light, Oxygen, or Voltage) domain containing blue-light photoreceptor ZEITLUPE (ZTL) directs circadian timing by degrading clock proteins in plants. Functions hinge upon allosteric differences coupled to the ZTL photocycle; however, structural and kinetic information was unavailable. Herein, we tune the ZTL photocycle over two orders of magnitude. These variants reveal that ZTL complexes with targets independent of light, but dictates enhanced protein degradation in the dark. In vivo experiments definitively show photocycle kinetics dictate the rate of clock component degradation, thereby impacting circadian period. Structural studies demonstrate that photocycle dependent activation of ZTL depends on an unusual dark-state conformation of ZTL. Crystal structures of ZTL LOV domain confirm delineation of structural and kinetic mechanisms and identify an evolutionarily selected allosteric hinge differentiating modes of PAS/LOV signal transduction. The combined biochemical, genetic and structural studies provide new mechanisms indicating how PAS/LOV proteins integrate environmental variables in complex networks. DOI: http://dx.doi.org/10.7554/eLife.21646.001 PMID:28244872

47 CFR Appendix B to Part 64 - Priority Access Service (PAS) for National Security and Emergency Preparedness (NSEP)

Code of Federal Regulations, 2013 CFR

2013-10-01

... providers as necessary to maintain the viability of the PAS system. 5. Maintain a database for PAS related... NSEP PAS database only to those having a need-to-know or who will not use the information for economic... selected for this priority should be responsible for ensuring the viability or reconstruction of the basic...

47 CFR Appendix B to Part 64 - Priority Access Service (PAS) for National Security and Emergency Preparedness (NSEP)

Code of Federal Regulations, 2011 CFR

2011-10-01

... providers as necessary to maintain the viability of the PAS system. 5. Maintain a database for PAS related... NSEP PAS database only to those having a need-to-know or who will not use the information for economic... selected for this priority should be responsible for ensuring the viability or reconstruction of the basic...

47 CFR Appendix B to Part 64 - Priority Access Service (PAS) for National Security and Emergency Preparedness (NSEP)

Code of Federal Regulations, 2014 CFR

2014-10-01

... providers as necessary to maintain the viability of the PAS system. 5. Maintain a database for PAS related... NSEP PAS database only to those having a need-to-know or who will not use the information for economic... selected for this priority should be responsible for ensuring the viability or reconstruction of the basic...

47 CFR Appendix B to Part 64 - Priority Access Service (PAS) for National Security and Emergency Preparedness (NSEP)

Code of Federal Regulations, 2012 CFR

2012-10-01

... providers as necessary to maintain the viability of the PAS system. 5. Maintain a database for PAS related... NSEP PAS database only to those having a need-to-know or who will not use the information for economic... selected for this priority should be responsible for ensuring the viability or reconstruction of the basic...

Pituitary Adenoma With Paraganglioma/Pheochromocytoma (3PAs) and Succinate Dehydrogenase Defects in Humans and Mice

PubMed Central

Xekouki, Paraskevi; Szarek, Eva; Bullova, Petra; Giubellino, Alessio; Quezado, Martha; Mastroyannis, Spyridon A.; Mastorakos, Panagiotis; Wassif, Christopher A.; Raygada, Margarita; Rentia, Nadia; Dye, Louis; Cougnoux, Antony; Koziol, Deloris; Sierra, Maria de La Luz; Lyssikatos, Charalampos; Belyavskaya, Elena; Malchoff, Carl; Moline, Jessica; Eng, Charis; Maher, Louis James; Pacak, Karel; Lodish, Maya

2015-01-01

Context: Germline mutations in genes coding succinate dehydrogenase (SDH) subunits A, B, C, and D have been identified in familial paragangliomas (PGLs)/pheochromocytomas (PHEOs) and other tumors. We described a GH-secreting pituitary adenoma (PA) caused by SDHD mutation in a patient with familial PGLs. Additional patients with PAs and SDHx defects have since been reported. Design: We studied 168 patients with unselected sporadic PA and with the association of PAs, PGLs, and/or pheochromocytomas, a condition we named the 3P association (3PAs) for SDHx germline mutations. We also studied the pituitary gland and hormonal profile of Sdhb+/− mice and their wild-type littermates at different ages. Results: No SDHx mutations were detected among sporadic PA, whereas three of four familial cases were positive for a mutation (75%). Most of the SDHx-deficient PAs were either prolactinomas or somatotropinomas. Pituitaries of Sdhb+/− mice older than 12 months had an increased number mainly of prolactin-secreting cells and several ultrastructural abnormalities such as intranuclear inclusions, altered chromatin nuclear pattern, and abnormal mitochondria. Igf-1 levels of mutant mice tended to be higher across age groups, whereas Prl and Gh levels varied according to age and sex. Conclusion: The present study confirms the existence of a new association that we termed 3PAs. It is due mostly to germline SDHx defects, although sporadic cases of 3PAs without SDHx defects also exist. Using Sdhb+/− mice, we provide evidence that pituitary hyperplasia in SDHx-deficient cells may be the initial abnormality in the cascade of events leading to PA formation. PMID:25695889

Searching for planetary nebulae at the Galactic halo via J-PAS and J-PLUS

NASA Astrophysics Data System (ADS)

Goncalves, Denise R.; Aparício-Villegas, Teresa; Akras, Stavros; Borges Fernandes, Marcelo; J-PAS Collaboration

2015-08-01

The Javalambre-Physics of the Accelerating Universe Astrophysical Survey (J-PAS) is a narrow-band imaging, very wide field cosmological survey to be carried out from a dedicated 2.5m telescope and a 4.7 sq.deg camera with 1.2Gpix. It will last 5 years and will observe 8500 sq.deg of Northern sky to a 5-σ magnitude depth for point sources, equivalent to i ~23.3 over an aperture of 2 arcsec2. The J-PAS filter system consists of 54 contiguous narrow band filters of 145-Å FWHM, from 3,500 to 10,000Å. Two broad-band filters will be added at the extremes, UV and IR, plus 3 SDSS g, r, and i filters. The Javalambre Photometric Local Universe Survye (J-PLUS) will be an auxiliary survey ofJ-PAS (mainly for calibration) with a dedicated 0.80m telescope. J-PLUS comprises 12 filters, including g, r, i and z SDSS ones. Though about 2,500 planetary nebulae (PNe, confirmed spectroscopically) are known in the Galaxy, only 14 objects have been convincingly identified as halo PNe. They were classified as such from their location, kinematics and chemistry. Halo PNe are able to reveal precious information for the study of low- and intermediate-mass star evolution and the early chemical conditions of the Galaxy. The characteristic low continuum and intense line emissions of PNe make them good objects to be searched by J-PAS, and even by J-PLUS. For instance, the halo PNe BoBn 1, DdDm 1 and PS 1, located somewhere between 11 and 24 kpc from the Sun, have B magnitudes of 16, 14 and 13.4, respectively. Such values are easily encompassed by J-PAS/J-PLUS, given the typical limit magnitude of the survey. Though covering a significantly smaller sky area, data from the ALHAMBRA survey were used to test our J-PAS/J-PLUS strategy to search for PNe. Our first results will be shown in this poster.

Pyrrolizidine alkaloids (PAs) in honey and pollen-legal regulation of PA levels in food and animal feed required.

PubMed

Kempf, Michael; Reinhard, Annika; Beuerle, Till

2010-01-01

Pyrrolizidine alkaloids (PAs) are secondary plant constituents that comprise about 400 different structures and occur in two major forms, a tertiary form and the corresponding N-oxide. PAs containing a 1,2-double bond are pre-toxins and metabolically activated by the action of hepatic P-450 enzymes to toxic pyrroles. Besides the acute toxic effects, the genotoxic and tumorigenicity potential of PAs was demonstrated in some eukaryotic model systems. Recently, the potential PA contamination of food and feeding stuff attracted recurrent great deals of attention. Humans are exposed to these toxins by consumption of herbal medicine, herbal teas, dietary supplements or food containing PA plant material. In numerous studies the potential threat to human health by PAs is stated. In pharmaceuticals, the use of these plants is regulated. Considering the PA concentrations observed especially in authentic honey from PA producing plants and pollen products, the results provoke an international regulation of PAs in food.

Exploratory studies of extended storage of apheresis platelets in a platelet additive solution (PAS)

PubMed Central

Corson, Jill; Jones, Mary Kay; Christoffel, Todd; Pellham, Esther; Bailey, S. Lawrence; Bolgiano, Doug

2014-01-01

To evaluate the poststorage viability of apheresis platelets stored for up to 18 days in 80% platelet additive solution (PAS)/20% plasma, 117 healthy subjects donated platelets using the Haemonetics MCS+, COBE Spectra (Spectra), or Trima Accel (Trima) systems. Control platelets from the same subjects were compared with their stored test PAS platelets by radiolabeling their stored and control platelets with either 51chromium or 111indium. Trima platelets met Food and Drug Administration poststorage platelet viability criteria for only 7 days vs almost 13 days for Haemonetics platelets; ie, platelet recoveries after these storage times averaged 44 ± 3% vs 49 ± 3% and survivals were 5.4 ± 0.3 vs 4.6 ± 0.3 days, respectively. The differences in storage duration are likely related to both the collection system and the storage bag. The Spectra and Trima platelets were hyperconcentrated during collection, and PAS was added, whereas the Haemonetics platelets were elutriated with PAS, which may have resulted in less collection injury. When Spectra and Trima platelets were stored in Haemonetics’ bags, poststorage viability was significantly improved. Platelet viability is better maintained in vitro than in vivo, allowing substantial increases in platelet storage times. However, implementation will require resolution of potential bacterial overgrowth during storage. PMID:24258816

Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.

PubMed

Kersting, Anna R; Mizrachi, Eshchar; Bornberg-Bauer, Erich; Myburg, Alexander A

2015-06-01

Eucalyptus is a pivotal genus within the rosid order Myrtales with distinct geographic history and adaptations. Comparative analysis of protein domain evolution in the newly sequenced Eucalyptus grandis genome and other rosid lineages sheds light on the adaptive mechanisms integral to the success of this genus of woody perennials. We reconstructed the ancestral domain content to elucidate the gain, loss and expansion of protein domains and domain arrangements in Eucalyptus in the context of rosid phylogeny. We used functional gene ontology (GO) annotation of genes to investigate the possible biological and evolutionary consequences of protein domain expansion. We found that protein modulation within the angiosperms occurred primarily on the level of expansion of certain domains and arrangements. Using RNA-Seq data from E. grandis, we showed that domain expansions have contributed to tissue-specific expression of tandemly duplicated genes. Our results indicate that tandem duplication of genes, a key feature of the Eucalyptus genome, has played an important role in the expansion of domains, particularly in proteins related to the specialization of reproduction and biotic and abiotic interactions affecting root and floral biology, and that tissue-specific expression of proteins with expanded domains has facilitated subfunctionalization in domain families. © 2014 University of Pretoria New Phytologist © 2014 New Phytologist Trust.

Bright blue-shifted fluorescent proteins with Cys in the GAF domain engineered from bacterial phytochromes: fluorescence mechanisms and excited-state dynamics.

PubMed

Hontani, Yusaku; Shcherbakova, Daria M; Baloban, Mikhail; Zhu, Jingyi; Verkhusha, Vladislav V; Kennis, John T M

2016-11-18

Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes (BphPs) are of great interest for in vivo imaging. They utilize biliverdin (BV) as a chromophore, which is a heme degradation product, and therefore they are straightforward to use in mammalian tissues. Here, we report on fluorescence properties of NIR FPs with key alterations in their BV binding sites. BphP1-FP, iRFP670 and iRFP682 have Cys residues in both PAS and GAF domains, rather than in the PAS domain alone as in wild-type BphPs. We found that NIR FP variants with Cys in the GAF or with Cys in both PAS and GAF show blue-shifted emission with long fluorescence lifetimes. In contrast, mutants with Cys in the PAS only or no Cys residues at all exhibit red-shifted emission with shorter lifetimes. Combining these results with previous biochemical and BphP1-FP structural data, we conclude that BV adducts bound to Cys in the GAF are the origin of bright blue-shifted fluorescence. We propose that the long fluorescence lifetime follows from (i) a sterically more constrained thioether linkage, leaving less mobility for ring A than in canonical BphPs, and (ii) that π-electron conjugation does not extend on ring A, making excited-state deactivation less sensitive to ring A mobility.

Covalently Linked Tandem Lesions in DNA

PubMed Central

Patrzyc, Helen B.; Dawidzik, Jean B.; Budzinski, Edwin E.; Freund, Harold G.; Wilton, John H.; Box, Harold C.

2013-01-01

Reactive oxygen species (ROS) generate a type of DNA damage called tandem lesions, two adjacent nucleotides both modified. A subcategory of tandem lesions consists of adjacent nucleotides linked by a covalent bond. Covalently linked tandem lesions generate highly characteristic liquid chromotography-tandem mass spectrometry (LC-MS/MS) elution profiles. We have used this property to comprehensively survey X-irradiated DNA for covalently linked tandem lesions. A total of 15 tandem lesions were detected in DNA irradiated in deoxygenated aqueous solution, five tandem lesions were detected in DNA that was irradiated in oxygenated solution. PMID:23106212

Laser diode bars based on strain-compensated AlGaPAs/GaAs heterostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marmalyuk, Aleksandr A; Ladugin, M A; Yarotskaya, I V

2012-01-31

Traditional (in the AlGaAs/GaAs system) and phosphorus-compensated (in the AlGaAs/AlGaPAs/GaAs system) laser heterostructures emitting at a wavelength of 850 nm are grown by MOVPE and studied. Laser diode bars are fabricated and their output characteristics are studied. The method used to grow heterolayers allowed us to control (minimise) mechanical stresses in the AlGaPAs/GaAs laser heterostructure, which made it possible to keep its curvature at the level of the initial curvature of the substrate. It is shown that the use of a compensated AlGaPAs/GaAs heterostructure improves the linear distribution of emitting elements in the near field of laser diode arrays andmore » allows the power - current characteristic to retain its slope at high pump currents owing to a uniform contact of all emitting elements with the heat sink. The radius of curvature of the grown compensated heterostructures turns out to be smaller than that of traditional heterostructures.« less

Comparison of multi-fiber reproducibility of PAS-MRI and Q-ball with empirical multiple b-value HARDI

NASA Astrophysics Data System (ADS)

Nath, Vishwesh; Schilling, Kurt G.; Blaber, Justin A.; Ding, Zhaohua; Anderson, Adam W.; Landman, Bennett A.

2017-02-01

Crossing fibers are prevalent in human brains and a subject of intense interest for neuroscience. Diffusion tensor imaging (DTI) can resolve tissue orientation but is blind to crossing fibers. Many advanced diffusion-weighted magnetic resolution imaging (MRI) approaches have been presented to extract crossing-fibers from high angular resolution diffusion imaging (HARDI), but the relative sensitivity and specificity of approaches remains unclear. Here, we examine two leading approaches (PAS and q-ball) in the context of a large-scale, single subject reproducibility study. A single healthy individual was scanned 11 times with 96 diffusion weighted directions and 10 reference volumes for each of five b-values (1000, 1500, 2000, 2500, 3000 s/mm2) for a total of 5830 volumes (over the course of three sessions). We examined the reproducibility of the number of fibers per voxel, volume fraction, and crossing-fiber angles. For each method, we determined the minimum resolvable angle for each acquisition. Reproducibility of fiber counts per voxel was generally high ( 80% consensus for PAS and 70% for q-ball), but there was substantial bias between individual repetitions and model estimated with all data ( 10% lower consensus for PAS and 15% lower for q-ball). Both PAS and q-ball predominantly discovered fibers crossing at near 90 degrees, but reproducibility was higher for PAS across most measures. Within voxels with low anisotropy, q-ball finds more intra-voxel structure; meanwhile, PAS resolves multiple fibers at greater than 75 degrees for more voxels. These results can inform researchers when deciding between HARDI approaches or interpreting findings across studies.

Intra-domain phage display (ID-PhD) of peptides and protein mini-domains censored from canonical pIII phage display.

PubMed

Tjhung, Katrina F; Deiss, Frédérique; Tran, Jessica; Chou, Ying; Derda, Ratmir

2015-01-01

In this paper, we describe multivalent display of peptide and protein sequences typically censored from traditional N-terminal display on protein pIII of filamentous bacteriophage M13. Using site-directed mutagenesis of commercially available M13KE phage cloning vector, we introduced sites that permit efficient cloning using restriction enzymes between domains N1 and N2 of the pIII protein. As infectivity of phage is directly linked to the integrity of the connection between N1 and N2 domains, intra-domain phage display (ID-PhD) allows for simple quality control of the display and the natural variations in the displayed sequences. Additionally, direct linkage to phage propagation allows efficient monitoring of sequence cleavage, providing a convenient system for selection and evolution of protease-susceptible or protease-resistant sequences. As an example of the benefits of such an ID-PhD system, we displayed a negatively charged FLAG sequence, which is known to be post-translationally excised from pIII when displayed on the N-terminus, as well as positively charged sequences which suppress production of phage when displayed on the N-terminus. ID-PhD of FLAG exhibited sub-nanomolar apparent Kd suggesting multivalent nature of the display. A TEV-protease recognition sequence (TEVrs) co-expressed in tandem with FLAG, allowed us to demonstrate that 99.9997% of the phage displayed the FLAG-TEVrs tandem and can be recognized and cleaved by TEV-protease. The residual 0.0003% consisted of phage clones that have excised the insert from their genome. ID-PhD is also amenable to display of protein mini-domains, such as the 33-residue minimized Z-domain of protein A. We show that it is thus possible to use ID-PhD for multivalent display and selection of mini-domain proteins (Affibodies, scFv, etc.).

Coupling of tandem Smad ubiquitination regulatory factor (Smurf) WW domains modulates target specificity.

PubMed

Chong, P Andrew; Lin, Hong; Wrana, Jeffrey L; Forman-Kay, Julie D

2010-10-26

Smad ubiquitination regulatory factor 2 (Smurf2) is an E3 ubiquitin ligase that participates in degradation of TGF-β receptors and other targets. Smurf2 WW domains recognize PPXY (PY) motifs on ubiquitin ligase target proteins or on adapters, such as Smad7, that bind to E3 target proteins. We previously demonstrated that the isolated WW3 domain of Smurf2, but not the WW2 domain, can directly bind to a Smad7 PY motif. We show here that the WW2 augments this interaction by binding to the WW3 and making auxiliary contacts with the PY motif and a novel E/D-S/T-P motif, which is N-terminal to all Smad PY motifs. The WW2 likely enhances the selectivity of Smurf2 for the Smad proteins. NMR titrations confirm that Smad1 and Smad2 are bound by Smurf2 with the same coupled WW domain arrangement used to bind Smad7. The analogous WW domains in the short isoform of Smurf1 recognize the Smad7 PY peptide using the same coupled mechanism. However, a longer Smurf1 isoform, which has an additional 26 residues in the inter-WW domain linker, is only partially able to use the coupled WW domain binding mechanism. The longer linker results in a decrease in affinity for the Smad7 peptide. Interdomain coupling of WW domains enhances selectivity and enables the tuning of interactions by isoform switching.

Coupling of tandem Smad ubiquitination regulatory factor (Smurf) WW domains modulates target specificity

PubMed Central

Chong, P. Andrew; Lin, Hong; Wrana, Jeffrey L.; Forman-Kay, Julie D.

2010-01-01

Smad ubiquitination regulatory factor 2 (Smurf2) is an E3 ubiquitin ligase that participates in degradation of TGF-β receptors and other targets. Smurf2 WW domains recognize PPXY (PY) motifs on ubiquitin ligase target proteins or on adapters, such as Smad7, that bind to E3 target proteins. We previously demonstrated that the isolated WW3 domain of Smurf2, but not the WW2 domain, can directly bind to a Smad7 PY motif. We show here that the WW2 augments this interaction by binding to the WW3 and making auxiliary contacts with the PY motif and a novel E/D-S/T-P motif, which is N-terminal to all Smad PY motifs. The WW2 likely enhances the selectivity of Smurf2 for the Smad proteins. NMR titrations confirm that Smad1 and Smad2 are bound by Smurf2 with the same coupled WW domain arrangement used to bind Smad7. The analogous WW domains in the short isoform of Smurf1 recognize the Smad7 PY peptide using the same coupled mechanism. However, a longer Smurf1 isoform, which has an additional 26 residues in the inter-WW domain linker, is only partially able to use the coupled WW domain binding mechanism. The longer linker results in a decrease in affinity for the Smad7 peptide. Interdomain coupling of WW domains enhances selectivity and enables the tuning of interactions by isoform switching. PMID:20937913

Anxiety in early Parkinson's disease: Validation of the Italian observer-rated version of the Parkinson Anxiety Scale (OR-PAS).

PubMed

Santangelo, Gabriella; Falco, Fabrizia; D'Iorio, Alfonsina; Cuoco, Sofia; Raimo, Simona; Amboni, Marianna; Pellecchia, Maria Teresa; Longo, Katia; Vitale, Carmine; Barone, Paolo

2016-08-15

Anxiety disorders are common in Parkinson's Disease (PD) and their identification is relevant even at early stages. The Parkinson Anxiety Scale (PAS) evaluates anxiety in PD; it was used only in the original validation study in PD patients mainly at 2-3 stages of Hoehn & Yahr system (H&Y). The study aimed to investigate psychometric properties of observer-rated version of the PAS (OR-PAS), prevalence rate of anxiety and its features, compared with diagnostic criteria in early PD patients. A sample of 101 PD patients with H&Y:1-2 underwent the OR-PAS. To assess convergent and divergent validity, PD patients underwent Beck Anxiety Inventory, and scales assessing depression, apathy, anhedonia and cognition. To diagnose anxiety disorders, Mini International Neuropsychiatric Inventory was used as gold standard. A "receiver operating characteristics" curve was obtained; positive and negative predictive values were calculated for different cut-off points of the OR-PAS and its subscales. There was no missing data, no floor and ceiling effects; mean score was 12.2±10.1; Cronbach's alpha was 0.899. The OR-PAS showed good convergent and divergent validity. Maximum discrimination was obtained with a cut-off score of 8.5. The anxiety occurred in 59 patients (58.4%). The OR-PAS is a reliable and valid screening instrument for assessing anxiety in patients at early PD. Anxiety was found in 58.4% of PD patients, demonstrating that anxiety occurs even at early stages. Copyright © 2016 Elsevier B.V. All rights reserved.

Orthogonal tandem catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lohr, Tracy L.; Marks, Tobin J.

2015-05-20

Tandem catalysis is a growing field that is beginning to yield important scientific and technological advances toward new and more efficient catalytic processes. 'One-pot' tandem reactions, where multiple catalysts and reagents, combined in a single reaction vessel undergo a sequence of precisely staged catalytic steps, are highly attractive from the standpoint of reducing both waste and time. Orthogonal tandem catalysis is a subset of one-pot reactions in which more than one catalyst is used to promote two or more mechanistically distinct reaction steps. This Perspective summarizes and analyses some of the recent developments and successes in orthogonal tandem catalysis, withmore » particular focus on recent strategies to address catalyst incompatibility. We also highlight the concept of thermodynamic leveraging by coupling multiple catalyst cycles to effect challenging transformations not observed in single-step processes, and to encourage application of this technique to energetically unfavourable or demanding reactions.« less

Step-Scan T-Cell Fourier Transform Infrared Photoacoustic Spectroscopy (FTIR-PAS) for Monitoring Environmental Air Pollutants

NASA Astrophysics Data System (ADS)

Liu, Lixian; Mandelis, Andreas; Melnikov, Alexander; Michaelian, Kirk; Huan, Huiting; Haisch, Christoph

2016-07-01

Air pollutants have adverse effects on the Earth's climate system. There is an urgent need for cost-effective devices capable of recognizing and detecting various ambient pollutants. An FTIR photoacoustic spectroscopy (FTIR-PAS) method based on a commercial FTIR spectrometer developed for air contamination monitoring will be presented. A resonant T-cell was determined to be the most appropriate resonator in view of the low-frequency requirement and space limitations in the sample compartment. Step-scan FTIR-PAS theory for regular cylinder resonator has been described as a reference for prediction of T-cell vibration principles. Both simulated amplitude and phase responses of the T-cell show good agreement with measurement data Carbon dioxide IR absorption spectra were used to demonstrate the capacity of the FTIR-PAS method to detect ambient pollutants. The theoretical detection limit for carbon dioxide was found to be 4 ppmv. A linear response to carbon dioxide concentration was found in the range from 2500 ppmv to 5000 ppmv. The results indicate that it is possible to use step-scan FTIR-PAS with a T-cell as a quantitative method for analysis of ambient contaminants.

Toxins vapC and pasB from prokaryotic TA modules remain active in mammalian cancer cells.

PubMed

Wieteska, Łukasz; Skulimowski, Aleksander; Cybula, Magdalena; Szemraj, Janusz

2014-09-30

Among the great number of addictive modules which have been discovered, only a few have been characterized. However, research concerning the adoption of toxins from these systems shows their great potential as a tool for molecular biology and medicine. In our study, we tested two different toxins derived from class II addictive modules, pasAB from plasmid pTF-FC2 (Thiobacillus ferrooxidans) and vapBC 2829Rv (Mycobacterium tuberculosis), in terms of their usefulness as growth inhibitors of human cancer cell lines, namely KYSE 30, MCF-7 and HCT 116. Transfection of the pasB and vapC genes into the cells was conducted with the use of two different expression systems. Cellular effects, such as apoptosis, necrosis and changes in the cell cycle, were tested by applying flow cytometry with immunofluorescence staining. Our findings demonstrated that toxins VapC and PasB demonstrate proapoptotic activity in the human cancer cells, regardless of the expression system used. As for the toxin PasB, observed changes were more subtle than for the VapC. The level of expression for both the genes was monitored by QPCR and did not reveal statistically significant differences within the same cell line.

An analysis of characteristics of post-authorisation studies registered on the ENCePP EU PAS Register

PubMed Central

Carroll, Robert; Ramagopalan, Sreeram V.; Cid-Ruzafa, Javier; Lambrelli, Dimitra; McDonald, Laura

2017-01-01

Background: The objective of this study was to investigate the study design characteristics of Post-Authorisation Studies (PAS) requested by the European Medicines Agency which were recorded on the European Union (EU) PAS Register held by the European Network of Centres for Pharmacoepidemiology and Pharmacovigilance (ENCePP). Methods: We undertook a cross-sectional descriptive analysis of all studies registered on the EU PAS Register as of 18 th October 2016. Results: We identified a total of 314 studies on the EU PAS Register, including 81 (26%) finalised, 160 (51%) ongoing and 73 (23%) planned. Of those studies identified, 205 (65%) included risk assessment in their scope, 133 (42%) included drug utilisation and 94 (30%) included effectiveness evaluation. Just over half of the studies (175; 56%) used primary data capture, 135 (43%) used secondary data and 4 (1%) used a hybrid design combining both approaches. Risk assessment and effectiveness studies were more likely to use primary data capture (60% and 85% respectively as compared to 39% and 14% respectively for secondary). The converse was true for drug utilisation studies where 59% were secondary vs. 39% for primary. For type 2 diabetes mellitus, database studies were more commonly used (80% vs 3% chart review, 3% hybrid and 13% primary data capture study designs) whereas for studies in oncology, primary data capture were more likely to be used (85% vs 4% chart review, and 11% database study designs). Conclusions: Results of this analysis show that PAS design varies according to study objectives and therapeutic area. PMID:29188016

Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.

PubMed

Kung, Camy C-H; Naik, Mandar T; Wang, Szu-Huan; Shih, Hsiu-Ming; Chang, Che-Chang; Lin, Li-Ying; Chen, Chia-Lin; Ma, Che; Chang, Chi-Fon; Huang, Tai-Huang

2014-08-15

The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.

Achieving 15% Tandem Polymer Solar Cells

DTIC Science & Technology

2015-06-23

solar cell structures – both polymer only and hybrid tandem cells to constantly pushing the envelope of solution processed solar cell ...performance – 11.6% polymer tandem cell , 7% transparent tandem polymer cell , and over 10% PCE hybrid tandem solar cells were achieved. In addition, AFOSR’s...final support also enabled us to explore novel hybrid perovskite solar cells in depth. For example, single junction cell efficiency

Experimental study on spatio-temporal behavior of a single particle forming a particle accumulation structure (PAS) in half-zone liquid bridge

NASA Astrophysics Data System (ADS)

Oba, Takeru; Ueno, Ichiro; Kaneko, Toshihiro

2017-11-01

We focus on particle behavior due to thermocapillary-driven convection in a half-zone liquid bridge of high-Prandtl number fluid. It has been known that the suspended particles exhibit a unique solid-like structure known as 'particle accumulation structure (PAS)' in a rotating frame of reference with traveling-type hydrothermal wave. It is said that PAS is caused by interaction between particles and the free surface of a half-zone liquid bridge. Such structures arise even under small Stokes number conditions. When observing PAS two-dimensionally, it looks like a closed single string, but the actual movement of particles is different. Therefore we employ three-dimensional particle tracking velocimetry to the half-zone liquid bridge of 2.5 mm in radius and 1.7 mm in height, and detect the particle behaviors close to the free surface. We explain the spatio-temporal correlation between the solid-like global structure of PAS and the local particle motions, and make comparisons with proposed physical models of PAS formation.

Evaluation of the Alphasense Optical Particle Counter (OPC-N2) and the Grimm Portable Aerosol Spectrometer (PAS-1.108)

PubMed Central

Sousan, Sinan; Koehler, Kirsten; Hallett, Laura; Peters, Thomas M.

2017-01-01

We compared the performance of a low-cost (∼$500), compact optical particle counter (OPC, OPC-N2, Alphasense) to another OPC (PAS-1.108, Grimm Technologies) and reference instruments. We measured the detection efficiency of the OPCs by size from 0.5 to 5 μm for monodispersed, polystyrene latex (PSL) spheres. We then compared number and mass concentrations measured with the OPCs to those measured with reference instruments for three aerosols: salt, welding fume and Arizona road dust. The OPC-N2 detection efficiency for monodispersed was similar to the PAS-1.108 for particles larger than 0.8 μm (minimum of 79% at 1 μm and maximum of 101% at 3 μm). For 0.5-μm particles, the detection efficiency of OPCN2 was underestimated at 78%, whereas PAS-1.108 overestimated concentrations by 183%. The mass concentrations from the OPCs were linear (r ≥ 0.97) with those from the reference instruments for all aerosols, although the slope and intercept were different. The mass concentrations were overestimated for dust (OPC-N2, slope = 1.6; PAS-1.108, slope = 2.7) and underestimated for welding fume (OPC-N2, slope = 0.05; PAS-1.108, slope = 0.4). The coefficient of variation (CV, precision) for OPC-N2 for all experiments was between 4.2% and 16%. These findings suggest that, given site-specific calibrations, the OPC-N2 can provide number and mass concentrations similar to the PAS-1.108 for particles larger than 1 μm. PMID:28871213

Evaluation of the Alphasense Optical Particle Counter (OPC-N2) and the Grimm Portable Aerosol Spectrometer (PAS-1.108).

PubMed

Sousan, Sinan; Koehler, Kirsten; Hallett, Laura; Peters, Thomas M

2016-01-01

We compared the performance of a low-cost (∼$500), compact optical particle counter (OPC, OPC-N2, Alphasense) to another OPC (PAS-1.108, Grimm Technologies) and reference instruments. We measured the detection efficiency of the OPCs by size from 0.5 to 5 μm for monodispersed, polystyrene latex (PSL) spheres. We then compared number and mass concentrations measured with the OPCs to those measured with reference instruments for three aerosols: salt, welding fume and Arizona road dust. The OPC-N2 detection efficiency for monodispersed was similar to the PAS-1.108 for particles larger than 0.8 μm (minimum of 79% at 1 μm and maximum of 101% at 3 μm). For 0.5-μm particles, the detection efficiency of OPCN2 was underestimated at 78%, whereas PAS-1.108 overestimated concentrations by 183%. The mass concentrations from the OPCs were linear (r ≥ 0.97) with those from the reference instruments for all aerosols, although the slope and intercept were different. The mass concentrations were overestimated for dust (OPC-N2, slope = 1.6; PAS-1.108, slope = 2.7) and underestimated for welding fume (OPC-N2, slope = 0.05; PAS-1.108, slope = 0.4). The coefficient of variation (CV, precision) for OPC-N2 for all experiments was between 4.2% and 16%. These findings suggest that, given site-specific calibrations, the OPC-N2 can provide number and mass concentrations similar to the PAS-1.108 for particles larger than 1 μm.

Patency of Saphenous Vein Grafts Using the PAS-Port System During Coronary Artery Bypass Surgery.

PubMed

Kubota, Hiroshi; Endo, Hidehito; Ishii, Hikaru; Tsuchiya, Hiroshi; Takahashi, Yu; Inaba, Yusuke; Noma, Mio; Yoshimoto, Akihiro; Higuchi, Satoshi; Kohshoh, Hideyasu; Taniai, Seiichi; Ishiguro, Haruhisa; Yoshino, Hideaki; Sudo, Kenichi

2017-08-01

Several proximal anastomosis devices have been developed to shorten the time required for a proximal anastomosis and to avoid aortic cross-/side-clamping during coronary artery bypass grafting. This study retrospectively examined the patency of saphenous vein grafts (SVGs) using the PAS-Port System (Cardia Inc, Redwood City, CA). From 2004 to 2014, 451 patients underwent coronary artery bypass graft operations requiring at least 1 proximal anastomosis using a PAS-Port device. A total of 802 PAS-Port devices were used, and 95.0% (762 of 802) were implanted successfully. Among the successfully implanted anastomoses, 76.8% (585 of 762) were evaluated using coronary angiography or multidimensional computed tomography, or both. The evaluations were performed between postoperative days 4 and 3,182 (mean, 319 ± 624 days). The early (1 to 365 days) and the midterm to long-term (more than 366 days) occlusion rates were examined. A complete postoperative clinical course was recorded for 70.7% of the patients. Overall, 93.8% (549 of 585) of the device-dependent SVGs were patent. The patency rates of device-dependent SVGs that were 1, 2, 3, 4, 5, 6, 7, and 8 years old were 90.1% ± 1.8%, 87.1% ± 2.3%, 86.1% ± 2.5%, 82.9% ± 3.3%, 80.6% ± 3.9%, 77.2% ± 5.0%, 77.2% ± 5.0%, and 70.2% ± 8.1%, respectively. The longest follow-up period was 3,182 days (8.7 years). The occlusion rate for device-dependent SVGs tended to decrease as the number of patients accumulated. The PAS-Port system provided acceptable SVG patency and clinical outcome for the early and midterm to long-term. There may be a learning curve for the use of PAS-Port device that affects the device-dependent SVG patency. Copyright © 2017 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

The HARP domain dictates the annealing helicase activity of HARP/SMARCAL1.

PubMed

Ghosal, Gargi; Yuan, Jingsong; Chen, Junjie

2011-06-01

Mutations in HepA-related protein (HARP, or SMARCAL1) cause Schimke immunoosseous dysplasia (SIOD). HARP has ATP-dependent annealing helicase activity, which helps to stabilize stalled replication forks and facilitate DNA repair during replication. Here, we show that the conserved tandem HARP (2HP) domain dictates this annealing helicase activity. Furthermore, chimeric proteins generated by fusing the 2HP domain of HARP with the SNF2 domain of BRG1 or HELLS show annealing helicase activity in vitro and, when targeted to replication forks, mimic the functions of HARP in vivo. We propose that the HARP domain endows HARP with this ATP-driven annealing helicase activity.

A comprehensive protein-protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1.

PubMed

DeMille, Desiree; Bikman, Benjamin T; Mathis, Andrew D; Prince, John T; Mackay, Jordan T; Sowa, Steven W; Hall, Tacie D; Grose, Julianne H

2014-07-15

Per-Arnt-Sim (PAS) kinase is a sensory protein kinase required for glucose homeostasis in yeast, mice, and humans, yet little is known about the molecular mechanisms of its function. Using both yeast two-hybrid and copurification approaches, we identified the protein-protein interactome for yeast PAS kinase 1 (Psk1), revealing 93 novel putative protein binding partners. Several of the Psk1 binding partners expand the role of PAS kinase in glucose homeostasis, including new pathways involved in mitochondrial metabolism. In addition, the interactome suggests novel roles for PAS kinase in cell growth (gene/protein expression, replication/cell division, and protein modification and degradation), vacuole function, and stress tolerance. In vitro kinase studies using a subset of 25 of these binding partners identified Mot3, Zds1, Utr1, and Cbf1 as substrates. Further evidence is provided for the in vivo phosphorylation of Cbf1 at T211/T212 and for the subsequent inhibition of respiration. This respiratory role of PAS kinase is consistent with the reported hypermetabolism of PAS kinase-deficient mice, identifying a possible molecular mechanism and solidifying the evolutionary importance of PAS kinase in the regulation of glucose homeostasis. © 2014 DeMille et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Faux-Pas Test: A Proposal of a Standardized Short Version.

PubMed

Fernández-Modamio, Mar; Arrieta-Rodríguez, Marta; Bengochea-Seco, Rosario; Santacoloma-Cabero, Iciar; Gómez de Tojeiro-Roce, Juan; García-Polavieja, Bárbara; González-Fraile, Eduardo; Martín-Carrasco, Manuel; Griffin, Kim; Gil-Sanz, David

2018-06-26

Previous research on theory of mind suggests that people with schizophrenia have difficulties with complex mentalization tasks that involve the integration of cognition and affective mental states. One of the tools most commonly used to assess theory of mind is the Faux-Pas Test. However, it presents two main methodological problems: 1) the lack of a standard scoring system; 2) the different versions are not comparable due to a lack of information on the stories used. These methodological problems make it difficult to draw conclusions about performance on this test by people with schizophrenia. The aim of this study was to develop a reduced version of the Faux-Pas test with adequate psychometric properties. The test was administered to control and clinical groups. Interrater and test-retest reliability were analyzed for each story in order to select the set of 10 stories included in the final reduced version. The shortened version showed good psychometric properties for controls and patients: test-retest reliability of 0.97 and 0.78, inter-rater reliability of 0.95 and 0.87 and Cronbach's alpha of 0.82 and 0.72.

Step-scan T cell-based differential Fourier transform infrared photoacoustic spectroscopy (DFTIR-PAS) for detection of ambient air contaminants

NASA Astrophysics Data System (ADS)

Liu, Lixian; Mandelis, Andreas; Huan, Huiting; Melnikov, Alexander

2016-10-01

A step-scan differential Fourier transform infrared photoacoustic spectroscopy (DFTIR-PAS) using a commercial FTIR spectrometer was developed theoretically and experimentally for air contaminant monitoring. The configuration comprises two identical, small-size and low-resonance-frequency T cells satisfying the conflicting requirements of low chopping frequency and limited space in the sample compartment. Carbon dioxide (CO2) IR absorption spectra were used to demonstrate the capability of the DFTIR-PAS method to detect ambient pollutants. A linear amplitude response to CO2 concentrations from 100 to 10,000 ppmv was observed, leading to a theoretical detection limit of 2 ppmv. The differential mode was able to suppress the coherent noise, thereby imparting the DFTIR-PAS method with a better signal-to-noise ratio and lower theoretical detection limit than the single mode. The results indicate that it is possible to use step-scan DFTIR-PAS with T cells as a quantitative method for high sensitivity analysis of ambient contaminants.

TANDEM: matching proteins with tandem mass spectra.

PubMed

Craig, Robertson; Beavis, Ronald C

2004-06-12

Tandem mass spectra obtained from fragmenting peptide ions contain some peptide sequence specific information, but often there is not enough information to sequence the original peptide completely. Several proprietary software applications have been developed to attempt to match the spectra with a list of protein sequences that may contain the sequence of the peptide. The application TANDEM was written to provide the proteomics research community with a set of components that can be used to test new methods and algorithms for performing this type of sequence-to-data matching. The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors.

A TALE-inspired computational screen for proteins that contain approximate tandem repeats.

PubMed

Perycz, Malgorzata; Krwawicz, Joanna; Bochtler, Matthias

2017-01-01

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.

Software for peak finding and elemental composition assignment for glycosaminoglycan tandem mass spectra.

PubMed

Hogan, John D; Klein, Joshua A; Wu, Jiandong; Chopra, Pradeep; Boons, Geert-Jan; Carvalho, Luis; Lin, Cheng; Zaia, Joseph

2018-04-03

Glycosaminoglycans (GAGs) covalently linked to proteoglycans (PGs) are characterized by repeating disaccharide units and variable sulfation patterns along the chain. GAG length and sulfation patterns impact disease etiology, cellular signaling, and structural support for cells. We and others have demonstrated the usefulness of tandem mass spectrometry (MS2) for assigning the structures of GAG saccharides; however, manual interpretation of tandem mass spectra is time-consuming, so computational methods must be employed. In the proteomics domain, the identification of monoisotopic peaks and charge states relies on algorithms that use averagine, or the average building block of the compound class being analyzed. While these methods perform well for protein and peptide spectra, they perform poorly on GAG tandem mass spectra, due to the fact that a single average building block does not characterize the variable sulfation of GAG disaccharide units. In addition, it is necessary to assign product ion isotope patterns in order to interpret the tandem mass spectra of GAG saccharides. To address these problems, we developed GAGfinder, the first tandem mass spectrum peak finding algorithm developed specifically for GAGs. We define peak finding as assigning experimental isotopic peaks directly to a given product ion composition, as opposed to deconvolution or peak picking, which are terms more accurately describing the existing methods previously mentioned. GAGfinder is a targeted, brute force approach to spectrum analysis that utilizes precursor composition information to generate all theoretical fragments. GAGfinder also performs peak isotope composition annotation, which is typically a subsequent step for averagine-based methods. Data are available via ProteomeXchange with identifier PXD009101. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Detecting long tandem duplications in genomic sequences.

PubMed

Audemard, Eric; Schiex, Thomas; Faraut, Thomas

2012-05-08

Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,(a) we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS  <  1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations.

PAs and NPs in an emergency room-linked acute care clinic.

PubMed

Currey, C J

1984-12-01

The use of hospital emergency rooms for nonurgent care during evenings hours often strains medical resources and may affect the quality of emergency care. One facility's effective use of an after-hours acute care clinic staffed by PAs and NPs to divert nonurgent problems away from its emergency room is outlined. PAs and NPs work during peak demand hours (evenings and weekends) under the supervision of an emergency room physician, and receive supplementary support from other emergency room personnel. Incoming patients are referred to the emergency room or acute care clinic, depending on the nature of their problems. Acute care clinic patients are then treated by the PA or NP and either released or referred to an emergency room physician, if their conditions warrant additional treatment. As a result, use of the acute care clinic has greatly reduced the amount of non-urgent medical treatment in the emergency room and has provided other advantages to both patients and staff as well. These advantages and the encouraging statistics following six months of the clinic's operation are discussed.

The protease ClpXP and the PAS-domain protein DivL regulate CtrA and gene transfer agent production in Rhodobacter capsulatus.

PubMed

Westbye, A B; Kater, L; Wiesmann, C; Ding, H; Yip, C K; Beatty, J T

2018-04-06

Several members of the Rhodobacterales ( Alphaproteobacteria ) produce a conserved horizontal gene transfer vector, called gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system to study GTA biology is the R. capsulatus GTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in the Alphaproteobacteria and is an essential regulator of RcGTA production: it controls production and maturation of the RcGTA particle and RcGTA release from cells. CtrA also controls the natural transformation-like system required for cells to receive RcGTA-donated DNA. Here, we report that a dysregulation of the CckA-ChpT-CtrA phosphorelay - either by loss of the PAS-domain protein DivL or by substituting the autophosphorylation residue of the hybrid histidine kinase CckA - decreased CtrA phosphorylation and greatly increased RcGTA protein production in R. capsulatus We show that a loss of the ClpXP protease or the three C-terminal residues of CtrA resulted in increased CtrA levels in R. capsulatus, and identify ClpX(P) as essential for maturation of RcGTA particles. Furthermore, we show that CtrA phosphorylation is important for head spike production. Our results provide novel insight into the regulation of CtrA and GTAs in the Rhodobacterales Importance Members of the Rhodobacterales are abundant in ocean and fresh water environments. The conserved GTA produced by many Rhodobacterales may have an important role in horizontal gene transfer (HGT) in aquatic environments and provide a significant contribution to their adaptation. GTA production is controlled by bacterial regulatory systems, including the conserved CckA-ChpT-CtrA phosphorelay, however several questions about GTA regulation remains. Our identification that a 'short' DivL homologue and ClpXP regulate CtrA in R. capsulatus extends the model of CtrA regulation from Caulobacter crescentus to a member

Mapping the Free Energy Landscape of PKA Inhibition and Activation: A Double-Conformational Selection Model for the Tandem cAMP-Binding Domains of PKA RIα

PubMed Central

Akimoto, Madoka; McNicholl, Eric Tyler; Ramkissoon, Avinash; Moleschi, Kody; Taylor, Susan S.; Melacini, Giuseppe

2015-01-01

Protein Kinase A (PKA) is the major receptor for the cyclic adenosine monophosphate (cAMP) secondary messenger in eukaryotes. cAMP binds to two tandem cAMP-binding domains (CBD-A and -B) within the regulatory subunit of PKA (R), unleashing the activity of the catalytic subunit (C). While CBD-A in RIα is required for PKA inhibition and activation, CBD-B functions as a “gatekeeper” domain that modulates the control exerted by CBD-A. Preliminary evidence suggests that CBD-B dynamics are critical for its gatekeeper function. To test this hypothesis, here we investigate by Nuclear Magnetic Resonance (NMR) the two-domain construct RIα (91–379) in its apo, cAMP2, and C-bound forms. Our comparative NMR analyses lead to a double conformational selection model in which each apo CBD dynamically samples both active and inactive states independently of the adjacent CBD within a nearly degenerate free energy landscape. Such degeneracy is critical to explain the sensitivity of CBD-B to weak interactions with C and its high affinity for cAMP. Binding of cAMP eliminates this degeneracy, as it selectively stabilizes the active conformation within each CBD and inter-CBD contacts, which require both cAMP and W260. The latter is contributed by CBD-B and mediates capping of the cAMP bound to CBD-A. The inter-CBD interface is dispensable for intra-CBD conformational selection, but is indispensable for full activation of PKA as it occludes C-subunit recognition sites within CBD-A. In addition, the two structurally homologous cAMP-bound CBDs exhibit marked differences in their residual dynamics profiles, supporting the notion that conservation of structure does not necessarily imply conservation of dynamics. PMID:26618408

Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins

PubMed Central

Jung, Huihun; Pena-Francesch, Abdon; Saadat, Alham; Sebastian, Aswathy; Kim, Dong Hwan; Hamilton, Reginald F.; Albert, Istvan; Allen, Benjamin D.; Demirel, Melik C.

2016-01-01

Many globular and structural proteins have repetitions in their sequences or structures. However, a clear relationship between these repeats and their contribution to the mechanical properties remains elusive. We propose a new approach for the design and production of synthetic polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions. Our designed sequences are based on a structural protein produced in squid suction cups that has a segmented copolymer structure with amorphous and crystalline domains. We produced segmented polypeptides with varying repeat number, while keeping the lengths and compositions of the amorphous and crystalline regions fixed. We showed that mechanical properties of these synthetic proteins could be tuned by modulating their molecular weights. Specifically, the toughness and extensibility of synthetic polypeptides increase as a function of the number of tandem repeats. This result suggests that the repetitions in native squid proteins could have a genetic advantage for increased toughness and flexibility. PMID:27222581

A TALE-inspired computational screen for proteins that contain approximate tandem repeats

PubMed Central

Krwawicz, Joanna

2017-01-01

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen. PMID:28617832

Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems

PubMed Central

Makarova, Kira S.; Wolf, Yuri I.

2017-01-01

ABSTRACT The two-component signal transduction (TCS) machinery is a key mechanism of sensing environmental changes in the prokaryotic world. TCS systems have been characterized thoroughly in bacteria but to a much lesser extent in archaea. Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data. We describe the domain architectures of the archaeal TCS components, including several novel output domains, and discuss the evolution of the archaeal TCS machinery. The distribution of TCS systems in archaea is strongly biased, with high levels of abundance in haloarchaea and thaumarchaea but none detected in the sequenced genomes from the phyla Crenarchaeota, Nanoarchaeota, and Korarchaeota. The archaeal sensor histidine kinases are generally similar to their well-studied bacterial counterparts but are often located in the cytoplasm and carry multiple PAS and/or GAF domains. In contrast, archaeal response regulators differ dramatically from the bacterial ones. Most archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. Instead, archaea encode multiple copies of response regulators containing either the stand-alone receiver (REC) domain or combinations of REC with PAS and/or GAF domains. Therefore, the prevailing mechanism of archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation. IMPORTANCE Although the Archaea represent a separate domain of life, their signaling systems have been assumed to be closely similar to the bacterial ones. A study of the domain architectures of the archaeal two-component signal transduction (TCS) machinery

Optical characterization of semiconductor materials by using FTIR-PAS

NASA Astrophysics Data System (ADS)

Arévalo, Fabiola; Saavedra, Renato; Paulraj, M.

2008-11-01

In this paper we discuss the procedures for photoacoustic measurements for semiconducting materials, including bulk samples like Gallium Antimonide (GaSb). The optical absorption at photon energies near the band gap was measured at room temperature using Fourier Transform Infrared Photoacoustic spectroscopy (FTIR-PAS). Measurements were performed using a NEXUS 670 FTIR-spectrometer (from Thermo Nicolet) with a MTEC model 300 PA cell (MTEC Photoacoustics, Inc.). Optical properties of the studied samples were determined from their room temperature PA spectra and band gaps were calculated directly from absorption spectra

The Tandem CARDs of NOD2: Intramolecular Interactions and Recognition of RIP2

PubMed Central

Fridh, Veronica; Rittinger, Katrin

2012-01-01

Caspase recruitment domains (CARDs) are homotypic protein interaction modules that link the stimulus-dependent assembly of large signaling platforms such as inflammasomes to the activation of downstream effectors that often include caspases and kinases and thereby play an important role in the regulation of inflammatory and apoptotic signaling pathways. NOD2 belongs to the NOD-like (NLR) family of intracellular pattern recognition receptors (PRR) and induces activation of the NF-κB pathway in response to the recognition of bacterial components. This process requires the specific recognition of the CARD of the protein kinase RIP2 by the tandem CARDs of NOD2. Here we demonstrate that the tandem CARDs of NOD2 are engaged in an intramolecular interaction that is important for the structural stability of this region. Using a combination of ITC and pull-down experiments we identify distinct surface areas that are involved in the intramolecular tandem CARD interaction and the interaction with the downstream effector RIP2. Our findings indicate that while CARDa of NOD2 might be the primary binding partner of RIP2 the two CARDs of NOD2 do not act independently of one another but may cooperate to from a binding surface that is distinct from that of single CARDs. PMID:22470564

Solution structure of leptospiral LigA4 Big domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Song; Zhang, Jiahai; Zhang, Xuecheng

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 Bigmore » 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{sup 2+} binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca{sup 2+}-binding site was identified by strains-all and NMR chemical shift perturbation.« less

Low-dose radiation pretreatment improves survival of human ceiling culture-derived proliferative adipocytes (ccdPAs) under hypoxia via HIF-1 alpha and MMP-2 induction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adachi, Naoki; Kubota, Yoshitaka, E-mail: kubota-cbu@umin.ac.jp; Kosaka, Kentarou

2015-08-07

Poor survival is a major problem of adipocyte transplantation. We previously reported that VEGF and MMPs secreted from transplanted adipocytes are essential for angiogenesis and adipogenesis. Pretreatment with low-dose (5 Gy) radiation (LDR) increased VEGF, MMP-2, and HIF-1 alpha mRNA expression in human ceiling culture-derived proliferative adipocytes (hccdPAs). Gene expression after LDR differed between adipose-derived stem cells (hASCs) and hccdPAs. Pretreatment with LDR improved the survival of hccdPAs under hypoxia, which is inevitable in the early stages after transplantation. Upregulation of VEGF and MMP-2 after LDR in hccdPAs is mediated by HIF-1 alpha expression. Our results suggest that pretreatment with LDRmore » may improve adipocyte graft survival in a clinical setting through upregulation of VEGF and MMP-2 via HIF-1 alpha. - Highlights: • Ceiling culture-derived proliferative adipocytes (ccdPAs) react to radiation. • Low-dose radiation (LDR) pretreatment improves survival of ccdPAs under hypoxia. • Gene expression after LDR differs between ccdPAs and adipose-derived stem cells. • LDR-induced increase in MMP-2 and VEGF is dependent on HIF-1 alpha induction. • LDR pretreatment may improve the adipocyte graft survival rate in clinical settings.« less

Rational design of alpha-helical tandem repeat proteins with closed architectures

PubMed Central

Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L.; Bradley, Philip

2015-01-01

Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials1,2. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks3,4. The overall architecture of tandem repeat protein structures – which is dictated by the internal geometry and local packing of the repeat building blocks – is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners5–9, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis10. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid11 repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the N- and C-termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering12–20, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that – to our knowledge – is not yet present in the protein structure database21. PMID:26675735

The JH2 domain and SH2-JH2 linker regulate JAK2 activity: A detailed kinetic analysis of wild type and V617F mutant kinase domains.

PubMed

Sanz Sanz, Arturo; Niranjan, Yashavanthi; Hammarén, Henrik; Ungureanu, Daniela; Ruijtenbeek, Rob; Touw, Ivo P; Silvennoinen, Olli; Hilhorst, Riet

2014-10-01

JAK2 tyrosine kinase regulates many cellular functions. Its activity is controlled by the pseudokinase (JH2) domain by still poorly understood mechanisms. The V617F mutation in the pseudokinase domain activates JAK2 and causes myeloproliferative neoplasms. We conducted a detailed kinetic analysis of recombinant JAK2 tyrosine kinase domain (JH1) and wild-type and V617F tandem kinase (JH1JH2) domains using peptide microarrays to define the functions of the kinase domains. The results show that i) JAK2 follows a random Bi-Bi reaction mechanism ii) JH2 domain restrains the activity of the JH1 domain by reducing the affinity for ATP and ATP competitive inhibitors iii) V617F decreases affinity for ATP but increases catalytic activity compared to wild-type and iv) the SH2-JH2 linker region participates in controlling activity by reducing the affinity for ATP. Copyright © 2014 Elsevier B.V. All rights reserved.

Short Tandem Repeat DNA Internet Database

National Institute of Standards and Technology Data Gateway

SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

FTIR-PAS: a powerful tool for characterising the chemical composition and predicting the labile C fraction of various organic waste products.

PubMed

Bekiaris, Georgios; Bruun, Sander; Peltre, Clément; Houot, Sabine; Jensen, Lars S

2015-05-01

Fourier transform infrared (FT-IR) spectroscopy has been used for several years as a fast, low-cost, reliable technique for characterising a large variety of materials. However, the strong influence of sample particle size and the inability to measure the absorption of very dark and opaque samples have made FTIR unsuitable for many waste materials. FTIR-photoacoustic spectroscopy (FTIR-PAS) can eliminate some of the shortcomings of traditional FTIR caused by scattering effects and reflection issues, and recent advances in PAS technology have made commercial instruments available. In this study, FTIR-PAS was used to characterise a wide range of organic waste products and predict their labile carbon fraction, which is normally determined from time-consuming assays. FTIR-PAS was found to be capable of predicting the labile fraction of carbon as efficiently as near infrared spectroscopy (NIR) and furthermore of identifying the compounds that are correlated with the predicted parameter, thus facilitating a more mechanistic interpretation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Concerted action of the PHD, chromo and motor domains regulates the human chromatin remodelling ATPase CHD4.

PubMed

Morra, Rosa; Lee, Benjamin M; Shaw, Heather; Tuma, Roman; Mancini, Erika J

2012-07-30

CHD4, the core subunit of the Nucleosome Remodelling and Deacetylase (NuRD) complex, is a chromatin remodelling ATPase that, in addition to a helicase domain, harbors tandem plant homeo finger and chromo domains. By using a panel of domain constructs we dissect their roles and demonstrate that DNA binding, histone binding and ATPase activities are allosterically regulated. Molecular shape reconstruction from small-angle X-ray scattering reveals extensive domain-domain interactions, which provide a structural explanation for the regulation of CHD4 activities by intramolecular domain communication. Our results demonstrate functional interdependency between domains within a chromatin remodeller. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Additive interaction between heterogeneous environmental quality domains (air, water, land, sociodemographic and built environment) on preterm birth

EPA Science Inventory

BACKGROUND Environmental exposures often occur in tandem; however, epidemiological research often focuses on singular exposures. Statistical interactions among broad, well-characterized environmental domains have not yet been evaluated in association with health. We address this ...

NMR assignments of the N-terminal domain of Nephila clavipes spidroin 1

PubMed Central

Parnham, Stuart; Gaines, William A.; Duggan, Brendan M.; Marcotte, William R.

2011-01-01

The building blocks of spider dragline silk are two fibrous proteins secreted from the major ampullate gland named spidroins 1 and 2 (MaSp1, MaSp2). These proteins consist of a large central domain composed of approximately 100 tandem copies of a 35–40 amino acid repeat sequence. Non-repetitive N and C-terminal domains, of which the C-terminal domain has been implicated to transition from soluble and insoluble states during spinning, flank the repetitive core. The N-terminal domain until recently has been largely unknown due to difficulties in cloning and expression. Here, we report nearly complete assignment for all 1H, 13C, and 15N resonances in the 14 kDa N-terminal domain of major ampullate spidroin 1 (MaSp1-N) of the golden orb-web spider Nephila clavipes. PMID:21152998

32 CFR 806b.11 - When to give Privacy Act Statements (PAS).

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 6 2011-07-01 2011-07-01 false When to give Privacy Act Statements (PAS). 806b... ADMINISTRATION PRIVACY ACT PROGRAM Collecting Personal Information § 806b.11 When to give Privacy Act Statements... information. Give a copy of the Privacy Act Statement if asked. Do not ask the person to sign the Privacy Act...

32 CFR 806b.11 - When to give Privacy Act Statements (PAS).

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 6 2013-07-01 2013-07-01 false When to give Privacy Act Statements (PAS). 806b... ADMINISTRATION PRIVACY ACT PROGRAM Collecting Personal Information § 806b.11 When to give Privacy Act Statements... information. Give a copy of the Privacy Act Statement if asked. Do not ask the person to sign the Privacy Act...

32 CFR 806b.11 - When to give Privacy Act Statements (PAS).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 6 2010-07-01 2010-07-01 false When to give Privacy Act Statements (PAS). 806b... ADMINISTRATION PRIVACY ACT PROGRAM Collecting Personal Information § 806b.11 When to give Privacy Act Statements... information. Give a copy of the Privacy Act Statement if asked. Do not ask the person to sign the Privacy Act...

Interaction between heterogeneous environmental quality domains (air, water, land, socio-demographic and built environment) on preterm birth.

EPA Science Inventory

Environmental exposures are often measured individually, though many occur in tandem. To address aggregate exposures, a county-level Environmental Quality Index (EQI) representing five environmental domains (air, water, land, built and sociodemographic) was constructed. Recent st...

An Investigation of Interrater Reliability for the Rorschach Performance Assessment System (R-PAS) in a Nonpatient U.S. Sample.

PubMed

Kivisalu, Trisha M; Lewey, Jennifer H; Shaffer, Thomas W; Canfield, Merle L

2016-01-01

The Rorschach Performance Assessment System (R-PAS) aims to provide an evidence-based approach to administration, coding, and interpretation of the Rorschach Inkblot Method (RIM). R-PAS analyzes individualized communications given by respondents to each card to code a wide pool of possible variables. Due to the large number of possible codes that can be assigned to these responses, it is important to consider the concordance rates among different assessors. This study investigated interrater reliability for R-PAS protocols. Data were analyzed from a nonpatient convenience sample of 50 participants who were recruited through networking, local marketing, and advertising efforts from January 2013 through October 2014. Blind recoding was used and discrepancies between the initial and blind coders' ratings were analyzed for each variable with SPSS yielding percent agreement and intraclass correlation values. Data for Location, Space, Contents, Synthesis, Vague, Pairs, Form Quality, Populars, Determinants, and Cognitive and Thematic codes are presented. Rates of agreement for 1,168 responses were higher for more simplistic coding (e.g., Location), whereas agreement was lower for more complex codes (e.g., Cognitive and Thematic codes). Overall, concordance rates achieved good to excellent agreement. Results suggest R-PAS is an effective method with high interrater reliability supporting its empirical basis.

Tandem Organic Light-Emitting Diodes.

PubMed

Fung, Man-Keung; Li, Yan-Qing; Liao, Liang-Sheng

2016-12-01

A tandem organic light-emitting diode (OLED) is an organic optoelectronic device that has two or more electroluminescence (EL) units connected electrically in series with unique intermediate connectors within the device. Researchers have studied this new OLED architecture with growing interest and have found that the current efficiency of a tandem OLED containing N EL units (N > 1) should be N times that of a conventional OLED containing only a single EL unit. Therefore, this new architecture is potentially useful for constructing high-efficiency, high-luminance, and long-lifetime OLED displays and organic solid-state lighting sources. In a tandem OLED, the intermediate connector plays a crucial role in determining the effectiveness of the stacked EL units. The interfaces in the connector control the inner charge generation and charge injection into the adjacent EL units. Meanwhile, the transparency and the thickness of the connector affect the light output of the device. Therefore, the intermediate connector should be made to meet both the electrical and optical requirements for achieving optimal performance. Here, recent advances in the research of the tandem OLEDs is discussed, with the main focus on material selection and interface studies in the intermediate connectors, as well as the optical design of the tandem OLEDs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Psychometric Properties and Norms of the German ABC-Community and PAS-ADD Checklist

ERIC Educational Resources Information Center

Zeilinger, Elisabeth L.; Weber, Germain; Haveman, Meindert J.

2011-01-01

Aim: The aim of the present study was to standardize and generate psychometric evidence of the German language versions of two well-established English language mental health instruments: the "Aberrant Behavior Checklist-Community" (ABC-C) and the "Psychiatric Assessment Schedule for Adults with Developmental Disabilities" (PAS-ADD) Checklist. New…

Peer Relations and the Understanding of Faux Pas: Longitudinal Evidence for Bidirectional Associations

ERIC Educational Resources Information Center

Banerjee, Robin; Watling, Dawn; Caputi, Marcella

2011-01-01

Research connecting children's understanding of mental states to their peer relations at school remains scarce. Previous work by the authors demonstrated that children's understanding of mental states in the context of a faux pas--a social blunder involving unintentional insult--is associated with concurrent peer rejection. The present report…

The presence of glutamate residues on the PAS sequence of the stimuli-sensitive nano-ferritin improves in vivo biodistribution and mitoxantrone encapsulation homogeneity.

PubMed

Falvo, Elisabetta; Malagrinò, Francesca; Arcovito, Alessandro; Fazi, Francesco; Colotti, Gianni; Tremante, Elisa; Di Micco, Patrizio; Braca, Aldo; Opri, Roberta; Giuffrè, Alessandro; Fracasso, Giulio; Ceci, Pierpaolo

2018-04-10

A genetically engineered human ferritin heavy chain (HFt)-based construct has been recently shown by our group to efficiently entrap and deliver doxorubicin to cancer cells. This construct, named HFt-MP-PAS, contained a tumor-selective sequence (MP) responsive to proteolytic cleavage by tumor proteases (MMPs), located between each HFt subunit and an outer shielding polypeptide sequence rich in proline (P), serine (S) and alanine (A) residues (PAS). HFt-MP-PAS displayed excellent therapeutic efficacy in xenogenic pancreatic and head and neck cancer models in vivo, leading to a significant increase in overall animal survivals. Here we report a new construct obtained by the genetic insertion of two glutamate residues in the PAS sequence of HFt-MP-PAS. Such new construct, named HFt-MP-PASE, is characterized by improved performances as drug biodistribution in a xenogenic pancreatic cancer model in vivo. Moreover, HFt-MP-PASE efficiently encapsulates the anti-cancer drug mitoxantrone (MIT), and the resulting MIT-loaded nanoparticles proved to be more soluble and monodispersed than the HFt-MP-PAS counterparts. Importantly, in vitro MIT-loaded HFt-MP-PASE kills several cancer cell lines of different origin (colon, breast, sarcoma and pancreas) at least as efficiently as the free drug. Finally, our MIT loaded protein nanocages allowed in vivo an impressive incrementing of the drug accumulation in the tumor with respect to the free drug. Copyright © 2018 Elsevier B.V. All rights reserved.

High voltage series connected tandem junction solar battery

DOEpatents

Hanak, Joseph J.

1982-01-01

A high voltage series connected tandem junction solar battery which comprises a plurality of strips of tandem junction solar cells of hydrogenated amorphous silicon having one optical path and electrically interconnected by a tunnel junction. The layers of hydrogenated amorphous silicon, arranged in a tandem configuration, can have the same bandgap or differing bandgaps. The tandem junction strip solar cells are series connected to produce a solar battery of any desired voltage.

Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.

PubMed

Galperin, Michael Y; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2018-04-01

The two-component signal transduction (TCS) machinery is a key mechanism of sensing environmental changes in the prokaryotic world. TCS systems have been characterized thoroughly in bacteria but to a much lesser extent in archaea. Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data. We describe the domain architectures of the archaeal TCS components, including several novel output domains, and discuss the evolution of the archaeal TCS machinery. The distribution of TCS systems in archaea is strongly biased, with high levels of abundance in haloarchaea and thaumarchaea but none detected in the sequenced genomes from the phyla Crenarchaeota , Nanoarchaeota , and Korarchaeota The archaeal sensor histidine kinases are generally similar to their well-studied bacterial counterparts but are often located in the cytoplasm and carry multiple PAS and/or GAF domains. In contrast, archaeal response regulators differ dramatically from the bacterial ones. Most archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. Instead, archaea encode multiple copies of response regulators containing either the stand-alone receiver (REC) domain or combinations of REC with PAS and/or GAF domains. Therefore, the prevailing mechanism of archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation. IMPORTANCE Although the Archaea represent a separate domain of life, their signaling systems have been assumed to be closely similar to the bacterial ones. A study of the domain architectures of the archaeal two-component signal transduction (TCS) machinery revealed an

Mathematical Justification of Expression-Based Pathway Activation Scoring (PAS).

PubMed

Aliper, Alexander M; Korzinkin, Michael B; Kuzmina, Natalia B; Zenin, Alexander A; Venkova, Larisa S; Smirnov, Philip Yu; Zhavoronkov, Alex A; Buzdin, Anton A; Borisov, Nikolay M

2017-01-01

Although modeling of activation kinetics for various cell signaling pathways has reached a high grade of sophistication and thoroughness, most such kinetic models still remain of rather limited practical value for biomedicine. Nevertheless, recent advancements have been made in application of signaling pathway science for real needs of prescription of the most effective drugs for individual patients. The methods for such prescription evaluate the degree of pathological changes in the signaling machinery based on two types of data: first, on the results of high-throughput gene expression profiling, and second, on the molecular pathway graphs that reflect interactions between the pathway members. For example, our algorithm OncoFinder evaluates the activation of molecular pathways on the basis of gene/protein expression data in the objects of the interest.Yet, the question of assessment of the relative importance for each gene product in a molecular pathway remains unclear unless one call for the methods of parameter sensitivity /stiffness analysis in the interactomic kinetic models of signaling pathway activation in terms of total concentrations of each gene product.Here we show two principal points: 1. First, the importance coefficients for each gene in pathways that were obtained using the extremely time- and labor-consuming stiffness analysis of full-scaled kinetic models generally differ from much easier-to-calculate expression-based pathway activation score (PAS) not more than by 30%, so the concept of PAS is kinetically justified. 2. Second, the use of pathway-based approach instead of distinct gene analysis, due to the law of large numbers, allows restoring the correlation between the similar samples that were examined using different transcriptome investigation techniques.

[Gardner syndrome--parent alienation syndrome (PAS). Diagnosis or family reality?].

PubMed

Namysłowska, Irena; Heitzman, Janusz; Siewierska, Anna

2009-01-01

The authors present characteristics of Parental Alienation Syndrome (PAS) proposed by Gardner as well as data, which may help to differentiate that syndrome with real psychological, physical and sexual abuse. The consequences of Gardner Syndrome for legal decisions in the court cases of child custody and the critique of this syndrome in forensic and psychiatric literature are also discussed, and several questions posed. Authors propose to treat Gardner Syndrome not as as a child disorder but as a specific, dynamic family situation, which occurs sometimes, during divorce and fight about child custody.

Effects of room airflow on accurate determination of PUF-PAS sampling rates in the indoor environment.

PubMed

Herkert, Nicholas J; Hornbuckle, Keri C

2018-05-23

Accurate and precise interpretation of concentrations from polyurethane passive samplers (PUF-PAS) is important as more studies show elevated concentrations of PCBs and other semivolatile air toxics in indoor air of schools and homes. If sufficiently reliable, these samplers may be used to identify local sources and human health risks. Here we report indoor air sampling rates (Rs) for polychlorinated biphenyl congeners (PCBs) predicted for a frequently used double-dome and a half-dome PUF-PAS design. Both our experimentally calibrated (1.10 ± 0.23 m3 d-1) and modeled (1.08 ± 0.04 m3 d-1) Rs for the double-dome samplers compare well with literature reports for similar rooms. We determined that variability of wind speeds throughout the room significantly (P < 0.001) effected uptake rates. We examined this effect using computational fluid dynamics modeling and 3-D sonic anemometer measurements and found the airflow dynamics to have a significant but small impact on the precision of calculated airborne concentrations. The PUF-PAS concentration measurements were within 27% and 10% of the active sampling concentration measurements for the double-dome and half-dome designs, respectively. While the half-dome samplers produced more consistent concentration measurements, we find both designs to perform well indoors.

Electromagnetic resonance modes on a two-dimensional tandem grating and its application for broadband absorption in the visible spectrum.

PubMed

Han, Sunwoo; Lee, Bong Jae

2016-01-25

In this work, we numerically investigate the electromagnetic resonances on two-dimensional tandem grating structures. The base of a tandem grating consists of an opaque Au substrate, a SiO(2) spacer, and a Au grating (concave type); that is, a well-known fishnet structure forming Au/SiO(2)/Au stack. A convex-type Au grating (i.e., topmost grating) is then attached on top of the base fishnet structure with or without additional SiO(2) spacer, resulting in two types of tandem grating structures. In order to calculate the spectral reflectance and local magnetic field distribution, the finite-difference time-domain method is employed. When the topmost Au grating is directly added onto the base fishnet structure, the surface plasmon and magnetic polariton in the base structure are branched out due to the geometric asymmetry with respect to the SiO(2) spacer. If additional SiO(2) spacer is added between the topmost Au grating and the base fishnet structure, new magnetic resonance modes appear due to coupling between two vertically aligned Au/SiO(2)/Au stacks. With the understanding of multiple electromagnetic resonance modes on the proposed tandem grating structures, we successfully design a broadband absorber made of Au and SiO(2) in the visible spectrum.

47 CFR 69.129 - Signalling for tandem switching.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. [59 FR 32930, June 27, 1994] ...

47 CFR 69.129 - Signalling for tandem switching.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. [59 FR 32930, June 27, 1994] ...

47 CFR 69.129 - Signalling for tandem switching.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 3 2013-10-01 2013-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. [59 FR 32930, June 27, 1994] ...

47 CFR 69.129 - Signalling for tandem switching.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 3 2012-10-01 2012-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. [59 FR 32930, June 27, 1994] ...

APE1 incision activity at abasic sites in tandem repeat sequences.

PubMed

Li, Mengxia; Völker, Jens; Breslauer, Kenneth J; Wilson, David M

2014-05-29

Repetitive DNA sequences, such as those present in microsatellites and minisatellites, telomeres, and trinucleotide repeats (linked to fragile X syndrome, Huntington disease, etc.), account for nearly 30% of the human genome. These domains exhibit enhanced susceptibility to oxidative attack to yield base modifications, strand breaks, and abasic sites; have a propensity to adopt non-canonical DNA forms modulated by the positions of the lesions; and, when not properly processed, can contribute to genome instability that underlies aging and disease development. Knowledge on the repair efficiencies of DNA damage within such repetitive sequences is therefore crucial for understanding the impact of such domains on genomic integrity. In the present study, using strategically designed oligonucleotide substrates, we determined the ability of human apurinic/apyrimidinic endonuclease 1 (APE1) to cleave at apurinic/apyrimidinic (AP) sites in a collection of tandem DNA repeat landscapes involving telomeric and CAG/CTG repeat sequences. Our studies reveal the differential influence of domain sequence, conformation, and AP site location/relative positioning on the efficiency of APE1 binding and strand incision. Intriguingly, our data demonstrate that APE1 endonuclease efficiency correlates with the thermodynamic stability of the DNA substrate. We discuss how these results have both predictive and mechanistic consequences for understanding the success and failure of repair protein activity associated with such oxidatively sensitive, conformationally plastic/dynamic repetitive DNA domains. Published by Elsevier Ltd.

Folding and Aggregation of Mucin Domains.

NASA Astrophysics Data System (ADS)

Urbanc, Brigita; Bansil, Rama; Turner, Bradley

2007-03-01

Mucin glycoproteins consist of tandem repeating glycosylated regions flanked by non-repetitive protein domains with little glycosylation. These non-repetitive domains are involved in polymerization of mucin via disulfide bonds and play an important role in the pH dependent gelation of gastric mucin, which is essential to protecting the stomach from autodigestion. We have examined the folding and aggregation of the non-repetitive sequence of von Willebrand factor vWF-C1 domain (67 amino acids) and PGM 2X (242 amino acids) using Discrete Molecular Dynamics (four-bead protein model with hydrogen bonding and amino acid-specific hydrophobic/hydrophilic and electrostatic interactions of side chains). Simulations of vWF C1 show 4-6 β-strands separated by turns/loops with more loops at lower pH. A simulation of several vWF C1 proteins at low pH shows aggregates still with a high content of β-strands and enhanced turn/loop regions. For the PGM 2X simulation the contact map shows several salt bridges enclosing hairpin turns. The implications of these simulations for describing the aggregation/gelation of PGM will be discussed.

Intramolecular trimerization, a novel strategy for making multispecific antibodies with controlled orientation of the antigen binding domains

PubMed Central

Alvarez-Cienfuegos, Ana; Nuñez-Prado, Natalia; Compte, Marta; Cuesta, Angel M.; Blanco-Toribio, Ana; Harwood, Seandean Lykke; Villate, Maider; Merino, Nekane; Bonet, Jaume; Navarro, Rocio; Muñoz-Briones, Clara; Sørensen, Karen Marie Juul; Mølgaard, Kasper; Oliva, Baldo; Sanz, Laura; Blanco, Francisco J.; Alvarez-Vallina, Luis

2016-01-01

Here, we describe a new strategy that allows the rapid and efficient engineering of mono and multispecific trivalent antibodies. By fusing single-domain antibodies from camelid heavy-chain-only immunoglobulins (VHHs) to the N-terminus of a human collagen XVIII trimerization domain (TIEXVIII) we produced monospecific trimerbodies that were efficiently secreted as soluble functional proteins by mammalian cells. The purified VHH-TIEXVIII trimerbodies were trimeric in solution and exhibited excellent antigen binding capacity. Furthermore, by connecting with two additional glycine-serine-based linkers three VHH-TIEXVIII modules on a single polypeptide chain, we present an approach for the rational design of multispecific tandem trimerbodies with defined stoichiometry and controlled orientation. Using this technology we report here the construction and characterization of a tandem VHH-based trimerbody capable of simultaneously binding to three different antigens: carcinoembryonic antigen (CEA), epidermal growth factor receptor (EGFR) and green fluorescence protein (GFP). Multispecific tandem VHH-based trimerbodies were well expressed in mammalian cells, had good biophysical properties and were capable of simultaneously binding their targeted antigens. Importantly, these antibodies were very effective in inhibiting the proliferation of human epidermoid carcinoma A431 cells. Multispecific VHH-based trimerbodies are therefore ideal candidates for future applications in various therapeutic areas. PMID:27345490

Structure of the USP15 N-terminal domains: a β-hairpin mediates close association between the DUSP and UBL domains.

PubMed

Harper, Stephen; Besong, Tabot M D; Emsley, Jonas; Scott, David J; Dreveny, Ingrid

2011-09-20

Ubiquitin specific protease 15 (USP15) functions in COP9 signalosome mediated regulation of protein degradation and cellular signaling through catalyzing the ubiquitin deconjugation reaction of a discrete number of substrates. It influences the stability of adenomatous polyposis coli, IκBα, caspase-3, and the human papillomavirus type 16 E6. USP15 forms a subfamily with USP4 and USP11 related through a shared presence of N-terminal "domain present in ubiquitin specific proteases" (DUSP) and "ubiquitin-like" (UBL) domains (DU subfamily). Here we report the 1.5 Å resolution crystal structure of the human USP15 N-terminal domains revealing a 80 Å elongated arrangement with the DU domains aligned in tandem. This architecture is generated through formation of a defined interface that is dominated by an intervening β-hairpin structure (DU finger) that engages in an intricate hydrogen-bonding network between the domains. The UBL domain is closely related to ubiquitin among β-grasp folds but is characterized by the presence of longer loop regions and different surface characteristics, indicating that this domain is unlikely to act as ubiquitin mimic. Comparison with the related murine USP4 DUSP-UBL crystal structure reveals that the main DU interdomain contacts are conserved. Analytical ultracentrifugation, small-angle X-ray scattering, and gel filtration experiments revealed that USP15 DU is monomeric in solution. Our data provide a framework to advance study of the structure and function of the DU subfamily. © 2011 American Chemical Society

Tandem Translation Classroom: A Case Study

ERIC Educational Resources Information Center

Kim, Dohun; Koh, Taejin

2018-01-01

The transition to student-centred learning, advances in teleconferencing tools, and active international student exchange programmes have stimulated tandem learning in many parts of the world. This pedagogical model is based on a mutual language exchange between tandem partners, where each student is a native speaker in the language the…

Variation in Venoms of Polybia Paulista Von Ihering and Polybia Occidentalis Olivier (Hymenoptera: Vespidae), Assessed by the FTIR-PAS Technique.

PubMed

Mendonça, A; Paula, M C; Fernandes, W D; Andrade, L H C; Lima, S M; Antonialli-Junior, W F

2017-02-01

Wasps are able to synthesize toxic compounds known as venoms, which form a part of a mechanism to overcome prey and also to defend their colonies. Study of the compounds that constitute these substances is essential in order to understand how this defense mechanism evolved, since there is evidence that the venoms can vary both intra- and interspecifically. Some studies have used liquid and gas chromatography as a reliable technique to analyze these compounds. However, the use of Fourier transform infrared photoacoustic spectroscopy (FTIR-PAS) to analyze the variations in venom's chemical profile has been proposed recently. This study evaluated whether the FTIR-PAS technique is effective for assessing the role of environmental factors on intra- and interspecific differences in the venom of the wasps Polybia paulista Von Ihering and Polybia occidentalis Olivier by FTIR-PAS. The colonies were collected in three municipalities of Mato Grosso do Sul, Brazil, in different types of environments. The results showed that the venoms of P. paulista and P. occidentalis differed significantly in profile. In addition, the intraspecific differences in the venom's chemical profile of P. paulista are related to the type of environment where they nested, regardless of the geographical distance between the nests. The FTIR-PAS technique proved to be reliable and effective to evaluate the variations in the venom's chemical profile in social wasps.

Thermodynamic characterization of tandem mismatches found in naturally occurring RNA

PubMed Central

Christiansen, Martha E.; Znosko, Brent M.

2009-01-01

Although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [Christiansen,M.E. and Znosko,B.M. (2008) Biochemistry, 47, 4329–4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. Since experimental data is preferred over a predictive model, the thermodynamic parameters for 25 frequently occurring tandem mismatches were determined. These new experimental values, on average, are 1.0 kcal/mol different from the values predicted for these mismatches using the previous model. The data for the sequence asymmetric tandem mismatches reported here were then combined with the data for 72 sequence asymmetric tandem mismatches that were published previously, and the parameters used to predict the thermodynamics of previously unmeasured sequence asymmetric tandem mismatches were updated. The average absolute difference between the measured values and the values predicted using these updated parameters is 0.5 kcal/mol. This updated model improves the prediction for tandem mismatches that were predicted rather poorly by the previous model. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA duplexes containing tandem mismatches, and, furthermore, should allow for improved prediction of secondary structure from sequence. PMID:19509311

Selecting tandem partners for silicon solar cells [Selecting tandem partners for silicon solar cells using spectral efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Zhengshan; Leilaeioun, Mehdi; Holman, Zachary

Combining silicon and other materials in tandem solar cells is one approach to enhancing the overall power conversion efficiency of the cells. Here, we argue that top cell partners for silicon tandem solar cells should be selected on the basis of their spectral efficiency — their efficiency resolved by wavelength.

Selecting tandem partners for silicon solar cells [Selecting tandem partners for silicon solar cells using spectral efficiency

DOE PAGES

Yu, Zhengshan; Leilaeioun, Mehdi; Holman, Zachary

2016-09-26

Combining silicon and other materials in tandem solar cells is one approach to enhancing the overall power conversion efficiency of the cells. Here, we argue that top cell partners for silicon tandem solar cells should be selected on the basis of their spectral efficiency — their efficiency resolved by wavelength.

Conformational Changes of an Interdomain Linker Mediate Mechanical Signal Transmission in Sensor Kinase BvgS

PubMed Central

Lesne, Elodie; Dupré, Elian; Locht, Camille

2017-01-01

ABSTRACT The whooping cough agent, Bordetella pertussis, controls the expression of its large virulence regulon in a coordinated manner through the two-component system BvgAS. BvgS is a dimeric, multidomain sensor kinase. Each monomer comprises, in succession, tandem periplasmic Venus flytrap (VFT) domains, a transmembrane segment, a cytoplasmic Per-Arnt-Sim (PAS) domain, a kinase module, and additional phosphorelay domains. BvgS shifts between kinase and phosphatase modes of activity in response to chemical modulators that modify the clamshell motions of the VFT domains. We have shown previously that this regulation involves a shift between distinct states of conformation and dynamics of the two-helix coiled-coil linker preceding the enzymatic module. In this work, we determined the mechanism of signal transduction across the membrane via a first linker, which connects the VFT and PAS domains of BvgS, using extensive cysteine cross-linking analyses and other approaches. Modulator perception by the periplasmic domains appears to trigger a small, symmetrical motion of the transmembrane segments toward the periplasm, causing rearrangements of the noncanonical cytoplasmic coiled coil that follows. As a consequence, the interface of the PAS domains is modified, which affects the second linker and eventually causes the shift of enzymatic activity. The major features of this first linker are well conserved among BvgS homologs, indicating that the mechanism of signal transduction unveiled here is likely to be generally relevant for this family of sensor kinases. IMPORTANCE Bordetella pertussis produces virulence factors coordinately regulated by the two-component system BvgAS. BvgS is a sensor kinase, and BvgA is a response regulator that activates gene transcription when phosphorylated by BvgS. Sensor kinases homologous to BvgS are also found in other pathogens. Our goal is to decipher the mechanisms of BvgS signaling, since these sensor kinases may represent new targets

Chemical shift assignments of the partially deuterated Fyn SH2-SH3 domain.

PubMed

Kieken, Fabien; Loth, Karine; van Nuland, Nico; Tompa, Peter; Lenaerts, Tom

2018-04-01

Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1 H, 15 N and 13 C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.

Binding affinity of the L-742,001 inhibitor to the endonuclease domain of A/H1N1/PA influenza virus variants: Molecular simulation approaches

NASA Astrophysics Data System (ADS)

Nguyen, Hung; Nguyen, Hoang Linh; Linh, Huynh Quang; Nguyen, Minh Tho

2018-01-01

The steered molecular dynamics (SMD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and free energy perturbation (FEP) methods were used to determine the binding affinity of the L-742,001 inhibitor to the endonuclease domain of the A/H1N1/PA influenza viruses (including wild type (WT) and three mutations I79L, E119D and F105S for both pH1N1 PA and PR8 PA viruses). Calculated results showed that the L-742,001 inhibitor not only binds to the PR8 PAs (1934 A influenza virus) better than to the pH1N1 PAs (2009 A influenza virus) but also more strongly interacts with the WT endonuclease domain than with three mutant variants for both pH1N1 PA and PR8 PA viruses. The binding affinities obtained by the SMD, MM-PBSA and FEP methods attain high correlation with available experimental data. Here the FEP method appears to provide a more accurate determination of the binding affinity than the SMD and MM-PBSA counterparts.

Tandem junction amorphous silicon solar cells

DOEpatents

Hanak, Joseph J.

1981-01-01

An amorphous silicon solar cell has an active body with two or a series of layers of hydrogenated amorphous silicon arranged in a tandem stacked configuration with one optical path and electrically interconnected by a tunnel junction. The layers of hydrogenated amorphous silicon arranged in tandem configuration can have the same bandgap or differing bandgaps.

Understanding pathogenic single-nucleotide polymorphisms in multidomain proteins – studies of isolated domains are not enough

PubMed Central

Randles, Lucy G; Dawes, Gwen J S; Wensley, Beth G; Steward, Annette; Nickson, Adrian A; Clarke, Jane

2013-01-01

Studying the effects of pathogenic mutations is more complex in multidomain proteins when compared with single domains: mutations occurring at domain boundaries may have a large effect on a neighbouring domain that will not be detected in a single-domain system. To demonstrate this, we present a study that utilizes well-characterized model protein domains from human spectrin to investigate the effect of disease-and non-disease-causing single point mutations occurring at the boundaries of human spectrin repeats. Our results show that mutations in the single domains have no clear correlation with stability and disease; however, when studied in a tandem model system, the disease-causing mutations are shown to disrupt stabilizing interactions that exist between domains. This results in a much larger decrease in stability than would otherwise have been predicted, and demonstrates the importance of studying such mutations in the correct protein context. PMID:23241237

Molecular recognition of the Tes LIM2-3 domains by the actin-related protein Arp7A.

PubMed

Boëda, Batiste; Knowles, Phillip P; Briggs, David C; Murray-Rust, Judith; Soriano, Erika; Garvalov, Boyan K; McDonald, Neil Q; Way, Michael

2011-04-01

Actin-related proteins (Arps) are a highly conserved family of proteins that have extensive sequence and structural similarity to actin. All characterized Arps are components of large multimeric complexes associated with chromatin or the cytoskeleton. In addition, the human genome encodes five conserved but largely uncharacterized "orphan" Arps, which appear to be mostly testis-specific. Here we show that Arp7A, which has 43% sequence identity with β-actin, forms a complex with the cytoskeletal proteins Tes and Mena in the subacrosomal layer of round spermatids. The N-terminal 65-residue extension to the actin-like fold of Arp7A interacts directly with Tes. The crystal structure of the 1-65(Arp7A)·LIM2-3(Tes)·EVH1(Mena) complex reveals that residues 28-49 of Arp7A contact the LIM2-3 domains of Tes. Two alanine residues from Arp7A that occupy equivalent apolar pockets in both LIM domains as well as an intervening GPAK linker that binds the LIM2-3 junction are critical for the Arp7A-Tes interaction. Equivalent occupied apolar pockets are also seen in the tandem LIM domain structures of LMO4 and Lhx3 bound to unrelated ligands. Our results indicate that apolar pocket interactions are a common feature of tandem LIM domain interactions, but ligand specificity is principally determined by the linker sequence.

When to suspect tinea; a histopathologic study of 103 cases of PAS-positive tinea.

PubMed

Elbendary, Amira; Valdebran, Manuel; Gad, AbdAllah; Elston, Dirk M

2016-10-01

The histopathologic features of tinea vary widely and its diagnosis could be easily missed if the index of suspicion is not high. We aimed in this study to detect histopathologic features that could be a clue for diagnosis We retrospectively reviewed 103 cases of tinea, confirmed by Periodic acid-Schiff (PAS) staining. For each case, gender, biopsy site, and pre-biopsy suspicion were recorded. The presence or absence of 17 microscopic features was noted. Concordance between pre-biopsy and histopathologic diagnosis was noted in 57.28% of cases, suggesting that the diagnosis is often not suspected clinically. Among the histopathologic features studied, a compact stratum corneum (either uniform or forming a layer beneath a basket weave stratum corneum), parakeratosis, mild spongiosis and neutrophils in the stratum corneum and within the blood vessels were the most frequent features noted. This study suggests histopathologic clues that should prompt the pathologist to order a PAS stain, especially when diagnosis is not suspected clinically. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

High-Efficiency Polycrystalline Thin Film Tandem Solar Cells.

PubMed

Kranz, Lukas; Abate, Antonio; Feurer, Thomas; Fu, Fan; Avancini, Enrico; Löckinger, Johannes; Reinhard, Patrick; Zakeeruddin, Shaik M; Grätzel, Michael; Buecheler, Stephan; Tiwari, Ayodhya N

2015-07-16

A promising way to enhance the efficiency of CIGS solar cells is by combining them with perovskite solar cells in tandem devices. However, so far, such tandem devices had limited efficiency due to challenges in developing NIR-transparent perovskite top cells, which allow photons with energy below the perovskite band gap to be transmitted to the bottom cell. Here, a process for the fabrication of NIR-transparent perovskite solar cells is presented, which enables power conversion efficiencies up to 12.1% combined with an average sub-band gap transmission of 71% for photons with wavelength between 800 and 1000 nm. The combination of a NIR-transparent perovskite top cell with a CIGS bottom cell enabled a tandem device with 19.5% efficiency, which is the highest reported efficiency for a polycrystalline thin film tandem solar cell. Future developments of perovskite/CIGS tandem devices are discussed and prospects for devices with efficiency toward and above 27% are given.

Thermal denaturation of the BRCT tandem repeat region of human tumour suppressor gene product BRCA1.

PubMed

Pyrpassopoulos, Serapion; Ladopoulou, Angela; Vlassi, Metaxia; Papanikolau, Yannis; Vorgias, Constantinos E; Yannoukakos, Drakoulis; Nounesis, George

2005-04-01

Reduced stability of the tandem BRCT domains of human BReast CAncer 1 (BRCA1) due to missense mutations may be critical for loss of function in DNA repair and damage-induced checkpoint control. In the present thermal denaturation study of the BRCA1 BRCT region, high-precision differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy provide evidence for the existence of a denatured state that is structurally very similar to the native. Consistency between theoretical structure-based estimates of the enthalpy (DeltaH) and heat capacity change (DeltaCp) and the calorimetric results is obtained when considering partial thermal unfolding contained in the region of the conserved hydrophobic pocket formed at the interface of the two BRCT repeats. The structural integrity of this region has been shown to be crucial for the interaction of BRCA1 with phosphorylated peptides. In addition, cancer-causing missense mutations located at the inter-BRCT-repeat interface have been linked to the destabilization of the tandem BRCT structure.

A novel source of MeV positron bunches driven by energetic protons for PAS application

NASA Astrophysics Data System (ADS)

Tan, Zongquan; Xu, Wenzhen; Liu, Yanfen; Xiao, Ran; Kong, Wei; Ye, Bangjiao

2014-11-01

This paper proposes a novel methodology of MeV positrons generation for PAS application. Feasibility of this proposal analyzed by G4Beamline and Transport have shown reasonable success. Using 2 Hz, 1.6 GeV, 100 ns and 1.5 μC/bunch proton bunches for bombarding a graphite target, about 100 ns e+ bunches are generated. Quasi-monochromatic positrons in the range of 1-10 MeV included in these bunches have a flux of >107/s, peak brightness of 1014/s. A magnetic-confinement beamline is utilized to transport the positrons and a "Fast Beam Chopper" is unprecedentedly extended to chop those relativistic bunches. The positron beam can be finally characterized by the energy range of 1-10 MeV and bunch width from one hundred ps up to 1 ns. Such ultrashort bunches can be useful in tomography-type positron annihilation spectroscopy (PAS) as well as other applications.

Proteins with an Euonymus lectin-like domain are ubiquitous in Embryophyta

PubMed Central

2009-01-01

Background Cloning of the Euonymus lectin led to the discovery of a novel domain that also occurs in some stress-induced plant proteins. The distribution and the diversity of proteins with an Euonymus lectin (EUL) domain were investigated using detailed analysis of sequences in publicly accessible genome and transcriptome databases. Results Comprehensive in silico analyses indicate that the recently identified Euonymus europaeus lectin domain represents a conserved structural unit of a novel family of putative carbohydrate-binding proteins, which will further be referred to as the Euonymus lectin (EUL) family. The EUL domain is widespread among plants. Analysis of retrieved sequences revealed that some sequences consist of a single EUL domain linked to an unrelated N-terminal domain whereas others comprise two in tandem arrayed EUL domains. A new classification system for these lectins is proposed based on the overall domain architecture. Evolutionary relationships among the sequences with EUL domains are discussed. Conclusion The identification of the EUL family provides the first evidence for the occurrence in terrestrial plants of a highly conserved plant specific domain. The widespread distribution of the EUL domain strikingly contrasts the more limited or even narrow distribution of most other lectin domains found in plants. The apparent omnipresence of the EUL domain is indicative for a universal role of this lectin domain in plants. Although there is unambiguous evidence that several EUL domains possess carbohydrate-binding activity further research is required to corroborate the carbohydrate-binding properties of different members of the EUL family. PMID:19930663

Form-Focused Interaction in Online Tandem Learning

ERIC Educational Resources Information Center

O'Rourke, Breffni

2005-01-01

Tandem language learning--a configuration involving pairs of learners with complementary target/native languages--is an underexploited but potentially very powerful use of computer-mediated communication (CMC) in second-language pedagogy. Tandem offers the benefits of authentic, culturally grounded interaction, while also promoting a pedagogical…

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.

Time-Domain Pure-state Polarization Analysis of Surface Waves Traversing California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, J; Walter, W R; Lay, T

A time-domain pure-state polarization analysis method is used to characterize surface waves traversing California parallel to the plate boundary. The method is applied to data recorded at four broadband stations in California from twenty-six large, shallow earthquakes which occurred since 1988, yielding polarization parameters such as the ellipticity, Euler angles, instantaneous periods, and wave incident azimuths. The earthquakes are located along the circum-Pacific margin and the ray paths cluster into two groups, with great-circle paths connecting stations MHC and PAS or CMB and GSC. The first path (MHC-PAS) is in the vicinity of the San Andreas Fault System (SAFS), andmore » the second (CMB-GSC) traverses the Sierra Nevada Batholith parallel to and east of the SAFS. Both Rayleigh and Love wave data show refractions due to lateral velocity heterogeneities under the path, indicating that accurate phase velocity and attenuation analysis requires array measurements. The Rayleigh waves are strongly affected by low velocity anomalies beneath Central California, with ray paths bending eastward as waves travel toward the south, while Love waves are less affected, providing observables to constrain the depth extent of the anomalies. Strong lateral gradients in the lithospheric structure between the continent and the ocean are the likely cause of the path deflections.« less

Electronic Tandem Language Learning (eTandem): A Third Approach to Second Language Learning for the 21st Century

ERIC Educational Resources Information Center

Cziko, Gary A.

2004-01-01

Tandem language learning occurs when two learners of different native languages work together to help each other learn the other language. First used in face-to-face contexts, Tandem is now increasingly being used by language-learning partners located in different countries who are linked via various forms of electronic communication, a context…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michael, Alicia K.; Fribourgh, Jennifer L.; Chelliah, Yogarany

The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ~24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here in this paper, we show that CRY1 binds directly to the PAS domain core of CLOCK: BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solutionmore » X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.« less

Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1

DOE PAGES

Michael, Alicia K.; Fribourgh, Jennifer L.; Chelliah, Yogarany; ...

2017-01-31

The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ~24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here in this paper, we show that CRY1 binds directly to the PAS domain core of CLOCK: BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solutionmore » X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.« less

Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication

NASA Astrophysics Data System (ADS)

Rustiguel, Joane K.; Soares, Ricardo O. S.; Meisburger, Steve P.; Davis, Katherine M.; Malzbender, Kristina L.; Ando, Nozomi; Dias-Baruffi, Marcelo; Nonato, Maria Cristina

2016-09-01

Galectins are proteins involved in diverse cellular contexts due to their capacity to decipher and respond to the information encoded by β-galactoside sugars. In particular, human galectin-4, normally expressed in the healthy gastrointestinal tract, displays differential expression in cancerous tissues and is considered a potential drug target for liver and lung cancer. Galectin-4 is a tandem-repeat galectin characterized by two carbohydrate recognition domains connected by a linker-peptide. Despite their relevance to cell function and pathogenesis, structural characterization of full-length tandem-repeat galectins has remained elusive. Here, we investigate galectin-4 using X-ray crystallography, small- and wide-angle X-ray scattering, molecular modelling, molecular dynamics simulations, and differential scanning fluorimetry assays and describe for the first time a structural model for human galectin-4. Our results provide insight into the structural role of the linker-peptide and shed light on the dynamic characteristics of the mechanism of carbohydrate recognition among tandem-repeat galectins.

A lecithin phosphatidylserine and phosphatidic acid complex (PAS) reduces symptoms of the premenstrual syndrome (PMS): Results of a randomized, placebo-controlled, double-blind clinical trial.

PubMed

Schmidt, Katja; Weber, Nicole; Steiner, Meir; Meyer, Nadin; Dubberke, Anne; Rutenberg, David; Hellhammer, Juliane

2018-04-01

Many women experience emotional and physical symptoms around the time of ovulation and more so before menstruation interfering with their daily normal life also known as premenstrual syndrome (PMS). Recent observational data suggest that supplementation with Lipogen's phosphatidylserine (PS) and phosphatidic acid (PA) complex (PAS) alleviates these PMS symptoms. The aim of this study was to confirm these observations on the effects of PAS on PMS symptom severity within a controlled clinical trial setting. Forty women aged 18-45 years with a diagnosis of PMS were assigned to either take PAS (containing 400 mg PS & 400 mg PA per day) or a matching placebo. The study comprised 5 on-site visits including 1 baseline menstrual cycle followed by 3 treatment cycles. Treatment intake was controlled for by using an electronic device, the Medication Event Monitoring System (MEMS ® ). Primary outcome of the study was the PMS symptoms severity as assessed by using the Daily Record of Severity of Problems (DRSP). Further, SIPS questionnaire (a German version of the Premenstrual Symptoms Screening Tool (PSST)), salivary hormone levels (cortisol awakening response (CAR) and evening cortisol levels) as well as serum levels (cortisol, estradiol, progesterone and corticosteroid binding globulin (CBG)) were assessed. PMS symptoms as assessed by the DRSP Total score showed a significantly better improvement (p = 0.001) over a 3 cycles PAS intake as compared to placebo. In addition, PAS treated women reported a greater improvement in physical (p = 0.002) and depressive symptoms (p = 0.068). They also reported a lower reduction of productivity (p = 0.052) and a stronger decrease in interference with relationships with others (p = 0.099) compared to the placebo group. No other DRSP scale or item showed significant results. Likewise, the reduction in the number of subjects fulfilling PMS or premenstrual dysphoric disorder (PMDD) criteria as classified by the SIPS did not

47 CFR 69.111 - Tandem-switched transport and tandem charge.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., geographically averaged on a study-area-wide basis, that the incumbent local exchange carrier experiences based... exchange carrier experiences based on the prior year's annual use. Tandem-switched transport transmission..., geographically averaged on a study-area-wide basis, that the incumbent local exchange carrier experiences based...

Tandem catalysis: a new approach to polymers.

PubMed

Robert, Carine; Thomas, Christophe M

2013-12-21

The creation of polymers by tandem catalysis represents an exciting frontier in materials science. Tandem catalysis is one of the strategies used by Nature for building macromolecules. Living organisms generally synthesize macromolecules by in vivo enzyme-catalyzed chain growth polymerization reactions using activated monomers that have been formed within cells during complex metabolic processes. However, these biological processes rely on highly complex biocatalysts, thus limiting their industrial applications. In order to obtain polymers by tandem catalysis, homogeneous and enzyme catalysts have played a leading role in the last two decades. In the following feature article, we will describe selected published efforts to achieve these research goals.

Peptide Analysis Using Tandem Mass Spectrometry

DTIC Science & Technology

1989-06-01

to give pyroglutamic acid during storage, eliminating ammonia. It is almost absent in the spectrum of a freshly-prepared sample and is not seen in...USING TANDEM MASS SPECTROMETRY INTRODUCTION S The objective of the project was to determine the complete amino acid sequence of the large polypeptide...Ubiquitin by use of fast atom bombardment (FAB) ionization and tandem mass spectrometry. The peptide containing 76 amino acid residues was available

Development of Physics Attitude Scale (PAS): An Instrument to Measure Students' Attitudes toward Physics

ERIC Educational Resources Information Center

Kaur, Daisy; Zhao, Yi

2017-01-01

The present study is focused on the detailed description of Physics Attitude Scale (PAS) to measure students' attitudes toward physics. The development of this new instrument involved extensive interviews with both the experts as well as the students. This was followed by expert reviews and pilot testing of the instrument. The duly revised draft…

ESI-MS, ESI-MS/MS fingerprint and LC-ESI-MS analysis of proathocyanidins from Bursera simaruba Sarg bark.

PubMed

Maldini, Mariateresa; Montoro, Paola; Piacente, Sonia; Pizza, Cosimo

2009-12-01

Direct flow injection/electrospray ionization/ion trap tandem mass spectrometry was used to investigate the presence of proanthocyanidins (PAs) in the methanolic extract of B. simaruba bark. Additionally, an LC-ESI-MS qualitative study was performed by using a monolithic stationary phase. The fragmentation pattern obtained evidenced the presence in B. simaruba bark of PAs belonging to the series of polymers of epicatechin, along with their glycosilated derivatives.

Crystal Structure of the Central Coiled-Coil Domain from Human Liprin-[beta]2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stafford, Ryan L.; Tang, Ming-Yun; Sawaya, Michael R.

2012-02-07

Liprins are a conserved family of scaffolding proteins important for the proper regulation and development of neuronal synapses. Humans have four liprin-{alpha}s and two liprin-{beta}s which all contain long coiled-coil domains followed by three tandem SAM domains. Complex interactions between the coiled-coil and SAM domains are thought to create liprin scaffolds, but the structural and biochemical properties of these domains remain largely uncharacterized. In this study we find that the human liprin-{beta}2 coiled-coil forms an extended dimer. Several protease-resistant subdomains within the liprin-{beta}1 and liprin-{beta}2 coiled-coils were also identified. A 2.0 {angstrom} crystal structure of the central, protease-resistant core ofmore » the liprin-{beta}2 coiled-coil reveals a parallel helix orientation. These studies represent an initial step toward determining the overall architecture of liprin scaffolds and understanding the molecular basis for their synaptic functions.« less

TRedD—A database for tandem repeats over the edit distance

PubMed Central

Sokol, Dina; Atagun, Firat

2010-01-01

A ‘tandem repeat’ in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats are common in the genomes of both eukaryotic and prokaryotic organisms. They are significant markers for human identity testing, disease diagnosis, sequence homology and population studies. In this article, we describe a new database, TRedD, which contains the tandem repeats found in the human genome. The database is publicly available online, and the software for locating the repeats is also freely available. The definition of tandem repeats used by TRedD is a new and innovative definition based upon the concept of ‘evolutive tandem repeats’. In addition, we have developed a tool, called TandemGraph, to graphically depict the repeats occurring in a sequence. This tool can be coupled with any repeat finding software, and it should greatly facilitate analysis of results. Database URL: http://tandem.sci.brooklyn.cuny.edu/ PMID:20624712

Extinction, seeing and sky transparency monitoring at the Observatorio Astrofísico de Javalambre for J-PAS and J-PLUS calibration and scheduling

NASA Astrophysics Data System (ADS)

Vázquez Ramió, H.; Díaz-Martín, M. C.; Varela, J.; Ederoclite, A.; Maícas, N. Lamadrid, J. L.; Abril, J.; Iglesias-Marzoa, R.; Rodríguez, S.; Tilve, V.; Cenarro, A. J.; Antón Bravo, J. L.; Bello Ferrer, R.; Cristóbal-Hornillos, D.; Guillén Civera, L.; Hernández-Fuertes, J.; Jiménez Mejías, D.; Lasso-Cabrera, N. M.; López Alegre, G.; López Sainz, A.; Luis-Simoes, R. M.; Marín-Franch, A.; Moles, M.; Rueda-Teruel, F.; Rueda-Teruel, S.; Suárez López, O.; Yanes-Díaz, A.

2015-05-01

The Javalambre-Physics of the Accelerating Universe Astrophysical Survey (J-PAS; see Benítez et al. 2014) and the Javalambre-Photometric Local Universe Survey (J-PLUS) will be conducted at the brand-new Observatorio Astrofísico de Javalambre (OAJ) in Teruel, Spain. J-PLUS is planned to start by the first half of 2015 while J-PAS first light is expected to happen along 2015. Besides the two main telescopes (with 2.5 m and 80 cm apertures), several smaller-sized facilities are present at the OAJ devoted to site characterization and supporting measurements to be used to calibrate the J-PAS and J-PLUS photometry and to feed up the OAJ's Sequencer with the integrated seeing and the sky transparency. These instruments are: i) an extinction monitor, an 11 " telescope estimating the atmospheric extinction to finally obtain the OAJ extinction curve, which is the initial step to J-PAS overall photometric calibration procedure; ii) an 8 " telescope implementing the Differential Image Motion Monitor (DIMM) technique to obtain the integrated seeing; and iii) an All-Sky Transmission MONitor (ASTMON), a roughly all-sky instrument providing the sky transparency as well as sky brightness and the atmospheric extinction too.

PTGBase: an integrated database to study tandem duplicated genes in plants.

PubMed

Yu, Jingyin; Ke, Tao; Tehrim, Sadia; Sun, Fengming; Liao, Boshou; Hua, Wei

2015-01-01

Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays. Many tandem duplication events have been studied in plant genomes; yet, there is a surprising shortage of efforts to systematically present the integration of large amounts of information about publicly deposited tandem duplicated gene data across the plant kingdom. To address this shortcoming, we developed the first plant tandem duplicated genes database, PTGBase. It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available. © The Author(s) 2015. Published by Oxford University Press.

Phosphotyrosine recognition domains: the typical, the atypical and the versatile

PubMed Central

2012-01-01

SH2 domains are long known prominent players in the field of phosphotyrosine recognition within signaling protein networks. However, over the years they have been joined by an increasing number of other protein domain families that can, at least with some of their members, also recognise pTyr residues in a sequence-specific context. This superfamily of pTyr recognition modules, which includes substantial fractions of the PTB domains, as well as much smaller, or even single member fractions like the HYB domain, the PKCδ and PKCθ C2 domains and RKIP, represents a fascinating, medically relevant and hence intensely studied part of the cellular signaling architecture of metazoans. Protein tyrosine phosphorylation clearly serves a plethora of functions and pTyr recognition domains are used in a similarly wide range of interaction modes, which encompass, for example, partner protein switching, tandem recognition functionalities and the interaction with catalytically active protein domains. If looked upon closely enough, virtually no pTyr recognition and regulation event is an exact mirror image of another one in the same cell. Thus, the more we learn about the biology and ultrastructural details of pTyr recognition domains, the more does it become apparent that nature cleverly combines and varies a few basic principles to generate a sheer endless number of sophisticated and highly effective recognition/regulation events that are, under normal conditions, elegantly orchestrated in time and space. This knowledge is also valuable when exploring pTyr reader domains as diagnostic tools, drug targets or therapeutic reagents to combat human diseases. PMID:23134684

Hybrid Tandem Solar Cells | Photovoltaic Research | NREL

Science.gov Websites

Hybrid Tandem Solar Cells Hybrid Tandem Solar Cells To achieve aggressive cost reductions in photovoltaics (PV) beyond the 6¢/kWh SunShot Initiative 2020 goal, module efficiency must be increased beyond on a silicon platform and that aim to provide viable prototypes for commercialization. PV Research

Generation of single domain antibody fragments derived from camelids and generation of manifold constructs.

PubMed

Vincke, Cécile; Gutiérrez, Carlos; Wernery, Ulrich; Devoogdt, Nick; Hassanzadeh-Ghassabeh, Gholamreza; Muyldermans, Serge

2012-01-01

Immunizing a camelid (camels and llamas) with soluble, properly folded proteins raises an affinity-matured immune response in the unique camelid heavy-chain only antibodies (HCAbs). The peripheral blood lymphocytes of the immunized animal are used to clone the antigen-binding antibody fragment from the HCAbs in a phage display vector. A representative aliquot of the library of these antigen-binding fragments is used to retrieve single domain antigen-specific binders by successive rounds of panning. These single domain antibody fragments are cloned in tandem to generate manifold constructs (bivalent, biparatopic or bispecific constructs) to increase their functional affinity, to increase specificity, or to connect two independent antigen molecules.

Monolithic Parallel Tandem Organic Photovoltaic Cell with Transparent Carbon Nanotube Interlayer

NASA Technical Reports Server (NTRS)

Tanaka, S.; Mielczarek, K.; Ovalle-Robles, R.; Wang, B.; Hsu, D.; Zakhidov, A. A.

2009-01-01

We demonstrate an organic photovoltaic cell with a monolithic tandem structure in parallel connection. Transparent multiwalled carbon nanotube sheets are used as an interlayer anode electrode for this parallel tandem. The characteristics of front and back cells are measured independently. The short circuit current density of the parallel tandem cell is larger than the currents of each individual cell. The wavelength dependence of photocurrent for the parallel tandem cell shows the superposition spectrum of the two spectral sensitivities of the front and back cells. The monolithic three-electrode photovoltaic cell indeed operates as a parallel tandem with improved efficiency.

ATP Binding to p97/VCP D1 Domain Regulates Selective Recruitment of Adaptors to Its Proximal N-Domain

PubMed Central

Chia, Wei Sheng; Chia, Diana Xueqi; Rao, Feng; Bar Nun, Shoshana; Geifman Shochat, Susana

2012-01-01

p97/Valosin-containing protein (VCP) is a member of the AAA-ATPase family involved in many cellular processes including cell division, intracellular trafficking and extraction of misfolded proteins in endoplasmic reticulum-associated degradation (ERAD). It is a homohexamer with each subunit containing two tandem D1 and D2 ATPase domains and N- and C-terminal regions that function as adaptor protein binding domains. p97/VCP is directed to its many different functional pathways by associating with various adaptor proteins. The regulation of the recruitment of the adaptor proteins remains unclear. Two adaptor proteins, Ufd1/Npl4 and p47, which bind exclusively to the p97/VCP N-domain and direct p97/VCP to either ERAD-related processes or homotypic fusion of Golgi fragments, were studied here. Surface plasmon resonance biosensor-based assays allowed the study of binding kinetics in real time. In competition experiments, it was observed that in the presence of ATP, Ufd1/Npl4 was able to compete more effectively with p47 for binding to p97/VCP. By using non-hydrolysable ATP analogues and the hexameric truncated p97/N-D1 fragment, it was shown that binding rather than hydrolysis of ATP to the proximal D1 domain strengthened the Ufd1/Npl4 association with the N-domain, thus regulating the recruitment of either Ufd1/Npl4 or p47. This novel role of ATP and an assigned function to the D1 AAA-ATPase domain link the multiple functions of p97/VCP to the metabolic status of the cell. PMID:23226521

ATP binding to p97/VCP D1 domain regulates selective recruitment of adaptors to its proximal N-domain.

PubMed

Chia, Wei Sheng; Chia, Diana Xueqi; Rao, Feng; Bar Nun, Shoshana; Geifman Shochat, Susana

2012-01-01

p97/Valosin-containing protein (VCP) is a member of the AAA-ATPase family involved in many cellular processes including cell division, intracellular trafficking and extraction of misfolded proteins in endoplasmic reticulum-associated degradation (ERAD). It is a homohexamer with each subunit containing two tandem D1 and D2 ATPase domains and N- and C-terminal regions that function as adaptor protein binding domains. p97/VCP is directed to its many different functional pathways by associating with various adaptor proteins. The regulation of the recruitment of the adaptor proteins remains unclear. Two adaptor proteins, Ufd1/Npl4 and p47, which bind exclusively to the p97/VCP N-domain and direct p97/VCP to either ERAD-related processes or homotypic fusion of Golgi fragments, were studied here. Surface plasmon resonance biosensor-based assays allowed the study of binding kinetics in real time. In competition experiments, it was observed that in the presence of ATP, Ufd1/Npl4 was able to compete more effectively with p47 for binding to p97/VCP. By using non-hydrolysable ATP analogues and the hexameric truncated p97/N-D1 fragment, it was shown that binding rather than hydrolysis of ATP to the proximal D1 domain strengthened the Ufd1/Npl4 association with the N-domain, thus regulating the recruitment of either Ufd1/Npl4 or p47. This novel role of ATP and an assigned function to the D1 AAA-ATPase domain link the multiple functions of p97/VCP to the metabolic status of the cell.

Inverted Three-Junction Tandem Thermophotovoltaic Modules

NASA Technical Reports Server (NTRS)

Wojtczuk, Steven

2012-01-01

An InGaAs-based three-junction (3J) tandem thermophotovoltaic (TPV) cell has been investigated to utilize more of the blackbody spectrum (from a 1,100 C general purpose heat source GPHS) efficiently. The tandem consists of three vertically stacked subcells, a 0.74-eV InGaAs cell, a 0.6- eV InGaAs cell, and a 0.55-eV InGaAs cell, as well as two interconnecting tunnel junctions. A greater than 20% TPV system efficiency was achieved by another group with a 1,040 C blackbody using a single-bandgap 0.6- eV InGaAs cell MIM (monolithic interconnected module) (30 lateral junctions) that delivered about 12 V/30 or 0.4 V/junction. It is expected that a three-bandgap tandem MIM will eventually have about 3 this voltage (1.15 V) and about half the current. A 4 A/cm2 would be generated by a single-bandgap 0.6-V InGaAs MIM, as opposed to the 2 A/cm2 available from the same spectrum when split among the three series-connected junctions in the tandem stack. This would then be about a 50% increase (3xVoc, 0.5xIsc) in output power if the proposed tandem replaced the single- bandgap MIM. The advantage of the innovation, if successful, would be a 50% increase in power conversion efficiency from radioisotope heat sources using existing thermophotovoltaics. Up to 50% more power would be generated for radioisotope GPHS deep space missions. This type of InGaAs multijunction stack could be used with terrestrial concentrator solar cells to increase efficiency from 41 to 45% or more.

Toxic pyrrolizidinalkaloids as undesired contaminants in food and feed: degradation of the PAs from Senecio jacobaea in silage.

PubMed

Becerra-Jiminez, J; Kuschak, M; Roeder, E; Wiedenfeld, H

2013-07-01

Pyrrolizidine alkaloids (PAs) can show a hazardous potential for men and animals. They can act as cancerogenic, mutagenic, teratogenic and fetotoxic agents. One pathway of a human intoxication is its occurence as contaminants in food and feed. Here, the contamination of cereals already led to severe and fatal intoxication episodes. Besides this, milk is of special concern as it is the main food for children which show a very high susceptibility for a PA intoxication. Milk can contain PAs in case the milk producing animals have access to contaminated feed. In this context it is of special interest whether the PA content of contaminated silage remains stable during the ensiling procedure or show a more or less high level of decomposition. We could show that ensiling will not lead to PA-free silage.

Psychometric properties and norms of the German ABC-Community and PAS-ADD Checklist.

PubMed

Zeilinger, Elisabeth L; Weber, Germain; Haveman, Meindert J

2011-01-01

The aim of the present study was to standardize and generate psychometric evidence of the German language versions of two well-established English language mental health instruments: the Aberrant Behavior Checklist-Community (ABC-C) and the Psychiatric Assessment Schedule for Adults with Developmental Disabilities (PAS-ADD) Checklist. New methods in this field were introduced: a simulation method for testing the factor structure and an exploration of long-term stability over two years. The checklists were both administered to a representative sample of 270 individuals with intellectual disability (ID) and, two years later in a second data collection, to 128 participants of the original sample. Principal component analysis and parallel analysis were performed. Reliability measures, long-term stability, subscale intercorrelations, as well as standardized norms were generated. Prevalence of mental health problems was examined. Psychometric properties were mostly excellent, with long-term stability showing moderate to strong effects. The original factor structure of the ABC-C was replicated. PAS-ADD Checklist produced a similar, but still different structure compared with findings from the English language area. The overall prevalence rate of mental health problems in the sample was about 20%. Considering the good results on the measured psychometric properties, the two checklists are recommended for the early detection of mental health problems in persons with ID. Copyright © 2011 Elsevier Ltd. All rights reserved.

Four Amino Acids within a Tandem QxVx Repeat in a Predicted Extended α-Helix of the Smad-Binding Domain of Sip1 Are Necessary for Binding to Activated Smad Proteins

PubMed Central

Conidi, Andrea; van den Berghe, Veronique; Leslie, Kris; Stryjewska, Agata; Xue, Hua; Chen, Ye-Guang; Seuntjens, Eve; Huylebroeck, Danny

2013-01-01

The zinc finger transcription factor Smad-interacting protein-1 (Sip1; Zeb2, Zfhx1b) plays an important role during vertebrate embryogenesis in various tissues and differentiating cell types, and during tumorigenesis. Previous biochemical analysis suggests that interactions with several partner proteins, including TGFβ family receptor-activated Smads, regulate the activities of Sip1 in the nucleus both as a DNA-binding transcriptional repressor and activator. Using a peptide aptamer approach we mapped in Sip1 its Smad-binding domain (SBD), initially defined as a segment of 51 amino acids, to a shorter stretch of 14 amino acids within this SBD. Modelling suggests that this short SBD stretch is part of an extended α-helix that may fit the binding to a hydrophobic corridor within the MH2 domain of activated Smads. Four amino acids (two polar Q residues and two non-polar V residues) that form the tandem repeat (QxVx)2 in this 14-residue stretch were found to be crucial for binding to both TGFβ/Nodal/Activin-Smads and BMP-Smads. A full-length Sip1 with collective mutation of these Q and V residues (to A) no longer binds to Smads, while it retains its binding activity to its cognate bipartite target DNA sequence. This missense mutant Sip1(AxAx)2 provides a new molecular tool to identify SBD (in)dependent target genes in Sip1-controlled TGFβ and/or BMP (de)regulated cellular, developmental and pathological processes. PMID:24146916

BRCT-domain protein BRIT1 influences class switch recombination

PubMed Central

Yen, Wei-Feng; Chaudhry, Ashutosh; Vaidyanathan, Bharat; Yewdell, William T.; Pucella, Joseph N.; Sharma, Rahul; Li, Kaiyi; Rudensky, Alexander Y.; Chaudhuri, Jayanta

2017-01-01

DNA double-strand breaks (DSBs) serve as obligatory intermediates for Ig heavy chain (Igh) class switch recombination (CSR). The mechanisms by which DSBs are resolved to promote long-range DNA end-joining while suppressing genomic instability inherently associated with DSBs are yet to be fully elucidated. Here, we use a targeted short-hairpin RNA screen in a B-cell lymphoma line to identify the BRCT-domain protein BRIT1 as an effector of CSR. We show that conditional genetic deletion of BRIT1 in mice leads to a marked increase in unrepaired Igh breaks and a significant reduction in CSR in ex vivo activated splenic B cells. We find that the C-terminal tandem BRCT domains of BRIT1 facilitate its interaction with phosphorylated H2AX and that BRIT1 is recruited to the Igh locus in an activation-induced cytidine deaminase (AID) and H2AX-dependent fashion. Finally, we demonstrate that depletion of another BRCT-domain protein, MDC1, in BRIT1-deleted B cells increases the severity of CSR defect over what is observed upon loss of either protein alone. Our results identify BRIT1 as a factor in CSR and demonstrate that multiple BRCT-domain proteins contribute to optimal resolution of AID-induced DSBs. PMID:28724724

Performance of a tandem-rotor/tandem-stator conical-flow compressor designed for a pressure ratio of 3

NASA Technical Reports Server (NTRS)

Wood, J. R.; Owen, A. K.; Schumann, L. F.

1982-01-01

A conical-flow compressor stage with a large radius change through the rotor was tested at three values of rotor tip clearance. The stage had a tandem rotor and a tandem stator. Peak efficiency at design speed was 0.774 at a pressure ratio of 2.613. The rotor was tested without the stator, and detailed survey data were obtained for each rotor blade row. Overall peak rotor efficiency was 0.871 at a pressure ratio of 2.952.

A tandem-based compact dual-energy gamma generator.

PubMed

Persaud, A; Kwan, J W; Leitner, M; Leung, K-N; Ludewigt, B; Tanaka, N; Waldron, W; Wilde, S; Antolak, A J; Morse, D H; Raber, T

2010-02-01

A dual-energy tandem-type gamma generator has been developed at E. O. Lawrence Berkeley National Laboratory and Sandia National Laboratories. The tandem accelerator geometry allows higher energy nuclear reactions to be reached, thereby allowing more flexible generation of MeV-energy gammas for active interrogation applications. Both positively charged ions and atoms of hydrogen are created from negative ions via a gas stripper. In this paper, we show first results of the working tandem-based gamma generator and that a gas stripper can be utilized in a compact source design. Preliminary results of monoenergetic gamma production are shown.

Immunogenicity of a recombinant fusion protein of tandem repeat epitopes of foot-and-mouth disease virus type Asia 1 for guinea pigs.

PubMed

Zhang, Q; Yang, Y Q; Zhang, Z Y; Li, L; Yan, W Y; Jiang, W J; Xin, A G; Lei, C X; Zheng, Z X

2002-01-01

In this study, the sequences of capsid protein VPI regions of YNAs1.1 and YNAs1.2 isolates of foot-and-mouth disease virus (FMDV) were analyzed and a peptide containing amino acids (aa) 133-158 of VP1 and aa 20-34 of VP4 of FMDV type Asia I was assumed to contain B and T cell epitopes, because it is hypervariable and includes a cell attachment site RGD located in the G-H loop. The DNA fragments encoding aa 133-158 of VP1 and aa 20-34 of VP4 of FMDV type Asia 1 were chemically synthesized and ligated into a tandem repeat of aa 133-158-20 approximately 34-133-158. In order to enhance its immunogenicity, the tandem repeat was inserted downstream of the beta-galactosidase gene in the expression vector pWR590. This insertion yielded a recombinant expression vector pAS1 encoding the fusion protein. The latter reacted with sera from FMDV type Asia 1-infected animals in vitro and elicited high levels of neutralizing antibodies in guinea pigs. The T cell proliferation in immunized animals increased following stimulation with the fusion protein. It is reported for the first time that a recombinant fusion protein vaccine was produced using B and T cell epitopes of FMDV type Asia 1 and that this fusion protein was immunogenic. The fusion protein reported here can serve as a candidate of fusion epitopes for design of a vaccine against FMDV type Asia 1.

Src binds cortactin through an SH2 domain cystine-mediated linkage.

PubMed

Evans, Jason V; Ammer, Amanda G; Jett, John E; Bolcato, Chris A; Breaux, Jason C; Martin, Karen H; Culp, Mark V; Gannett, Peter M; Weed, Scott A

2012-12-15

Tyrosine-kinase-based signal transduction mediated by modular protein domains is critical for cellular function. The Src homology (SH)2 domain is an important conductor of intracellular signaling that binds to phosphorylated tyrosines on acceptor proteins, producing molecular complexes responsible for signal relay. Cortactin is a cytoskeletal protein and tyrosine kinase substrate that regulates actin-based motility through interactions with SH2-domain-containing proteins. The Src kinase SH2 domain mediates cortactin binding and tyrosine phosphorylation, but how Src interacts with cortactin is unknown. Here we demonstrate that Src binds cortactin through cystine bonding between Src C185 in the SH2 domain within the phosphotyrosine binding pocket and cortactin C112/246 in the cortactin repeats domain, independent of tyrosine phosphorylation. Interaction studies show that the presence of reducing agents ablates Src-cortactin binding, eliminates cortactin phosphorylation by Src, and prevents Src SH2 domain binding to cortactin. Tandem MS/MS sequencing demonstrates cystine bond formation between Src C185 and cortactin C112/246. Mutational studies indicate that an intact cystine binding interface is required for Src-mediated cortactin phosphorylation, cell migration, and pre-invadopodia formation. Our results identify a novel phosphotyrosine-independent binding mode between the Src SH2 domain and cortactin. Besides Src, one quarter of all SH2 domains contain cysteines at or near the analogous Src C185 position. This provides a potential alternative mechanism to tyrosine phosphorylation for cysteine-containing SH2 domains to bind cognate ligands that may be widespread in propagating signals regulating diverse cellular functions.

Src binds cortactin through an SH2 domain cystine-mediated linkage

PubMed Central

Evans, Jason V.; Ammer, Amanda G.; Jett, John E.; Bolcato, Chris A.; Breaux, Jason C.; Martin, Karen H.; Culp, Mark V.; Gannett, Peter M.; Weed, Scott A.

2012-01-01

Summary Tyrosine-kinase-based signal transduction mediated by modular protein domains is critical for cellular function. The Src homology (SH)2 domain is an important conductor of intracellular signaling that binds to phosphorylated tyrosines on acceptor proteins, producing molecular complexes responsible for signal relay. Cortactin is a cytoskeletal protein and tyrosine kinase substrate that regulates actin-based motility through interactions with SH2-domain-containing proteins. The Src kinase SH2 domain mediates cortactin binding and tyrosine phosphorylation, but how Src interacts with cortactin is unknown. Here we demonstrate that Src binds cortactin through cystine bonding between Src C185 in the SH2 domain within the phosphotyrosine binding pocket and cortactin C112/246 in the cortactin repeats domain, independent of tyrosine phosphorylation. Interaction studies show that the presence of reducing agents ablates Src-cortactin binding, eliminates cortactin phosphorylation by Src, and prevents Src SH2 domain binding to cortactin. Tandem MS/MS sequencing demonstrates cystine bond formation between Src C185 and cortactin C112/246. Mutational studies indicate that an intact cystine binding interface is required for Src-mediated cortactin phosphorylation, cell migration, and pre-invadopodia formation. Our results identify a novel phosphotyrosine-independent binding mode between the Src SH2 domain and cortactin. Besides Src, one quarter of all SH2 domains contain cysteines at or near the analogous Src C185 position. This provides a potential alternative mechanism to tyrosine phosphorylation for cysteine-containing SH2 domains to bind cognate ligands that may be widespread in propagating signals regulating diverse cellular functions. PMID:23097045

Solar-to-Chemical Energy Conversion with Photoelectrochemical Tandem Cells.

PubMed

Sivula, Kevin

2013-01-01

Efficiently and inexpensively converting solar energy into chemical fuels is an important goal towards a sustainable energy economy. An integrated tandem cell approach could reasonably convert over 20% of the sun's energy directly into chemical fuels like H2 via water splitting. Many different systems have been investigated using various combinations of photovoltaic cells and photoelectrodes, but in order to be economically competitive with the production of H2 from fossil fuels, a practical water splitting tandem cell must optimize cost, longevity and performance. In this short review, the practical aspects of solar fuel production are considered from the perspective of a semiconductor-based tandem cell and the latest advances with a very promising technology - metal oxide photoelectrochemical tandem cells - are presented.

Interactions of U24 from Roseolovirus with WW domains: canonical vs noncanonical.

PubMed

Sang, Yurou; Zhang, Rui; Creagh, A Louise; Haynes, Charles A; Straus, Suzana K

2017-06-01

U24 is a C-terminal membrane-anchored protein found in both human herpes virus type 6 and 7 (HHV-6 and HHV-7), with an N-terminal segment that is rich in prolines (PPxY motif in both HHV-6A and 7; PxxP motif in HHV-6A). Previous work has shown that U24 interacts strongly with Nedd4 WW domains, in particular, hNedd4L-WW3*. It was also shown that this interaction depends strongly on the nature of the amino acids that are upstream from the PY motif in U24. In this contribution, data was obtained from pull-downs, isothermal titration calorimetry, and NMR to further determine what modulates U24:WW domain interactions. Specifically, 3 non-canonical WW domains from human Smad ubiquitination regulatory factor (Smurf), namely hSmurf2-WW2, hSmurf2-WW3, and a tandem construct hSmurf2-WW2 + 3, were studied. Overall, the interactions between U24 and these Smurf WW domains were found to be weaker than those in U24:Nedd4 WW domain pairs, suggesting that U24 function is tightly linked to specific E3 ubiqitin ligases.

TRAP: automated classification, quantification and annotation of tandemly repeated sequences.

PubMed

Sobreira, Tiago José P; Durham, Alan M; Gruber, Arthur

2006-02-01

TRAP, the Tandem Repeats Analysis Program, is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. TRAP uses the results of the Tandem Repeats Finder program to perform a global analysis of the satellite content of DNA sequences, permitting researchers to easily assess the tandem repeat content for both individual sequences and whole genomes. The results can be generated in convenient formats such as HTML and comma-separated values. TRAP can also be used to automatically generate annotation data in the format of feature table and GFF files.

The C-terminal extension of human RTEL1, mutated in Hoyeraal-Hreidarsson syndrome, contains harmonin-N-like domains.

PubMed

Faure, Guilhem; Revy, Patrick; Schertzer, Michael; Londono-Vallejo, Arturo; Callebaut, Isabelle

2014-06-01

Several studies have recently shown that germline mutations in RTEL1, an essential DNA helicase involved in telomere regulation and DNA repair, cause Hoyeraal-Hreidarsson syndrome (HHS), a severe form of dyskeratosis congenita. Using original new softwares, facilitating the delineation of the different domains of the protein and the identification of remote relationships for orphan domains, we outline here that the C-terminal extension of RTEL1, downstream of its catalytic domain and including several HHS-associated mutations, contains a yet unidentified tandem of harmonin-N-like domains, which may serve as a hub for partner interaction. This finding highlights the potential critical role of this region for the function of RTEL1 and gives insights into the impact that the identified mutations would have on the structure and function of these domains. © 2013 Wiley Periodicals, Inc.

Unexpected peaks in tandem mass spectra due to reaction of product ions with residual water in mass spectrometer collision cells.

PubMed

Neta, Pedatsur; Farahani, Mahnaz; Simón-Manso, Yamil; Liang, Yuxue; Yang, Xiaoyu; Stein, Stephen E

2014-12-15

Certain product ions in electrospray ionization tandem mass spectrometry are found to react with residual water in the collision cell. This reaction often leads to the formation of ions that cannot be formed directly from the precursor ions, and this complicates the mass spectra and may distort MRM (multiple reaction monitoring) results. Various drugs, pesticides, metabolites, and other compounds were dissolved in acetonitrile/water/formic acid and studied by electrospray ionization mass spectrometry to record their MS(2) and MS(n) spectra in several mass spectrometers (QqQ, QTOF, IT, and Orbitrap HCD). Certain product ions were found to react with residual water in collision cells. The reaction was confirmed by MS(n) studies and the rate of reaction was determined in the IT instrument using zero collision energy and variable activation times. Examples of product ions reacting with water include phenyl and certain substituted phenyl cations, benzoyl-type cations formed from protonated folic acid and similar compounds by loss of the glutamate moiety, product ions formed from protonated cyclic siloxanes by loss of methane, product ions formed from organic phosphates, and certain negative ions. The reactions of product ions with residual water varied greatly in their rate constant and in the extent of reaction (due to isomerization). Various types of product ions react with residual water in mass spectrometer collision cells. As a result, tandem mass spectra may contain unexplained peaks and MRM results may be distorted by the occurrence of such reactions. These often unavoidable reactions must be taken into account when annotating peaks in tandem mass spectra and when interpreting MRM results. Published in 2014. This article is a U.S. Government work and is in the public domain in the USA. Published in 2014. This article is a U.S. Government work and is in the public domain in the USA.

Schwann Cell Migration Induced by Earthworm Extract via Activation of PAs and MMP2/9 Mediated through ERK1/2 and p38

PubMed Central

Chang, Yung-Ming; Shih, Ying-Ting; Chen, Yueh-Sheng; Liu, Chien-Liang; Fang, Wen-Kuei; Tsai, Chang-Hai; Tsai, Fuu-Jen; Kuo, Wei-Wen; Lai, Tung-Yuan; Huang, Chih-Yang

2011-01-01

The earthworm, which has stasis removal and wound-healing functions, is a widely used Chinese herbal medicine in China. Schwann cell migration is critical for the regeneration of injured nerves. Schwann cells provide an essentially supportive activity for neuron regeneration. However, the molecular migration mechanisms induced by earthworms in Schwann cells remain unclear. Here, we investigate the roles of MAPK (ERK1/2, JNK and p38) pathways for earthworm-induced matrix-degrading proteolytic enzyme (PAs and MMP2/9) production in Schwann cells. Moreover, earthworm induced phosphorylation of ERK1/2 and p38, but not JNK, activate the downstream signaling expression of PAs and MMPs in a time-dependent manner. Earthworm-stimulated ERK1/2 and p38 phosphorylation was attenuated by pretreatment with U0126 and SB203580, resulting in migration and uPA-related signal pathway inhibition. The results were confirmed using small interfering ERK1/2 and p38 RNA. These results demonstrated that earthworms can stimulate Schwann cell migration and up-regulate PAs and MMP2/9 expression mediated through the MAPK pathways, ERK1/2 and p38. Taken together, our data suggests the MAPKs (ERK1/2, p38)-, PAs (uPA, tPA)-, MMP (MMP2, MMP9) signaling pathway of Schwann cells regulated by earthworms might play a major role in Schwann cell migration and nerve regeneration. PMID:19808845

YY1 as a controlling factor for the Peg3 and Gnas imprinted domains

PubMed Central

Kim, Jeong Do; Hinz, Angela K.; Choo, Jung Ha; Stubbs, Lisa; Kim, Joomyeong

2007-01-01

Imprinting Control Regions (ICRs) often harbor tandem arrays of transcription factor binding sites, as demonstrated by the identification of multiple YY1 binding sites within the ICRs of Peg3, Nespas, and Xist/Tsix domains. In the current study, we have sought to characterize possible roles of YY1 in transcriptional control and epigenetic modification of these imprinted domains. RNA interference-based knockdown experiments in Neuro2A cells resulted in overall transcriptional up-regulation of most of the imprinted genes within the Peg3 domain and also, concomitantly, caused significant loss in the DNA methylation of Peg3-DMR (Differentially Methylated Regions). A similar overall and coordinated expression change was also observed for the imprinted genes of the Gnas domain: up-regulation of Nespas and down-regulation of Nesp and Gnasxl. YY1 knockdown also resulted in changes in the expression levels of Xist and Snrpn. These results support the idea that YY1 plays a major role, as a trans factor, for the control of these imprinted domains. PMID:17067777

Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution.

PubMed

Ponting, C P; Mott, R; Bork, P; Copley, R R

2001-12-01

Sequence database searching methods such as BLAST, are invaluable for predicting molecular function on the basis of sequence similarities among single regions of proteins. Searches of whole databases however, are not optimized to detect multiple homologous regions within a single polypeptide. Here we have used the prospero algorithm to perform self-comparisons of all predicted Drosophila melanogaster gene products. Predicted repeats, and their homologs from all species, were analyzed further to detect hitherto unappreciated evolutionary relationships. Results included the identification of novel tandem repeats in the human X-linked retinitis pigmentosa type-2 gene product, repeated segments in cystinosin, associated with a defect in cystine transport, and 'nested' homologous domains in dysferlin, whose gene is mutated in limb girdle muscular dystrophy. Novel signaling domain families were found that may regulate the microtubule-based cytoskeleton and ubiquitin-mediated proteolysis, respectively. Two families of glycosyl hydrolases were shown to contain internal repetitions that hint at their evolution via a piecemeal, modular approach. In addition, three examples of fruit fly genes were detected with tandem exons that appear to have arisen via internal duplication. These findings demonstrate how completely sequenced genomes can be exploited to further understand the relationships between molecular structure, function, and evolution.

Targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae.

PubMed

Takahashi, Tadashi; Sato, Atsushi; Ogawa, Masahiro; Hanya, Yoshiki; Oguma, Tetsuya

2014-08-01

We describe here the first successful construction of a targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had a 5'-deleted pyrG upstream of the region targeted for tandem chromosomal duplication and a 3'-deleted pyrG downstream of the target region. Consequently,strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks(DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under nonselective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method.

Structure of Myo7b/USH1C complex suggests a general PDZ domain binding mode by MyTH4-FERM myosins

PubMed Central

Li, Jianchao; He, Yunyun; Weck, Meredith L.; Lu, Qing; Tyska, Matthew J.; Zhang, Mingjie

2017-01-01

Unconventional myosin 7a (Myo7a), myosin 7b (Myo7b), and myosin 15a (Myo15a) all contain MyTH4-FERM domains (myosin tail homology 4-band 4.1, ezrin, radixin, moesin; MF) in their cargo binding tails and are essential for the growth and function of microvilli and stereocilia. Numerous mutations have been identified in the MyTH4-FERM tandems of these myosins in patients suffering visual and hearing impairment. Although a number of MF domain binding partners have been identified, the molecular basis of interactions with the C-terminal MF domain (CMF) of these myosins remains poorly understood. Here we report the high-resolution crystal structure of Myo7b CMF in complex with the extended PDZ3 domain of USH1C (a.k.a., Harmonin), revealing a previously uncharacterized interaction mode both for MyTH4-FERM tandems and for PDZ domains. We predicted, based on the structure of the Myo7b CMF/USH1C PDZ3 complex, and verified that Myo7a CMF also binds to USH1C PDZ3 using a similar mode. The structure of the Myo7b CMF/USH1C PDZ complex provides mechanistic explanations for >20 deafness-causing mutations in Myo7a CMF. Taken together, these findings suggest that binding to PDZ domains, such as those from USH1C, PDZD7, and Whirlin, is a common property of CMFs of Myo7a, Myo7b, and Myo15a. PMID:28439001

A history of PAs in the US Public Health Service.

PubMed

McKinnon, Mark F; Elizondo, Epifanio; Bonfiglio, Susan M; Hunter-Buskey, Robin N; Placide, Frances P; Bunnell, Rebecca A

2016-12-01

Since 1798, the men and women of the Commissioned Corps of the US Public Health Service (USPHS), one of the seven US uniformed services, have served on the front lines of public health. Two hundred years after the start of the USPHS, the first physician assistant (PA) entered the service to carry on the tradition of protecting, promoting, and advancing the health and safety of the nation. These dedicated clinicians are involved in healthcare delivery to underserved and vulnerable populations, disease control and prevention, biomedical research, food and drug regulation, and national and international response efforts for natural and man-made disasters. This article describes how PAs in the Commissioned Corps of the USPHS have impacted the health and safety of not only the United States but also the international community.

Programmable Logic Device (PLD) Design Description for the Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio System (STRS) Radio

NASA Technical Reports Server (NTRS)

Shalkhauser, Mary Jo W.

2017-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework for software defined radios (SDRs) to abstract the application software from the radio platform hardware. The STRS standard aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. To promote the use of the STRS architecture for future NASA advanced exploration missions, NASA Glenn Research Center (GRC) developed an STRS compliant SDR on a radio platform used by the Advance Exploration System program at the Johnson Space Center (JSC) in their Integrated Power, Avionics, and Software (iPAS) laboratory. At the conclusion of the development, the software and hardware description language (HDL) code was delivered to JSC for their use in their iPAS test bed to get hands-on experience with the STRS standard, and for development of their own STRS Waveforms on the now STRS compliant platform.The iPAS STRS Radio was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RIACS) platform, currently being used for radio development at JSC. The platform consists of a Xilinx ML605 Virtex-6 FPGA board, an Analog Devices FMCOMMS1-EBZ RF transceiver board, and an Embedded PC (Axiomtek eBox 620-110-FL) running the Ubuntu 12.4 operating system. Figure 1 shows the RIACS platform hardware. The result of this development is a very low cost STRS compliant platform that can be used for waveform developments for multiple applications.The purpose of this document is to describe the design of the HDL code for the FPGA portion of the iPAS STRS Radio particularly the design of the FPGA wrapper and the test waveform.

Alpha particle confinement in tandem mirrors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devoto, R.S.; Ohnishi, M.; Kerns, J.

1980-10-10

Mechanisms leading to loss of alpha particles from non-axisymmetric tandem mirrors are considered. Stochastic diffusion due to bounce-drift resonances, which can cause rapid radial losses of high-energy alpha particles, can be suppressed by imposing a 20% rise in axisymmetric fields before the quadrupole transition sections. Alpha particles should then be well-confined until thermal energies when they enter the resonant plateau require. A fast code for computation of drift behavior in reactors is described. Sample calculations are presented for resonant particles in a proposed coil set for the Tandem Mirror Next Step.

Tandem mobile robot system

DOEpatents

Buttz, James H.; Shirey, David L.; Hayward, David R.

2003-01-01

A robotic vehicle system for terrain navigation mobility provides a way to climb stairs, cross crevices, and navigate across difficult terrain by coupling two or more mobile robots with a coupling device and controlling the robots cooperatively in tandem.

Tandem internal models execute motor learning in the cerebellum.

PubMed

Honda, Takeru; Nagao, Soichi; Hashimoto, Yuji; Ishikawa, Kinya; Yokota, Takanori; Mizusawa, Hidehiro; Ito, Masao

2018-06-25

In performing skillful movement, humans use predictions from internal models formed by repetition learning. However, the computational organization of internal models in the brain remains unknown. Here, we demonstrate that a computational architecture employing a tandem configuration of forward and inverse internal models enables efficient motor learning in the cerebellum. The model predicted learning adaptations observed in hand-reaching experiments in humans wearing a prism lens and explained the kinetic components of these behavioral adaptations. The tandem system also predicted a form of subliminal motor learning that was experimentally validated after training intentional misses of hand targets. Patients with cerebellar degeneration disease showed behavioral impairments consistent with tandemly arranged internal models. These findings validate computational tandemization of internal models in motor control and its potential uses in more complex forms of learning and cognition. Copyright © 2018 the Author(s). Published by PNAS.

Quality evaluation of tandem mass spectral libraries.

PubMed

Oberacher, Herbert; Weinmann, Wolfgang; Dresen, Sebastian

2011-06-01

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

Nanocrystal assembly for tandem catalysis

DOEpatents

Yang, Peidong; Somorjai, Gabor; Yamada, Yusuke; Tsung, Chia-Kuang; Huang, Wenyu

2014-10-14

The present invention provides a nanocrystal tandem catalyst comprising at least two metal-metal oxide interfaces for the catalysis of sequential reactions. One embodiment utilizes a nanocrystal bilayer structure formed by assembling sub-10 nm platinum and cerium oxide nanocube monolayers on a silica substrate. The two distinct metal-metal oxide interfaces, CeO.sub.2--Pt and Pt--SiO.sub.2, can be used to catalyze two distinct sequential reactions. The CeO.sub.2--Pt interface catalyzed methanol decomposition to produce CO and H.sub.2, which were then subsequently used for ethylene hydroformylation catalyzed by the nearby Pt--SiO.sub.2 interface. Consequently, propanal was selectively produced on this nanocrystal bilayer tandem catalyst.

The B-Box Domain Protein BBX21 Promotes Photomorphogenesis.

PubMed

Xu, Dongqing; Jiang, Yan; Li, Jian; Holm, Magnus; Deng, Xing Wang

2018-03-01

B-box-containing (BBX) proteins play critical roles in a variety of cellular and developmental processes in plants. BBX21 (also known as SALT TOLERANCE HOMOLOG2), which contains two B-box domains in tandem at the N terminus, has been previously demonstrated as a key component involved in the COP1-HY5 signaling hub. However, the exact molecular and physiological roles of B-box domains in BBX21 are largely unclear. Here, we found that structurally disruption of the second B-box domain, but not the first one, in BBX21 completely abolishes its biological and physiological activity in conferring hyperphotomorphogenetic phenotype in Arabidopsis ( Arabidopsis thaliana ). Intact B-box domains in BBX21 are not required for interaction with COP1 and its degradation by COP1 via the 26S proteasome system. However, disruption of the second B-box of BBX21 nearly impairs its ability for binding of T/G-box within the HY5 promoter both in vitro and in vivo, as well as controlling HY5 and HY5-regulated gene expression in Arabidopsis seedlings. Taken together, this study provides a mechanistic framework in which BBX21 directly binds to the T/G-box present in the HY5 promoter possibly through its second B-box domain, which in turn controls HY5 and HY5-regulated gene expression to promote photomorphogenesis. © 2018 American Society of Plant Biologists. All Rights Reserved.

Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics

PubMed Central

Motta, Stefano

2018-01-01

Hypoxia inducible factors (HIFs) are transcription factors belonging to the basic helix−loop−helix PER-ARNT-SIM (bHLH-PAS) protein family with a role in sensing oxygen levels in the cell. Under hypoxia, the HIF-α degradation pathway is blocked and dimerization with the aryl hydrocarbon receptor nuclear translocator (ARNT) makes HIF-α transcriptionally active. Due to the common hypoxic environment of tumors, inhibition of this mechanism by destabilization of HIF-α:ARNT dimerization has been proposed as a promising therapeutic strategy. Following the discovery of a druggable cavity within the PAS-B domain of HIF-2α, research efforts have been directed to identify artificial ligands that can impair heterodimerization. Although the crystallographic structures of the HIF-2α:ARNT complex have elucidated the dimer architecture and the 0X3-inhibitor placement within the HIF-2α PAS-B, unveiling the inhibition mechanism requires investigation of how ligand-induced perturbations could dynamically propagate through the structure and affect dimerization. To this end, we compared evolutionary features, intrinsic dynamics and energetic properties of the dimerization interfaces of HIF-2α:ARNT in both the apo and holo forms. Residue conservation analysis highlighted inter-domain connecting elements that have a role in dimerization. Analysis of domain contributions to the dimerization energy demonstrated the importance of bHLH and PAS-A of both partners and of HIF-2α PAS-B domain in dimer stabilization. Among quaternary structure oscillations revealed by Molecular Dynamics simulations, the hinge-bending motion of the ARNT PAS-B domain around the flexible PAS-A/PAS-B linker supports a general model for ARNT dimerization in different heterodimers. Comparison of the HIF-2α:ARNT dynamics in the apo and 0X3-bound forms indicated a model of inhibition where the HIF-2α-PAS-B interfaces are destabilised as a result of water-bridged ligand-protein interactions and these local

A three-domain Kazal-type serine proteinase inhibitor exhibiting domain inhibitory and bacteriostatic activities from freshwater crayfish Procambarus clarkii.

PubMed

Li, Xin-Cang; Wang, Xian-Wei; Wang, Zong-Heng; Zhao, Xiao-Fan; Wang, Jin-Xing

2009-12-01

In crustaceans, Kazal-type serine proteinase inhibitors in hemolymph are believed to function as regulators of the host-defense reactions or inhibitors against proteinases from microorganisms. In this study, we report a Kazal-type serine proteinase inhibitor, named hcPcSPI1, from freshwater crayfish (Procambarus clarkii). We found that hcPcSPI1 is composed of a putative signal peptide, an RGD motif, and three tandem Kazal-type domains with the domain P1 residues L, L and E, respectively. Mainly, hcPcSPI1 was detected in hemocytes as well as in the heart, gills, and intestine at both the mRNA and protein levels. Quantitative real-time PCR analysis showed that hcPcSPI1 in hemocytes was upregulated by the stimulation of Esherichia coli (8099) or became decreased after a white spot syndrome virus (WSSV) challenge. In addition, hcPcSPI1 and its three independent domains were overexpressed and purified to explore their potential functions. All four proteins inhibited subtilisin A and proteinase K, but not alpha-chymotypsin or trypsin. Recombinant hcPcSPI1 could firmly attach to Gram-negative bacteria E. coli and Klebsiella pneumoniae; Gram-positive bacteria Bacillus subtilis, Bacillus thuringiensis and Staphylococcus aureus; fungi Candida albicans and Saccharomyce cerevisiae, and only domain 1 was responsible for the binding to E. coli and S. aureus. In addition, recombinant hcPcSPI1 was also found to possess bacteriostatic activity against the B. subtilis and B. thuringiensis. Domains 2 and 3 contributed mainly to these bacteriostatic activities. All results suggested that hcPcSPI1 might play important roles in the innate immunity of crayfish.

Single-task and dual-task tandem gait test performance after concussion.

PubMed

Howell, David R; Osternig, Louis R; Chou, Li-Shan

2017-07-01

To compare single-task and dual-task tandem gait test performance between athletes after concussion with controls on observer-timed, spatio-temporal, and center-of-mass (COM) balance control measurements. Ten participants (19.0±5.5years) were prospectively identified and completed a tandem gait test protocol within 72h of concussion and again 1 week, 2 weeks, 1 month, and 2 months post-injury. Seven uninjured controls (20.0±4.5years) completed the same protocol in similar time increments. Tandem gait test trials were performed with (dual-task) and without (single-task) concurrently performing a cognitive test as whole-body motion analysis was performed. Outcome variables included test completion time, average tandem gait velocity, cadence, and whole-body COM frontal plane displacement. Concussion participants took significantly longer to complete the dual-task tandem gait test than controls throughout the first 2 weeks post-injury (mean time=16.4 [95% CI: 13.4-19.4] vs. 10.1 [95% CI: 6.4-13.7] seconds; p=0.03). Single-task tandem gait times were significantly lower 72h post-injury (p=0.04). Dual-task cadence was significantly lower for concussion participants than controls (89.5 [95% CI: 68.6-110.4] vs. 127.0 [95% CI: 97.4-156.6] steps/minute; p=0.04). Moderately-high to high correlations between tandem gait test time and whole-body COM medial-lateral displacement were detected at each time point during dual-task gait (r s =0.70-0.93; p=0.03-0.001). Adding a cognitive task during the tandem gait test resulted in longer detectable deficits post-concussion compared to the traditional single-task tandem gait test. As a clinical tool to assess dynamic motor function, tandem gait may assist with return to sport decisions after concussion. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

47 CFR Appendix B to Part 64 - Priority Access Service (PAS) for National Security and Emergency Preparedness (NSEP)

Code of Federal Regulations, 2010 CFR

2010-10-01

... leadership; (iii) Disaster shelter coordination and management; and (iv) Critical Disaster Field Office... telecommunications management and response functions during emergency/disaster situations. 3. Initiate PAS requests... priorities, priority one being the highest. The five priority levels are: 1. Executive Leadership and Policy...

Characterization of Conserved Tandem Donor Sites and Intronic Motifs Required for Alternative Splicing in Corticosteroid Receptor Genes

PubMed Central

Qian, Xiaoxiao; Matthews, Laura; Lightman, Stafford; Ray, David; Norman, Michael

2015-01-01

Alternative splicing events from tandem donor sites result in mRNA variants coding for additional amino acids in the DNA binding domain of both the glucocorticoid (GR) and mineralocorticoid (MR) receptors. We now show that expression of both splice variants is extensively conserved in mammalian species, providing strong evidence for their functional significance. An exception to the conservation of the MR tandem splice site (an A at position +5 of the MR+12 donor site in the mouse) was predicted to decrease U1 small nuclear RNA binding. In accord with this prediction, we were unable to detect the MR+12 variant in this species. The one exception to the conservation of the GR tandem splice site, an A at position +3 of the platypus GRγ donor site that was predicted to enhance binding of U1 snRNA, was unexpectedly associated with decreased expression of the variant from the endogenous gene as well as a minigene. An intronic pyrimidine motif present in both GR and MR genes was found to be critical for usage of the downstream donor site, and overexpression of TIA1/TIAL1 RNA binding proteins, which are known to bind such motifs, led to a marked increase in the proportion of GRγ and MR+12. These results provide striking evidence for conservation of a complex splicing mechanism that involves processes other than stochastic spliceosome binding and identify a mechanism that would allow regulation of variant expression. PMID:19819975

Negotiating Multiple Identities through eTandem Learning Experiences

ERIC Educational Resources Information Center

Yang, Se Jeong; Yi, Youngjoo

2017-01-01

Much of eTandem research has investigated either linguistic or cross-cultural aspects of second language (L2) learning, but relatively little is known about issues of identity construction in an eTandem context. Situating the study within theories and research of language learner identity, we examined ways in which two adult L2 learners (a Korean…

The immunoglobulin-like domains 1 and 2 of the protein tyrosine phosphatase LAR adopt an unusual horseshoe-like conformation

PubMed Central

Biersmith, Bridget H.; Hammel, Michal; Geisbrecht, Erika R.; Bouyain, Samuel

2011-01-01

Neurogenesis depends on exquisitely regulated interactions between macromolecules on the cell surface and in the extracellular matrix. In particular, interactions between proteoglycans and members of the type IIa subgroup of receptor protein tyrosine phosphatases underlie critical developmental processes such as the formation of synapses at the neuromuscular junction and the migration of axons to their appropriate targets. We report here the crystal structures of the first and second immunoglobulin-like domains of the Drosophila type IIa receptor Dlar and its mouse homologue LAR. These two domains adopt an unusual antiparallel arrangement that has not been previously observed in tandem repeats of immunoglobulin-like domains and that is presumably conserved in all type IIa receptor protein tyrosine phosphatases. PMID:21402080

Tandem robot control system and method for controlling mobile robots in tandem

DOEpatents

Hayward, David R.; Buttz, James H.; Shirey, David L.

2002-01-01

A control system for controlling mobile robots provides a way to control mobile robots, connected in tandem with coupling devices, to navigate across difficult terrain or in closed spaces. The mobile robots can be controlled cooperatively as a coupled system in linked mode or controlled individually as separate robots.

SYMTRAN - A Time-dependent Symmetric Tandem Mirror Transport Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hua, D; Fowler, T

2004-06-15

A time-dependent version of the steady-state radial transport model in symmetric tandem mirrors in Ref. [1] has been coded up and first tests performed. Our code, named SYMTRAN, is an adaptation of the earlier SPHERE code for spheromaks, now modified for tandem mirror physics. Motivated by Post's new concept of kinetic stabilization of symmetric mirrors, it is an extension of the earlier TAMRAC rate-equation code omitting radial transport [2], which successfully accounted for experimental results in TMX. The SYMTRAN code differs from the earlier tandem mirror radial transport code TMT in that our code is focused on axisymmetric tandem mirrorsmore » and classical diffusion, whereas TMT emphasized non-ambipolar transport in TMX and MFTF-B due to yin-yang plugs and non-symmetric transitions between the plugs and axisymmetric center cell. Both codes exhibit interesting but different non-linear behavior.« less

PAs reduce rounding interruptions in the pediatric intensive care unit.

PubMed

Hascall, Rebecca L; Perkins, R Serene; Kmiecik, Lauren; Gupta, Priya R; Shelak, Carolyn F; Demirel, Shaban; Buchholz, Mark T

2018-06-01

We investigated the proportion of encounters that were interrupted during family-centered rounds in the pediatric intensive care unit (PICU) to determine whether the use of a physician assistant (PA) significantly affected the proportion of interrupted encounters. We evaluated 2,657 rounding encounters in our 24-bed regional referral unit. The duration of each rounding encounter and total rounding duration were recorded. The presence or absence of a PA during each rounding encounter, the occurrence of an interruption, and other potential predictors of interruptions were recorded. The presence of a PA during PICU rounds was significantly associated (P < .001) with a 35.4% lower likelihood of an interruption. Family-centered rounds in the PICU are less likely to be interrupted when a PA is present. PAs help physicians and improve rounding efficiency by safely and effectively handling certain interruptions.

An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon).

PubMed

Ba, Hengxing; Wu, Lang; Liu, Zongyue; Li, Chunyi

2016-01-01

Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.

Cooperative cell motility during tandem locomotion of amoeboid cells

PubMed Central

Bastounis, Effie; Álvarez-González, Begoña; del Álamo, Juan C.; Lasheras, Juan C.; Firtel, Richard A.

2016-01-01

Streams of migratory cells are initiated by the formation of tandem pairs of cells connected head to tail to which other cells subsequently adhere. The mechanisms regulating the transition from single to streaming cell migration remain elusive, although several molecules have been suggested to be involved. In this work, we investigate the mechanics of the locomotion of Dictyostelium tandem pairs by analyzing the spatiotemporal evolution of their traction adhesions (TAs). We find that in migrating wild-type tandem pairs, each cell exerts traction forces on stationary sites (∼80% of the time), and the trailing cell reuses the location of the TAs of the leading cell. Both leading and trailing cells form contractile dipoles and synchronize the formation of new frontal TAs with ∼54-s time delay. Cells not expressing the lectin discoidin I or moving on discoidin I–coated substrata form fewer tandems, but the trailing cell still reuses the locations of the TAs of the leading cell, suggesting that discoidin I is not responsible for a possible chemically driven synchronization process. The migration dynamics of the tandems indicate that their TAs’ reuse results from the mechanical synchronization of the leading and trailing cells’ protrusions and retractions (motility cycles) aided by the cell–cell adhesions. PMID:26912787

DNA Damage by Ionizing Radiation: Tandem Double Lesions by Charged Particles

NASA Technical Reports Server (NTRS)

Huo, Winifred M.; Chaban, Galina M.; Wang, Dunyou; Dateo, Christopher E.

2005-01-01

Oxidative damages by ionizing radiation are the source of radiation-induced carcinogenesis, damage to the central nervous system, lowering of the immune response, as well as other radiation-induced damages to human health. Monte Carlo track simulations and kinetic modeling of radiation damages to the DNA employ available molecular and cellular data to simulate the biological effect of high and low LET radiation io the DNA. While the simulations predict single and double strand breaks and base damages, so far all complex lesions are the result of stochastic coincidence from independent processes. Tandem double lesions have not yet been taken into account. Unlike the standard double lesions that are produced by two separate attacks by charged particles or radicals, tandem double lesions are produced by one single attack. The standard double lesions dominate at the high dosage regime. On the other hand, tandem double lesions do not depend on stochastic coincidences and become important at the low dosage regime of particular interest to NASA. Tandem double lesions by hydroxyl radical attack of guanine in isolated DNA have been reported at a dosage of radiation as low as 10 Gy. The formation of two tandem base lesions was found to be linear with the applied doses, a characteristic of tandem lesions. However, tandem double lesions from attack by a charged particle have not been reported.

The crystal structures of EAP domains from Staphylococcus aureus reveal an unexpected homology to bacterial superantigens.

PubMed

Geisbrecht, Brian V; Hamaoka, Brent Y; Perman, Benjamin; Zemla, Adam; Leahy, Daniel J

2005-04-29

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 A 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.

A tandem mirror hybrid plume plasma propulsion facility

NASA Technical Reports Server (NTRS)

Yang, T. F.; Krueger, W. A.; Peng, S.; Urbahn, J.; Chang-Diaz, F. R.

1988-01-01

This paper discusses a novel concept in electrodeless plasma propulsion, in which the materials problems are ameliorated by an electrodeless magnetic confinement scheme borrowed from the tandem mirror approach to controlled thermonuclear fusion. The concept also features a two-stage magnetic nozzle with an annular hypersonic coaxial gas injector near the throat. The nozzle produces hybrid plume by the coaxial injection of hypersonic neutral gas, and the gas layer thus formed protects the material walls from the hot plasma and, through increased collisions, helps detach it from the diverging magnetic field. The tandem mirror plasma propulsion facility is capable of delivering a variable I(sp). The results of numerical simulation of this concept are presented together with those from an experimental tandem-mirror plasma propulsion device.

Coiled-coil coactivators play a structural role mediating interactions in hypoxia-inducible factor heterodimerization

DOE PAGES

Guo, Yirui; Scheuermann, Thomas H.; Partch, Carrie L.; ...

2015-01-27

The hypoxia-inducible factor complex (HIF-α·aryl hydrocarbon receptor nuclear translocator (ARNT)) requires association with several transcription coactivators for a successful cellular response to hypoxic stress. In addition to the conventional global transcription coactivator CREB-binding protein/p300 (CBP/p300) that binds to the HIF-α transactivation domain, a new group of transcription coactivators called the coiled-coil coactivators (CCCs) interact directly with the second PER-ARNT-SIM (PAS) domain of ARNT (ARNT PAS-B). These less studied transcription coactivators play essential roles in the HIF-dependent hypoxia response, and CCC misregulation is associated with several forms of cancer. To better understand CCC protein recruitment by the heterodimeric HIF transcription factor,more » we used x-ray crystallography, NMR spectroscopy, and biochemical methods to investigate the structure of the ARNT PAS-B domain in complex with the C-terminal fragment of a coiled-coil coactivator protein, transforming acidic coiled-coil coactivator 3 (TACC3). We found that the HIF-2α PAS-B domain also directly interacts with TACC3, motivating an NMR data-derived model suggesting a means by which TACC3 could form a ternary complex with HIF-2α PAS-B and ARNT PAS-B via β-sheet/coiled-coil interactions. Furthermore, these findings suggest that TACC3 could be recruited as a bridge to cooperatively mediate between the HIF-2α PAS-B·ARNT PAS-B complex, thereby participating more directly in HIF-dependent gene transcription than previously anticipated.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Yirui; Scheuermann, Thomas H.; Partch, Carrie L.

The hypoxia-inducible factor complex (HIF-α·aryl hydrocarbon receptor nuclear translocator (ARNT)) requires association with several transcription coactivators for a successful cellular response to hypoxic stress. In addition to the conventional global transcription coactivator CREB-binding protein/p300 (CBP/p300) that binds to the HIF-α transactivation domain, a new group of transcription coactivators called the coiled-coil coactivators (CCCs) interact directly with the second PER-ARNT-SIM (PAS) domain of ARNT (ARNT PAS-B). These less studied transcription coactivators play essential roles in the HIF-dependent hypoxia response, and CCC misregulation is associated with several forms of cancer. To better understand CCC protein recruitment by the heterodimeric HIF transcription factor,more » we used x-ray crystallography, NMR spectroscopy, and biochemical methods to investigate the structure of the ARNT PAS-B domain in complex with the C-terminal fragment of a coiled-coil coactivator protein, transforming acidic coiled-coil coactivator 3 (TACC3). We found that the HIF-2α PAS-B domain also directly interacts with TACC3, motivating an NMR data-derived model suggesting a means by which TACC3 could form a ternary complex with HIF-2α PAS-B and ARNT PAS-B via β-sheet/coiled-coil interactions. Furthermore, these findings suggest that TACC3 could be recruited as a bridge to cooperatively mediate between the HIF-2α PAS-B·ARNT PAS-B complex, thereby participating more directly in HIF-dependent gene transcription than previously anticipated.« less

The Psychiatric Assessment Schedule for Adult with Developmental Disability (PAS-ADD) Checklist: Reliability and Validity of French Version

ERIC Educational Resources Information Center

Gerber, F.; Carminati, G. Galli

2013-01-01

Background: The lack of psychometric measures of psychopathology especially in intellectual disabilities (ID) population was addressed by creation of the Psychiatric Assessment Schedule for Adult with Developmental Disability (PAS-ADD-10) in Moss et?al. This schedule is a structured interview designed for professionals in psychopathology. The…

The evolution and function of protein tandem repeats in plants.

PubMed

Schaper, Elke; Anisimova, Maria

2015-04-01

Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing.

PubMed

Ivanov, Alexey V; Peng, Hongzhuang; Yurchenko, Vyacheslav; Yap, Kyoko L; Negorev, Dmitri G; Schultz, David C; Psulkowski, Elyse; Fredericks, William J; White, David E; Maul, Gerd G; Sadofsky, Moshe J; Zhou, Ming-Ming; Rauscher, Frank J

2007-12-14

Tandem PHD and bromodomains are often found in chromatin-associated proteins and have been shown to cooperate in gene silencing. Each domain can bind specifically modified histones: the mechanisms of cooperation between these domains are unknown. We show that the PHD domain of the KAP1 corepressor functions as an intramolecular E3 ligase for sumoylation of the adjacent bromodomain. The RING finger-like structure of the PHD domain is required for both Ubc9 binding and sumoylation and directs modification to specific lysine residues in the bromodomain. Sumoylation is required for KAP1-mediated gene silencing and functions by directly recruiting the SETDB1 histone methyltransferase and the CHD3/Mi2 component of the NuRD complex via SUMO-interacting motifs. Sumoylated KAP1 stimulates the histone methyltransferase activity of SETDB1. These data provide a mechanistic explanation for the cooperation of PHD and bromodomains in gene regulation and describe a function of the PHD domain as an intramolecular E3 SUMO ligase.

Monitoring Bilingualism: Pedagogical Implications of the Bilingual Tandem Analyser

ERIC Educational Resources Information Center

Schwienhorst, Klaus; Borgia, Alexandre

2006-01-01

Tandem learning is the collaborative learning partnership of two language learners with complementary language combinations, for example an Irish student learning German and a German student learning English. One of the major principles in tandem learning, apart from reciprocity and learner autonomy, is balanced bilingualism. While learners may…

High Performance Tandem Perovskite/Polymer Solar Cells

NASA Astrophysics Data System (ADS)

Liu, Yao; Bag, Monojit; Page, Zachariah; Renna, Lawrence; Kim, Paul; Choi, Jaewon; Emrick, Todd; Venkataraman, D.; Russell, Thomas

Combining perovskites with other inorganic materials, such as copper indium gallium diselenide (CIGS) or silicon, is enabling significant improvement in solar cell device performance. Here, we demonstrate a highly efficient hybrid tandem solar cell fabricated through a facile solution deposition approach to give a perovskite front sub-cell and a polymer:fullerene blend back sub-cell. This methodology eliminates the adverse effects of thermal annealing during perovskite fabrication on polymer solar cells. The record tandem solar cell efficiency of 15.96% is 40% greater than the corresponding perovskite-based single junction device and 65% greater than the polymer-based single junction device, while mitigating deleterious hysteresis effects often associated with perovskite solar cells. The hybrid tandem devices demonstrate the synergistic effects arising from the combination of perovskite and polymer-based materials for solar cells. This work was supported by the Department of Energy-supported Energy Frontier Research Center at the University of Massachusetts (DE-SC0001087). The authors acknowledge the W.M. Keck Electron Microscopy.

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface.

PubMed

Fleming, Patrick J; Patel, Dhilon S; Wu, Emilia L; Qi, Yifei; Yeom, Min Sun; Sousa, Marcelo Carlos; Fleming, Karen G; Im, Wonpil

2016-06-21

The outer membrane of Gram-negative bacteria is an asymmetric membrane with lipopolysaccharides on the external leaflet and phospholipids on the periplasmic leaflet. This outer membrane contains mainly β-barrel transmembrane proteins and lipidated periplasmic proteins (lipoproteins). The multisubunit protein β-barrel assembly machine (BAM) catalyzes the insertion and folding of the β-barrel proteins into this membrane. In Escherichia coli, the BAM complex consists of five subunits, a core transmembrane β-barrel with a long periplasmic domain (BamA) and four lipoproteins (BamB/C/D/E). The BamA periplasmic domain is composed of five globular subdomains in tandem called POTRA motifs that are key to BAM complex formation and interaction with the substrate β-barrel proteins. The BAM complex is believed to undergo conformational cycling while facilitating insertion of client proteins into the outer membrane. Reports describing variable conformations and dynamics of the periplasmic POTRA domain have been published. Therefore, elucidation of the conformational dynamics of the POTRA domain in full-length BamA is important to understand the function of this molecular complex. Using molecular dynamics simulations, we present evidence that the conformational flexibility of the POTRA domain is modulated by binding to the periplasmic surface of a native lipid membrane. Furthermore, membrane binding of the POTRA domain is compatible with both BamB and BamD binding, suggesting that conformational selection of different POTRA domain conformations may be involved in the mechanism of BAM-facilitated insertion of outer membrane β-barrel proteins. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A Dual-Intein Autoprocessing Domain that Directs Synchronized Protein Co-Expression in Both Prokaryotes and Eukaryotes

PubMed Central

Zhang, Bei; Rapolu, Madhusudhan; Liang, Zhibin; Han, Zhenlin; Williams, Philip G.; Su, Wei Wen

2015-01-01

Being able to coordinate co-expression of multiple proteins is necessary for a variety of important applications such as assembly of protein complexes, trait stacking, and metabolic engineering. Currently only few options are available for multiple recombinant protein co-expression, and most of them are not applicable to both prokaryotic and eukaryotic hosts. Here, we report a new polyprotein vector system that is based on a pair of self-excising mini-inteins fused in tandem, termed the dual-intein (DI) domain, to achieve synchronized co-expression of multiple proteins. The DI domain comprises an Ssp DnaE mini-intein N159A mutant and an Ssp DnaB mini-intein C1A mutant connected in tandem by a peptide linker to mediate efficient release of the flanking proteins via autocatalytic cleavage. Essentially complete release of constituent proteins, GFP and RFP (mCherry), from a polyprotein precursor, in bacterial, mammalian, and plant hosts was demonstrated. In addition, successful co-expression of GFP with chloramphenicol acetyltransferase, and thioredoxin with RFP, respectively, further substantiates the general applicability of the DI polyprotein system. Collectively, our results demonstrate the DI-based polyprotein technology as a highly valuable addition to the molecular toolbox for multi-protein co-expression which finds vast applications in biotechnology, biosciences, and biomedicine. PMID:25712612

Safety evaluation for packaging for the transport of K Basin sludge samples in the PAS-1 cask

DOE Office of Scientific and Technical Information (OSTI.GOV)

SMITH, R.J.

1998-11-17

This safety evaluation for packaging authorizes the shipment of up to two 4-L sludge samples to and from the 325 Lab or 222-S Lab for characterization. The safety of this shipment is based on the current U.S. Department of Energy Certification of Compliance (CoC) for the PAS-1 cask, USA/9184/B(U) (DOE).

rTANDEM, an R/Bioconductor package for MS/MS protein identification.

PubMed

Fournier, Frédéric; Joly Beauparlant, Charles; Paradis, René; Droit, Arnaud

2014-08-01

rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor. rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/. The packages are under open licenses (GPL-3 and Artistice-1.0). frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Stability studies of extracellular domain two of neural-cadherin.

PubMed

Vunnam, Nagamani; McCool, John K; Williamson, Michael; Pedigo, Susan

2011-12-01

Neural- (NCAD) and epithelial- (ECAD) cadherin are calcium-dependent cell-adhesive molecules, and are localized at excitatory and inhibitory synapses respectively. They play an important role in synaptogenesis, synapse maintenance and plasticity. The extracellular region plays a critical role in cadherin-mediated cell adhesion, and has five tandemly repeated ectodomains (EC1-EC5). Calcium binding is required for dimer formation between first two N-terminal domains (EC1-EC2). Despite similarity in the primary structure, the extracellular domains of NCAD and ECAD have different intrinsic stability, dimerization affinity and kinetics of disassembly. To investigate the origin of these differences, we are characterizing the modular domains individually. Here, we report studies of NCAD2, EC2 of NCAD. This domain is important for calcium binding and is the physical linkage between the dimerization interface in EC1 and the membrane proximal modular domains. Thermal-denaturation studies show that NCAD2 is less stable than ECAD2 and less influenced by the adjoining 7-residue, N- and C-terminal linker segments. In addition the NCAD2 constructs are less influenced by added salt. This difference is likely due to variation in the overall number and distribution of charges on these anionic proteins. Our studies indicate that despite their sequence similarity and apparently passive role in adhesive dimer formation, EC2 of E- and N-cadherins are distinctly different and may contribute to the differences in energetics and kinetics of dimerization. Copyright © 2011 Elsevier B.V. All rights reserved.

Anaortic off-pump versus clampless off-pump using the PAS-Port device versus conventional coronary artery bypass grafting: mid-term results from a matched propensity score analysis of 5422 unselected patients.

PubMed

Furukawa, Nobuyuki; Kuss, Oliver; Preindl, Konstantin; Renner, André; Aboud, Anas; Hakim-Meibodi, Kavous; Benzinger, Michael; Pühler, Thomas; Ensminger, Stephan; Fujita, Buntaro; Becker, Tobias; Gummert, Jan F; Börgermann, Jochen

2017-10-01

Meta-analyses from observational and randomized studies have demonstrated benefits of off-pump surgery for hard and surrogate endpoints. In some of them, increased re-revascularization was noted in the off-pump groups, which could impact their long-term survival. Therefore, we analyzed the course of all patients undergoing isolated coronary surgery regarding the major cardiac and cerebrovascular event (MACCE) criteria. A prospective register was taken from a high-volume off-pump center recording all anaortic off-pump (ANA), clampless off-pump (PAS-Port) and conventional (CONV) coronary artery bypass operations between July 2009 and June 2015. Propensity Score Matching was performed based on 28 preoperative risk variables. We identified 935 triplets (N = 2805). Compared with CONV, in-hospital mortality of both the ANA group (OR for ANA [95% CI] 0.25 [0.06; 0.83], P = 0.021), and the PAS-Port group was lower (OR for PAS-Port [95% CI] 0.50 [0.17; 1.32], P = 0.17). In the mid-term follow-up there were no significant differences between the groups regarding mortality (HR for ANA [95%-CI] 0.83 [0.55-1.26], P = 0.38; HR for PAS-Port [95%-CI] 1.06 [0.70-1.59], P = 0.79), incidence of stroke (HR for ANA 0.81 [0.43-1.53], P = 0.52; HR for PAS-Port 0.78 [0.41-1.50], P = 0.46), myocardial infarction (HR for ANA 0.53 [0.22-1.31], P = 0.17; HR for PAS-Port 0.78 [0.37-1.66], P = 0.52) or re-revascularization rate (HR for ANA 0.99 [0.67-1.44], P = 0.94; HR for PAS-Port 0.95 [0.65-1.38], P = 0.77). Both off-pump clampless techniques were associated with lower in-hospital mortality compared with conventional CABG. The mid-term course showed no difference with regard to the MACCE criteria between anaortic off-pump, clampless off-pump using PAS-Port and conventional CABG. © The Author 2017. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Semi-transparent perovskite solar cells for tandems with silicon and CIGS

DOE PAGES

Bailie, Colin D.; Christoforo, M. Greyson; Mailoa, Jonathan P.; ...

2014-12-23

A promising approach for upgrading the performance of an established low-bandgap solar technology without adding much cost is to deposit a high bandgap polycrystalline semiconductor on top to make a tandem solar cell. We use a transparent silver nanowire electrode on perovskite solar cells to achieve a semi-transparent device. We place the semi-transparent cell in a mechanically-stacked tandem configuration onto copper indium gallium diselenide (CIGS) and low-quality multicrystalline silicon (Si) to achieve solid-state polycrystalline tandem solar cells with a net improvement in efficiency over the bottom cell alone. Furthermore, this work paves the way for integrating perovskites into a low-costmore » and high-efficiency (>25%) tandem cell.« less

A recombinant fusion protein and DNA vaccines against foot-and-mouth disease virus type Asia 1 infection in guinea pigs.

PubMed

Zhang, Q; Zhu, M W; Yang, Y Q; Shao, M; Zhang, Z Y; Lan, H Y; Yan, W Y; Wu, J J; Zheng, Z X

2003-01-01

On the basis of amino acid (aa) sequence of the tandem repeat 133-158-20-34-133-158 which consisted of aa 133-158 of VP1 and aa 20-34 of VP4 of Foot-and-mouth disease virus (FMDV) type Asia 1 a recombinant prokaryotic expression vector pAS1-P encoding a fusion protein and eukaryotic expression vectors pAS1-E and pAS1-EdeltaCpG-ODN representing DNA vaccines were constructed. Guinea pigs immunized with these vaccines showed both neutralizing antibody and T cell proliferation responses. FMDV challenge tests for the first time showed that the recombinant fusion protein and pAS1-E and pAS1-EdeltaCpG-ODN vaccines protected 86%, 60% and 43% of guinea pigs from FMDV type Asia1 challenge, respectively. The results also indicated that the immune response of animals treated with the vector pAS1-E containing an oligodeoxynucleotide (ODN), which consisted of immunostimulatory cytosine-phosphate-guanosine (CpG) motifs, was augmented by CpG ODN.

A Forecast Skill Comparison between CliPAS One-Tier and Two-Tier Hindcast Experiments

NASA Astrophysics Data System (ADS)

Lee, J.; Wang, B.; Kang, I.

2006-05-01

A 24-year (1981-2004) MME hindcast experimental dataset is produced under the "Climate Prediction and Its Application to Society" (CliPAS) project sponsored by Korean Meteorological Administration (KMA). This dataset consists of 5 one-tier model systems from National Aeronautics and Space Administration (NASA), National Center for Environmental Prediction (NCEP), Frontier Research Center for Global Change (FRCGC), Seoul National University (SNU), and University of Hawaii (UH) and 5 two-tier model systems from Florida State University (FSU), Geophysical Fluid Dynamic Lab (GFDL), SNU, and UH. Multi-model Ensemble (MME) Forecast skills of seasonal precipitation and atmospheric circulation are compared between CliPAS one-tier and two-tier hindcast experiments for seasonal mean precipitation and atmospheric circulation. For winter prediction, two-tier MME has a comparable skill to one-tier MME. However, it is demonstrated that in the Asian-Australian monsoon (A-AM) heavy precipitation regions, one-tier systems are superior to two-tier systems in summer season. The reason is that inclusion of the local warm pool- monsoon interaction in the one-tier system improves the ENSO teleconnection with monsoon regions. Both one-tier and two-tier MME fail to predict Indian monsoon circulation, while they have a significantly good skill for the broad scale monsoon circulation defined by Webster and Yang index. One-tier system has a much better skill to predict the monsoon circulation over the western North pacific where air-sea interaction plays an important role than two-tier system.

Economic viability of thin-film tandem solar modules in the United States

NASA Astrophysics Data System (ADS)

Sofia, Sarah E.; Mailoa, Jonathan P.; Weiss, Dirk N.; Stanbery, Billy J.; Buonassisi, Tonio; Peters, I. Marius

2018-05-01

Tandem solar cells are more efficient but more expensive per unit area than established single-junction (SJ) solar cells. To understand when specific tandem architectures should be utilized, we evaluate the cost-effectiveness of different II-VI-based thin-film tandem solar cells and compare them to the SJ subcells. Levelized cost of electricity (LCOE) and energy yield are calculated for four technologies: industrial cadmium telluride and copper indium gallium selenide, and their hypothetical two-terminal (series-connected subcells) and four-terminal (electrically independent subcells) tandems, assuming record SJ quality subcells. Different climatic conditions and scales (residential and utility scale) are considered. We show that, for US residential systems with current balance-of-system costs, the four-terminal tandem has the lowest LCOE because of its superior energy yield, even though it has the highest US per watt (US W-1) module cost. For utility-scale systems, the lowest LCOE architecture is the cadmium telluride single junction, the lowest US W-1 module. The two-terminal tandem requires decreased subcell absorber costs to reach competitiveness over the four-terminal one.

Typing Clostridium difficile strains based on tandem repeat sequences

PubMed Central

2009-01-01

Background Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies. Results This report presents results from a systematic screen for variation in repetitive DNA in the genome of C. difficile. We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. Based on an investigation of 154 C. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. Conclusion We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile. Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. PMID:19133124

Solution-processed parallel tandem polymer solar cells using silver nanowires as intermediate electrode.

PubMed

Guo, Fei; Kubis, Peter; Li, Ning; Przybilla, Thomas; Matt, Gebhard; Stubhan, Tobias; Ameri, Tayebeh; Butz, Benjamin; Spiecker, Erdmann; Forberich, Karen; Brabec, Christoph J

2014-12-23

Tandem architecture is the most relevant concept to overcome the efficiency limit of single-junction photovoltaic solar cells. Series-connected tandem polymer solar cells (PSCs) have advanced rapidly during the past decade. In contrast, the development of parallel-connected tandem cells is lagging far behind due to the big challenge in establishing an efficient interlayer with high transparency and high in-plane conductivity. Here, we report all-solution fabrication of parallel tandem PSCs using silver nanowires as intermediate charge collecting electrode. Through a rational interface design, a robust interlayer is established, enabling the efficient extraction and transport of electrons from subcells. The resulting parallel tandem cells exhibit high fill factors of ∼60% and enhanced current densities which are identical to the sum of the current densities of the subcells. These results suggest that solution-processed parallel tandem configuration provides an alternative avenue toward high performance photovoltaic devices.

Tandem Repeated Irritation Test (TRIT) Studies and Clinical Relevance: Post 2006.

PubMed

Reddy, Rasika; Maibach, Howard

2018-06-11

Single or multiple applications of irritants can lead to occupational contact dermatitis, and most commonly irritant contact dermatitis (ICD). Tandem irritation, the sequential application of two irritants to a target skin area, has been studied using the Tandem Repeated Irritation Test (TRIT) to provide a more accurate representation of skin irritation. Here we present an update to Kartono's review on tandem irritation studies since 2006 [1]. We surveyed the literature available on PubMed, Embase, Google Scholar, and the UCSF Dermatology library databases since 2006. The studies included discuss the tandem effects of common chemical irritants, organic solvents, occlusion as well as clinical relevance - and enlarge our ability to discern whether multiple chemical exposures are more or less likely to enhance irritation.

Flow field interactions between two tandem cyclists

NASA Astrophysics Data System (ADS)

Barry, Nathan; Burton, David; Sheridan, John; Thompson, Mark; Brown, Nicholas A. T.

2016-12-01

Aerodynamic drag is the primary resistive force acting on cyclists at racing speeds. Many events involve cyclists travelling in very close proximity. Previous studies have shown that interactions result in significant drag reductions for inline cyclists. However, the interaction between cyclist leg position (pedalling) and the vortical flow structures that contribute significantly to the drag on an isolated cyclist has not previously been quantified or described for tandem cyclists of varying separation. To this end, scale model cyclists were constructed for testing in a water channel for inline tandem configurations. Particle image velocimetry was used to capture time-averaged velocity fields around two tandem cyclists. Perhaps surprisingly, the wake of a trailing cyclist maintains strong similarity to the characteristic wake of a single cyclist despite a significant disturbance to the upstream flow. Together with streamwise velocity measurements through the wake and upstream of the trailing cyclist, this work supports previous findings, which showed that the trailing cyclist drag reduction is primarily due to upstream sheltering effects reducing the stagnation pressure on forward-facing surfaces.

Stacking multiple connecting functional materials in tandem organic light-emitting diodes

NASA Astrophysics Data System (ADS)

Zhang, Tao; Wang, Deng-Ke; Jiang, Nan; Lu, Zheng-Hong

2017-02-01

Tandem device is an important architecture in fabricating high performance organic light-emitting diodes and organic photovoltaic cells. The key element in making a high performance tandem device is the connecting materials stack, which plays an important role in electric field distribution, charge generation and charge injection. For a tandem organic light-emitting diode (OLED) with a simple Liq/Al/MoO3 stack, we discovered that there is a significant current lateral spreading causing light emission over an extremely large area outside the OLED pixel when the Al thickness exceeds 2 nm. This spread light emission, caused by an inductive electric field over one of the device unit, limits one’s ability to fabricate high performance tandem devices. To resolve this issue, a new connecting materials stack with a C60 fullerene buffer layer is reported. This new structure permits optimization of the Al metal layer in the connecting stack and thus enables us to fabricate an efficient tandem OLED having a high 155.6 cd/A current efficiency and a low roll-off (or droop) in current efficiency.

Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit.

PubMed

Liu, Jiuyang; Zhang, Shuya; Liu, Mingqing; Liu, Yaqian; Nshogoza, Gilbert; Gao, Jia; Ma, Rongsheng; Yang, Yang; Wu, Jihui; Zhang, Jiahai; Li, Fudong; Ruan, Ke

2018-04-12

As a reader of di-methylated arginine on various proteins, such as histone, RNA polymerase II, PIWI and Fragile X mental retardation protein, the Tudor domain of Tudor domain-containing protein 3 (TDRD3) mediates transcriptional activation in nucleus and formation of stress granules in the cytoplasm. Despite the TDRD3 implication in cancer cell proliferation and invasion, warheads to block the di-methylated arginine recognition pocket of the TDRD3 Tudor domain have not yet been uncovered. Here we identified 14 small molecule hits against the TDRD3 Tudor domain through NMR fragment-based screening. These hits were further cross-validated by using competitive fluorescence polarization and isothermal titration calorimetry experiments. The crystal structure of the TDRD3 Tudor domain in complex with hit 1 reveals a distinct binding mode from the nature substrate. Hit 1 protrudes into the aromatic cage of the TDRD3 Tudor domain, where the aromatic residues are tilted to accommodate a sandwich-like π-π interaction. The side chain of the conserved residue N596 swings away 3.1 Å to form a direct hydrogen bond with hit 1. Moreover, this compound shows a decreased affinity against the single Tudor domain of survival motor neuron protein, but no detectable binding to neither the tandem Tudor domain of TP53-binding protein 1 nor the extended Tudor domain of staphylococcal nuclease domain-containing protein 1. Our work depicts the structural plasticity of the TDRD3 Tudor domain and paves the way for the subsequent structure-guided discovery of selective inhibitors targeting Tudor domains. Structural data are available in the PDB under the accession number 5YJ8. © 2018 Federation of European Biochemical Societies.

[Polymorphic loci and polymorphism analysis of short tandem repeats within XNP gene].

PubMed

Liu, Qi-Ji; Gong, Yao-Qin; Guo, Chen-Hong; Chen, Bing-Xi; Li, Jiang-Xia; Guo, Yi-Shou

2002-01-01

To select polymorphic short tandem repeat markers within X-linked nuclear protein (XNP) gene, genomic clones which contain XNP gene were recognized by homologous analysis with XNP cDNA. By comparing the cDNA with genomic DNA, non-exonic sequences were identified, and short tandem repeats were selected from non-exonic sequences by using BCM search Launcher. Polymorphisms of the short tandem repeats in Chinese population were evaluated by PCR amplification and PAGE. Five short tandem repeats were identified from XNP gene, two of which were polymorphic. Four and 11 alleles were observed in Chinese population for XNPSTR1 and XNPSTR4, respectively. Heterozygosities were 47% for XNPSTR1 and 70% for XNPSTR4. XNPSTR1 and XNPSTR4 localized within 3' end and intron 10, respectively. Two polymorphic short tandem repeats have been identified within XNP gene and will be useful for linkage analysis and gene diagnosis of XNP gene.

Low-Cost CdTe/Silicon Tandem Solar Cells

DOE PAGES

Tamboli, Adele C.; Bobela, David C.; Kanevce, Ana; ...

2017-09-06

Achieving higher photovoltaic efficiency in single-junction devices is becoming increasingly difficult, but tandem modules offer the possibility of significant efficiency improvements. By device modeling we show that four-terminal CdTe/Si tandem solar modules offer the prospect of 25%-30% module efficiency, and technoeconomic analysis predicts that these efficiency gains can be realized at costs per Watt that are competitive with CdTe and Si single junction alternatives. The cost per Watt of the modeled tandems is lower than crystalline silicon, but slightly higher than CdTe alone. But, these higher power modules reduce area-related balance of system costs, providing increased value especially in area-constrainedmore » applications. This avenue for high-efficiency photovoltaics enables improved performance on a near-term timeframe, as well as a path to further reduced levelized cost of electricity as module and cell processes continue to advance.« less

Low-Cost CdTe/Silicon Tandem Solar Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamboli, Adele C.; Bobela, David C.; Kanevce, Ana

Achieving higher photovoltaic efficiency in single-junction devices is becoming increasingly difficult, but tandem modules offer the possibility of significant efficiency improvements. By device modeling we show that four-terminal CdTe/Si tandem solar modules offer the prospect of 25%-30% module efficiency, and technoeconomic analysis predicts that these efficiency gains can be realized at costs per Watt that are competitive with CdTe and Si single junction alternatives. The cost per Watt of the modeled tandems is lower than crystalline silicon, but slightly higher than CdTe alone. But, these higher power modules reduce area-related balance of system costs, providing increased value especially in area-constrainedmore » applications. This avenue for high-efficiency photovoltaics enables improved performance on a near-term timeframe, as well as a path to further reduced levelized cost of electricity as module and cell processes continue to advance.« less

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

PubMed Central

Glunčić, Matko; Paar, Vladimir

2013-01-01

The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012.exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of α-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of ‘magnifying glass’ effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes). PMID:22977183

Your Way to a Better Theory of Mind: A Healthy Diet Relates to Better Faux Pas Recognition in Older Adults.

PubMed

Ruffman, Ted; Zhang, Julie; Taumoepeau, Mele; Skeaff, Sheila

2016-01-01

Aging is characterized by a well-documented worsening of general cognition, and also a decline in social understanding such as the ability to recognize emotions or detect socially inappropriate behavior (faux pas). Several studies have demonstrated that lifestyle factors (diet, exercise, social integration, smoking) tend to offset general cognitive decline, and we examined whether they also help to offset age-related declines in social cognition. There were 56 participants aged 60 years or over. General cognition was measured using a matrices task and the Mini-Mental State Examination (MMSE). Emotion recognition was measured by the matching of faces to emotion sounds and bodies to sounds. Faux pas recognition was measured by 16 videos, examining participants' ability to differentiate appropriate and inappropriate social behavior. Diet, exercise, social integration, and smoking habits were measured via questionnaires. For general cognition, diet, pr = .32, p < .02, smoking, pr = -.32, p = .02, and education, pr = .48, p < .001, explained unique variance in matrices performance. For social cognition, even after accounting for participants' education, age, exercise habits, smoking, and social integration, a healthy diet explained independent variance in the ability to identify appropriate social behavior, pr = .29, p = .04. We replicated previous research in finding that lifestyle factors were related to fluid intelligence. In addition, we obtained the novel finding that a healthy diet is associated with better recognition of faux pas in older adults, likely acting through facilitation of brain health, and providing initial support for a means of enhancing social functioning and well-being in old age.

Perovskite-perovskite tandem photovoltaics with optimized band gaps

NASA Astrophysics Data System (ADS)

Eperon, Giles E.; Leijtens, Tomas; Bush, Kevin A.; Prasanna, Rohit; Green, Thomas; Wang, Jacob Tse-Wei; McMeekin, David P.; Volonakis, George; Milot, Rebecca L.; May, Richard; Palmstrom, Axel; Slotcavage, Daniel J.; Belisle, Rebecca A.; Patel, Jay B.; Parrott, Elizabeth S.; Sutton, Rebecca J.; Ma, Wen; Moghadam, Farhad; Conings, Bert; Babayigit, Aslihan; Boyen, Hans-Gerd; Bent, Stacey; Giustino, Feliciano; Herz, Laura M.; Johnston, Michael B.; McGehee, Michael D.; Snaith, Henry J.

2016-11-01

We demonstrate four- and two-terminal perovskite-perovskite tandem solar cells with ideally matched band gaps. We develop an infrared-absorbing 1.2-electron volt band-gap perovskite, FA0.75Cs0.25Sn0.5Pb0.5I3, that can deliver 14.8% efficiency. By combining this material with a wider-band gap FA0.83Cs0.17Pb(I0.5Br0.5)3 material, we achieve monolithic two-terminal tandem efficiencies of 17.0% with >1.65-volt open-circuit voltage. We also make mechanically stacked four-terminal tandem cells and obtain 20.3% efficiency. Notably, we find that our infrared-absorbing perovskite cells exhibit excellent thermal and atmospheric stability, not previously achieved for Sn-based perovskites. This device architecture and materials set will enable “all-perovskite” thin-film solar cells to reach the highest efficiencies in the long term at the lowest costs.

A hybrid-domain approach for modeling climate data time series

NASA Astrophysics Data System (ADS)

Wen, Qiuzi H.; Wang, Xiaolan L.; Wong, Augustine

2011-09-01

In order to model climate data time series that often contain periodic variations, trends, and sudden changes in mean (mean shifts, mostly artificial), this study proposes a hybrid-domain (HD) algorithm, which incorporates a time domain test and a newly developed frequency domain test through an iterative procedure that is analogue to the well known backfitting algorithm. A two-phase competition procedure is developed to address the confounding issue between modeling periodic variations and mean shifts. A variety of distinctive features of climate data time series, including trends, periodic variations, mean shifts, and a dependent noise structure, can be modeled in tandem using the HD algorithm. This is particularly important for homogenization of climate data from a low density observing network in which reference series are not available to help preserve climatic trends and long-term periodic variations, preventing them from being mistaken as artificial shifts. The HD algorithm is also powerful in estimating trend and periodicity in a homogeneous data time series (i.e., in the absence of any mean shift). The performance of the HD algorithm (in terms of false alarm rate and hit rate in detecting shifts/cycles, and estimation accuracy) is assessed via a simulation study. Its power is further illustrated through its application to a few climate data time series.

Stacking multiple connecting functional materials in tandem organic light-emitting diodes

PubMed Central

Zhang, Tao; Wang, Deng-Ke; Jiang, Nan; Lu, Zheng-Hong

2017-01-01

Tandem device is an important architecture in fabricating high performance organic light-emitting diodes and organic photovoltaic cells. The key element in making a high performance tandem device is the connecting materials stack, which plays an important role in electric field distribution, charge generation and charge injection. For a tandem organic light-emitting diode (OLED) with a simple Liq/Al/MoO3 stack, we discovered that there is a significant current lateral spreading causing light emission over an extremely large area outside the OLED pixel when the Al thickness exceeds 2 nm. This spread light emission, caused by an inductive electric field over one of the device unit, limits one’s ability to fabricate high performance tandem devices. To resolve this issue, a new connecting materials stack with a C60 fullerene buffer layer is reported. This new structure permits optimization of the Al metal layer in the connecting stack and thus enables us to fabricate an efficient tandem OLED having a high 155.6 cd/A current efficiency and a low roll-off (or droop) in current efficiency. PMID:28225028

Electrical and optical analyses of tandem organic light-emitting diodes with organic charge-generation layer

NASA Astrophysics Data System (ADS)

Kim, Bong Sung; Chae, Heeyeop; Chung, Ho Kyoon; Cho, Sung Min

2018-06-01

The electrical and optical properties of tandem organic light-emitting diodes (OLEDs), in which a fluorescent and phosphorescent emitting units are connected by an organic charge-generation layer (CGL), were experimentally analyzed. To investigate the internal properties of the tandem OLEDs, we fabricated and compared two single, two homo-tandem, and two hetero-tandem OLEDs using the fluorescent and phosphorescent units. From the experimental results of the OLEDs obtained at the same current density, the voltage across the CGL as well as the individual emission spectra and luminance of each unit of tandem OLEDs were obtained and compared with the theoretical simulation results. The analysis method proposed in this study can be utilized as a method to verify the accuracy of optical or electrical computer simulation of tandem OLED and it will be useful to understand the overall electrical and optical characteristics of tandem OLEDs.

Alpinia oxyphylla Miquel fruit extract activates MAPK-mediated signaling of PAs and MMP2/9 to induce Schwann cell migration and nerve regeneration.

PubMed

Chang, Yung-Ming; Ye, Chi-Xin; Ho, Tsung-Jung; Tsai, Te-Neng; Chiu, Ping-Ling; Tsai, Chin-Chuan; Lin, Yueh-Min; Kuo, Chia-Hua; Tsai, Fuu-Jen; Tsai, Chang-Hai; Huang, Chih-Yang

2014-05-01

This study investigates the molecular mechanisms by which Alpiniae oxyphyllae fructus (AOF) promotes neuron regeneration. A piece of silicone rubber was guided across a 15 mm gap in the sciatic nerve of a rat. This nerve gap was then filled with different concentrations of AOF extract (0-200 mg/ml). We investigated the role of MAPK (ERK1/2, JNK and p38) pathways for AOF-induced matrix-degrading proteolytic enzyme (PAs and MMP2/9) production in RSC96 Schwann cells. The results showed that AOF increased the expressions of uPA, tPA, MMP-9, and MAPKs in vivo. In vitro, our results show that treatment with AOF extract induces ERK1/2, JNK, and p38 phosphorylation to activate the downstream PAs and MMPs signaling expression. AOF-stimulated ERK1/2, JNK, and p38 phosphorylation attenuated by individual pretreatment with siRNAs or inhibitors (U0126, SP600125 and SB203580), resulting in migration and uPA-related signal pathway inhibition. Taken together our data suggests the MAPKs (ERK1/2, JNK and p38), PAs (uPA, tPA), MMP (MMP2, MMP9) regenerative and migration signaling pathway of Schwann cells regulated by AOF extract might play a major role in Schwann cell migration and damaged peripheral nerve regeneration.

Protein arginine methyltransferase 7 has a novel homodimer-like structure formed by tandem repeats.

PubMed

Hasegawa, Morio; Toma-Fukai, Sachiko; Kim, Jun-Dal; Fukamizu, Akiyoshi; Shimizu, Toshiyuki

2014-05-21

Protein arginine methyltransferase 7 (PRMT7) is a member of a family of enzymes that catalyze the transfer of methyl groups from S-adenosyl-l-methionine to nitrogen atoms on arginine residues. Here, we describe the crystal structure of Caenorhabditis elegans PRMT7 in complex with its reaction product S-adenosyl-L-homocysteine. The structural data indicated that PRMT7 harbors two tandem repeated PRMT core domains that form a novel homodimer-like structure. S-adenosyl-L-homocysteine bound to the N-terminal catalytic site only; the C-terminal catalytic site is occupied by a loop that inhibits cofactor binding. Mutagenesis demonstrated that only the N-terminal catalytic site of PRMT7 is responsible for cofactor binding. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

[French translations and adaptations of questionnaires of magical thinking (MIS, Eckblad and Chapman, 1983) and perception disorders (PAS, Chapman et al., 1978)].

PubMed

Dumas, P; Saoud, M; Gutknecht, C; Dalery, J; d'Amato, T

1999-01-01

Meehl used the term "schizotype" to refer to individuals who possess an underlying vulnerability for schizophrenia. Because of the extremely varying degrees of the schizotype's clinical expression, he recommended assessing schizotypic signs through objective measures rather than clinical judgement. In this way, Chapman et al. have developed symptom-oriented scales based on Meehl's manual, such as the Social Anhedonia (SA) and Physical Anhedonia (PhA) Scales, the Magical Ideation Scale (MIS), the Perceptual Aberration Scale (PAS) and the Impulsive Nonconformity Scale (IN). Whereas Chapman's scales of psychosis proneness are the most internationally used instruments for the assessment of schizotypy, some of them, such as MIS and PAS, were still not available in French. Therefore, the first aim of this report was to offer French translations of the Magical Ideation and the Perceptual Aberration Scales; the agreement of the original authors were obtained for both translated versions and their back translations. The second aim of our study was to establish French norms for each of these scales. The preliminary norms presented here [MIS: 19/30 (for females) and 20/30 (for males); PAS: 18/35 (for both genders)] were obtained by administering both scales to a sample of 134 French students. They are very close to those found by Chapman et al. for University of Wisconsin undergraduate students. We will confirm them with a larger sample of French students.

TandEM: Titan and Enceladus mission

USGS Publications Warehouse

Coustenis, A.; Atreya, S.K.; Balint, T.; Brown, R.H.; Dougherty, M.K.; Ferri, F.; Fulchignoni, M.; Gautier, D.; Gowen, R.A.; Griffith, C.A.; Gurvits, L.I.; Jaumann, R.; Langevin, Y.; Leese, M.R.; Lunine, J.I.; McKay, C.P.; Moussas, X.; Muller-Wodarg, I.; Neubauer, F.; Owen, T.C.; Raulin, F.; Sittler, E.C.; Sohl, F.; Sotin, Christophe; Tobie, G.; Tokano, T.; Turtle, E.P.; Wahlund, J.-E.; Waite, J.H.; Baines, K.H.; Blamont, J.; Coates, A.J.; Dandouras, I.; Krimigis, T.; Lellouch, E.; Lorenz, R.D.; Morse, A.; Porco, C.C.; Hirtzig, M.; Saur, J.; Spilker, T.; Zarnecki, J.C.; Choi, E.; Achilleos, N.; Amils, R.; Annan, P.; Atkinson, D.H.; Benilan, Y.; Bertucci, C.; Bezard, B.; Bjoraker, G.L.; Blanc, M.; Boireau, L.; Bouman, J.; Cabane, M.; Capria, M.T.; Chassefiere, E.; Coll, P.; Combes, M.; Cooper, J.F.; Coradini, A.; Crary, F.; Cravens, T.; Daglis, I.A.; de Angelis, E.; De Bergh, C.; de Pater, I.; Dunford, C.; Durry, G.; Dutuit, O.; Fairbrother, D.; Flasar, F.M.; Fortes, A.D.; Frampton, R.; Fujimoto, M.; Galand, M.; Grasset, O.; Grott, M.; Haltigin, T.; Herique, A.; Hersant, F.; Hussmann, H.; Ip, W.; Johnson, R.; Kallio, E.; Kempf, S.; Knapmeyer, M.; Kofman, W.; Koop, R.; Kostiuk, T.; Krupp, N.; Kuppers, M.; Lammer, H.; Lara, L.-M.; Lavvas, P.; Le, Mouelic S.; Lebonnois, S.; Ledvina, S.; Li, Ji; Livengood, T.A.; Lopes, R.M.; Lopez-Moreno, J. -J.; Luz, D.; Mahaffy, P.R.; Mall, U.; Martinez-Frias, J.; Marty, B.; McCord, T.; Salvan, C.M.; Milillo, A.; Mitchell, D.G.; Modolo, R.; Mousis, O.; Nakamura, M.; Neish, Catherine D.; Nixon, C.A.; Mvondo, D.N.; Orton, G.; Paetzold, M.; Pitman, J.; Pogrebenko, S.; Pollard, W.; Prieto-Ballesteros, O.; Rannou, P.; Reh, K.; Richter, L.; Robb, F.T.; Rodrigo, R.; Rodriguez, S.; Romani, P.; Bermejo, M.R.; Sarris, E.T.; Schenk, P.; Schmitt, B.; Schmitz, N.; Schulze-Makuch, D.; Schwingenschuh, K.; Selig, A.; Sicardy, B.; Soderblom, L.; Spilker, L.J.; Stam, D.; Steele, A.; Stephan, K.; Strobel, D.F.; Szego, K.; Szopa,

2009-01-01

TandEM was proposed as an L-class (large) mission in response to ESA’s Cosmic Vision 2015–2025 Call, and accepted for further studies, with the goal of exploring Titan and Enceladus. The mission concept is to perform in situ investigations of two worlds tied together by location and properties, whose remarkable natures have been partly revealed by the ongoing Cassini–Huygens mission. These bodies still hold mysteries requiring a complete exploration using a variety of vehicles and instruments. TandEM is an ambitious mission because its targets are two of the most exciting and challenging bodies in the Solar System. It is designed to build on but exceed the scientific and technological accomplishments of the Cassini–Huygens mission, exploring Titan and Enceladus in ways that are not currently possible (full close-up and in situ coverage over long periods of time). In the current mission architecture, TandEM proposes to deliver two medium-sized spacecraft to the Saturnian system. One spacecraft would be an orbiter with a large host of instruments which would perform several Enceladus flybys and deliver penetrators to its surface before going into a dedicated orbit around Titan alone, while the other spacecraft would carry the Titan in situ investigation components, i.e. a hot-air balloon (Montgolfière) and possibly several landing probes to be delivered through the atmosphere.

TandEM: Titan and Enceladus mission

NASA Astrophysics Data System (ADS)

Coustenis, A.; Atreya, S. K.; Balint, T.; Brown, R. H.; Dougherty, M. K.; Ferri, F.; Fulchignoni, M.; Gautier, D.; Gowen, R. A.; Griffith, C. A.; Gurvits, L. I.; Jaumann, R.; Langevin, Y.; Leese, M. R.; Lunine, J. I.; McKay, C. P.; Moussas, X.; Müller-Wodarg, I.; Neubauer, F.; Owen, T. C.; Raulin, F.; Sittler, E. C.; Sohl, F.; Sotin, C.; Tobie, G.; Tokano, T.; Turtle, E. P.; Wahlund, J.-E.; Waite, J. H.; Baines, K. H.; Blamont, J.; Coates, A. J.; Dandouras, I.; Krimigis, T.; Lellouch, E.; Lorenz, R. D.; Morse, A.; Porco, C. C.; Hirtzig, M.; Saur, J.; Spilker, T.; Zarnecki, J. C.; Choi, E.; Achilleos, N.; Amils, R.; Annan, P.; Atkinson, D. H.; Bénilan, Y.; Bertucci, C.; Bézard, B.; Bjoraker, G. L.; Blanc, M.; Boireau, L.; Bouman, J.; Cabane, M.; Capria, M. T.; Chassefière, E.; Coll, P.; Combes, M.; Cooper, J. F.; Coradini, A.; Crary, F.; Cravens, T.; Daglis, I. A.; de Angelis, E.; de Bergh, C.; de Pater, I.; Dunford, C.; Durry, G.; Dutuit, O.; Fairbrother, D.; Flasar, F. M.; Fortes, A. D.; Frampton, R.; Fujimoto, M.; Galand, M.; Grasset, O.; Grott, M.; Haltigin, T.; Herique, A.; Hersant, F.; Hussmann, H.; Ip, W.; Johnson, R.; Kallio, E.; Kempf, S.; Knapmeyer, M.; Kofman, W.; Koop, R.; Kostiuk, T.; Krupp, N.; Küppers, M.; Lammer, H.; Lara, L.-M.; Lavvas, P.; Le Mouélic, S.; Lebonnois, S.; Ledvina, S.; Li, J.; Livengood, T. A.; Lopes, R. M.; Lopez-Moreno, J.-J.; Luz, D.; Mahaffy, P. R.; Mall, U.; Martinez-Frias, J.; Marty, B.; McCord, T.; Menor Salvan, C.; Milillo, A.; Mitchell, D. G.; Modolo, R.; Mousis, O.; Nakamura, M.; Neish, C. D.; Nixon, C. A.; Nna Mvondo, D.; Orton, G.; Paetzold, M.; Pitman, J.; Pogrebenko, S.; Pollard, W.; Prieto-Ballesteros, O.; Rannou, P.; Reh, K.; Richter, L.; Robb, F. T.; Rodrigo, R.; Rodriguez, S.; Romani, P.; Ruiz Bermejo, M.; Sarris, E. T.; Schenk, P.; Schmitt, B.; Schmitz, N.; Schulze-Makuch, D.; Schwingenschuh, K.; Selig, A.; Sicardy, B.; Soderblom, L.; Spilker, L. J.; Stam, D.; Steele, A.; Stephan, K.; Strobel, D. F.; Szego, K.; Szopa, C.; Thissen, R.; Tomasko, M. G.; Toublanc, D.; Vali, H.; Vardavas, I.; Vuitton, V.; West, R. A.; Yelle, R.; Young, E. F.

2009-03-01

TandEM was proposed as an L-class (large) mission in response to ESA’s Cosmic Vision 2015-2025 Call, and accepted for further studies, with the goal of exploring Titan and Enceladus. The mission concept is to perform in situ investigations of two worlds tied together by location and properties, whose remarkable natures have been partly revealed by the ongoing Cassini-Huygens mission. These bodies still hold mysteries requiring a complete exploration using a variety of vehicles and instruments. TandEM is an ambitious mission because its targets are two of the most exciting and challenging bodies in the Solar System. It is designed to build on but exceed the scientific and technological accomplishments of the Cassini-Huygens mission, exploring Titan and Enceladus in ways that are not currently possible (full close-up and in situ coverage over long periods of time). In the current mission architecture, TandEM proposes to deliver two medium-sized spacecraft to the Saturnian system. One spacecraft would be an orbiter with a large host of instruments which would perform several Enceladus flybys and deliver penetrators to its surface before going into a dedicated orbit around Titan alone, while the other spacecraft would carry the Titan in situ investigation components, i.e. a hot-air balloon (Montgolfière) and possibly several landing probes to be delivered through the atmosphere.

Tandem microwave waste remediation and decontamination system

DOEpatents

Wicks, George G.; Clark, David E.; Schulz, Rebecca L.

1999-01-01

The invention discloses a tandem microwave system consisting of a primary chamber in which microwave energy is used for the controlled combustion of materials. A second chamber is used to further treat the off-gases from the primary chamber by passage through a susceptor matrix subjected to additional microwave energy. The direct microwave radiation and elevated temperatures provide for significant reductions in the qualitative and quantitative emissions of the treated off gases. The tandem microwave system can be utilized for disinfecting wastes, sterilizing materials, and/or modifying the form of wastes to solidify organic or inorganic materials. The simple design allows on-site treatment of waste by small volume waste generators.

Optimizing a tandem disk model

NASA Astrophysics Data System (ADS)

Healey, J. V.

1983-08-01

The optimum values of the solidity ratio, tip speed ratio (TSR), and the preset angle of attack, the corresponding distribution, and the breakdown mechanism for a tandem disk model for a crosswind machine such as a Darrieus are examined analytically. Equations are formulated for thin blades with zero drag in consideration of two plane rectangular disks, both perpendicular to the wind flow. Power coefficients are obtained for both disks and comparisons are made between a single-disk system and a two-disk system. The power coefficient for the tandem disk model is shown to be a sum of the coefficients of the individual disks, with a maximum value of twice the Betz limit at an angle of attack of -1 deg and the TSR between 4-7. The model, applied to the NACA 0012 profile, gives a maximum power coefficient of 0.967 with a solidity ratio of 0.275 and highly limited ranges for the angle of attack and TSR.

Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling

NASA Astrophysics Data System (ADS)

Egea-Jimenez, Antonio Luis; Gallardo, Rodrigo; Garcia-Pino, Abel; Ivarsson, Ylva; Wawrzyniak, Anna Maria; Kashyap, Rudra; Loris, Remy; Schymkowitz, Joost; Rousseau, Frederic; Zimmermann, Pascale

2016-07-01

PDZ domain-containing proteins work as intracellular scaffolds to control spatio-temporal aspects of cell signalling. This function is supported by the ability of their PDZ domains to bind other proteins such as receptors, but also phosphoinositide lipids important for membrane trafficking. Here we report a crystal structure of the syntenin PDZ tandem in complex with the carboxy-terminal fragment of Frizzled 7 and phosphatidylinositol 4,5-bisphosphate (PIP2). The crystal structure reveals a tripartite interaction formed via the second PDZ domain of syntenin. Biophysical and biochemical experiments establish co-operative binding of the tripartite complex and identify residues crucial for membrane PIP2-specific recognition. Experiments with cells support the importance of the syntenin-PIP2 interaction for plasma membrane targeting of Frizzled 7 and c-jun phosphorylation. This study contributes to our understanding of the biology of PDZ proteins as key players in membrane compartmentalization and dynamics.

Ubiquitin Regulates Caspase Recruitment Domain-mediated Signaling by Nucleotide-binding Oligomerization Domain-containing Proteins NOD1 and NOD2*

PubMed Central

Ver Heul, Aaron M.; Fowler, C. Andrew; Ramaswamy, S.; Piper, Robert C.

2013-01-01

NOD1 and NOD2 (nucleotide-binding oligomerization domain-containing proteins) are intracellular pattern recognition receptors that activate inflammation and autophagy. These pathways rely on the caspase recruitment domains (CARDs) within the receptors, which serve as protein interaction platforms that coordinately regulate immune signaling. We show that NOD1 CARD binds ubiquitin (Ub), in addition to directly binding its downstream targets receptor-interacting protein kinase 2 (RIP2) and autophagy-related protein 16-1 (ATG16L1). NMR spectroscopy and structure-guided mutagenesis identified a small hydrophobic surface of NOD1 CARD that binds Ub. In vitro, Ub competes with RIP2 for association with NOD1 CARD. In vivo, we found that the ligand-stimulated activity of NOD1 with a mutant CARD lacking Ub binding but retaining ATG16L1 and RIP2 binding is increased relative to wild-type NOD1. Likewise, point mutations in the tandem NOD2 CARDs at positions analogous to the surface residues defining the Ub interface on NOD1 resulted in loss of Ub binding and increased ligand-stimulated NOD2 signaling. These data suggest that Ub binding provides a negative feedback loop upon NOD-dependent activation of RIP2. PMID:23300079

Structure and catalytic regulatory function of ubiquitin specific protease 11 N-terminal and ubiquitin-like domains.

PubMed

Harper, Stephen; Gratton, Hayley E; Cornaciu, Irina; Oberer, Monika; Scott, David J; Emsley, Jonas; Dreveny, Ingrid

2014-05-13

The ubiquitin specific protease 11 (USP11) is implicated in DNA repair, viral RNA replication, and TGFβ signaling. We report the first characterization of the USP11 domain architecture and its role in regulating the enzymatic activity. USP11 consists of an N-terminal "domain present in USPs" (DUSP) and "ubiquitin-like" (UBL) domain, together referred to as DU domains, and the catalytic domain harboring a second UBL domain. Crystal structures of the DU domains show a tandem arrangement with a shortened β-hairpin at the two-domain interface and altered surface characteristics compared to the homologues USP4 and USP15. A conserved VEVY motif is a signature feature at the two-domain interface that shapes a potential protein interaction site. Small angle X-ray scattering and gel filtration experiments are consistent with the USP11DU domains and full-length USP11 being monomeric. Unexpectedly, we reveal, through kinetic assays of a series of deletion mutants, that the catalytic activity of USP11 is not regulated through intramolecular autoinhibition or activation by the N-terminal DU or UBL domains. Moreover, ubiquitin chain cleavage assays with all eight linkages reveal a preference for Lys(63)-, Lys(6)-, Lys(33)-, and Lys(11)-linked chains over Lys(27)-, Lys(29)-, and Lys(48)-linked and linear chains consistent with USP11's function in DNA repair pathways that is mediated by the protease domain. Our data support a model whereby USP11 domains outside the catalytic core domain serve as protein interaction or trafficking modules rather than a direct regulatory function of the proteolytic activity. This highlights the diversity of USPs in substrate recognition and regulation of ubiquitin deconjugation.

Dynamics of tandem bubble interaction in a microfluidic channel

PubMed Central

Yuan, Fang; Sankin, Georgy; Zhong, Pei

2011-01-01

The dynamics of tandem bubble interaction in a microfluidic channel (800 × 21 μm, W × H) have been investigated using high-speed photography, with resultant fluid motion characterized by particle imaging velocimetry. A single or tandem bubble is produced reliably via laser absorption by micron-sized gold dots (6 μm in diameter with 40 μm in separation distance) coated on a glass surface of the microfluidic channel. Using two pulsed Nd:YAG lasers at λ = 1064 nm and ∼10 μJ/pulse, the dynamics of tandem bubble interaction (individual maximum bubble diameter of 50 μm with a corresponding collapse time of 5.7 μs) are examined at different phase delays. In close proximity (i.e., interbubble distance = 40 μm or γ = 0.8), the tandem bubbles interact strongly with each other, leading to asymmetric deformation of the bubble walls and jet formation, as well as the production of two pairs of vortices in the surrounding fluid rotating in opposite directions. The direction and speed of the jet (up to 95 m/s), as well as the orientation and strength of the vortices can be varied by adjusting the phase delay. PMID:22088007

Dynamics of tandem bubble interaction in a microfluidic channel.

PubMed

Yuan, Fang; Sankin, Georgy; Zhong, Pei

2011-11-01

The dynamics of tandem bubble interaction in a microfluidic channel (800  ×  21 μm, W × H) have been investigated using high-speed photography, with resultant fluid motion characterized by particle imaging velocimetry. A single or tandem bubble is produced reliably via laser absorption by micron-sized gold dots (6 μm in diameter with 40 μm in separation distance) coated on a glass surface of the microfluidic channel. Using two pulsed Nd:YAG lasers at λ = 1064 nm and ∼10 μJ/pulse, the dynamics of tandem bubble interaction (individual maximum bubble diameter of 50 μm with a corresponding collapse time of 5.7 μs) are examined at different phase delays. In close proximity (i.e., interbubble distance = 40 μm or γ = 0.8), the tandem bubbles interact strongly with each other, leading to asymmetric deformation of the bubble walls and jet formation, as well as the production of two pairs of vortices in the surrounding fluid rotating in opposite directions. The direction and speed of the jet (up to 95 m/s), as well as the orientation and strength of the vortices can be varied by adjusting the phase delay.

On the Relativistic Correction of Particles Trajectory in Tandem Type Electrostatic Accelerator

NASA Astrophysics Data System (ADS)

Minárik, Stanislav

2015-08-01

A constant potential is applied to the acceleration of the ion-beam in the tandem type electrostatic accelerator. However, not just one voltage is applied, but instead a number of applications can be made in succession by means of the tandem arrangement of high voltage tubes. This number of voltage applications, which is the number of so-called "stages" of a tandem accelerator, may be two, three, or four, depending on the chosen design. Electrostatic field with approximately constant intensity acts on ions in any stage. In general, non-relativistic dynamics is used for the description of the ion transport in tandem accelerator. Energies of accelerated ions are too low and relativistic effects cannot be commonly observed by standard experimental technique. Estimation of possible relativistic correction of ion trajectories is therefore only a matter of calculation. In this note, we briefly present such calculation. Our aim is to show how using the relativistic dynamics modifies the particles trajectory in tandem type accelerator and what parameters determine this modification.

Simulation of two dimensional electrophoresis and tandem mass spectrometry for teaching proteomics.

PubMed

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations-2D electrophoresis and tandem mass spectrometry. The two simulations are integrated together and are designed to teach the concept of proteome analysis of prokaryotic and eukaryotic organisms. 2DE-Tandem MS can be used as a freestanding simulation, or in conjunction with a wet lab, to introduce proteomics in the undergraduate classroom. 2DE Tandem MS is a free program available on Sourceforge at https://sourceforge.net/projects/jbf/. It was developed using Java Swing and functions in Mac OSX, Windows, and Linux, ensuring that every student sees a consistent and informative graphical user interface no matter the computer platform they choose. Java must be installed on the host computer to run 2DE Tandem MS. Example classroom exercises are provided in the Supporting Information. Copyright © 2012 Wiley Periodicals, Inc.

Separate necdin domains bind ARNT2 and HIF1{alpha} and repress transcription

DOE Office of Scientific and Technical Information (OSTI.GOV)

Friedman, Eitan R.; Fan Chenming

2007-11-09

PWS is caused by the loss of expression of a set of maternally imprinted genes including NECDIN (NDN). NDN is expressed in post-mitotic neurons and plays an essential role in PWS as mouse models lacking only the Ndn gene mimic aspects of this disease. Patients haploid for SIM1 develop a PW-like syndrome. Here, we report that NDN directly interacts with ARNT2, a bHLH-PAS protein and dimer partner for SIM1. We also found that NDN can interact with HIF1{alpha}. We showed that NDN can repress transcriptional activation mediated by ARNT2:SIM1 as well as ARNT2:HIF1{alpha}. The N-terminal 115 residues of NDN aremore » sufficient for interaction with the bHLH domains of ARNT2 or HIF1{alpha} but not for transcriptional repression. Using GAL4-NDN fusion proteins, we determined that NDN possesses multiple repression domains. We thus propose that NDN regulates neuronal function and hypoxic response by regulating the activities of the ARNT2:SIM1 and ARNT2:HIF1{alpha} dimers, respectively.« less

Step-scan differential Fourier transform infrared photoacoustic spectroscopy (DFTIR-PAS): a spectral deconvolution method for weak absorber detection in the presence of strongly overlapping background absorptions.

PubMed

Liu, Lixian; Mandelis, Andreas; Huan, Huiting; Michaelian, Kirk H

2017-04-01

The determination of small absorption coefficients of trace gases in the atmosphere constitutes a challenge for analytical air contaminant measurements, especially in the presence of strongly absorbing backgrounds. A step-scan differential Fourier transform infrared photoacoustic spectroscopy (DFTIR-PAS) method was developed to suppress the coherent external noise and spurious photoacoustic (PA) signals caused by strongly absorbing backgrounds. The infrared absorption spectra of acetylene (C₂H₂) and local air were used to verify the performance of the step-scan DFTIR-PAS method. A linear amplitude response to C₂H₂ concentrations from 100 to 5000 ppmv was observed, leading to a theoretical detection limit of 5 ppmv. The differential mode was capable of eliminating the coherent noise and dominant background gas signals, thereby revealing the presence of the otherwise hidden C₂H₂ weak absorption. Thus, the step-scan DFTIR-PAS modality was demonstrated to be an effective approach for monitoring weakly absorbing gases with absorption bands overlapped by strongly absorbing background species.

Structure of the E2 DNA-binding domain from human papillomavirus serotype 31 at 2.4 A.

PubMed

Bussiere, D E; Kong, X; Egan, D A; Walter, K; Holzman, T F; Lindh, F; Robins, T; Giranda, V L

1998-11-01

The papillomaviruses are a family of small double-stranded DNA viruses which exclusively infect epithelial cells and stimulate the proliferation of those cells. A key protein within the papillomavirus life-cycle is known as the E2 (Early 2) protein and is responsible for regulating viral transcription from all viral promoters as well as for replication of the papillomavirus genome in tandem with another protein known as E1. The E2 protein itself consists of three functional domains: an N-terminal trans-activation domain, a proline-rich linker, and a C-terminal DNA-binding domain. The first crystal structure of the human papillomavirus, serotype 31 (HPV-31), E2 DNA-binding domain has been determined at 2.4 A resolution. The HPV DNA-binding domain monomer consists of two beta-alpha-beta repeats of approximately equal length and is arranged as to have an anti-parallel beta-sheet flanked by the two alpha-helices. The monomers form the functional in vivo dimer by association of the beta-sheets of each monomer so as to form an eight-stranded anti-parallel beta-barrel at the center of the dimer, with the alpha-helices lining the outside of the barrel. The overall structure of HVP-31 E2 DNA-binding domain is similar to both the bovine papillomavirus E2-binding domain and the Epstein-Barr nuclear antigen-1 DNA-binding domain.

iPAS: AES Flight System Technology Maturation for Human Spaceflight

NASA Technical Reports Server (NTRS)

Othon, William L.

2014-01-01

In order to realize the vision of expanding human presence in space, NASA will develop new technologies that can enable future crewed spacecraft to go far beyond Earth orbit. These technologies must be matured to the point that future project managers can accept the risk of incorporating them safely and effectively within integrated spacecraft systems, to satisfy very challenging mission requirements. The technologies must also be applied and managed within an operational context that includes both on-board crew and mission support on Earth. The Advanced Exploration Systems (AES) Program is one part of the NASA strategy to identify and develop key capabilities for human spaceflight, and mature them for future use. To support this initiative, the Integrated Power Avionics and Software (iPAS) environment has been developed that allows engineers, crew, and flight operators to mature promising technologies into applicable capabilities, and to assess the value of these capabilities within a space mission context. This paper describes the development of the integration environment to support technology maturation and risk reduction, and offers examples of technology and mission demonstrations executed to date.

Development of an advanced spacecraft tandem mass spectrometer

NASA Astrophysics Data System (ADS)

Drew, Russell C.

1992-03-01

The purpose of this research was to apply current advanced technology in electronics and materials to the development of a miniaturized Tandem Mass Spectrometer that would have the potential for future development into a package suitable for spacecraft use. The mass spectrometer to be used as a basis for the tandem instrument would be a magnetic sector instrument, of Nier-Johnson configuration, as used on the Viking Mars Lander mission. This instrument configuration would then be matched with a suitable second stage MS to provide the benefits of tandem MS operation for rapid identification of unknown organic compounds. This tandem instrument is configured with a newly designed GC system to aid in separation of complex mixtures prior to MS analysis. A number of important results were achieved in the course of this project. Among them were the development of a miniaturized GC subsystem, with a unique desorber-injector, fully temperature feedback controlled oven with powered cooling for rapid reset to ambient conditions, a unique combination inlet system to the MS that provides for both membrane sampling and direct capillary column sample transfer, a compact and ruggedized alignment configuration for the MS, an improved ion source design for increased sensitivity, and a simple, rugged tandem MS configuration that is particularly adaptable to spacecraft use because of its low power and low vacuum pumping requirements. The potential applications of this research include use in manned spacecraft like the space station as a real-time detection and warning device for the presence of potentially harmful trace contaminants of the spacecraft atmosphere, use as an analytical device for evaluating samples collected on the Moon or a planetary surface, or even use in connection with monitoring potentially hazardous conditions that may exist in terrestrial locations such as launch pads, environmental test chambers or other sensitive areas. Commercial development of the technology

Development of an advanced spacecraft tandem mass spectrometer

NASA Technical Reports Server (NTRS)

Drew, Russell C.

1992-01-01

The purpose of this research was to apply current advanced technology in electronics and materials to the development of a miniaturized Tandem Mass Spectrometer that would have the potential for future development into a package suitable for spacecraft use. The mass spectrometer to be used as a basis for the tandem instrument would be a magnetic sector instrument, of Nier-Johnson configuration, as used on the Viking Mars Lander mission. This instrument configuration would then be matched with a suitable second stage MS to provide the benefits of tandem MS operation for rapid identification of unknown organic compounds. This tandem instrument is configured with a newly designed GC system to aid in separation of complex mixtures prior to MS analysis. A number of important results were achieved in the course of this project. Among them were the development of a miniaturized GC subsystem, with a unique desorber-injector, fully temperature feedback controlled oven with powered cooling for rapid reset to ambient conditions, a unique combination inlet system to the MS that provides for both membrane sampling and direct capillary column sample transfer, a compact and ruggedized alignment configuration for the MS, an improved ion source design for increased sensitivity, and a simple, rugged tandem MS configuration that is particularly adaptable to spacecraft use because of its low power and low vacuum pumping requirements. The potential applications of this research include use in manned spacecraft like the space station as a real-time detection and warning device for the presence of potentially harmful trace contaminants of the spacecraft atmosphere, use as an analytical device for evaluating samples collected on the Moon or a planetary surface, or even use in connection with monitoring potentially hazardous conditions that may exist in terrestrial locations such as launch pads, environmental test chambers or other sensitive areas. Commercial development of the technology

Theoretical study of optical properties of anti phase domains in GaP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tea, E., E-mail: etea.contact@gmail.com; FOTON INSA-Rennes; Vidal, J.

III-V/Si heterostructures are currently investigated for silicon photonics and solar energy conversion. In particular, dilute nitride alloy GaAsPN grown on a GaP/Si platform exhibits lattice match with Si and an optimal band gap configuration for tandem solar cell devices. However, monolithic “coherent” growth of the GaP thin layer on Si suffers from the nucleation of extended structural defects, which can hamper device operation as well as the GaP/Si interface level and through their propagation inside the overall heterostructure. However, the effect of such structural defects on optical and transport properties is actually not well understood in details. In this letter,more » we investigate the anti phase domains defect (also called inversion domains) by means of ab initio calculations giving insights into the alteration of optical and transport properties of GaP due to the defective GaP/Si interface.« less

Identification of hidden relationships from the coupling of hydrophobic cluster analysis and domain architecture information.

PubMed

Faure, Guilhem; Callebaut, Isabelle

2013-07-15

Describing domain architecture is a critical step in the functional characterization of proteins. However, some orphan domains do not match any profile stored in dedicated domain databases and are thereby difficult to analyze. We present here an original novel approach, called TREMOLO-HCA, for the analysis of orphan domain sequences and inspired from our experience in the use of Hydrophobic Cluster Analysis (HCA). Hidden relationships between protein sequences can be more easily identified from the PSI-BLAST results, using information on domain architecture, HCA plots and the conservation degree of amino acids that may participate in the protein core. This can lead to reveal remote relationships with known families of domains, as illustrated here with the identification of a hidden Tudor tandem in the human BAHCC1 protein and a hidden ET domain in the Saccharomyces cerevisiae Taf14p and human AF9 proteins. The results obtained in such a way are consistent with those provided by HHPRED, based on pairwise comparisons of HHMs. Our approach can, however, be applied even in absence of domain profiles or known 3D structures for the identification of novel families of domains. It can also be used in a reverse way for refining domain profiles, by starting from known protein domain families and identifying highly divergent members, hitherto considered as orphan. We provide a possible integration of this approach in an open TREMOLO-HCA package, which is fully implemented in python v2.7 and is available on request. Instructions are available at http://www.impmc.upmc.fr/∼callebau/tremolohca.html. isabelle.callebaut@impmc.upmc.fr Supplementary Data are available at Bioinformatics online.

Catalytic domains of the LAR and CD45 protein tyrosine phosphatases from Escherichia coli expression systems: Purification and characterization for specificity and mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Hyeongjin; Ramer, S.E.; Itoh, Michiyasu

1992-01-14

The cytoplasmic domains of two human transmembrane protein tyrosine phosphatases (PTPases), LAR and CD45, have been expressed in Escherichia coli, purified to near-homogeneity, and compared for catalytic efficiency toward several phosphotyrosine-containing peptide substrates. A 615-residue LAR fragment (LAR-D1D2) containing both tandemly repeated PTPase domains shows almost identical specific activity and high catalytic efficiency as the 40-kDa single-domain LAR-D1 fragment, consistent with a single functional active site in the 70-kDa LAR-D1D2 enzyme. A 90-kDa fragment of the human leukocyte CD45 PTPase, containing two similar tandemly repeated PTPase domains, shows parallel specificity to LAR-D1 and LAR-D1D2 with a high k{sub cat}/K{sub M}more » value for a phosphotyrosyl undecapeptide. Sufficient purified LAR-D1 and LAR-D1D2 PTPases were available to demonstrate enzymatic exchange of {sup 18}O from {sup 18}O{sub 4} inorganic phosphate into H{sub 2} {sup 16}O at rates of {approximately}1 {times} 10{sup {minus}2} s{sup {minus}1}. The oxygen-18 exchange probably proceeds via a phosphoenzyme intermediate. Brief incubation of all three PTPase fragments with a ({sup 32}P)phosphotyrosyl peptide substrate prior to quench with SDS sample buffer and gel electrophoresis led to autoradiographic detection of {sup 32}P-labeled enzymes. Pulse/chase studies on the LAR {sup 32}P-enzyme showed turnover of the labeled phosphoryl group.« less

A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils

NASA Astrophysics Data System (ADS)

Louros, Nikolaos N.; Baltoumas, Fotis A.; Hamodrakas, Stavros J.; Iconomidou, Vassiliki A.

2016-02-01

Pmel17 is a multidomain protein involved in biosynthesis of melanin. This process is facilitated by the formation of Pmel17 amyloid fibrils that serve as a scaffold, important for pigment deposition in melanosomes. A specific luminal domain of human Pmel17, containing 10 tandem imperfect repeats, designated as repeat domain (RPT), forms amyloid fibrils in a pH-controlled mechanism in vitro and has been proposed to be essential for the formation of the fibrillar matrix. Currently, no three-dimensional structure has been resolved for the RPT domain of Pmel17. Here, we examine the structure of the RPT domain by performing sequence threading. The resulting model was subjected to energy minimization and validated through extensive molecular dynamics simulations. Structural analysis indicated that the RPT model exhibits several distinct properties of β-solenoid structures, which have been proposed to be polymerizing components of amyloid fibrils. The derived model is stabilized by an extensive network of hydrogen bonds generated by stacking of highly conserved polar residues of the RPT domain. Furthermore, the key role of invariant glutamate residues is proposed, supporting a pH-dependent mechanism for RPT domain assembly. Conclusively, our work attempts to provide structural insights into the RPT domain structure and to elucidate its contribution to Pmel17 amyloid fibril formation.

Design and long-term monitoring of DSC/CIGS tandem solar module

NASA Astrophysics Data System (ADS)

Vildanova, M. F.; Nikolskaia, A. B.; Kozlov, S. S.; Shevaleevskiy, O. I.

2015-11-01

This paper describes the design and development of tandem dye-sensitized/Cu(In, Ga)Se (DSC/CIGS) PV modules. The tandem PV module comprised of the top DSC module and a bottom commercial 0,8 m2 CIGS module. The top DSC module was made of 10 DSC mini-modules with the field size of 20 × 20 cm2 each. Tandem DSC/CIGS PV modules were used for providing the long-term monitoring of energy yield and electrical parameters in comparison with standalone CIGS modules under outdoor conditions. The outdoor test facility, containing solar modules of both types and a measurement unit, was located on the roof of the Institute of Biochemical Physics in Moscow. The data obtained during monitoring within the 2014 year period has shown the advantages of the designed tandem DSC/CIGS PV-modules over the conventional CIGS modules, especially for cloudy weather and low-intensity irradiation conditions.

A 170kDa multi-domain cystatin of Fasciola gigantica is active in the male reproductive system.

PubMed

Geadkaew, Amornrat; Kosa, Nanthawat; Siricoon, Sinee; Grams, Suksiri Vichasri; Grams, Rudi

2014-09-01

Cystatins are functional as intra- and extracellular inhibitors of cysteine proteases and are expressed as single or multi-domain proteins. We have previously described two single domain type 1 cystatins in the trematode Fasciola gigantica that are released into the parasite's intestinal tract and exhibit inhibitory activity against endogenous and host cathepsin L and B proteases. In contrast, the here presented 170kDa multi-domain cystatin (FgMDC) comprises signal peptide and 12 tandem repeated cystatin-like domains with similarity to type 2 single domain cystatins. The domains show high sequence divergence with identity values often <20% and at only 26.8% between the highest matching domains 6 and 10. Several domains contain degenerated QVVAG core motifs and/or lack other important residues of active type 2 cystatins. Domain-specific antisera detected multiple forms of FgMDC ranging from <10 to >120kDa molecular mass in immunoblots of parasite crude extracts and ES product with different banding patterns for each antiserum demonstrating complex processing of the proprotein. The four domains with the highest conserved QVVAG motifs were expressed in Escherichia coli and the refolded recombinant proteins blocked cysteine protease activity in the parasite's ES product. Strikingly, immunohistochemical analysis using seven domain-specific antisera localized FgMDC in testis lobes and sperm. It is speculated that the processed cystatin-like domains have function analogous to the mammalian group of male reproductive tissue-specific type 2 cystatins and are functional in spermiogenesis and fertilization. Copyright © 2014 Elsevier B.V. All rights reserved.

De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.

PubMed

Liu, Xiaowen; Dekker, Lennard J M; Wu, Si; Vanduijn, Martijn M; Luider, Theo M; Tolić, Nikola; Kou, Qiang; Dvorkin, Mikhail; Alexandrova, Sonya; Vyatkina, Kira; Paša-Tolić, Ljiljana; Pevzner, Pavel A

2014-07-03

There are two approaches for de novo protein sequencing: Edman degradation and mass spectrometry (MS). Existing MS-based methods characterize a novel protein by assembling tandem mass spectra of overlapping peptides generated from multiple proteolytic digestions of the protein. Because each tandem mass spectrum covers only a short peptide of the target protein, the key to high coverage protein sequencing is to find spectral pairs from overlapping peptides in order to assemble tandem mass spectra to long ones. However, overlapping regions of peptides may be too short to be confidently identified. High-resolution mass spectrometers have become accessible to many laboratories. These mass spectrometers are capable of analyzing molecules of large mass values, boosting the development of top-down MS. Top-down tandem mass spectra cover whole proteins. However, top-down tandem mass spectra, even combined, rarely provide full ion fragmentation coverage of a protein. We propose an algorithm, TBNovo, for de novo protein sequencing by combining top-down and bottom-up MS. In TBNovo, a top-down tandem mass spectrum is utilized as a scaffold, and bottom-up tandem mass spectra are aligned to the scaffold to increase sequence coverage. Experiments on data sets of two proteins showed that TBNovo achieved high sequence coverage and high sequence accuracy.

Single P-N junction tandem photovoltaic device

DOEpatents

Walukiewicz, Wladyslaw [Kensington, CA; Ager, III, Joel W.; Yu, Kin Man [Lafayette, CA

2012-03-06

A single P-N junction solar cell is provided having two depletion regions for charge separation while allowing the electrons and holes to recombine such that the voltages associated with both depletion regions of the solar cell will add together. The single p-n junction solar cell includes an alloy of either InGaN or InAlN formed on one side of the P-N junction with Si formed on the other side in order to produce characteristics of a two junction (2J) tandem solar cell through only a single P-N junction. A single P-N junction solar cell having tandem solar cell characteristics will achieve power conversion efficiencies exceeding 30%.

Single P-N junction tandem photovoltaic device

DOEpatents

Walukiewicz, Wladyslaw [Kensington, CA; Ager, III, Joel W.; Yu, Kin Man [Lafayette, CA

2011-10-18

A single P-N junction solar cell is provided having two depletion regions for charge separation while allowing the electrons and holes to recombine such that the voltages associated with both depletion regions of the solar cell will add together. The single p-n junction solar cell includes an alloy of either InGaN or InAlN formed on one side of the P-N junction with Si formed on the other side in order to produce characteristics of a two junction (2J) tandem solar cell through only a single P-N junction. A single P-N junction solar cell having tandem solar cell characteristics will achieve power conversion efficiencies exceeding 30%.

Efficient Monolithic Perovskite/Silicon Tandem Solar Cell with Cell Area >1 cm(2).

PubMed

Werner, Jérémie; Weng, Ching-Hsun; Walter, Arnaud; Fesquet, Luc; Seif, Johannes Peter; De Wolf, Stefaan; Niesen, Bjoern; Ballif, Christophe

2016-01-07

Monolithic perovskite/crystalline silicon tandem solar cells hold great promise for further performance improvement of well-established silicon photovoltaics; however, monolithic tandem integration is challenging, evidenced by the modest performances and small-area devices reported so far. Here we present first a low-temperature process for semitransparent perovskite solar cells, yielding efficiencies of up to 14.5%. Then, we implement this process to fabricate monolithic perovskite/silicon heterojunction tandem solar cells yielding efficiencies of up to 21.2 and 19.2% for cell areas of 0.17 and 1.22 cm(2), respectively. Both efficiencies are well above those of the involved subcells. These single-junction perovskite and tandem solar cells are hysteresis-free and demonstrate steady performance under maximum power point tracking for several minutes. Finally, we present the effects of varying the intermediate recombination layer and hole transport layer thicknesses on tandem cell photocurrent generation, experimentally and by transfer matrix simulations.

PASBio: predicate-argument structures for event extraction in molecular biology

PubMed Central

Wattarujeekrit, Tuangthong; Shah, Parantu K; Collier, Nigel

2004-01-01

Background The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sentence structure. A consensus in the IE community is emerging on the necessity for exploiting deeper knowledge structures such as through the relations between a verb and its arguments shown by predicate-argument structure (PAS). PAS is of interest as structures typically correspond to events of interest and their participating entities. For this to be realized within IE a key knowledge component is the definition of PAS frames. PAS frames for non-technical domains such as newswire are already being constructed in several projects such as PropBank, VerbNet, and FrameNet. Knowledge from PAS should enable more accurate applications in several areas where sentence understanding is required like machine translation and text summarization. In this article, we explore the need to adapt PAS for the MB domain and specify PAS frames to support IE, as well as outlining the major issues that require consideration in their construction. Results We introduce PASBio by extending a model based on PropBank to the MB domain. The hypothesis we explore is that PAS holds the key for understanding relationships describing the roles of genes and gene products in mediating their biological functions. We chose predicates describing gene expression, molecular interactions and signal transduction events with the aim of covering a number of research areas in MB. Analysis was performed on sentences containing a set of verbal predicates from MEDLINE and full text journals. Results confirm the necessity to analyze

The production and characterization of novel heavy-chain antibodies against the tandem repeat region of MUC1 mucin.

PubMed

Rahbarizadeh, Fatemeh; Rasaee, Mohammad J; Forouzandeh, Mehdi; Allameh, Abdolamir; Sarrami, Ramin; Nasiry, Habib; Sadeghizadeh, Majid

2005-01-01

Camelidae are known to produce immunoglobulins (Igs) devoid of light chains and constant heavy-chain domains (CH1). Antigen-specific fragments of these heavy-chain IgGs (VHH) are of great interest in biotechnology applications. This paper describes the first example of successfully raised heavy-chain antibodies in Camelus dromedarius (single-humped camel) and Camelus bactrianus (two-humped camel) against a MUC1 related peptide that is found to be an important epitope expressed in cancerous tissue. Camels were immunized against a synthetic peptide corresponding to the tandem repeat region of MUC1 mucin and cancerous tissue preparation obtained from patients suffering from breast carcinoma. Three IgG subclasses with different binding properties to protein A and G were purified by affinity chromatography. Both conventional and heavy-chain IgG antibodies were produced in response to MUC1-related peptide. The elicited antibodies could react specifically with the tandem repeat region of MUC1 mucin in an enzyme linked immunosorbant assay (ELISA). Anti-peptide antibodies were purified after passing antiserum over two affinity chromatography columns. Using ELISA, immunocytochemistry and Western blotting, the interaction of purified antibodies with different antigens was evaluated. The antibodies were observed to be selectively bound to antigens namely: MUC1 peptide (tandem repeat region), human milk fat globule membrane (HMFG), deglycosylated human milk fat globule membrane (D-HMFG), homogenized cancerous breast tissue and a native MUC1 purified from ascitic fluid. Ka values of specific polyclonal antipeptide antibodies were estimated in C. dromedarius and C. bactrianus, as 7 x 10(10) M(-1) and 1.4 x 10(10) M(-1) respectively.

The Effects of the Paired Associates Strategy (PAS) on the Recall of Factual Information by Postsecondary Students with Learning Disabilities

ERIC Educational Resources Information Center

Patwa, Shamim S.; Chafouleas, Sandra M.; Madaus, Joseph W.

2005-01-01

Despite the success of independence-oriented interventions such as strategy instruction (SI) in secondary populations, very little research has examined the effectiveness of SI at the postsecondary level. Thus, we sought to determine if one form of SI, the Paired Associates Strategy (PAS), improved the recall of factual information by…

Hybrid tandem quantum dot/organic photovoltaic cells with complementary near infrared absorption

NASA Astrophysics Data System (ADS)

Kim, Taesoo; Palmiano, Elenita; Liang, Ru-Ze; Hu, Hanlin; Murali, Banavoth; Kirmani, Ahmad R.; Firdaus, Yuliar; Gao, Yangqin; Sheikh, Arif; Yuan, Mingjian; Mohammed, Omar F.; Hoogland, Sjoerd; Beaujuge, Pierre M.; Sargent, Edward H.; Amassian, Aram

2017-05-01

Monolithically integrated hybrid tandem solar cells that effectively combine solution-processed colloidal quantum dot (CQD) and organic bulk heterojunction subcells to achieve tandem performance that surpasses the individual subcell efficiencies have not been demonstrated to date. In this work, we demonstrate hybrid tandem cells with a low bandgap PbS CQD subcell harvesting the visible and near-infrared photons and a polymer:fullerene—poly (diketopyrrolopyrrole-terthiophene) (PDPP3T):[6,6]-phenyl-C60-butyric acid methyl ester (PC61BM)—top cell absorbing effectively the red and near-infrared photons of the solar spectrum in a complementary fashion. The two subcells are connected in series via an interconnecting layer (ICL) composed of a metal oxide layer, a conjugated polyelectrolyte, and an ultrathin layer of Au. The ultrathin layer of Au forms nano-islands in the ICL, reducing the series resistance, increasing the shunt resistance, and enhancing the device fill-factor. The hybrid tandems reach a power conversion efficiency (PCE) of 7.9%, significantly higher than the PCE of the corresponding individual single cells, representing one of the highest efficiencies reported to date for hybrid tandem solar cells based on CQD and polymer subcells.

Optical enhancement of a printed organic tandem solar cell using diffractive nanostructures.

PubMed

Mayer, Jan A; Offermans, Ton; Chrapa, Marek; Pfannmöller, Martin; Bals, Sara; Ferrini, Rolando; Nisato, Giovanni

2018-03-19

Solution processable organic tandem solar cells offer a promising approach to achieve cost-effective, lightweight and flexible photovoltaics. In order to further enhance the efficiency of optimized organic tandem cells, diffractive light-management nanostructures were designed for an optimal redistribution of the light as function of both wavelength and propagation angles in both sub-cells. As the fabrication of these optical structures is compatible with roll-to-roll production techniques such as hot-embossing or UV NIL imprinting, they present an optimal cost-effective solution for printed photovoltaics. Tandem cells with power conversion efficiencies of 8-10% were fabricated in the ambient atmosphere by doctor blade coating, selected to approximate the conditions during roll-to-roll manufacturing. Application of the light management structure onto an 8.7% efficient encapsulated tandem cell boosted the conversion efficiency of the cell to 9.5%.

PHD Domain-Mediated E3 Ligase Activity Directs Intramolecular Sumoylation of an Adjacent Bromodomain which is Required for Gene Silencing

PubMed Central

Ivanov, Alexey V.; Peng, Hongzhuang; Yurchenko, Vyacheslav; Yap, Kyoko L.; Negorev, Dmitri G.; Schultz, David C.; Psulkowski, Elyse; Fredericks, William J.; White, David E.; Maul, Gerd G.; Sadofsky, Moshe J.; Zhou, Ming-Ming; Rauscher, Frank J.

2015-01-01

SUMMARY Tandem PHD and bromodomains are often found in chromatin-associated proteins and have been shown to cooperate in gene silencing. Each domain can bind specifically modified histones: the mechanisms of cooperation between these domains are unknown. We show that the PHD domain of the KAP1 corepressor functions as an intramolecular E3 ligase for sumoylation of the adjacent bromodomain. The RING finger-like structure of the PHD domain is required for both Ubc9 binding and sumoylation and directs modification to specific lysine residues in the bromodomain. Sumoylation is required for KAP1-mediated gene silencing and functions by directly recruiting the SETDB1 histone methyltransferase and the CHD3/Mi2 component of the NuRD complex via SUMO interacting motifs. Sumoylated KAP1 stimulates the histone methyltransferase activity of SETDB1. These data provide a mechanistic explanation for the cooperation of PHD and bromodomains in gene regulation and describe a new function of the PHD domain as an intramolecular E3 SUMO ligase. PMID:18082607

The dual PH domain protein Opy1 functions as a sensor and modulator of PtdIns(4,5)P₂ synthesis.

PubMed

Ling, Yading; Stefan, Christopher J; Macgurn, Jason A; Audhya, Anjon; Emr, Scott D

2012-06-29

Phosphatidylinositol-4,5-bisphosphate, PtdIns(4,5)P(2), is an essential signalling lipid that regulates key processes such as endocytosis, exocytosis, actin cytoskeletal organization and calcium signalling. Maintaining proper levels of PtdIns(4,5)P(2) at the plasma membrane (PM) is crucial for cell survival and growth. We show that the conserved PtdIns(4)P 5-kinase, Mss4, forms dynamic, oligomeric structures at the PM that we term PIK patches. The dynamic assembly and disassembly of Mss4 PIK patches may provide a mechanism to precisely modulate Mss4 kinase activity, as needed, for localized regulation of PtdIns(4,5)P(2) synthesis. Furthermore, we identify a tandem PH domain-containing protein, Opy1, as a novel Mss4-interacting protein that partially colocalizes with PIK patches. Based upon genetic, cell biological, and biochemical data, we propose that Opy1 functions as a coincidence detector of the Mss4 PtdIns(4)P 5-kinase and PtdIns(4,5)P(2) and serves as a negative regulator of PtdIns(4,5)P(2) synthesis at the PM. Our results also suggest that additional conserved tandem PH domain-containing proteins may play important roles in regulating phosphoinositide signalling.

Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE, a regulator of ABA responses unique to basal land plants and required for desiccation tolerance

DOE PAGES

Stevenson, Sean Ross; Kamisugi, Yasuko; Trinh, Chi H.; ...

2016-05-18

The anatomically simple plants that first colonized land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA nonresponsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR) gene encoding a modular protein kinase comprising an N-terminal PAS domain, a central EDR domain, and a C-terminal MAPKKK-like domain. anr mutants fail to accumulate dehydration tolerance-associated gene products in response to drought, ABA, or osmotic stress and do not acquire ABA-dependent desiccation tolerance. Themore » crystal structure of the PAS domain, determined to 1.7-Å resolution, shows a conserved PAS-fold that dimerizes through a weak dimerization interface. Targeted mutagenesis of a conserved tryptophan residue within the PAS domain generates plants with ABA nonresponsive growth and strongly attenuated ABA-responsive gene expression, whereas deleting this domain retains a fully ABA-responsive phenotype. ANR orthologs are found in early-diverging land plant lineages and aquatic algae but are absent from more recently diverged vascular plants. Lastly, we propose that ANR genes represent an ancestral adaptation that enabled drought stress survival of the first terrestrial colonizers but were lost during land plant evolution.« less

Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE, a regulator of ABA responses unique to basal land plants and required for desiccation tolerance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stevenson, Sean Ross; Kamisugi, Yasuko; Trinh, Chi H.

The anatomically simple plants that first colonized land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA nonresponsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR) gene encoding a modular protein kinase comprising an N-terminal PAS domain, a central EDR domain, and a C-terminal MAPKKK-like domain. anr mutants fail to accumulate dehydration tolerance-associated gene products in response to drought, ABA, or osmotic stress and do not acquire ABA-dependent desiccation tolerance. Themore » crystal structure of the PAS domain, determined to 1.7-Å resolution, shows a conserved PAS-fold that dimerizes through a weak dimerization interface. Targeted mutagenesis of a conserved tryptophan residue within the PAS domain generates plants with ABA nonresponsive growth and strongly attenuated ABA-responsive gene expression, whereas deleting this domain retains a fully ABA-responsive phenotype. ANR orthologs are found in early-diverging land plant lineages and aquatic algae but are absent from more recently diverged vascular plants. Lastly, we propose that ANR genes represent an ancestral adaptation that enabled drought stress survival of the first terrestrial colonizers but were lost during land plant evolution.« less

Modified tandem gratings anastigmatic imaging spectrometer with oblique incidence for spectral broadband

NASA Astrophysics Data System (ADS)

Cui, Chengguang; Wang, Shurong; Huang, Yu; Xue, Qingsheng; Li, Bo; Yu, Lei

2015-09-01

A modified spectrometer with tandem gratings that exhibits high spectral resolution and imaging quality for solar observation, monitoring, and understanding of coastal ocean processes is presented in this study. Spectral broadband anastigmatic imaging condition, spectral resolution, and initial optical structure are obtained based on geometric aberration theory. Compared with conventional tandem gratings spectrometers, this modified design permits flexibility in selecting gratings. A detailed discussion of the optical design and optical performance of an ultraviolet spectrometer with tandem gratings is also included to explain the advantage of oblique incidence for spectral broadband.

The chitin-binding domain of a GH-18 chitinase from Vibrio harveyi is crucial for chitin-chitinase interactions.

PubMed

Suginta, Wipa; Sirimontree, Paknisa; Sritho, Natchanok; Ohnuma, Takayuki; Fukamizo, Tamo

2016-12-01

Vibrio harveyi chitinase A (VhChiA) is a GH-18 glycosyl hydrolase with a structure containing three distinct domains: i) the N-terminal chitin-binding domain; ii) the (α/β) 8 TIM barrel catalytic domain; and iii) the α+β insertion domain. In this study, we cloned the gene fragment encoding the chitin-binding domain of VhChiA, termed ChBD Vh ChiA . The recombinant ChBD Vh ChiA was heterologously expressed in E. coli BL21 strain Tuner(DE3)pLacI host cells, and purified to homogeneity. CD measurements suggested that ChBD Vh ChiA contained β-sheets as major structural components and fluorescence spectroscopy showed that the protein domain was folded correctly, and suitable for functional characterization. Chitin binding assays showed that ChBD Vh ChiA bound to both α- and β-chitins, with the greatest affinity for β-colloidal chitin, but barely bound to polymeric chitosan. These results identified the tandem N-acetamido functionality on chitin chains as the specific sites of enzyme-substrate interactions. The binding affinity of the isolated domain was significantly lower than that of intact VhChiA, suggesting that the catalytic domain works synergistically with the chitin-binding domain to guide the polymeric substrate into the substrate binding cleft. These data confirm the physiological role of the chitin-binding domain of the marine bacterial GH-18 chitinase A in chitin-chitinase interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Tandem photovoltaic solar cells and increased solar energy conversion efficiency

NASA Technical Reports Server (NTRS)

Loferski, J. J.

1976-01-01

Tandem photovoltaic cells, as proposed by Jackson (1955) to increase the efficiency of solar energy conversion, involve the construction of a system of stacked p/n homojunction photovoltaic cells composed of different semiconductors. It had been pointed out by critics, however, that the total power which could be extracted from the cells in the stack placed side by side was substantially greater than the power obtained from the stacked cells. A reexamination of the tandem cell concept in view of the development of the past few years is conducted. It is concluded that the use of tandem cell systems in flat plate collectors, as originally envisioned by Jackson, may yet become feasible as a result of the development of economically acceptable solar cells for large scale terrestrial power generation.

Recruitment of mRNA-destabilizing protein TIS11 to stress granules is mediated by its zinc finger domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murata, Tomiyasu; Morita, Noriyoshi; Hikita, Kiyomi

2005-02-15

TIS11, a member of the CCCH zinc finger protein family, was found to be distributed throughout cells with a preferential cytoplasmic localization when transiently expressed in COS-7 cells. Upon treatment with heat shock, TIS11 became localized in discrete particles in the cytoplasm of the transfectants. We showed the TIS11-positive particles to be stress granules (SGs), which are known to be formed in the cytoplasm of eukaryotic cells in response to environmental stresses. By deletion studies using the green fluorescent protein fusion system, we mapped a functional stress granule (SG) localization signal to a region containing two tandem repeats of themore » zinc finger motif of TIS11. Site-directed mutations of Tyr105/Tyr113, Gly109/Gly 114, and Phe119 in the first zinc finger motif diminished the ability of this TIS11 domain to direct SG localization. Importantly, when the zinc-chelating Cys residues in either the first or second zinc finger were mutated to Ala residues, the recruitment of the TIS11 zinc finger region to SG was significantly inhibited by the mutation and was completely abolished by the mutation in both zinc fingers. These results suggest that recruitment of TIS11 to heat shock-induced SG is governed by the tandem zinc finger domains of this protein.« less

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains.

PubMed

Van Bortle, Kevin; Ramos, Edward; Takenaka, Naomi; Yang, Jingping; Wahi, Jessica E; Corces, Victor G

2012-11-01

Several multiprotein DNA complexes capable of insulator activity have been identified in Drosophila melanogaster, yet only CTCF, a highly conserved zinc finger protein, and the transcription factor TFIIIC have been shown to function in mammals. CTCF is involved in diverse nuclear activities, and recent studies suggest that the proteins with which it associates and the DNA sequences that it targets may underlie these various roles. Here we show that the Drosophila homolog of CTCF (dCTCF) aligns in the genome with other Drosophila insulator proteins such as Suppressor of Hairy wing [SU(HW)] and Boundary Element Associated Factor of 32 kDa (BEAF-32) at the borders of H3K27me3 domains, which are also enriched for associated insulator proteins and additional cofactors. RNAi depletion of dCTCF and combinatorial knockdown of gene expression for other Drosophila insulator proteins leads to a reduction in H3K27me3 levels within repressed domains, suggesting that insulators are important for the maintenance of appropriate repressive chromatin structure in Polycomb (Pc) domains. These results shed new insights into the roles of insulators in chromatin domain organization and support recent models suggesting that insulators underlie interactions important for Pc-mediated repression. We reveal an important relationship between dCTCF and other Drosophila insulator proteins and speculate that vertebrate CTCF may also align with other nuclear proteins to accomplish similar functions.

Numerical investigation & comparison of a tandem-bladed turbocharger centrifugal compressor stage with conventional design

NASA Astrophysics Data System (ADS)

Danish, Syed Noman; Qureshi, Shafiq Rehman; EL-Leathy, Abdelrahman; Khan, Salah Ud-Din; Umer, Usama; Ma, Chaochen

2014-12-01

Extensive numerical investigations of the performance and flow structure in an unshrouded tandem-bladed centrifugal compressor are presented in comparison to a conventional compressor. Stage characteristics are explored for various tip clearance levels, axial spacings and circumferential clockings. Conventional impeller was modified to tandem-bladed design with no modifications in backsweep angle, meridional gas passage and camber distributions in order to have a true comparison with conventional design. Performance degradation is observed for both the conventional and tandem designs with increase in tip clearance. Linear-equation models for correlating stage characteristics with tip clearance are proposed. Comparing two designs, it is clearly evident that the conventional design shows better performance at moderate flow rates. However; near choke flow, tandem design gives better results primarily because of the increase in throat area. Surge point flow rate also seems to drop for tandem compressor resulting in increased range of operation.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.

PubMed

Melters, Daniël P; Bradnam, Keith R; Young, Hugh A; Telis, Natalie; May, Michael R; Ruby, J Graham; Sebra, Robert; Peluso, Paul; Eid, John; Rank, David; Garcia, José Fernando; DeRisi, Joseph L; Smith, Timothy; Tobias, Christian; Ross-Ibarra, Jeffrey; Korf, Ian; Chan, Simon W L

2013-01-30

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

PubMed Central

2013-01-01

Background Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Results Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. Conclusions While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes. PMID:23363705

Tandem SUMO fusion vectors for improving soluble protein expression and purification.

PubMed

Guerrero, Fernando; Ciragan, Annika; Iwaï, Hideo

2015-12-01

Availability of highly purified proteins in quantity is crucial for detailed biochemical and structural investigations. Fusion tags are versatile tools to facilitate efficient protein purification and to improve soluble overexpression of proteins. Various purification and fusion tags have been widely used for overexpression in Escherichia coli. However, these tags might interfere with biological functions and/or structural investigations of the protein of interest. Therefore, an additional purification step to remove fusion tags by proteolytic digestion might be required. Here, we describe a set of new vectors in which yeast SUMO (SMT3) was used as the highly specific recognition sequence of ubiquitin-like protease 1, together with other commonly used solubility enhancing proteins, such as glutathione S-transferase, maltose binding protein, thioredoxin and trigger factor for optimizing soluble expression of protein of interest. This tandem SUMO (T-SUMO) fusion system was tested for soluble expression of the C-terminal domain of TonB from different organisms and for the antiviral protein scytovirin. Copyright © 2015 Elsevier Inc. All rights reserved.

Peptide Identification by Database Search of Mixture Tandem Mass Spectra*

PubMed Central

Wang, Jian; Bourne, Philip E.; Bandeira, Nuno

2011-01-01

In high-throughput proteomics the development of computational methods and novel experimental strategies often rely on each other. In certain areas, mass spectrometry methods for data acquisition are ahead of computational methods to interpret the resulting tandem mass spectra. Particularly, although there are numerous situations in which a mixture tandem mass spectrum can contain fragment ions from two or more peptides, nearly all database search tools still make the assumption that each tandem mass spectrum comes from one peptide. Common examples include mixture spectra from co-eluting peptides in complex samples, spectra generated from data-independent acquisition methods, and spectra from peptides with complex post-translational modifications. We propose a new database search tool (MixDB) that is able to identify mixture tandem mass spectra from more than one peptide. We show that peptides can be reliably identified with up to 95% accuracy from mixture spectra while considering only a 0.01% of all possible peptide pairs (four orders of magnitude speedup). Comparison with current database search methods indicates that our approach has better or comparable sensitivity and precision at identifying single-peptide spectra while simultaneously being able to identify 38% more peptides from mixture spectra at significantly higher precision. PMID:21862760

Tunable color parallel tandem organic light emitting devices with carbon nanotube and metallic sheet interlayers

NASA Astrophysics Data System (ADS)

Oliva, Jorge; Papadimitratos, Alexios; Desirena, Haggeo; De la Rosa, Elder; Zakhidov, Anvar A.

2015-11-01

Parallel tandem organic light emitting devices (OLEDs) were fabricated with transparent multiwall carbon nanotube sheets (MWCNT) and thin metal films (Al, Ag) as interlayers. In parallel monolithic tandem architecture, the MWCNT (or metallic films) interlayers are an active electrode which injects similar charges into subunits. In the case of parallel tandems with common anode (C.A.) of this study, holes are injected into top and bottom subunits from the common interlayer electrode; whereas in the configuration of common cathode (C.C.), electrons are injected into the top and bottom subunits. Both subunits of the tandem can thus be monolithically connected functionally in an active structure in which each subunit can be electrically addressed separately. Our tandem OLEDs have a polymer as emitter in the bottom subunit and a small molecule emitter in the top subunit. We also compared the performance of the parallel tandem with that of in series and the additional advantages of the parallel architecture over the in-series were: tunable chromaticity, lower voltage operation, and higher brightness. Finally, we demonstrate that processing of the MWCNT sheets as a common anode in parallel tandems is an easy and low cost process, since their integration as electrodes in OLEDs is achieved by simple dry lamination process.

Tandem betatron

DOEpatents

Keinigs, Rhonald K.

1992-01-01

Two betatrons are provided in tandem for alternately accelerating an electron beam to avoid the single flux swing limitation of conventional betatrons and to accelerate the electron beam to high energies. The electron beam is accelerated in a first betatron during a period of increasing magnetic flux. The eletron beam is extracted from the first betatron as a peak magnetic flux is reached and then injected into a second betatron at a time of minimum magnetic flux in the second betatron. The cycle may be repeated until the desired electron beam energy is obtained. In one embodiment, the second betatron is axially offset from the first betatron to provide for electron beam injection directly at the axial location of the beam orbit in the second betatron.

Tandem resonator reflectance modulator

DOEpatents

Fritz, I.J.; Wendt, J.R.

1994-09-06

A wide band optical modulator is grown on a substrate as tandem Fabry-Perot resonators including three mirrors spaced by two cavities. The absorption of one cavity is changed relative to the absorption of the other cavity by an applied electric field, to cause a change in total reflected light, as light reflecting from the outer mirrors is in phase and light reflecting from the inner mirror is out of phase with light from the outer mirrors. 8 figs.

LIM domain protein TES changes its conformational states in different cellular compartments.

PubMed

Zhong, Yingli; Zhu, Jiaolian; Wang, Yan; Zhou, Jianlin; Ren, Kaiqun; Ding, Xiaofeng; Zhang, Jian

2009-01-01

The human TESTIN (TES) is a putative tumor suppressor and localizes to the cytoplasm as a component of focal adhesions and cell contacts. TES contains a PET domain in the NH(2)-terminus and three tandem LIM domains in the COOH-terminus. It has been hypothesized that interactions between two termini of TES might lead to a "closed" conformational state of the protein. Here, we provide evidence for different conformational states of TES. We confirmed that the NH(2)-terminus of TES can interact with its third LIM domain in the COOH-terminus by GST pull-down assays. In addition, antisera against the full-length or two truncations of TES were prepared to examine the relationship between the conformation and cellular distribution of the protein. We found that these antisera recognize different regions of TES and showed that TES is co-localised with the marker protein B23 in nucleolus, in addition to its localization in endoplasmic reticulum (ER). Furthermore, our co-immunoprecipitation (co-IP) analysis of TES and B23 demonstrated their co-existence in the same complex. Taken together, our results suggest that TES has different conformational states in different cellular compartments, and a "closed" conformational state of TES may be involved in nucleolar localization.

Tandem Repeat Proteins Inspired By Squid Ring Teeth

NASA Astrophysics Data System (ADS)

Pena-Francesch, Abdon

Proteins are large biomolecules consisting of long chains of amino acids that hierarchically assemble into complex structures, and provide a variety of building blocks for biological materials. The repetition of structural building blocks is a natural evolutionary strategy for increasing the complexity and stability of protein structures. However, the relationship between amino acid sequence, structure, and material properties of protein systems remains unclear due to the lack of control over the protein sequence and the intricacies of the assembly process. In order to investigate the repetition of protein building blocks, a recently discovered protein from squids is examined as an ideal protein system. Squid ring teeth are predatory appendages located inside the suction cups that provide a strong grasp of prey, and are solely composed of a group of proteins with tandem repetition of building blocks. The objective of this thesis is the understanding of sequence, structure and property relationship in repetitive protein materials inspired in squid ring teeth for the first time. Specifically, this work focuses on squid-inspired structural proteins with tandem repeat units in their sequence (i.e., repetition of alternating building blocks) that are physically cross-linked via beta-sheet structures. The research work presented here tests the hypothesis that, in these systems, increasing the number of building blocks in the polypeptide chain decreases the protein network defects and improves the material properties. Hence, the sequence, nanostructure, and properties (thermal, mechanical, and conducting) of tandem repeat squid-inspired protein materials are examined. Spectroscopic structural analysis, advanced materials characterization, and entropic elasticity theory are combined to elucidate the structure and material properties of these repetitive proteins. This approach is applied not only to native squid proteins but also to squid-inspired synthetic polypeptides

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

PubMed Central

Van Bortle, Kevin; Ramos, Edward; Takenaka, Naomi; Yang, Jingping; Wahi, Jessica E.; Corces, Victor G.

2012-01-01

Several multiprotein DNA complexes capable of insulator activity have been identified in Drosophila melanogaster, yet only CTCF, a highly conserved zinc finger protein, and the transcription factor TFIIIC have been shown to function in mammals. CTCF is involved in diverse nuclear activities, and recent studies suggest that the proteins with which it associates and the DNA sequences that it targets may underlie these various roles. Here we show that the Drosophila homolog of CTCF (dCTCF) aligns in the genome with other Drosophila insulator proteins such as Suppressor of Hairy wing [SU(HW)] and Boundary Element Associated Factor of 32 kDa (BEAF-32) at the borders of H3K27me3 domains, which are also enriched for associated insulator proteins and additional cofactors. RNAi depletion of dCTCF and combinatorial knockdown of gene expression for other Drosophila insulator proteins leads to a reduction in H3K27me3 levels within repressed domains, suggesting that insulators are important for the maintenance of appropriate repressive chromatin structure in Polycomb (Pc) domains. These results shed new insights into the roles of insulators in chromatin domain organization and support recent models suggesting that insulators underlie interactions important for Pc-mediated repression. We reveal an important relationship between dCTCF and other Drosophila insulator proteins and speculate that vertebrate CTCF may also align with other nuclear proteins to accomplish similar functions. PMID:22722341

Better load-weight distribution is needed for tandem-axle logging trucks

Treesearch

John E. Baumgras

1976-01-01

To determine the GVW and axle weights of tandem-axle logging trucks hauling into two West Virginia sawmills, 543 truckloads of hardwood sawlogs were weighed. The results showed that less than 2 percent of the truckloads exceeded the 48,000 pound GVW limit. While 58 percent of the truckloads exceeded the 32,000 pound tandem-axle weight limit, the front-axle weights...

Flexible and fragmentable tandem photosensitive nanocrystal skins

NASA Astrophysics Data System (ADS)

Akhavan, S.; Uran, C.; Bozok, B.; Gungor, K.; Kelestemur, Y.; Lesnyak, V.; Gaponik, N.; Eychmüller, A.; Demir, H. V.

2016-02-01

We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of single monolayers of colloidal water-soluble CdTe and CdHgTe nanocrystals (NCs) in adjacent junctions on a Kapton polymer tape. Owing to the usage of a single NC layer in each junction, noise generation was significantly reduced while keeping the resulting PNS films considerably transparent. In each junction, photogenerated excitons are dissociated at the interface of the semi-transparent Al electrode and the NC layer, with holes migrating to the contact electrode and electrons trapped in the NCs. As a result, the tandem PNSs lead to an open-circuit photovoltage buildup equal to the sum of those of the two single junctions, exhibiting a total voltage buildup of 128.4 mV at an excitation intensity of 75.8 μW cm-2 at 350 nm. Furthermore, we showed that these flexible PNSs could be bent over 3.5 mm radius of curvature and cut out in arbitrary shapes without damaging the operation of individual parts and without introducing any significant loss in the total sensitivity. These findings indicate that the NC skins are promising as building blocks to make low-cost, flexible, large-area UV/visible sensing platforms with highly efficient full-spectrum conversion.We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of

A Silicon–Singlet Fission Tandem Solar Cell Exceeding 100% External Quantum Efficiency with High Spectral Stability

PubMed Central

2017-01-01

After 60 years of research, silicon solar cell efficiency saturated close to the theoretical limit, and radically new approaches are needed to further improve the efficiency. The use of tandem systems raises this theoretical power conversion efficiency limit from 34% to 45%. We present the advantageous spectral stability of using voltage-matched tandem solar cells with respect to their traditional series-connected counterparts and experimentally demonstrate how singlet fission can be used to produce simple voltage-matched tandems. Our singlet fission silicon–pentacene tandem solar cell shows efficient photocurrent addition. This allows the tandem system to benefit from carrier multiplication and to produce an external quantum efficiency exceeding 100% at the main absorption peak of pentacene. PMID:28261671

The structure of Zika virus NS5 reveals a conserved domain conformation

DOE PAGES

Wang, Boxiao; Tan, Xiao -Feng; Thurmond, Stephanie; ...

2017-03-27

The recent outbreak of Zika virus (ZIKV) has imposed a serious threat to public health. Here we report the crystal structure of the ZIKV NS5 protein in complex with S-adenosyl-L-homocysteine, in which the tandem methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains stack into one of the two alternative conformations of flavivirus NS5 proteins. In conclusion, the activity of this NS5 protein is verified through a de novo RdRp assay on a subgenomic ZIKV RNA template. Importantly, our structural analysis leads to the identification of a potential drug-binding site of ZIKV NS5, which might facilitate the development of novel antiviralsmore » for ZIKV.« less

Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling.

PubMed

D'Cruz, Akshay A; Kershaw, Nadia J; Chiang, Jessica J; Wang, May K; Nicola, Nicos A; Babon, Jeffrey J; Gack, Michaela U; Nicholson, Sandra E

2013-12-01

TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp(488) and Trp(621)) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs.

Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling

PubMed Central

D'Cruz, Akshay A.; Kershaw, Nadia J.; Chiang, Jessica J.; Wang, May K.; Nicola, Nicos A.; Babon, Jeffrey J.; Gack, Michaela U.; Nicholson, Sandra E.

2014-01-01

TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp488 and Trp621) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs. PMID:24015671

C1q/TNF-related Protein 4 (CTRP4) Is a Unique Secreted Protein with Two Tandem C1q Domains That Functions in the Hypothalamus to Modulate Food Intake and Body Weight*

PubMed Central

Byerly, Mardi S.; Petersen, Pia S.; Ramamurthy, Santosh; Seldin, Marcus M.; Lei, Xia; Provost, Elayne; Wei, Zhikui; Ronnett, Gabriele V.; Wong, G. William

2014-01-01

CTRP4 is a unique member of the C1q family, possessing two tandem globular C1q domains. Its physiological function is poorly defined. Here, we show that CTRP4 is an evolutionarily conserved, ∼34-kDa secretory protein expressed in the brain. In human, mouse, and zebrafish brain, CTRP4 expression begins early in development and is widespread in the central nervous system. Neurons, but not astrocytes, express and secrete CTRP4, and secreted proteins form higher-order oligomeric complexes. CTRP4 is also produced by peripheral tissues and circulates in blood. Its serum levels are increased in leptin-deficient obese (ob/ob) mice. Functional studies suggest that CTRP4 acts centrally to modulate energy metabolism. Refeeding following an overnight fast induced the expression of CTRP4 in the hypothalamus. Central administration of recombinant protein suppressed food intake and altered the whole-body energy balance in both chow-fed and high-fat diet-fed mice. Suppression of food intake by CTRP4 is correlated with a decreased expression of orexigenic neuropeptide (Npy and Agrp) genes in the hypothalamus. These results establish CTRP4 as a novel nutrient-responsive central regulator of food intake and energy balance. PMID:24366864

Functional Characterisation of the WW Minimal Domain for Delivering Therapeutic Proteins by Adenovirus Dodecahedron

PubMed Central

Villegas-Méndez, Ana; Fender, Pascal; Garin, Marina I.; Rothe, Romy; Liguori, Lavinia; Marques, Bruno; Lenormand, Jean-Luc

2012-01-01

Protein transduction offers a great therapeutic potential by efficient delivery of biologically active cargo into cells. The Adenovirus Dd (Dodecahedron) has recently been shown to deliver proteins fused to the tandem WW2-3-4 structural domains from the E3 ubiquitin ligase Nedd4. In this study, we conclusively show that Dd is able to efficiently deliver cargo inside living cells, which mainly localize in fast moving endocytic vesicles, supporting active transport along the cytoskeleton. We further improve this delivery system by expressing a panel of 13 WW-GFP mutant forms to characterize their binding properties towards Dd. We identified the domain WW3 and its mutant form WW3_10_13 to be sufficient for optimal binding to Dd. We greatly minimise the interacting WW modules from 20 to 6 kDa without compromising its efficient delivery by Dd. Using these minimal WW domains fused to the tumor suppressor p53 protein, we show efficient cellular uptake and distribution into cancer cells, leading to specific induction of apoptosis in these cells. Taken together, these findings represent a step further towards the development of a Dd-based delivery system for future therapeutic application. PMID:23028993

High Fractional Occupancy of a Tandem Maf Recognition Element and Its Role in Long-Range β-Globin Gene Regulation

PubMed Central

Stees, Jared R.; Hossain, Mir A.; Sunose, Tomoki; Kudo, Yasushi; Pardo, Carolina E.; Nabilsi, Nancy H.; Darst, Russell P.; Poudyal, Rosha; Igarashi, Kazuhiko; Kladde, Michael P.

2015-01-01

Enhancers and promoters assemble protein complexes that ultimately regulate the recruitment and activity of RNA polymerases. Previous work has shown that at least some enhancers form stable protein complexes, leading to the formation of enhanceosomes. We analyzed protein-DNA interactions in the murine β-globin gene locus using the methyltransferase accessibility protocol for individual templates (MAPit). The data show that a tandem Maf recognition element (MARE) in locus control region (LCR) hypersensitive site 2 (HS2) reveals a remarkably high degree of occupancy during differentiation of mouse erythroleukemia cells. Most of the other transcription factor binding sites in LCR HS2 or in the adult β-globin gene promoter regions exhibit low fractional occupancy, suggesting highly dynamic protein-DNA interactions. Targeting of an artificial zinc finger DNA-binding domain (ZF-DBD) to the HS2 tandem MARE caused a reduction in the association of MARE-binding proteins and transcription complexes at LCR HS2 and the adult βmajor-globin gene promoter but did not affect expression of the βminor-globin gene. The data demonstrate that a stable MARE-associated footprint in LCR HS2 is important for the recruitment of transcription complexes to the adult βmajor-globin gene promoter during erythroid cell differentiation. PMID:26503787

A tandem mirror plasma source for hybrid plume plasma studies

NASA Technical Reports Server (NTRS)

Yang, T. F.; Chang, F. R.; Miller, R. H.; Wenzel, K. W.; Krueger, W. A.

1985-01-01

A tandem mirror device to be considered as a hot plasma source for the hybrid plume rocket concept is discussed. The hot plamsa from this device is injected into an exhaust duct, which will interact with an annular hypersonic layer of neutral gas. The device can be used to study the dynamics of the hybrid plume, and to verify the numerical predictions obtained with computer codes. The basic system design is also geared towards low weight and compactness, and high power density at the exhaust. The basic structure of the device consists of four major subsystems: (1) an electric power supply; (2) a low temperature, high density plasma gun, such as a stream gun, an MPD source or gas cell; (3) a power booster in the form of a tandem mirror machine; and (4) an exhaust nozzle arrangement. The configuration of the tandem mirror section is shown.

Impeller tandem blade study with grid embedding for local grid refinement

NASA Technical Reports Server (NTRS)

Bache, George

1992-01-01

Flow non-uniformity at the discharge of high power density impellers can result in significant unsteady interactions between impeller blades and downstream diffuser vanes. These interactions result in degradation of both performance and pump reliability. The MSFC Pump Technology Team has recognized the importance of resolving this problem and has thus initiated the development and testing of a high head coefficient impeller. One of the primary goals of this program is to improve impeller performance and discharge flow uniformity. The objective of the present work is complimentary. Flow uniformity and performance gains were sought through the application of a tandem blade arrangement. The approach adopted was to numerically establish flow characteristics at the impeller discharge for the baseline MSFC impeller and then parametrically evaluate tandem blade configurations. A tandem design was sought that improves both impeller performance and discharge uniformity. The Navier-Stokes solver AEROVISC was used to conduct the study. Grid embedding is used to resolve local gradients while attempting to minimize model size. Initial results indicate that significant gains in flow uniformity can be achieved through the tandem blade concept and that blade clocking rather than slot location is the primary driver for flow uniformity.

Progress in Tandem Solar Cells Based on Hybrid Organic-Inorganic Perovskites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Bo; Zheng, Xiaopeng; Bai, Yang

Owing to their high efficiency, low-cost solution-processability, and tunable bandgap, perovskite solar cells (PSCs) made of hybrid organic-inorganic perovskite (HOIP) thin films are promising top-cell candidates for integration with bottom-cells based on Si or other low-bandgap solar-cell materials to boost the power conversion efficiency (PCE) beyond the Shockley-Quiesser (S-Q) limit. In this review, recent progress in such tandem solar cells based on the emerging PSCs is summarized and reviewed critically. Notable achievements for different tandem solar cell configurations including mechanically-stacked, optical coupling, and monolithically-integrated with PSCs as top-cells are described in detail. Highly-efficient semitransparent PSC top-cells with high transmittance inmore » near-infrared (NIR) region are critical for tandem solar cells. Different types of transparent electrodes with high transmittance and low sheet-resistance for PSCs are reviewed, which presents a grand challenge for PSCs. The strategies to obtain wide-bandgap PSCs with good photo-stability are discussed. In conclusion, the PCE reduction due to reflection loss, parasitic absorption, electrical loss, and current mismatch are analyzed to provide better understanding of the performance of PSC-based tandem solar cells.« less

Progress in Tandem Solar Cells Based on Hybrid Organic-Inorganic Perovskites

DOE PAGES

Chen, Bo; Zheng, Xiaopeng; Bai, Yang; ...

2017-03-06

Owing to their high efficiency, low-cost solution-processability, and tunable bandgap, perovskite solar cells (PSCs) made of hybrid organic-inorganic perovskite (HOIP) thin films are promising top-cell candidates for integration with bottom-cells based on Si or other low-bandgap solar-cell materials to boost the power conversion efficiency (PCE) beyond the Shockley-Quiesser (S-Q) limit. In this review, recent progress in such tandem solar cells based on the emerging PSCs is summarized and reviewed critically. Notable achievements for different tandem solar cell configurations including mechanically-stacked, optical coupling, and monolithically-integrated with PSCs as top-cells are described in detail. Highly-efficient semitransparent PSC top-cells with high transmittance inmore » near-infrared (NIR) region are critical for tandem solar cells. Different types of transparent electrodes with high transmittance and low sheet-resistance for PSCs are reviewed, which presents a grand challenge for PSCs. The strategies to obtain wide-bandgap PSCs with good photo-stability are discussed. In conclusion, the PCE reduction due to reflection loss, parasitic absorption, electrical loss, and current mismatch are analyzed to provide better understanding of the performance of PSC-based tandem solar cells.« less

Simulation of Two Dimensional Electrophoresis and Tandem Mass Spectrometry for Teaching Proteomics

ERIC Educational Resources Information Center

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

An approach for configuring space photovoltaic tandem arrays based on cell layer performance

NASA Technical Reports Server (NTRS)

Flora, C. S.; Dillard, P. A.

1991-01-01

Meeting solar array performance goals of 300 W/Kg requires use of solar cells with orbital efficiencies greater than 20 percent. Only multijunction cells and cell layers operating in tandem produce this required efficiency. An approach for defining solar array design concepts that use tandem cell layers involve the following: transforming cell layer performance at standard test conditions to on-orbit performance; optimizing circuit configuration with tandem cell layers; evaluating circuit sensitivity to cell current mismatch; developing array electrical design around selected circuit; and predicting array orbital performance including seasonal variations.

Modeling the Performance Limitations and Prospects of Perovskite/Si Tandem Solar Cells under Realistic Operating Conditions

PubMed Central

2017-01-01

Perovskite/Si tandem solar cells have the potential to considerably out-perform conventional solar cells. Under standard test conditions, perovskite/Si tandem solar cells already outperform the Si single junction. Under realistic conditions, however, as we show, tandem solar cells made from current record cells are hardly more efficient than the Si cell alone. We model the performance of realistic perovskite/Si tandem solar cells under real-world climate conditions, by incorporating parasitic cell resistances, nonradiative recombination, and optical losses into the detailed-balance limit. We show quantitatively that when optimizing these parameters in the perovskite top cell, perovskite/Si tandem solar cells could reach efficiencies above 38% under realistic conditions, even while leaving the Si cell untouched. Despite the rapid efficiency increase of perovskite solar cells, our results emphasize the need for further material development, careful device design, and light management strategies, all necessary for highly efficient perovskite/Si tandem solar cells. PMID:28920081

Modeling the Performance Limitations and Prospects of Perovskite/Si Tandem Solar Cells under Realistic Operating Conditions.

PubMed

Futscher, Moritz H; Ehrler, Bruno

2017-09-08

Perovskite/Si tandem solar cells have the potential to considerably out-perform conventional solar cells. Under standard test conditions, perovskite/Si tandem solar cells already outperform the Si single junction. Under realistic conditions, however, as we show, tandem solar cells made from current record cells are hardly more efficient than the Si cell alone. We model the performance of realistic perovskite/Si tandem solar cells under real-world climate conditions, by incorporating parasitic cell resistances, nonradiative recombination, and optical losses into the detailed-balance limit. We show quantitatively that when optimizing these parameters in the perovskite top cell, perovskite/Si tandem solar cells could reach efficiencies above 38% under realistic conditions, even while leaving the Si cell untouched. Despite the rapid efficiency increase of perovskite solar cells, our results emphasize the need for further material development, careful device design, and light management strategies, all necessary for highly efficient perovskite/Si tandem solar cells.

Monolithic tandem solar cell

DOEpatents

Wanlass, M.W.

1994-06-21

A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, (c) a second photoactive subcell on the first subcell; and (d) an optically transparent prismatic cover layer over the second subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched. 9 figs.

Monolithic tandem solar cell

DOEpatents

Wanlass, Mark W.

1994-01-01

A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, (c) a second photoactive subcell on the first subcell; and (d) an optically transparent prismatic cover layer over the second subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched.

47 CFR 69.713 - Common line, traffic-sensitive, and tandem-switched transport services.

Code of Federal Regulations, 2010 CFR

2010-10-01

...-switched transport services. 69.713 Section 69.713 Telecommunication FEDERAL COMMUNICATIONS COMMISSION..., traffic-sensitive, and tandem-switched transport services. (a) Scope. This paragraph governs requests for...)(2) of this chapter. (3) The traffic-sensitive components of tandem-switched transport services, as...

47 CFR 69.713 - Common line, traffic-sensitive, and tandem-switched transport services.

Code of Federal Regulations, 2011 CFR

2011-10-01

...-switched transport services. 69.713 Section 69.713 Telecommunication FEDERAL COMMUNICATIONS COMMISSION..., traffic-sensitive, and tandem-switched transport services. (a) Scope. This paragraph governs requests for...)(2) of this chapter. (3) The traffic-sensitive components of tandem-switched transport services, as...

Structure of an Antibody in Complex with Its Mucin Domain Linear Epitope That Is Protective against Ebola Virus

PubMed Central

Olal, Daniel; Kuehne, Ana I.; Bale, Shridhar; Halfmann, Peter; Hashiguchi, Takao; Fusco, Marnie L.; Lee, Jeffrey E.; King, Liam B.; Kawaoka, Yoshihiro; Dye, John M.

2012-01-01

Antibody 14G7 is protective against lethal Ebola virus challenge and recognizes a distinct linear epitope in the prominent mucin-like domain of the Ebola virus glycoprotein GP. The structure of 14G7 in complex with its linear peptide epitope has now been determined to 2.8 Å. The structure shows that this GP sequence forms a tandem β-hairpin structure that binds deeply into a cleft in the antibody-combining site. A key threonine at the apex of one turn is critical for antibody interaction and is conserved among all Ebola viruses. This work provides further insight into the mechanism of protection by antibodies that target the protruding, highly accessible mucin-like domain of Ebola virus and the structural framework for understanding and characterizing candidate immunotherapeutics. PMID:22171276

Structure of an antibody in complex with its mucin domain linear epitope that is protective against Ebola virus.

PubMed

Olal, Daniel; Kuehne, Ana I; Bale, Shridhar; Halfmann, Peter; Hashiguchi, Takao; Fusco, Marnie L; Lee, Jeffrey E; King, Liam B; Kawaoka, Yoshihiro; Dye, John M; Saphire, Erica Ollmann

2012-03-01

Antibody 14G7 is protective against lethal Ebola virus challenge and recognizes a distinct linear epitope in the prominent mucin-like domain of the Ebola virus glycoprotein GP. The structure of 14G7 in complex with its linear peptide epitope has now been determined to 2.8 Å. The structure shows that this GP sequence forms a tandem β-hairpin structure that binds deeply into a cleft in the antibody-combining site. A key threonine at the apex of one turn is critical for antibody interaction and is conserved among all Ebola viruses. This work provides further insight into the mechanism of protection by antibodies that target the protruding, highly accessible mucin-like domain of Ebola virus and the structural framework for understanding and characterizing candidate immunotherapeutics.

Characterisation of single domain ATP-binding cassette protien homologues of Theileria parva.

PubMed

Kibe, M K; Macklin, M; Gobright, E; Bishop, R; Urakawa, T; ole-MoiYoi, O K

2001-09-01

Two distinct genes encoding single domain, ATP-binding cassette transport protein homologues of Theileria parva were cloned and sequenced. Neither of the genes is tandemly duplicated. One gene, TpABC1, encodes a predicted protein of 593 amino acids with an N-terminal hydrophobic domain containing six potential membrane-spanning segments. A single discontinuous ATP-binding element was located in the C-terminal region of TpABC1. The second gene, TpABC2, also contains a single C-terminal ATP-binding motif. Copies of TpABC2 were present at four loci in the T. parva genome on three different chromosomes. TpABC1 exhibited allelic polymorphism between stocks of the parasite. Comparison of cDNA and genomic sequences revealed that TpABC1 contained seven short introns, between 29 and 84 bp in length. The full-length TpABC1 protein was expressed in insect cells using the baculovirus system. Application of antibodies raised against the recombinant antigen to western blots of T. parva piroplasm lysates detected an 85 kDa protein in this life-cycle stage.

A Comparative Analysis between GaN-Based Current and Voltage Mode Class-D and E PAs for Communications

DTIC Science & Technology

2017-03-01

power level (5-10W) transmitters. The designs are analyzed and compared with respect to non-idealities such as bondwire effects and input signal duty...Hence, sub-optimum class- E/inverse class-E designs were implemented in this work and compared with respect to reduced duty cycle performance...inverse class E PA achieves 61.5% efficiency for medium power levels (37.7dBm) at 880MHz. The three designed PAs have been compared with respect to

Studies of the Lateral-Directional Flying Qualities of a Tandem Helicopter in Forward Flight

NASA Technical Reports Server (NTRS)

Amer, Kenneth B; Tapscott, Robert J

1954-01-01

An investigation of the lateral-directional flying qualities of a tandem-rotor helicopter in forward flight was undertaken to determine desirable goals for helicopter lateral-directional flying qualities and possible methods of achieving these goals in the tandem-rotor helicopter. Comparison between directional stability as measured in flight and rotor-off model tests in a wind tunnel shows qualitative agreement and, hence, indicates such wind-tunnel test, despite the absence of the rotors, to be one effective method of studying means of improving the directional stability of the tandem helicopter. Flight-test measurements of turns and oscillations, in conjunction with analytical studies, suggest possible practical methods of achieving the goals of satisfactory turn and oscillatory characteristics in the tandem helicopter.

Electrolytes Based on TEMPO–Co Tandem Redox Systems Outperform Single Redox Systems in Dye‐sensitized Solar Cells

PubMed Central

Cong, Jiayan; Hao, Yan; Boschloo, Gerrit

2014-01-01

Abstract A new TEMPO–Co tandem redox system with TEMPO and Co(bpy)3 2+/3+ has been investigated for the use in dye‐sensitized solar cells (DSSCs). A large open‐circuit voltage (V OC) increase, from 862 mV to 965 mV, was observed in the tandem redox system, while the short‐circuit current density (J SC) was maintained. The conversion efficiency was observed to increase from 7.1 % for cells containing the single Co(bpy)3 2+/3+ redox couple, to 8.4 % for cells containing the TEMPO–Co tandem redox system. The reason for the increase in V OC and overall efficiency is ascribed to the involvement of partial regeneration of the sensitizing dye molecules by TEMPO. This assumption can be verified through the observed much faster regeneration dynamics exhibited in the presence of the tandem system. Using the tandem redox system, the faster recombination problem of the single TEMPO redox couple is resolved and the mass‐transport of the metal‐complex‐based electrolyte is also improved. This TEMPO–Co tandem system is so far the most effienct tandem redox electrolyte reported not involving iodine. The current results show a promising future for tandem system as replacements for single redox systems in electrolytes for DSSCs. PMID:25504818

Proteolytic dissection of Zab, the Z-DNA-binding domain of human ADAR1

NASA Technical Reports Server (NTRS)

Schwartz, T.; Lowenhaupt, K.; Kim, Y. G.; Li, L.; Brown, B. A. 2nd; Herbert, A.; Rich, A.

1999-01-01

Zalpha is a peptide motif that binds to Z-DNA with high affinity. This motif binds to alternating dC-dG sequences stabilized in the Z-conformation by means of bromination or supercoiling, but not to B-DNA. Zalpha is part of the N-terminal region of double-stranded RNA adenosine deaminase (ADAR1), a candidate enzyme for nuclear pre-mRNA editing in mammals. Zalpha is conserved in ADAR1 from many species; in each case, there is a second similar motif, Zbeta, separated from Zalpha by a more divergent linker. To investigate the structure-function relationship of Zalpha, its domain structure was studied by limited proteolysis. Proteolytic profiles indicated that Zalpha is part of a domain, Zab, of 229 amino acids (residues 133-361 in human ADAR1). This domain contains both Zalpha and Zbeta as well as a tandem repeat of a 49-amino acid linker module. Prolonged proteolysis revealed a minimal core domain of 77 amino acids (positions 133-209), containing only Zalpha, which is sufficient to bind left-handed Z-DNA; however, the substrate binding is strikingly different from that of Zab. The second motif, Zbeta, retains its structural integrity only in the context of Zab and does not bind Z-DNA as a separate entity. These results suggest that Zalpha and Zbeta act as a single bipartite domain. In the presence of substrate DNA, Zab becomes more resistant to proteases, suggesting that it adopts a more rigid structure when bound to its substrate, possibly with conformational changes in parts of the protein.

Medical expertise, existential suffering and ending life.

PubMed

Varelius, Jukka

2014-02-01

In this article, I assess the position that voluntary euthanasia (VE) and physician-assisted suicide (PAS) ought not to be accepted in the cases of persons who suffer existentially but who have no medical condition, because existential questions do not fall within the domain of physicians' professional expertise. I maintain that VE and PAS based on suffering arising from medical conditions involves existential issues relevantly similar to those confronted in connection with existential suffering. On that basis I conclude that if VE and PAS based on suffering arising from medical conditions is taken to fall within the domain of medical expertise, it is not consistent to use the view that physicians' professional expertise does not extend to existential questions as a reason for denying requests for VE and PAS from persons who suffer existentially but have no medical condition.

Structure of the mouse galectin-4 N-terminal carbohydrate-recognition domain reveals the mechanism of oligosaccharide recognition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krejciríková, Veronika; Pachl, Petr; Fábry, Milan

2011-11-18

Galectin-4, a member of the tandem-repeat subfamily of galectins, participates in cell-membrane interactions and plays an important role in cell adhesion and modulation of immunity and malignity. The oligosaccharide specificity of the mouse galectin-4 carbohydrate-recognition domains (CRDs) has been reported previously. In this work, the structure and binding properties of the N-terminal domain CRD1 were further investigated and the crystal structure of CRD1 in complex with lactose was determined at 2.1 {angstrom} resolution. The lactose-binding affinity was characterized by fluorescence measurements and two lactose-binding sites were identified: a high-affinity site with a K{sub d} value in the micromolar range (K{submore » d1} = 600 {+-} 70 {mu}M) and a low-affinity site with K{sub d2} = 28 {+-} 10 mM.« less

Monolithic tandem solar cell

DOEpatents

Wanlass, Mark W.

1991-01-01

A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, and (c) a second photoactive subcell on the first subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched. The solar cell can be provided as a two-terminal device or a three-terminal device.

Highly loaded multi-stage fan drive turbine-tandem blade configuration design

NASA Technical Reports Server (NTRS)

Evans, D. C.; Wolfmeyer, G. W.

1972-01-01

The results of the tandem blade configuration design study are reported. The three stage constant-inside-diameter turbine utilizes tandem blading in the stage two and stage three vanes and in the stage three blades. All other bladerows use plain blades. Blading detailed design is discussed, and design data are summarized. Steady-state stresses and vibratory behavior are discussed, and the results of the mechanical design analysis are presented.

Waveform Developer's Guide for the Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio System (STRS) Radio

NASA Technical Reports Server (NTRS)

Shalkhauser, Mary Jo W.; Roche, Rigoberto

2017-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework for software defined radios (SDRs) to abstract the application software from the radio platform hardware. The STRS standard aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. To promote the use of the STRS architecture for future NASA advanced exploration missions, NASA Glenn Research Center (GRC) developed an STRS-compliant SDR on a radio platform used by the Advance Exploration System program at the Johnson Space Center (JSC) in their Integrated Power, Avionics, and Software (iPAS) laboratory. The iPAS STRS Radio was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RIACS) platform, currently being used for radio development at JSC. The platform consists of a Xilinx(Trademark) ML605 Virtex(Trademark)-6 FPGA board, an Analog Devices FMCOMMS1-EBZ RF transceiver board, and an Embedded PC (Axiomtek(Trademark) eBox 620-110-FL) running the Ubuntu 12.4 operating system. The result of this development is a very low cost STRS compliant platform that can be used for waveform developments for multiple applications. The purpose of this document is to describe how to develop a new waveform using the RIACS platform and the Very High Speed Integrated Circuits (VHSIC) Hardware Description Language (VHDL) FPGA wrapper code and the STRS implementation on the Axiomtek processor.

Hardware Interface Description for the Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio Ssystem (STRS) Radio

NASA Technical Reports Server (NTRS)

Shalkhauser, Mary Jo W.; Roche, Rigoberto

2017-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework for software defined radios (SDRs) to abstract the application software from the radio platform hardware. The STRS standard aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. To promote the use of the STRS architecture for future NASA advanced exploration missions, NASA Glenn Research Center (GRC) developed an STRS-compliant SDR on a radio platform used by the Advance Exploration System program at the Johnson Space Center (JSC) in their Integrated Power, Avionics, and Software (iPAS) laboratory. The iPAS STRS Radio was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RIACS) platform, currently being used for radio development at JSC. The platform consists of a Xilinx ML605 Virtex-6 FPGA board, an Analog Devices FMCOMMS1-EBZ RF transceiver board, and an Embedded PC (Axiomtek eBox 620-110-FL) running the Ubuntu 12.4 operating system. Figure 1 shows the RIACS platform hardware. The result of this development is a very low cost STRS compliant platform that can be used for waveform developments for multiple applications.The purpose of this document is to describe how to develop a new waveform using the RIACS platform and the Very High Speed Integrated Circuits (VHSIC) Hardware Description Language (VHDL) FPGA wrapper code and the STRS implementation on the Axiomtek processor.

Mammalian Per-Arnt-Sim proteins in environmental adaptation.

PubMed

McIntosh, Brian E; Hogenesch, John B; Bradfield, Christopher A

2010-01-01

The Per-Arnt-Sim (PAS) domain is conserved across the kingdoms of life and found in an ever-growing list of proteins. This domain can bind to and sense endogenous or xenobiotic small molecules such as molecular oxygen, cellular metabolites, or polyaromatic hydrocarbons. Members of this family are often found in pathways that regulate responses to environmental change; in mammals these include the hypoxia, circadian, and dioxin response pathways. These pathways function in development and throughout life to regulate cellular, organ, and whole-organism adaptive responses. Remarkably, in the case of the clock, this adaptation includes anticipation of environmental change. In this review, we summarize the roles of PAS domain-containing proteins in mammals. We provide structural evidence that functionally classifies both known and unknown biological roles. Finally, we discuss the role of PAS proteins in anticipation of and adaptation to environmental change.

Low driving voltage simplified tandem organic light-emitting devices by using exciplex-forming hosts

NASA Astrophysics Data System (ADS)

Zhou, Dong-Ying; Cui, Lin-Song; Zhang, Ying-Jie; Liao, Liang-Sheng; Aziz, Hany

2014-10-01

Tandem organic light-emitting devices (OLEDs), i.e., OLEDs containing multiple electroluminescence (EL) units that are vertically stacked, are attracting significant interest because of their ability to realize high current efficiency and long operational lifetime. However, stacking multiple EL units in tandem OLEDs increases driving voltage and complicates fabrication process relative to their standard single unit counterparts. In this paper, we demonstrate low driving voltage tandem OLEDs via utilizing exciplex-forming hosts in the EL units instead of conventional host materials. The use of exciplex-forming hosts reduces the charge injection barriers and the trapping of charges on guest molecules, resulting in the lower driving voltage. The use of exciplex-forming hosts also allows using fewer layers, hence simpler EL configuration which is beneficial for reducing the fabrication complexity of tandem OLEDs.

Mechanical design of the first proximal Ig domain of human cardiac titin revealed by single molecule force spectroscopy.

PubMed

Li, Hongbin; Fernandez, Julio M

2003-11-14

The elastic I-band part of muscle protein titin contains two tandem immunoglobulin (Ig) domain regions of distinct mechanical properties. Until recently, the only known structure was that of the I27 module of the distal region, whose mechanical properties have been reported in detail. Recently, the structure of the first proximal domain, I1, has been resolved at 2.1A. In addition to the characteristic beta-sandwich structure of all titin Ig domains, the crystal structure of I1 showed an internal disulfide bridge that was proposed to modulate its mechanical extensibility in vivo. Here, we use single molecule force spectroscopy and protein engineering to examine the mechanical architecture of this domain. In contrast to the predictions made from the X-ray crystal structure, we find that the formation of a disulfide bridge in I1 is a relatively rare event in solution, even under oxidative conditions. Furthermore, our studies of the mechanical stability of I1 modules engineered with point mutations reveal significant differences between the mechanical unfolding of the I1 and I27 modules. Our study illustrates the varying mechanical architectures of the titin Ig modules.

Portable Tandem Mass Spectrometer Analyzer

DTIC Science & Technology

1991-07-01

The planned instrument was to be small enough to be portable in small vehicles and was to be able to use either an atmospheric pressure ion source or a...conventional electron impact/chemical ionization ion source. In order to accomplish these developments an atmospheric pressure ionization source was...developed for a compact, commercially available tandem quadrupole mass spectrometer. This ion source could be readily exchanged with the conventional

Fragile X Mental Retardation Syndrome: Structure of the KH1-KH2 Domains of Fragile X Mental Retardation Protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valverde,R.; Poznyakova, I.; Kajander, T.

Fragile X syndrome is the most common form of inherited mental retardation in humans, with an estimated prevalence of about 1 in 4000 males. Although several observations indicate that the absence of functional Fragile X Mental Retardation Protein (FMRP) is the underlying basis of Fragile X syndrome, the structure and function of FMRP are currently unknown. Here, we present an X-ray crystal structure of the tandem KH domains of human FMRP, which reveals the relative orientation of the KH1 and KH2 domains and the location of residue Ile304, whose mutation to Asn is associated with a particularly severe incidence ofmore » Fragile X syndrome. We show that the Ile304Asn mutation both perturbs the structure and destabilizes the protein.« less

Interpreting the Need for Initial Support to Perform Tandem Stance Tests of Balance

PubMed Central

Brach, Jennifer S.; Perera, Subashan; Wert, David M.; VanSwearingen, Jessie M.; Studenski, Stephanie A.

2012-01-01

Background Geriatric rehabilitation reimbursement increasingly requires documented deficits on standardized measures. Tandem stance performance can characterize balance, but protocols are not standardized. Objective The purpose of this study was to explore the impact of: (1) initial support to stabilize in position and (2) maximum hold time on tandem stance tests of balance in older adults. Design A cross-sectional secondary analysis of observational cohort data was conducted. Methods One hundred seventeen community-dwelling older adults (71% female, 12% black) were assigned to 1 of 3 groups based on the need for initial support to perform tandem stance: (1) unable even with support, (2) able only with support, and (3) able without support. The able without support group was further stratified on hold time in seconds: (1) <10 (low), (2) 10 to 29, (medium), and (3) 30 (high). Groups were compared on primary outcomes (gait speed, Timed “Up & Go” Test performance, and balance confidence) using analysis of variance. Results Twelve participants were unable to perform tandem stance, 14 performed tandem stance only with support, and 91 performed tandem stance without support. Compared with the able without support group, the able with support group had statistically or clinically worse performance and balance confidence. No significant differences were found between the able with support group and the unable even with support group on these same measures. Extending the hold time to 30 seconds in a protocol without initial support eliminated ceiling effects for 16% of the study sample. Limitations Small comparison groups, use of a secondary analysis, and lack of generalizability of results were limitations of the study. Conclusions Requiring initial support to stabilize in tandem stance appears to reflect meaningful deficits in balance-related mobility measures, so failing to consider support may inflate balance estimates and confound hold time comparisons

A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.

PubMed

Liu, Wei; Zhang, Jingfeng; Fan, Jing-Song; Tria, Giancarlo; Grüber, Gerhard; Yang, Daiwen

2016-05-10

Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Single-stage experimental evaluation of tandem-airfoil rotor and stator blading for compressors, part 8

NASA Technical Reports Server (NTRS)

Brent, J. A.; Clemmons, D. R.

1974-01-01

An experimental investigation was conducted with an 0.8 hub/tip ratio, single-stage, axial flow compressor to determine the potential of tandem-airfoil blading for improving the efficiency and stable operating range of compressor stages. The investigation included testing of a baseline stage with single-airfoil blading and two tandem-blade stages. The overall performance of the baseline stage and the tandem-blade stage with a 20-80% loading split was considerably below the design prediction. The other tandem-blade stage, which had a rotor with a 50-50% loading split, came within 4.5% of the design pressure rise (delta P(bar)/P(bar) sub 1) and matched the design stage efficiency. The baseline stage with single-airfoil blading, which was designed to account for the actual rotor inlet velocity profile and the effects of axial velocity ratio and secondary flow, achieved the design predicted performance. The corresponding tandem-blade stage (50-50% loading split in both blade rows) slightly exceeded the design pressure rise but was 1.5 percentage points low in efficiency. The tandem rotors tested during both phases demonstrated higher pressure rise and efficiency than the corresponding single-airfoil rotor, with identical inlet and exit airfoil angles.

Approach for ochratoxin A fast screening in spices using clean-up tandem immunoassay columns with confirmation by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS).

PubMed

Goryacheva, I Yu; De Saeger, S; Lobeau, M; Eremin, S A; Barna-Vetró, I; Van Peteghem, C

2006-09-01

An approach for ochratoxin A (OTA) fast cost-effective screening based on clean-up tandem immunoassay columns was developed and optimized for OTA detection with a cut-off level of 10 microg kg(-1) in spices. Two procedures were tested and applied for OTA detection. Column with bottom detection immunolayer was optimized for OTA determination in Capsicum ssp. spices. A modified clean-up tandem immunoassay procedure with top detection immunolayer was successfully applied for all tested spices. Its main advantages were decreasing of the number of analysis steps and quantity of antibody and also minimizing of matrix effects. The total duration of the extraction and analysis was about 40 min for six samples. Chilli, red pepper, pili-pili, cayenne, paprika, nutmeg, ginger, white pepper and black pepper samples were analyzed for OTA contamination by the proposed clean-up tandem immunoassay procedures. Clean-up tandem immunoassay results were confirmed by HPLC-MS/MS with immunoaffinity column clean-up. Among 17 tested Capsicum ssp. spices, 6 samples (35%) contained OTA in a concentration exceeding the 10 microg kg(-1) limit discussed by the European Commission. All tested nutmeg (n=8), ginger (n=5), white pepper (n=7) and black pepper (n=6) samples did not contain OTA above this action level.

The Thioredoxin Domain of Neisseria Gonorrhoeae PilB can use Electrons from DsbD to Reduce Downstream Methionine Sulfoxide Reductases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brot,N.; Collet, J.; Johnson, L.

2006-01-01

The PilB protein from Neisseria gonorrhoeae is located in the periplasm and made up of three domains. The N-terminal, thioredoxin-like domain (NT domain) is fused to tandem methionine sulfoxide reductase A and B domains (MsrA/B). We show that the {alpha} domain of Escherichia coli DsbD is able to reduce the oxidized NT domain, which suggests that DsbD in Neisseria can transfer electrons from the cytoplasmic thioredoxin to the periplasm for the reduction of the MsrA/B domains. An analysis of the available complete genomes provides further evidence for this proposition in other bacteria where DsbD/CcdA, Trx, MsrA, and MsrB gene homologsmore » are all located in a gene cluster with a common transcriptional direction. An examination of wild-type PilB and a panel of Cys to Ser mutants of the full-length protein and the individually expressed domains have also shown that the NT domain more efficiently reduces the MsrA/B domains when in the polyprotein context. Within this framework there does not appear to be a preference for the NT domain to reduce the proximal MsrA domain over MsrB domain. Finally, we report the 1.6 {angstrom} crystal structure of the NT domain. This structure confirms the presence of a surface loop that makes it different from other membrane-tethered, Trx-like molecules including TlpA, CcmG and ResA. Subtle differences are observed in this loop when compared to the N. meningitidis NT domain structure. The data taken together supports the formation of specific NT domain interactions with the MsrA/B domains and its in vivo recycling partner, DsbD.« less

Artificial urinary sphincter revision for urethral atrophy: Comparing single cuff downsizing and tandem cuff placement.

PubMed

Linder, Brian J; Viers, Boyd R; Ziegelmann, Matthew J; Rivera, Marcelino E; Elliott, Daniel S

2017-01-01

To compare outcomes for single urethral cuff downsizing versus tandem cuff placement during artificial urinary sphincter (AUS) revision for urethral atrophy. We identified 1778 AUS surgeries performed at our institution from 1990-2014. Of these, 406 were first AUS revisions, including 69 revisions for urethral atrophy. Multiple clinical and surgical variables were evaluated for potential association with device outcomes following revision, including surgical revision strategy (downsizing a single urethral cuff versus placing tandem urethral cuffs). Of the 69 revision surgeries for urethral atrophy at our institution, 56 (82%) were tandem cuff placements, 12 (18%) were single cuff downsizings and one was relocation of a single cuff. When comparing tandem cuff placements and single cuff downsizings, the cohorts were similar with regard to age (p=0.98), body-mass index (p=0.95), prior pelvic radiation exposure (p=0.73) and length of follow-up (p=0.12). Notably, there was no difference in 3-year overall device survival compared between single cuff and tandem cuff revisions (60% versus 76%, p=0.94). Likewise, no significant difference was identified for tandem cuff placement (ref. single cuff) when evaluating the risk of any tertiary surgery (HR 0.95, 95% CI 0.32-4.12, p=0.94) or urethral erosion/device infection following revision (HR 0.79, 95% CI 0.20-5.22, p=0.77). There was no significant difference in overall device survival in patients undergoing single cuff downsizing or tandem cuff placement during AUS revision for urethral atrophy. Copyright® by the International Brazilian Journal of Urology.

76 FR 40935 - Vertical Tandem Lifts in Marine Terminals; Extension of the Office of Management and Budget's...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-12

...] Vertical Tandem Lifts in Marine Terminals; Extension of the Office of Management and Budget's (OMB... Standard on Vertical Tandem Lifts (VTLs) in Marine Terminals (29 CFR part 1917). The collection of... on Vertical Tandem Lifts for Marine Terminals (29 CFR part 1917). OSHA is proposing to increase the...

Achieving high performance polymer tandem solar cells via novel materials design

NASA Astrophysics Data System (ADS)

Dou, Letian

Organic photovoltaic (OPV) devices show great promise in low-cost, flexible, lightweight, and large-area energy-generation applications. Nonetheless, most of the materials designed today always suffer from the inherent disadvantage of not having a broad absorption range, and relatively low mobility, which limit the utilization of the full solar spectrum. Tandem solar cells provide an effective way to harvest a broader spectrum of solar radiation by combining two or more solar cells with different absorption bands. However, for polymer solar cells, the performance of tandem devices lags behind single-layer solar cells mainly due to the lack of suitable low-bandgap polymers (near-IR absorbing polymers). In this dissertation, in order to achieve high performance, we focus on design and synthesis of novel low bandgap polymers specifically for tandem solar cells. In Chapter 3, I demonstrate highly efficient single junction and tandem polymer solar cells featuring a spectrally matched low-bandgap conjugated polymer (PBDTT-DPP: bandgap, ˜1.44 eV). The polymer has a backbone based on alternating benzodithiophene and diketopyrrolopyrrole units. A single-layer device based on the polymer provides a power conversion efficiency of ˜6%. When the polymer is applied to tandem solar cells, a power conversion efficiency of 8.62% is achieved, which was the highest certified efficiency for a polymer solar cell. To further improve this material system, in Chapter 4, I show that the reduction of the bandgap and the enhancement of the charge transport properties of the low bandgap polymer PBDTT-DPP can be accomplished simultaneously by substituting the sulfur atoms on the DPP unit with selenium atoms. The newly designed polymer PBDTT-SeDPP (Eg = 1.38 eV) shows excellent photovoltaic performance in single junction devices with PCEs over 7% and photo-response up to 900 nm. Tandem polymer solar cells based on PBDTT-SeDPP are also demonstrated with a 9.5% PCE, which are more than 10

Aryl hydrocarbon receptor (AHR): "pioneer member" of the basic-helix/loop/helix per-Arnt-sim (bHLH/PAS) family of "sensors" of foreign and endogenous signals.

PubMed

Nebert, Daniel W

2017-07-01

The basic-helix/loop/helix per-Arnt-sim (bHLH/PAS) family comprises many transcription factors, found throughout all three kingdoms of life; bHLH/PAS members "sense" innumerable intracellular and extracellular "signals" - including endogenous compounds, foreign chemicals, gas molecules, redox potential, photons (light), gravity, heat, and osmotic pressure. These signals then initiate downstream signaling pathways involved in responding to that signal. The term "PAS", abbreviation for "per-Arnt-sim" was first coined in 1991. Although the mouse Arnt gene was not identified until 1991, evidence of its co-transcriptional binding partner, aryl hydrocarbon receptor (AHR), was first reported in 1974 as a "sensor" of foreign chemicals, up-regulating cytochrome P450 family 1 (CYP1) and other enzyme activities that usually metabolize the signaling chemical. Within a few years, AHR was proposed also to participate in inflammation. The mouse [Ah] locus was shown (1973-1989) to be relevant to chemical carcinogenesis, mutagenesis, toxicity and teratogenesis, the mouse Ahr gene was cloned in 1992, and the first Ahr(-/-) knockout mouse line was reported in 1995. After thousands of studies from the early 1970s to present day, we now realize that AHR participates in dozens of signaling pathways involved in critical-life processes, affecting virtually every organ and cell-type in the animal, including many invertebrates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates

PubMed Central

Baudouin-Gonzalez, Luís; Santos, Marília A; Tempesta, Camille; Sucena, Élio; Roch, Fernando; Tanaka, Kohtaro

2017-01-01

Abstract Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. We have directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 Ma. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, we show that they diverged from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. Our analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. We argue that our findings will encourage studying cis-regulatory evolution at the whole-locus level to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression. PMID:28961967

Psychometric Evaluation of a Dutch Version of the Mini PAS-ADD for Assessing Psychiatric Disorders in Adults with Different Levels of Intellectual Disability

ERIC Educational Resources Information Center

Janssen, R.; Maes, B.

2013-01-01

Background: People with intellectual disabilities (ID) have an increased vulnerability to develop psychiatric problems. Moreover, the early recognition and the accurate diagnosis of psychiatric disorders in the population of persons with ID are challenging. Method: A Dutch version of the Mini PAS-ADD, which is a screening instrument for…

Spondylodiscite granulomateuse: surtout la tuberculose mais ne pas omettre le lymphome

PubMed Central

Zinebi, Ali; Rkiouak, Adil; Akhouad, Yousef; Reggad, Ahmed; Kasmy, Zohour; Boudlal, Mostafa; Lho, Abdelhamid Nait; Rabhi, Moncef; Sinaa, Mohamed; Ennibi, Khalid; Chaari, Jilali

2016-01-01

Les douleurs lombaires relèvent d'étiologies multiples dont le diagnostic peut être source de grandes difficultés. Le lymphome rachidien primitif est rare et son diagnostic nécessite une biopsie souvent scanoguidée. Un homme de 30 ans, était hospitalisé pour lombalgies inflammatoires évoluant dans un contexte d'altération de l'état général avec à l'examen des douleurs à la palpation des apophyses épineux L2L3, sans syndrome tumoral périphérique. Le bilan biologique montrait un syndrome inflammatoire. Le bilan morphologique était en faveur d'une spondylodiscite. La première biopsie montrait une ostéite granulomateuse. L'aggravation clinique et radiologique sous anti bacillaire a mené à reconsidérer le diagnostic et la deuxième biopsie confirme le diagnostic du lymphome. Le diagnostic de tuberculose osseuse en particulier vertébrale nécessite une confirmation bactériologique et ou histologique pour ne pas méconnaître un lymphome osseux primitif. PMID:28292061

Tandem UIMs confer Lys48 ubiquitin chain substrate preference to deubiquitinase USP25

PubMed Central

Kawaguchi, Kohei; Uo, Kazune; Tanaka, Toshiaki; Komada, Masayuki

2017-01-01

Ubiquitin-specific protease (USP) 25, belonging to the USP family of deubiquitinases, harbors two tandem ubiquitin-interacting motifs (UIMs), a ~20-amino-acid α-helical stretch that binds to ubiquitin. However, the role of the UIMs in USP25 remains unclear. Here we show that the tandem UIM region binds to Lys48-, but not Lys63-, linked ubiquitin chains, where the two UIMs played a critical and cooperative role. Purified USP25 exhibited higher ubiquitin isopeptidase activity to Lys48-, than to Lys63-, linked ubiquitin chains. Mutations that disrupted the ubiquitin-binding ability of the tandem UIMs resulted in a reduced ubiquitin isopeptidase activity of USP25, suggesting a role for the UIMs in exerting the full catalytic activity of USP25. Moreover, when mutations that convert the binding preference from Lys48- to Lys63-linked ubiquitin chains were introduced into the tandem UIM region, the USP25 mutants acquired elevated and reduced isopeptidase activity toward Lys63- and Lys48-linked ubiquitin chains, respectively. These results suggested that the binding preference of the tandem UIMs toward Lys48-linked ubiquitin chains contributes not only to the full catalytic activity but also to the ubiquitin chain substrate preference of USP25, possibly by selectively holding the Lys48-linked ubiquitin chain substrates in the proximity of the catalytic core. PMID:28327663

Conservation of the Human Integrin-Type Beta-Propeller Domain in Bacteria

PubMed Central

Chouhan, Bhanupratap; Denesyuk, Alexander; Heino, Jyrki; Johnson, Mark S.; Denessiouk, Konstantin

2011-01-01

Integrins are heterodimeric cell-surface receptors with key functions in cell-cell and cell-matrix adhesion. Integrin α and β subunits are present throughout the metazoans, but it is unclear whether the subunits predate the origin of multicellular organisms. Several component domains have been detected in bacteria, one of which, a specific 7-bladed β-propeller domain, is a unique feature of the integrin α subunits. Here, we describe a structure-derived motif, which incorporates key features of each blade from the X-ray structures of human αIIbβ3 and αVβ3, includes elements of the FG-GAP/Cage and Ca2+-binding motifs, and is specific only for the metazoan integrin domains. Separately, we searched for the metazoan integrin type β-propeller domains among all available sequences from bacteria and unicellular eukaryotic organisms, which must incorporate seven repeats, corresponding to the seven blades of the β-propeller domain, and so that the newly found structure-derived motif would exist in every repeat. As the result, among 47 available genomes of unicellular eukaryotes we could not find a single instance of seven repeats with the motif. Several sequences contained three repeats, a predicted transmembrane segment, and a short cytoplasmic motif associated with some integrins, but otherwise differ from the metazoan integrin α subunits. Among the available bacterial sequences, we found five examples containing seven sequential metazoan integrin-specific motifs within the seven repeats. The motifs differ in having one Ca2+-binding site per repeat, whereas metazoan integrins have three or four sites. The bacterial sequences are more conserved in terms of motif conservation and loop length, suggesting that the structure is more regular and compact than those example structures from human integrins. Although the bacterial examples are not full-length integrins, the full-length metazoan-type 7-bladed β-propeller domains are present, and sometimes two tandem

N719 dye-sensitized organophotocatalysis: enantioselective tandem Michael addition/oxyamination of aldehydes.

PubMed

Yoon, Hyo-Sang; Ho, Xuan-Huong; Jang, Jiyeon; Lee, Hwa-Jung; Kim, Seung-Joo; Jang, Hye-Young

2012-07-06

A remarkably efficient photosensitizer, N719 dye, was used in asymmetric tandem Michael addition/oxyamination of aldehydes, rendering α,β-substituted aldehydes in good yields with excellent levels of enantioselectivity and diastereoselectivity. This is the first report of a multiorganocatalytic reaction involving iminium catalysis and photoinduced singly occupied molecular orbital (SOMO) catalysis. This reaction is expected to expand the scope of tandem organocatalytic reactions.

InP/Ga0.47In0.53As monolithic, two-junction, three-terminal tandem solar cells

NASA Technical Reports Server (NTRS)

Wanlaas, M. W.; Gessert, T. A.; Horner, G. S.; Emery, K. A.; Coutts, T. J.

1991-01-01

The work presented has focussed on increasing the efficiency of InP-based solar cells through the development of a high-performance InP/Ga(0.47)In(0.53)As two-junction, three-terminal monolithic tandem cell. Such a tandem is particularly suited to space applications where a radiation-hard top cell (i.e., InP) is required. Furthermore, the InP/Ga(0.47)In(0.53)As materials system is lattice matched and offers a top cell/bottom cell bandgap differential (0.60 eV at 300 K) suitable for high tandem cell efficiencies under AMO illumination. A three-terminal configuration was chosen since it allows for independent power collection from each subcell in the monolithic stack, thus minimizing the adverse impact of radiation damage on the overall tandem efficiency. Realistic computer modeling calculations predict an efficiency boost of 7 to 11 percent from the Ga(0.47)In(0.53)As bottom cell under AMO illumination (25 C) for concentration ratios in the 1 to 1000 range. Thus, practical AMO efficiencies of 25 to 32 percent appear possible with the InP/Ga(0.47)In(0.53)As tandem cell. Prototype n/p/n InP/Ga(0.47)In(0.53)As monolithic tandem cells were fabricated and tested successfully. Using an aperture to define the illuminated areas, efficiency measurements performed on a non-optimized device under standard global illumination conditions (25 C) with no antireflection coating (ARC) give 12.2 percent for the InP top cell and 3.2 percent for the Ga(0.47)In(0.53)As bottom cell, yielding an overall tandem efficiency of 15.4 percent. With an ARC, the tandem efficiency could reach approximately 22 percent global and approximately 20 percent AMO. Additional details regarding the performance of individual InP and Ga(0.47)In(0.53)As component cells, fabrication and operation of complete tandem cells and methods for improving the tandem cell performance, are also discussed.

A review of recent progress in heterogeneous silicon tandem solar cells

NASA Astrophysics Data System (ADS)

Yamaguchi, Masafumi; Lee, Kan-Hua; Araki, Kenji; Kojima, Nobuaki

2018-04-01

Silicon solar cells are the most established solar cell technology and are expected to dominate the market in the near future. As state-of-the-art silicon solar cells are approaching the Shockley-Queisser limit, stacking silicon solar cells with other photovoltaic materials to form multi-junction devices is an obvious pathway to further raise the efficiency. However, many challenges stand in the way of fully realizing the potential of silicon tandem solar cells because heterogeneously integrating silicon with other materials often degrades their qualities. Recently, above or near 30% silicon tandem solar cell has been demonstrated, showing the promise of achieving high-efficiency and low-cost solar cells via silicon tandem. This paper reviews the recent progress of integrating solar cell with other mainstream solar cell materials. The first part of this review focuses on the integration of silicon with III-V semiconductor solar cells, which is a long-researched topic since the emergence of III-V semiconductors. We will describe the main approaches—heteroepitaxy, wafer bonding and mechanical stacking—as well as other novel approaches. The second part introduces the integration of silicon with polycrystalline thin-film solar cells, mainly perovskites on silicon solar cells because of its rapid progress recently. We will also use an analytical model to compare the material qualities of different types of silicon tandem solar cells and project their practical efficiency limits.

High energy collisions on tandem time-of-flight mass spectrometers†

PubMed Central

Cotter, Robert J.

2013-01-01

Long before the introduction of matrix-assisted laser desorption (MALDI), electrospray ionization (ESI), Orbitraps and any of the other tools that are now used ubiquitously for proteomics and metabolomics, the highest performance mass spectrometers were sector instruments, providing high resolution mass measurements by combining an electrostatic energy analyzer (E) with a high field magnet (B). In its heyday, the four sector mass spectrometer (or EBEB) was the crown jewel, providing the highest performance tandem mass spectrometry using single, high energy collisions to induce fragmentation. During a time in which quadrupole and tandem triple quadrupole instruments were also enjoying increased usage and popularity, there were nonetheless some clear advantages for sectors over their low collision energy counterparts. Time-of-flight mass spectrometers are high voltage, high vacuum instruments that have much in common with sectors and have inspired the development of tandem instruments exploiting single high energy collisions. In this retrospective we recount our own journey to produce high performance time-of-flights and tandems, describing the basic theory, problems and the advantages for such instruments. An experiment testing impulse collision theory (ICT) underscores the similarities with sector mass spectrometers where this concept was first developed. Applications provide examples of more extensive fragmentation, side chain cleavages and charge-remote fragmentation, also characteristic of high energy sector mass spectrometers. Moreover, the so-called curved-field reflectron has enabled the design of instruments that are simpler, collect and focus all of the ions, and may provide the future technology for the clinic, for tissue imaging and the characterization of microorganisms. PMID:23519928

Programmable DNA-binding proteins from Burkholderia provide a fresh perspective on the TALE-like repeat domain

PubMed Central

de Lange, Orlando; Wolf, Christina; Dietze, Jörn; Elsaesser, Janett; Morbitzer, Robert; Lahaye, Thomas

2014-01-01

The tandem repeats of transcription activator like effectors (TALEs) mediate sequence-specific DNA binding using a simple code. Naturally, TALEs are injected by Xanthomonas bacteria into plant cells to manipulate the host transcriptome. In the laboratory TALE DNA binding domains are reprogrammed and used to target a fused functional domain to a genomic locus of choice. Research into the natural diversity of TALE-like proteins may provide resources for the further improvement of current TALE technology. Here we describe TALE-like proteins from the endosymbiotic bacterium Burkholderia rhizoxinica, termed Bat proteins. Bat repeat domains mediate sequence-specific DNA binding with the same code as TALEs, despite less than 40% sequence identity. We show that Bat proteins can be adapted for use as transcription factors and nucleases and that sequence preferences can be reprogrammed. Unlike TALEs, the core repeats of each Bat protein are highly polymorphic. This feature allowed us to explore alternative strategies for the design of custom Bat repeat arrays, providing novel insights into the functional relevance of non-RVD residues. The Bat proteins offer fertile grounds for research into the creation of improved programmable DNA-binding proteins and comparative insights into TALE-like evolution. PMID:24792163

10.2% power conversion efficiency polymer tandem solar cells consisting of two identical sub-cells.

PubMed

You, Jingbi; Chen, Chun-Chao; Hong, Ziruo; Yoshimura, Ken; Ohya, Kenichiro; Xu, Run; Ye, Shenglin; Gao, Jing; Li, Gang; Yang, Yang

2013-08-07

Polymer tandem solar cells with 10.2% power conversion efficiency are demonstrated via stacking two PDTP-DFBT:PC₇₁ BM bulk heterojunctions, connected by MoO₃/PEDOT:PSS/ZnO as an interconnecting layer. The tandem solar cells increase the power conversion efficiency of the PDTP-DFBT:PC₇₁ BM system from 8.1% to 10.2%, successfully demonstrating polymer tandem solar cells with identical sub-cells of double-digit efficiency. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Tandem Catalyst with Multiple Metal Oxide Interfaces Produced by Atomic Layer Deposition.

PubMed

Ge, Huibin; Zhang, Bin; Gu, Xiaomin; Liang, Haojie; Yang, Huimin; Gao, Zhe; Wang, Jianguo; Qin, Yong

2016-06-13

Ideal heterogeneous tandem catalysts necessitate the rational design and integration of collaborative active sites. Herein, we report on the synthesis of a new tandem catalyst with multiple metal-oxide interfaces based on a tube-in-tube nanostructure using template-assisted atomic layer deposition, in which Ni nanoparticles are supported on the outer surface of the inner Al2 O3 nanotube (Ni/Al2 O3 interface) and Pt nanoparticles are attached to the inner surface of the outer TiO2 nanotube (Pt/TiO2 interface). The tandem catalyst shows remarkably high catalytic efficiency in nitrobenzene hydrogenation over Pt/TiO2 interface with hydrogen formed in situ by the decomposition of hydrazine hydrate over Ni/Al2 O3 interface. This can be ascribed to the synergy effect of the two interfaces and the confined nanospace favoring the instant transfer of intermediates. The tube-in-tube tandem catalyst with multiple metal-oxide interfaces represents a new concept for the design of highly efficient and multifunctional nanocatalysts. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Old and New Techniques as a Safe Hybrid Approach for Carotid Tandem Lesions.

PubMed

Barillà, David; Massara, Mafalda; Alberti, Antonino; Volpe, Alberto; Cutrupi, Andrea; Versace, Paolo; Volpe, Pietro

2016-04-01

Carotid revascularization is performed to prevent stroke. Carotid tandem lesions represent a challenge for treatment, and a hybrid approach may result effective. A high-risk 65-year-old woman presented with a "tandem lesion" of left common and internal carotid artery. She was deemed unfit for "simple" standard carotid endarterectomy (CEA). A "single-step" safe hybrid procedure was scheduled for the patient. A "Cormier" carotid vein graft bypass with a retrograde stenting was performed under local anesthesia. The "safe hybrid procedure" for tandem lesions of the common and internal carotid artery is effective and suitable in high-risk patients in a high-volume centers. Copyright © 2016 Elsevier Inc. All rights reserved.

Two-terminal monolithic InP-based tandem solar cells with tunneling intercell ohmic connections

NASA Technical Reports Server (NTRS)

Shen, C. C.; Chang, P. T.; Emery, K. A.

1991-01-01

A monolithic two-terminal InP/InGaAsP tandem solar cell was successfully fabricated. This tandem solar cell consists of a p/n InP homojunction top subcell and a 0.95 eV p/n InGaAsP homojunction bottom subcell. A patterned 0.95 eV n(+)/p(+) InGaAsP tunnel diode was employed as an intercell ohmic connection. The solar cell structure was prepared by two-step liquid phase epitaxial growth. Under one sun, AM1.5 global illumination, the best tandem cell delivered a conversion efficiency of 14.8 pct.

Aerodynamic Characteristics of Tube-Launched Tandem Wing Unmanned Aerial Vehicle

NASA Astrophysics Data System (ADS)

Rosid, Nurhayyan H.; Irsyad Lukman, E.; Fadlillah, M. Ahmad; Agoes Moelyadi, M.

2018-04-01

Tube Launched UAV with expandable tandem-wing configuration becomes one of the most interesting topic to be investigated. Folding wing mechanism is used due to the requirements that the UAV should be folded into tubular launcher. This paper focuses on investigating the aerodynamics characteristics because of the effects of folding wing mechanism, tandem wing configuration, and rapid deploying process from tube launcher. The aerodynamic characteristics investigation is conducted using computational fluid dynamics (CFD) at low Reynolds numbers (Re < 200000). The results of the simulation are used for the development of ITB Tube-launched UAV prototype and for future studies.

Cloning and analysis of the Glwc-1 and Glwc-2 genes encoding putative blue light photoreceptor from Ganoderma lucidum.

PubMed

Xu, Xinran; Chen, Xiangdong; Yu, Wumengxiao; Liu, Yu; Zhang, Weiwei; Lan, Jin

2017-08-01

Blue light plays an important role during the growth of Ganoderma lucidum, one of the best-known medicinal macrofungi in China. In the present study, we cloned Glwc-1 and Glwc-2, the homologue of the blue light photoreceptors Ncwc-1 and Ncwc-2 of Neurospora crassa, from G. lucidum. The deduced amino acid sequence of Glwc-1 contained the similar function domains as NcWC-1 including LOV, PAS B, PAS C, and PAC domains. The deduced amino acid sequence of Glwc-2 contained PAS domain and GATA-type zinc finger (Znf) domain as well as NcWC-2. Phylogenetic analysis based on fungal WC-1 and WC-2 supported GlWC-1 and GlWC-2 were blue light receptors. The expression of Glwc-1 and Glwc-2 indicated that they might play an important role during the primordium differentiation process of G. lucidum, and the external blue light stimulation increased the expression of Glwc-1 and Glwc-2. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements

PubMed Central

Peterson, Thomas

2013-01-01

Tandem direct duplications are a common feature of the genomes of eukaryotes ranging from yeast to human, where they comprise a significant fraction of copy number variations. The prevailing model for the formation of tandem direct duplications is non-allelic homologous recombination (NAHR). Here we report the isolation of a series of duplications and reciprocal deletions isolated de novo from a maize allele containing two Class II Ac/Ds transposons. The duplication/deletion structures suggest that they were generated by alternative transposition reactions involving the termini of two nearby transposable elements. The deletion/duplication breakpoint junctions contain 8 bp target site duplications characteristic of Ac/Ds transposition events, confirming their formation directly by an alternative transposition mechanism. Tandem direct duplications and reciprocal deletions were generated at a relatively high frequency (∼0.5 to 1%) in the materials examined here in which transposons are positioned nearby each other in appropriate orientation; frequencies would likely be much lower in other genotypes. To test whether this mechanism may have contributed to maize genome evolution, we analyzed sequences flanking Ac/Ds and other hAT family transposons and identified three small tandem direct duplications with the structural features predicted by the alternative transposition mechanism. Together these results show that some class II transposons are capable of directly inducing tandem sequence duplications, and that this activity has contributed to the evolution of the maize genome. PMID:23966872

Improve definition of titanium tandems in MR-guided high dose rate brachytherapy for cervical cancer using proton density weighted MRI

PubMed Central

2013-01-01

Background For cervical cancer patients treated with MR-guided high dose rate brachytherapy, the accuracy of radiation delivery depends on accurate localization of both tumors and the applicator, e.g. tandem and ovoid. Standard T2-weighted (T2W) MRI has good tumor-tissue contrast. However, it suffers from poor uterus-tandem contrast, which makes the tandem delineation very challenging. In this study, we evaluated the possibility of using proton density weighted (PDW) MRI to improve the definition of titanium tandems. Methods Both T2W and PDW MRI images were obtained from each cervical cancer patient. Imaging parameters were kept the same between the T2W and PDW sequences for each patient except the echo time (90 ms for T2W and 5.5 ms for PDW) and the slice thickness (0.5 cm for T2W and 0.25 cm for PDW). Uterus-tandem contrast was calculated by the equation C = (Su-St)/Su, where Su and St represented the average signal in the uterus and the tandem, respectively. The diameter of the tandem was measured 1.5 cm away from the tip of the tandem. The tandem was segmented by the histogram thresholding technique. Results PDW MRI could significantly improve the uterus-tandem contrast compared to T2W MRI (0.42±0.24 for T2W MRI, 0.77±0.14 for PDW MRI, p=0.0002). The average difference between the measured and physical diameters of the tandem was reduced from 0.20±0.15 cm by using T2W MRI to 0.10±0.11 cm by using PDW MRI (p=0.0003). The tandem segmented from the PDW image looked more uniform and complete compared to that from the T2W image. Conclusions Compared to the standard T2W MRI, PDW MRI has better uterus-tandem contrast. The information provided by PDW MRI is complementary to those provided by T2W MRI. Therefore, we recommend adding PDW MRI to the simulation protocol to assist tandem delineation process for cervical cancer patients. PMID:23327682

The "Bologna-München" Tandem--Experiencing Interculturality

ERIC Educational Resources Information Center

De Martino, Sandro

2016-01-01

This case study describes the "Bologna-München" Tandem, a cross-border collaboration which began in 2011. The aim of the collaboration is to give students studying Italian at the Ludwig- Maximilians-University in Munich and students studying German at the University of Bologna the opportunity to experience interculturality through…

A Comparison of Tandem Walk Performance Between Bed Rest Subjects and Astronauts

NASA Technical Reports Server (NTRS)

Miller, Chris; Peters, Brian; Kofman, Igor; Philips, Tiffany; Batson, Crystal; Cerisano, Jody; Fisher, Elizabeth; Mulavara, Ajitkumar; Feiveson, Alan; Reschke, Millard;

5. GENERAL VIEW OF UNITEDTOD TWIN TANDEM STEAM ENGINE. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

5. GENERAL VIEW OF UNITED-TOD TWIN TANDEM STEAM ENGINE. - Republic Iron & Steel Company, Youngstown Works, Blooming Mill & Blooming Mill Engines, North of Poland Avenue, Youngstown, Mahoning County, OH

Fluoroscopic percutaneous brush cytology, forceps biopsy and both in tandem for diagnosis of malignant biliary obstruction.

PubMed

Boos, Johannes; Yoo, Raphael J; Steinkeler, Jennifer; Ayata, Gamze; Ahmed, Muneeb; Sarwar, Ammar; Weinstein, Jeffrey; Faintuch, Salomao; Brook, Olga R

2018-02-01

To evaluate percutaneous brush cytology, forceps biopsy and a tandem procedure consisting of both, in the diagnosis of malignant biliary obstruction. A retrospective review of consecutive patients who underwent biliary brush cytology and/or forceps biopsy between 01/2010 and 09/2014 was performed. The cytology and pathology results were compared to the composite outcome (including radiological, pathological and clinical data). Cost for tandem procedure compared to brush cytology and forceps biopsy alone was calculated. A total of 232 interventions in 129 patients (70.8 ± 11.0 years) were included. Composite outcome showed malignancy in 94/129 (72.9%) patients. Sensitivity for brush cytology, forceps biopsy and tandem procedure was 40.6% (95% CI 32.6-48.7%), 42.7% (32.4-53.0%) and 55.8% (44.7-66.9%) with 100% specificity, respectively. There were 9/43 (20.9%) additional cancers diagnosed when forceps biopsy was performed in addition to brush cytology, while there were 13/43 (30.2%) more cancers diagnosed when brush cytology was performed in addition to forceps biopsy. Additional costs per additionally diagnosed malignancy if tandem approach is to be utilised in all cases was $704.96. Using brush cytology and forceps biopsy in tandem improves sensitivity compared to brush cytology and forceps biopsy alone in the diagnosis of malignant biliary obstruction. • Tandem procedure improves sensitivity compared to brush cytology and forceps biopsy. • Brush cytology may help to overcome "crush artefacts" from forceps biopsy. • The cost per diagnosed malignancy may warrant tandem procedure in all patients.

Evaluating the economic viability of CdTe/CIS and CIGS/CIS tandem photovoltaic modules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nanayakkara, Sanjini U.; Horowitz, Kelsey; Kanevce, Ana

In this paper, we analyze the potential cost competitiveness of two frameless, glass–glass thin-film tandem photovoltaic module structures, cadmium telluride (CdTe)/CuInSe 2 (CIS) and CuIn 0.3Ga 0.7Se 2 (CIGS)/CIS, based on the demonstrated cost of manufacturing the respective component cell technologies in high volume. To consider multiple economic scenarios, we base the CdTe/CIS module efficiency on the current industrial production of CdTe modules, while for CIGS/CIS, we use an aspirational estimate for CIGS efficiency. We focus on four-terminal mechanically stacked structures, thus avoiding the need to achieve current matching between the two cells. The top cell in such a tandemmore » must have a transparent back contact, which has not been successfully implemented to date. However, for the purpose of understanding the economic viability of both tandems, we assume that this can be implemented at a cost similar to that of sputtered indium tin oxide. The cost of both tandem module structures was found to be nearly identical on an equal-area basis and approximately $30/m 2 higher than the single-junction alternatives. Both tandem modules are about 4% (absolute) more efficient than a module by using the top-cell material alone. We find that these tandem modules might reduce total system cost by as much as 11% in applications having a high area-related balance-of-system cost, such as area-constrained residential systems; however, the relative advantage of tandems decreases in the cases where balance-of-system costs are lower, such as in commercial and utility scale systems.« less

Evaluating the economic viability of CdTe/CIS and CIGS/CIS tandem photovoltaic modules

DOE PAGES

Nanayakkara, Sanjini U.; Horowitz, Kelsey; Kanevce, Ana; ...

2017-01-20

In this paper, we analyze the potential cost competitiveness of two frameless, glass–glass thin-film tandem photovoltaic module structures, cadmium telluride (CdTe)/CuInSe 2 (CIS) and CuIn 0.3Ga 0.7Se 2 (CIGS)/CIS, based on the demonstrated cost of manufacturing the respective component cell technologies in high volume. To consider multiple economic scenarios, we base the CdTe/CIS module efficiency on the current industrial production of CdTe modules, while for CIGS/CIS, we use an aspirational estimate for CIGS efficiency. We focus on four-terminal mechanically stacked structures, thus avoiding the need to achieve current matching between the two cells. The top cell in such a tandemmore » must have a transparent back contact, which has not been successfully implemented to date. However, for the purpose of understanding the economic viability of both tandems, we assume that this can be implemented at a cost similar to that of sputtered indium tin oxide. The cost of both tandem module structures was found to be nearly identical on an equal-area basis and approximately $30/m 2 higher than the single-junction alternatives. Both tandem modules are about 4% (absolute) more efficient than a module by using the top-cell material alone. We find that these tandem modules might reduce total system cost by as much as 11% in applications having a high area-related balance-of-system cost, such as area-constrained residential systems; however, the relative advantage of tandems decreases in the cases where balance-of-system costs are lower, such as in commercial and utility scale systems.« less

R&D issues in scale-up and manufacturing of amorphous silicon tandem modules

NASA Astrophysics Data System (ADS)

Arya, R. R.; Carlson, D. E.; Chen, L. F.; Ganguly, G.; He, M.; Lin, G.; Middya, R.; Wood, G.; Newton, J.; Bennett, M.; Jackson, F.; Willing, F.

1999-03-01

R & D on amorphous silicon based tandem junction devices has improved the throughtput, the material utilization, and the performance of devices on commercial tin oxide coated glass. The tandem junction technology has been scaled-up to produce 8.6 Ft2 monolithically integrated modules in manufacturing at the TF1 plant. Optimization of performance and stability of these modules is ongoing.

Allostery Mediates Ligand Binding to WWOX Tumor Suppressor via a Conformational Switch

PubMed Central

Schuchardt, Brett J.; Mikles, David C.; Bhat, Vikas; McDonald, Caleb B.; Sudol, Marius; Farooq, Amjad

2014-01-01

While being devoid of the ability to recognize ligands itself, the WW2 domain is believed to aid ligand binding to WW1 domain in the context of WW1-WW2 tandem module of WWOX tumor suppressor. In an effort to test the generality of this hypothesis, we have undertaken here a detailed biophysical analysis of the binding of WW domains of WWOX alone and in the context of WW1-WW2 tandem module to an array of putative PPXY ligands. Our data show that while the WW1 domain of WWOX binds to all ligands in a physiologically-relevant manner, the WW2 domain does not. Moreover, ligand binding to WW1 domain in the context of WW1-WW2 tandem module is two-to-three-fold stronger than when treated alone. We also provide evidence that the WW domains within the WW1-WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. Of particular note is the observation that the physical association of WW2 domain with WW1 blocks access to ligand. Consequently, ligand binding to WW1 domain not only results in the displacement of WW2 lid but also disrupts the physical association of WW domains in the liganded conformation. Taken together, our study underscores a key role of allosteric communication in the ability of WW2 orphan domain to chaperone physiological action of WW1 domain within the context of the WW1-WW2 tandem module of WWOX. PMID:25703206

Displacement of particles in microfluidics by laser-generated tandem bubbles

NASA Astrophysics Data System (ADS)

Lautz, Jaclyn; Sankin, Georgy; Yuan, Fang; Zhong, Pei

2010-11-01

The dynamic interaction between laser-generated tandem bubble and individual polystyrene particles of 2 and 10 μm in diameter is studied in a microfluidic channel (25 μm height) by high-speed imaging and particle image velocimetry. The asymmetric collapse of the tandem bubble produces a pair of microjets and associated long-lasting vortices that can propel a single particle to a maximum velocity of 1.4 m/s in 30 μs after the bubble collapse with a resultant directional displacement up to 60 μm in 150 μs. This method may be useful for high-throughput cell sorting in microfluidic devices.

Setup for irradiation and characterization of materials and Si particle detectors at cryogenic temperatures

NASA Astrophysics Data System (ADS)

Väyrynen, S.; Pusa, P.; Sane, P.; Tikkanen, P.; Räisänen, J.; Kuitunen, K.; Tuomisto, F.; Härkönen, J.; Kassamakov, I.; Tuominen, E.; Tuovinen, E.

2007-03-01

A novel facility for proton irradiation with sample cryocooling has been developed at the Accelerator Laboratory of Helsinki University (equipped with a 5 MV tandem accelerator). The setup enables unique experiments to be carried out within the temperature range of 10-300 K. The setup has been constructed for "on-line" studies of vacancies with positron annihilation spectroscopy (PAS) including the option for optical ionization of the vacancies, and for current-voltage ( IV) measurements of irradiated silicon particle detectors. The setup is described in detail and typical performance characteristics are provided. The facility functionality was tested by performing PAS experiments with high-resistivity silicon and by IV measurements for two types of irradiated silicon particle detectors.

Evaluation of the kinase domain of c-KIT in canine cutaneous mast cell tumors

PubMed Central

Webster, Joshua D; Kiupel, Matti; Yuzbasiyan-Gurkan, Vilma

2006-01-01

Background Mutations in the c-KIT proto-oncogene have been implicated in the progression of several neoplastic diseases, including gastrointestinal stromal tumors and mastocytosis in humans, and cutaneous mast cell tumors (MCTs) in canines. Mutations in human mastocytosis patients primarily occur in c-KIT exon 17, which encodes a portion of its kinase domain. In contrast, deletions and internal tandem duplication (ITD) mutations are found in the juxtamembrane domain of c-KIT in approximately 15% of canine MCTs. In addition, ITD c-KIT mutations are significantly associated with aberrant KIT protein localization in canine MCTs. However, some canine MCTs have aberrant KIT localization but lack ITD c-KIT mutations, suggesting that other mutations or other factors may be responsible for aberrant KIT localization in these tumors. Methods In order to characterize the prevalence of mutations in the phospho-transferase portion of c-KIT's kinase domain in canine MCTs exons 16–20 of 33 canine MCTs from 33 dogs were amplified and sequenced. Additionally, in order to determine if mutations in c-KIT exon 17 are responsible for aberrant KIT localization in MCTs that lack juxtamembrane domain c-KIT mutations, c-KIT exon 17 was amplified and sequenced from 18 canine MCTs that showed an aberrant KIT localization pattern but did not have ITD c-KIT mutations. Results No mutations or polymorphisms were identified in exons 16–20 of any of the MCTs examined. Conclusion In conclusion, mutations in the phospho-transferase portion of c-KIT's kinase domain do not play an important role in the progression of canine cutaneous MCTs, or in the aberrant localization of KIT in canine MCTs. PMID:16579858

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

USDA-ARS?s Scientific Manuscript database

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres comprise of megabase-scale arrays of tandem repeats. The true prevalence of centromere tandem repeats, and whether they exhibit conserved seque...

Monolithic Perovskite Silicon Tandem Solar Cells with Advanced Optics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goldschmidt, Jan C.; Bett, Alexander J.; Bivour, Martin

2016-11-14

For high efficiency monolithic perovskite silicon tandem solar cells, we develop low-temperature processes for the perovskite top cell, rear-side light trapping, optimized perovskite growth, transparent contacts and adapted characterization methods.

Perovskite Solar Cells with Large-Area CVD-Graphene for Tandem Solar Cells.

PubMed

Lang, Felix; Gluba, Marc A; Albrecht, Steve; Rappich, Jörg; Korte, Lars; Rech, Bernd; Nickel, Norbert H

2015-07-16

Perovskite solar cells with transparent contacts may be used to compensate for thermalization losses of silicon solar cells in tandem devices. This offers a way to outreach stagnating efficiencies. However, perovskite top cells in tandem structures require contact layers with high electrical conductivity and optimal transparency. We address this challenge by implementing large-area graphene grown by chemical vapor deposition as a highly transparent electrode in perovskite solar cells, leading to identical charge collection efficiencies. Electrical performance of solar cells with a graphene-based contact reached those of solar cells with standard gold contacts. The optical transmission by far exceeds that of reference devices and amounts to 64.3% below the perovskite band gap. Finally, we demonstrate a four-terminal tandem device combining a high band gap graphene-contacted perovskite top solar cell (Eg = 1.6 eV) with an amorphous/crystalline silicon bottom solar cell (Eg = 1.12 eV).

The First Tandem, All-exciplex-based WOLED

NASA Astrophysics Data System (ADS)

Hung, Wen-Yi; Fang, Guan-Cheng; Lin, Shih-Wei; Cheng, Shuo-Hsien; Wong, Ken-Tsung; Kuo, Ting-Yi; Chou, Pi-Tai

2014-06-01

Exploiting our recently developed bilayer interface methodology, together with a new wide energy-gap, low LUMO acceptor (A) and the designated donor (D) layers, we succeeded in fabricating an exciplex-based organic light-emitting diode (OLED) systematically tuned from blue to red. Further optimization rendered a record-high blue exciplex OLED with ηext of 8%. We then constructed a device structure configured by two parallel blend layers of mCP/PO-T2T and DTAF/PO-T2T, generating blue and yellow exciplex emission, respectively. The resulting device demonstrates for the first time a tandem, all-exciplex-based white-light OLED (WOLED) with excellent efficiencies ηext: 11.6%, ηc: 27.7 cd A-1, and ηp: 15.8 ml W-1 with CIE(0.29, 0.35) and CRI 70.6 that are nearly independent of EL intensity. The tandem architecture and blend-layer D/A (1:1) configuration are two key elements that fully utilize the exciplex delay fluorescence, providing a paragon for the use of low-cost, abundant organic compounds en route to commercial WOLEDs.

Wasatch: An architecture-proof multiphysics development environment using a Domain Specific Language and graph theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saad, Tony; Sutherland, James C.

To address the coding and software challenges of modern hybrid architectures, we propose an approach to multiphysics code development for high-performance computing. This approach is based on using a Domain Specific Language (DSL) in tandem with a directed acyclic graph (DAG) representation of the problem to be solved that allows runtime algorithm generation. When coupled with a large-scale parallel framework, the result is a portable development framework capable of executing on hybrid platforms and handling the challenges of multiphysics applications. In addition, we share our experience developing a code in such an environment – an effort that spans an interdisciplinarymore » team of engineers and computer scientists.« less

Wasatch: An architecture-proof multiphysics development environment using a Domain Specific Language and graph theory

DOE PAGES

Saad, Tony; Sutherland, James C.

2016-05-04

To address the coding and software challenges of modern hybrid architectures, we propose an approach to multiphysics code development for high-performance computing. This approach is based on using a Domain Specific Language (DSL) in tandem with a directed acyclic graph (DAG) representation of the problem to be solved that allows runtime algorithm generation. When coupled with a large-scale parallel framework, the result is a portable development framework capable of executing on hybrid platforms and handling the challenges of multiphysics applications. In addition, we share our experience developing a code in such an environment – an effort that spans an interdisciplinarymore » team of engineers and computer scientists.« less

Inter-subunit interactions across the upper voltage sensing-pore domain interface contribute to the concerted pore opening transition of Kv channels.

PubMed

Shem-Ad, Tzilhav; Irit, Orr; Yifrach, Ofer

2013-01-01

The tight electro-mechanical coupling between the voltage-sensing and pore domains of Kv channels lies at the heart of their fundamental roles in electrical signaling. Structural data have identified two voltage sensor pore inter-domain interaction surfaces, thus providing a framework to explain the molecular basis for the tight coupling of these domains. While the contribution of the intra-subunit lower domain interface to the electro-mechanical coupling that underlies channel opening is relatively well understood, the contribution of the inter-subunit upper interface to channel gating is not yet clear. Relying on energy perturbation and thermodynamic coupling analyses of tandem-dimeric Shaker Kv channels, we show that mutation of upper interface residues from both sides of the voltage sensor-pore domain interface stabilizes the closed channel state. These mutations, however, do not affect slow inactivation gating. We, moreover, find that upper interface residues form a network of state-dependent interactions that stabilize the open channel state. Finally, we note that the observed residue interaction network does not change during slow inactivation gating. The upper voltage sensing-pore interaction surface thus only undergoes conformational rearrangements during channel activation gating. We suggest that inter-subunit interactions across the upper domain interface mediate allosteric communication between channel subunits that contributes to the concerted nature of the late pore opening transition of Kv channels.

Pwp2 mediates UTP-B assembly via two structurally independent domains.

PubMed

Boissier, Fanny; Schmidt, Christina Maria; Linnemann, Jan; Fribourg, Sébastien; Perez-Fernandez, Jorge

2017-06-09

The SSU processome constitutes a large ribonucleoprotein complex involved in the early steps of ribosome biogenesis. UTP-B is one of the first multi-subunit protein complexes that associates with the pre-ribosomal RNA to form the SSU processome. To understand the molecular basis of the hierarchical assembly of the SSU-processome, we have undergone a structural and functional analysis of the UTP-B subunit Pwp2p. We show that Pwp2p is required for the proper assembly of UTP-B and for a productive association of UTP-B with pre-rRNA. These two functions are mediated by two distinct structural domains. The N-terminal domain of Pwp2p folds into a tandem WD-repeat (tWD) that associates with Utp21p, Utp18p, and Utp6p to form a core complex. The CTDs of Pwp2p and Utp21p mediate the assembly of the heterodimer Utp12p:Utp13p that is required for the stable incorporation of the UTP-B complex in the SSU processome. Finally, we provide evidence suggesting a role of UTP-B as a platform for the binding of assembly factors during the maturation of 20S rRNA precursors.

Bifacial tandem solar cells

DOEpatents

Wojtczuk, Steven J.; Chiu, Philip T.; Zhang, Xuebing; Gagnon, Edward; Timmons, Michael

2016-06-14

A method of fabricating on a semiconductor substrate bifacial tandem solar cells with semiconductor subcells having a lower bandgap than the substrate bandgap on one side of the substrate and with subcells having a higher bandgap than the substrate on the other including, first, growing a lower bandgap subcell on one substrate side that uses only the same periodic table group V material in the dislocation-reducing grading layers and bottom subcells as is present in the substrate and after the initial growth is complete and then flipping the substrate and growing the higher bandgap subcells on the opposite substrate side which can be of different group V material.

Optimizing Algorithm Choice for Metaproteomics: Comparing X!Tandem and Proteome Discoverer for Soil Proteomes

NASA Astrophysics Data System (ADS)

Diaz, K. S.; Kim, E. H.; Jones, R. M.; de Leon, K. C.; Woodcroft, B. J.; Tyson, G. W.; Rich, V. I.

2014-12-01

The growing field of metaproteomics links microbial communities to their expressed functions by using mass spectrometry methods to characterize community proteins. Comparison of mass spectrometry protein search algorithms and their biases is crucial for maximizing the quality and amount of protein identifications in mass spectral data. Available algorithms employ different approaches when mapping mass spectra to peptides against a database. We compared mass spectra from four microbial proteomes derived from high-organic content soils searched with two search algorithms: 1) Sequest HT as packaged within Proteome Discoverer (v.1.4) and 2) X!Tandem as packaged in TransProteomicPipeline (v.4.7.1). Searches used matched metagenomes, and results were filtered to allow identification of high probability proteins. There was little overlap in proteins identified by both algorithms, on average just ~24% of the total. However, when adjusted for spectral abundance, the overlap improved to ~70%. Proteome Discoverer generally outperformed X!Tandem, identifying an average of 12.5% more proteins than X!Tandem, with X!Tandem identifying more proteins only in the first two proteomes. For spectrally-adjusted results, the algorithms were similar, with X!Tandem marginally outperforming Proteome Discoverer by an average of ~4%. We then assessed differences in heat shock proteins (HSP) identification by the two algorithms by BLASTing identified proteins against the Heat Shock Protein Information Resource, because HSP hits typically account for the majority signal in proteomes, due to extraction protocols. Total HSP identifications for each of the 4 proteomes were approximately ~15%, ~11%, ~17%, and ~19%, with ~14% for total HSPs with redundancies removed. Of the ~15% average of proteins from the 4 proteomes identified as HSPs, ~10% of proteins and spectra were identified by both algorithms. On average, Proteome Discoverer identified ~9% more HSPs than X!Tandem.

Indium Zinc Oxide Mediated Wafer Bonding for III-V/Si Tandem Solar Cells