Direct Protein Interactions Are Responsible for Ikaros-GATA and Ikaros-Cdk9 Cooperativeness in Hematopoietic Cells

PubMed Central

Bottardi, Stefania; Mavoungou, Lionel; Bourgoin, Vincent; Mashtalir, Nazar; Affar, El Bachir

2013-01-01

Ikaros (Ik) is a critical regulator of hematopoietic gene expression. Here, we established that the Ik interactions with GATA transcription factors and cyclin-dependent kinase 9 (Cdk9), a component of the positive transcription elongation factor b (P-TEFb), are required for transcriptional activation of Ik target genes. A detailed dissection of Ik-GATA and Ik-Cdk9 protein interactions indicated that the C-terminal zinc finger domain of Ik interacts directly with the C-terminal zinc fingers of GATA1, GATA2, and GATA3, whereas the N-terminal zinc finger domain of Ik is required for interaction with the kinase and T-loop domains of Cdk9. The relevance of these interactions was demonstrated in vivo in COS-7 and primary hematopoietic cells, in which Ik facilitated Cdk9 and GATA protein recruitment to gene promoters and transcriptional activation. Moreover, the oncogenic isoform Ik6 did not efficiently interact with Cdk9 or GATA proteins in vivo and perturbed Cdk9/P-TEFb recruitment to Ik target genes, thereby affecting transcription elongation. Finally, characterization of a novel nuclear Ik isoform revealed that Ik exon 6 is dispensable for interactions with Mi2 and GATA proteins but is essential for the Cdk9 interaction. Thus, Ik is central to the Ik-GATA-Cdk9 regulatory network, which is broadly utilized for gene regulation in hematopoietic cells. PMID:23732910

Direct protein interactions are responsible for Ikaros-GATA and Ikaros-Cdk9 cooperativeness in hematopoietic cells.

PubMed

Bottardi, Stefania; Mavoungou, Lionel; Bourgoin, Vincent; Mashtalir, Nazar; Affar, El Bachir; Milot, Eric

2013-08-01

Ikaros (Ik) is a critical regulator of hematopoietic gene expression. Here, we established that the Ik interactions with GATA transcription factors and cyclin-dependent kinase 9 (Cdk9), a component of the positive transcription elongation factor b (P-TEFb), are required for transcriptional activation of Ik target genes. A detailed dissection of Ik-GATA and Ik-Cdk9 protein interactions indicated that the C-terminal zinc finger domain of Ik interacts directly with the C-terminal zinc fingers of GATA1, GATA2, and GATA3, whereas the N-terminal zinc finger domain of Ik is required for interaction with the kinase and T-loop domains of Cdk9. The relevance of these interactions was demonstrated in vivo in COS-7 and primary hematopoietic cells, in which Ik facilitated Cdk9 and GATA protein recruitment to gene promoters and transcriptional activation. Moreover, the oncogenic isoform Ik6 did not efficiently interact with Cdk9 or GATA proteins in vivo and perturbed Cdk9/P-TEFb recruitment to Ik target genes, thereby affecting transcription elongation. Finally, characterization of a novel nuclear Ik isoform revealed that Ik exon 6 is dispensable for interactions with Mi2 and GATA proteins but is essential for the Cdk9 interaction. Thus, Ik is central to the Ik-GATA-Cdk9 regulatory network, which is broadly utilized for gene regulation in hematopoietic cells.

Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation

PubMed Central

Zhang, Qingzhu; Wang, Dong; Lang, Zhaobo; He, Li; Yang, Lan; Zeng, Liang; Li, Yanqiang; Zhao, Cheng; Huang, Huan; Zhang, Heng; Zhang, Huiming; Zhu, Jian-Kang

2016-01-01

DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hybrids displayed nonadditive DNA methylation levels, termed methylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differentially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interactions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution. PMID:27382183

microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein.

PubMed

Pinder, Benjamin D; Smibert, Craig A

2013-01-01

Argonaute (Ago) proteins are typically recruited to target messenger RNAs via an associated small RNA such as a microRNA (miRNA). Here, we describe a new mechanism of Ago recruitment through the Drosophila Smaug RNA-binding protein. We show that Smaug interacts with the Ago1 protein, and that Ago1 interacts with and is required for the translational repression of the Smaug target, nanos mRNA. The Ago1/nanos mRNA interaction does not require a miRNA, but it does require Smaug. Taken together, our data suggest a model whereby Smaug directly recruits Ago1 to nanos mRNA in a miRNA-independent manner, thereby repressing translation.

Interaction mining and skill-dependent recommendations for multi-objective team composition

PubMed Central

Dorn, Christoph; Skopik, Florian; Schall, Daniel; Dustdar, Schahram

2011-01-01

Web-based collaboration and virtual environments supported by various Web 2.0 concepts enable the application of numerous monitoring, mining and analysis tools to study human interactions and team formation processes. The composition of an effective team requires a balance between adequate skill fulfillment and sufficient team connectivity. The underlying interaction structure reflects social behavior and relations of individuals and determines to a large degree how well people can be expected to collaborate. In this paper we address an extended team formation problem that does not only require direct interactions to determine team connectivity but additionally uses implicit recommendations of collaboration partners to support even sparsely connected networks. We provide two heuristics based on Genetic Algorithms and Simulated Annealing for discovering efficient team configurations that yield the best trade-off between skill coverage and team connectivity. Our self-adjusting mechanism aims to discover the best combination of direct interactions and recommendations when deriving connectivity. We evaluate our approach based on multiple configurations of a simulated collaboration network that features close resemblance to real world expert networks. We demonstrate that our algorithm successfully identifies efficient team configurations even when removing up to 40% of experts from various social network configurations. PMID:22298939

Chromatin Protein HP1α Interacts with the Mitotic Regulator Borealin Protein and Specifies the Centromere Localization of the Chromosomal Passenger Complex*

PubMed Central

Liu, Xing; Song, Zhenwei; Huo, Yuda; Zhang, Jiahai; Zhu, Tongge; Wang, Jianyu; Zhao, Xuannv; Aikhionbare, Felix; Zhang, Jiancun; Duan, Hequan; Wu, Jihui; Dou, Zhen; Shi, Yunyu; Yao, Xuebiao

2014-01-01

Accurate mitosis requires the chromosomal passenger protein complex (CPC) containing Aurora B kinase, borealin, INCENP, and survivin, which orchestrates chromosome dynamics. However, the chromatin factors that specify the CPC to the centromere remain elusive. Here we show that borealin interacts directly with heterochromatin protein 1α (HP1α) and that this interaction is mediated by an evolutionarily conserved PXVXL motif in the C-terminal borealin with the chromo shadow domain of HP1α. This borealin-HP1α interaction recruits the CPC to the centromere and governs an activation of Aurora B kinase judged by phosphorylation of Ser-7 in CENP-A, a substrate of Aurora B. Consistently, modulation of the motif PXVXL leads to defects in CPC centromere targeting and aberrant Aurora B activity. On the other hand, the localization of the CPC in the midzone is independent of the borealin-HP1α interaction, demonstrating the spatial requirement of HP1α in CPC localization to the centromere. These findings reveal a previously unrecognized but direct link between HP1α and CPC localization in the centromere and illustrate the critical role of borealin-HP1α interaction in orchestrating an accurate cell division. PMID:24917673

Resistance to mitomycin C requires direct interaction between the Fanconi anemia proteins FANCA and FANCG in the nucleus through an arginine-rich domain.

PubMed

Kruyt, F A; Abou-Zahr, F; Mok, H; Youssoufian, H

1999-11-26

Fanconi anemia (FA) is a genetically heterogeneous disorder characterized by bone marrow failure, birth defects, and chromosomal instability. Because FA cells are sensitive to mitomycin C (MMC), FA gene products could be involved in cellular defense mechanisms. The FANCA and FANCG proteins deficient in FA groups A and G interact directly with each other. We have localized the mutual interaction domains of these proteins to amino acids 18-29 of FANCA and to two noncontiguous carboxyl-terminal domains of FANCG encompassing amino acids 400-475 and 585-622. Site-directed mutagenesis of FANCA residues 18-29 revealed a novel arginine-rich interaction domain (RRRAWAELLAG). By alanine mutagenesis, Arg(1), Arg(2), and Leu(8) but not Arg(3), Trp(5), and Glu(7) appeared to be critical for binding to FANCG. Similar immunolocalization for FANCA and FANCG suggested that these proteins interact in vivo. Moreover, targeting of FANCA to the nucleus or the cytoplasm with nuclear localization and nuclear export signals, respectively, showed concordance between the localization patterns of FANCA and FANCG. The complementation function of FANCA was abolished by mutations in its FANCG-binding domain. Conversely, stable expression of FANCA mutants encoding intact FANCG interaction domains induced hypersensitivity to MMC in HeLa cells. These results demonstrate that FANCA-FANCG complexes are required for cellular resistance to MMC. Because the FANCC protein deficient in FA group C works within the cytoplasm, we suggest that FANCC and the FANCA-FANCG complexes suppress MMC cytotoxicity within distinct cellular compartments.

Directed Interaction Between Monkey Premotor and Posterior Parietal Cortex During Motor-Goal Retrieval from Working Memory

PubMed Central

Martínez-Vázquez, Pablo; Gail, Alexander

2018-01-01

Abstract Goal-directed behavior requires cognitive control of action, putatively by means of frontal-lobe impact on posterior brain areas. We investigated frontoparietal directed interaction (DI) in monkeys during memory-guided rule-based reaches, to test if DI supports motor-goal selection or working memory (WM) processes. We computed DI between the parietal reach region (PRR) and dorsal premotor cortex (PMd) with a Granger-causality measure of intracortical local field potentials (LFP). LFP mostly in the beta (12–32 Hz) and low-frequency (f≤10Hz) ranges contributed to DI. During movement withholding, beta-band activity in PRR had a Granger-causal effect on PMd independent of WM content. Complementary, low-frequency PMd activity had a transient Granger-causing effect on PRR specifically during WM retrieval of spatial motor goals, while no DI was associated with preliminary motor-goal selection. Our results support the idea that premotor and posterior parietal cortices interact functionally to achieve cognitive control during goal-directed behavior, in particular, that frontal-to-parietal interaction occurs during retrieval of motor-goal information from spatial WM. PMID:29481586

Directed Interaction Between Monkey Premotor and Posterior Parietal Cortex During Motor-Goal Retrieval from Working Memory.

PubMed

Martínez-Vázquez, Pablo; Gail, Alexander

2018-05-01

Goal-directed behavior requires cognitive control of action, putatively by means of frontal-lobe impact on posterior brain areas. We investigated frontoparietal directed interaction (DI) in monkeys during memory-guided rule-based reaches, to test if DI supports motor-goal selection or working memory (WM) processes. We computed DI between the parietal reach region (PRR) and dorsal premotor cortex (PMd) with a Granger-causality measure of intracortical local field potentials (LFP). LFP mostly in the beta (12-32 Hz) and low-frequency (f≤10Hz) ranges contributed to DI. During movement withholding, beta-band activity in PRR had a Granger-causal effect on PMd independent of WM content. Complementary, low-frequency PMd activity had a transient Granger-causing effect on PRR specifically during WM retrieval of spatial motor goals, while no DI was associated with preliminary motor-goal selection. Our results support the idea that premotor and posterior parietal cortices interact functionally to achieve cognitive control during goal-directed behavior, in particular, that frontal-to-parietal interaction occurs during retrieval of motor-goal information from spatial WM.

PREMER: a Tool to Infer Biological Networks.

PubMed

Villaverde, Alejandro F; Becker, Kolja; Banga, Julio R

2017-10-04

Inferring the structure of unknown cellular networks is a main challenge in computational biology. Data-driven approaches based on information theory can determine the existence of interactions among network nodes automatically. However, the elucidation of certain features - such as distinguishing between direct and indirect interactions or determining the direction of a causal link - requires estimating information-theoretic quantities in a multidimensional space. This can be a computationally demanding task, which acts as a bottleneck for the application of elaborate algorithms to large-scale network inference problems. The computational cost of such calculations can be alleviated by the use of compiled programs and parallelization. To this end we have developed PREMER (Parallel Reverse Engineering with Mutual information & Entropy Reduction), a software toolbox that can run in parallel and sequential environments. It uses information theoretic criteria to recover network topology and determine the strength and causality of interactions, and allows incorporating prior knowledge, imputing missing data, and correcting outliers. PREMER is a free, open source software tool that does not require any commercial software. Its core algorithms are programmed in FORTRAN 90 and implement OpenMP directives. It has user interfaces in Python and MATLAB/Octave, and runs on Windows, Linux and OSX (https://sites.google.com/site/premertoolbox/).

Self-interacting inelastic dark matter: a viable solution to the small scale structure problems

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

Blennow, Mattias; Clementz, Stefan; Herrero-Garcia, Juan, E-mail: emb@kth.se, E-mail: scl@kth.se, E-mail: juan.herrero-garcia@adelaide.edu.au

2017-03-01

Self-interacting dark matter has been proposed as a solution to the small-scale structure problems, such as the observed flat cores in dwarf and low surface brightness galaxies. If scattering takes place through light mediators, the scattering cross section relevant to solve these problems may fall into the non-perturbative regime leading to a non-trivial velocity dependence, which allows compatibility with limits stemming from cluster-size objects. However, these models are strongly constrained by different observations, in particular from the requirements that the decay of the light mediator is sufficiently rapid (before Big Bang Nucleosynthesis) and from direct detection. A natural solution tomore » reconcile both requirements are inelastic endothermic interactions, such that scatterings in direct detection experiments are suppressed or even kinematically forbidden if the mass splitting between the two-states is sufficiently large. Using an exact solution when numerically solving the Schrödinger equation, we study such scenarios and find regions in the parameter space of dark matter and mediator masses, and the mass splitting of the states, where the small scale structure problems can be solved, the dark matter has the correct relic abundance and direct detection limits can be evaded.« less

Exploring interaction with 3D volumetric displays

NASA Astrophysics Data System (ADS)

Grossman, Tovi; Wigdor, Daniel; Balakrishnan, Ravin

2005-03-01

Volumetric displays generate true volumetric 3D images by actually illuminating points in 3D space. As a result, viewing their contents is similar to viewing physical objects in the real world. These displays provide a 360 degree field of view, and do not require the user to wear hardware such as shutter glasses or head-trackers. These properties make them a promising alternative to traditional display systems for viewing imagery in 3D. Because these displays have only recently been made available commercially (e.g., www.actuality-systems.com), their current use tends to be limited to non-interactive output-only display devices. To take full advantage of the unique features of these displays, however, it would be desirable if the 3D data being displayed could be directly interacted with and manipulated. We investigate interaction techniques for volumetric display interfaces, through the development of an interactive 3D geometric model building application. While this application area itself presents many interesting challenges, our focus is on the interaction techniques that are likely generalizable to interactive applications for other domains. We explore a very direct style of interaction where the user interacts with the virtual data using direct finger manipulations on and around the enclosure surrounding the displayed 3D volumetric image.

G-protein-coupled receptor-2-interacting protein-1 is required for endothelial cell directional migration and tumor angiogenesis via cortactin-dependent lamellipodia formation.

PubMed

Majumder, Syamantak; Sowden, Mark P; Gerber, Scott A; Thomas, Tamlyn; Christie, Christine K; Mohan, Amy; Yin, Guoyong; Lord, Edith M; Berk, Bradford C; Pang, Jinjiang

2014-02-01

Recent evidence suggests G-protein-coupled receptor-2-interacting protein-1 (GIT1) overexpression in several human metastatic tumors, including breast, lung, and prostate. Tumor metastasis is associated with an increase in angiogenesis. We have showed previously that GIT1 is required for postnatal angiogenesis during lung development. However, the functional role of GIT1 in pathological angiogenesis during tumor growth is unknown. In the present study, we show inhibition of angiogenesis in matrigel implants as well as reduced tumor angiogenesis and melanoma tumor growth in GIT1-knockout mice. We demonstrate that this is a result of impaired directional migration of GIT1-depleted endothelial cells toward a vascular endothelial growth factor gradient. Cortactin-mediated lamellipodia formation in the leading edge is critical for directional migration. We observed a significant reduction in cortactin localization and lamellipodia formation in the leading edge of GIT1-depleted endothelial cells. We specifically identified that the Spa homology domain (aa 250-420) of GIT1 is required for GIT1-cortactin complex localization to the leading edge. The mechanisms involved extracellular signal-regulated kinases 1 and 2-mediated Cortactin-S405 phosphorylation and activation of Rac1/Cdc42. Finally, using gain of function studies, we show that a constitutively active mutant of cortactin restored directional migration of GIT1-depleted cells. Our data demonstrated that a GIT1-cortactin association through GIT1-Spa homology domain is required for cortactin localization to the leading edge and is essential for endothelial cell directional migration and tumor angiogenesis.

Ubc13 and COOH Terminus of Hsp70-interacting Protein (CHIP) Are Required for Growth Hormone Receptor Endocytosis*

PubMed Central

Slotman, Johan A.; da Silva Almeida, Ana C.; Hassink, Gerco C.; van de Ven, Robert H. A.; van Kerkhof, Peter; Kuiken, Hendrik J.; Strous, Ger J.

2012-01-01

Growth hormone receptor (GHR) endocytosis is a highly regulated process that depends on the binding and activity of the multimeric ubiquitin ligase, SCFβTrCP (Skp Cullin F-box). Despite a specific interaction between β-transducin repeat-containing protein (βTrCP) and the GHR, and a strict requirement for ubiquitination activity, the receptor is not an obligatory target for SCFβTrCP-directed Lys48 polyubiquitination. We now show that also Lys63-linked ubiquitin chain formation is required for GHR endocytosis. We identified both the ubiquitin-conjugating enzyme Ubc13 and the ubiquitin ligase COOH terminus of Hsp70 interacting protein (CHIP) as being connected to this process. Ubc13 activity and its interaction with CHIP precede endocytosis of GHR. In addition to βTrCP, CHIP interacts specifically with the cytosolic tails of the dimeric GHR, identifying both Ubc13 and CHIP as novel factors in the regulation of cell surface availability of GHR. PMID:22433856

Direct Simulation of Friction Forces for Heavy Ions Interacting with a Warm Magnetized Electron Distribution

NASA Astrophysics Data System (ADS)

Bruhwiler, D. L.; Busby, R.; Fedotov, A. V.; Ben-Zvi, I.; Cary, J. R.; Stoltz, P.; Burov, A.; Litvinenko, V. N.; Messmer, P.; Abell, D.; Nieter, C.

2005-06-01

A proposed luminosity upgrade to RHIC includes a novel electron cooling section, which would use ˜55 MeV electrons to cool fully-ionized 100 GeV/nucleon gold ions. High-current bunched electron beams are required for the RHIC cooler, resulting in very high transverse temperatures and relatively low values for the magnetized cooling logarithm. The accuracy of analytical formulae in this regime requires careful examination. Simulations of the friction coefficient, using the VORPAL code, for single gold ions passing once through the interaction region, are compared with theoretical calculations. Charged particles are advanced using a fourth-order Hermite predictor-corrector algorithm. The fields in the beam frame are obtained from direct calculation of Coulomb's law, which is more efficient than multipole-type algorithms for less than ˜106 particles. Because the interaction time is so short, it is necessary to suppress the diffusive aspect of the ion dynamics through the careful use of positrons in the simulations.

Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness.

PubMed

Reiter, Johannes G; Hilbe, Christian; Rand, David G; Chatterjee, Krishnendu; Nowak, Martin A

2018-02-07

Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze "crosstalk" between a player's concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person's decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games.

Dynamic Network-Based Relevance Score Reveals Essential Proteins and Functional Modules in Directed Differentiation

PubMed Central

Wu, Chia-Chou; Lin, Che

2015-01-01

The induction of stem cells toward a desired differentiation direction is required for the advancement of stem cell-based therapies. Despite successful demonstrations of the control of differentiation direction, the effective use of stem cell-based therapies suffers from a lack of systematic knowledge regarding the mechanisms underlying directed differentiation. Using dynamic modeling and the temporal microarray data of three differentiation stages, three dynamic protein-protein interaction networks were constructed. The interaction difference networks derived from the constructed networks systematically delineated the evolution of interaction variations and the underlying mechanisms. A proposed relevance score identified the essential components in the directed differentiation. Inspection of well-known proteins and functional modules in the directed differentiation showed the plausibility of the proposed relevance score, with the higher scores of several proteins and function modules indicating their essential roles in the directed differentiation. During the differentiation process, the proteins and functional modules with higher relevance scores also became more specific to the neuronal identity. Ultimately, the essential components revealed by the relevance scores may play a role in controlling the direction of differentiation. In addition, these components may serve as a starting point for understanding the systematic mechanisms of directed differentiation and for increasing the efficiency of stem cell-based therapies. PMID:25977693

Transgenic Mice Expressing an Inhibitory Truncated Form of p300 Exhibit Long-Term Memory Deficits

ERIC Educational Resources Information Center

Oliveira, Ana M. M.; Wood, Marcelo A.; McDonough, Conor B.; Abel, Ted

2007-01-01

The formation of many forms of long-term memory requires several molecular mechanisms including regulation of gene expression. The mechanisms directing transcription require not only activation of individual transcription factors but also recruitment of transcriptional coactivators. CBP and p300 are transcriptional coactivators that interact with…

Centrobin–tubulin interaction is required for centriole elongation and stability

PubMed Central

Gudi, Radhika; Zou, Chaozhong; Li, Jun

2011-01-01

Centrobin is a daughter centriole protein that is essential for centrosome duplication. However, the molecular mechanism by which centrobin functions during centriole duplication remains undefined. In this study, we show that centrobin interacts with tubulin directly, and centrobin–tubulin interaction is pivotal for the function of centrobin during centriole duplication. We found that centrobin is recruited to the centriole biogenesis site via its interaction with tubulins during the early stage of centriole biogenesis, and its recruitment is dependent on hSAS-6 but not centrosomal P4.1–associated protein (CPAP) and CP110. The function of centrobin is also required for the elongation of centrioles, which is likely mediated by its interaction with tubulin. Furthermore, disruption of centrobin–tubulin interaction led to destabilization of existing centrioles and the preformed procentriole-like structures induced by CPAP expression, indicating that centrobin–tubulin interaction is critical for the stability of centrioles. Together, our study demonstrates that centrobin facilitates the elongation and stability of centrioles via its interaction with tubulins. PMID:21576394

The cognitive benefits of interacting with nature.

PubMed

Berman, Marc G; Jonides, John; Kaplan, Stephen

2008-12-01

We compare the restorative effects on cognitive functioning of interactions with natural versus urban environments. Attention restoration theory (ART) provides an analysis of the kinds of environments that lead to improvements in directed-attention abilities. Nature, which is filled with intriguing stimuli, modestly grabs attention in a bottom-up fashion, allowing top-down directed-attention abilities a chance to replenish. Unlike natural environments, urban environments are filled with stimulation that captures attention dramatically and additionally requires directed attention (e.g., to avoid being hit by a car), making them less restorative. We present two experiments that show that walking in nature or viewing pictures of nature can improve directed-attention abilities as measured with a backwards digit-span task and the Attention Network Task, thus validating attention restoration theory.

A Maximum NEC Criterion for Compton Collimation to Accurately Identify True Coincidences in PET

PubMed Central

Chinn, Garry; Levin, Craig S.

2013-01-01

In this work, we propose a new method to increase the accuracy of identifying true coincidence events for positron emission tomography (PET). This approach requires 3-D detectors with the ability to position each photon interaction in multi-interaction photon events. When multiple interactions occur in the detector, the incident direction of the photon can be estimated using the Compton scatter kinematics (Compton Collimation). If the difference between the estimated incident direction of the photon relative to a second, coincident photon lies within a certain angular range around colinearity, the line of response between the two photons is identified as a true coincidence and used for image reconstruction. We present an algorithm for choosing the incident photon direction window threshold that maximizes the noise equivalent counts of the PET system. For simulated data, the direction window removed 56%–67% of random coincidences while retaining > 94% of true coincidences from image reconstruction as well as accurately extracted 70% of true coincidences from multiple coincidences. PMID:21317079

Direct visualization reveals kinetics of meiotic chromosome synapsis

DOE PAGES

Rog, Ofer; Dernburg, Abby  F.

2015-03-17

The synaptonemal complex (SC) is a conserved protein complex that stabilizes interactions along homologous chromosomes (homologs) during meiosis. The SC regulates genetic exchanges between homologs, thereby enabling reductional division and the production of haploid gametes. Here, we directly observe SC assembly (synapsis) by optimizing methods for long-term fluorescence recording in C. elegans. We report that synapsis initiates independently on each chromosome pair at or near pairing centers—specialized regions required for homolog associations. Once initiated, the SC extends rapidly and mostly irreversibly to chromosome ends. Quantitation of SC initiation frequencies and extension rates reveals that initiation is a rate-limiting step inmore » homolog interactions. Eliminating the dynein-driven chromosome movements that accompany synapsis severely retards SC extension, revealing a new role for these conserved motions. This work provides the first opportunity to directly observe and quantify key aspects of meiotic chromosome interactions and will enable future in vivo analysis of germline processes.« less

Interactions between late acting proteins required for peptidoglycan synthesis during sporulation

PubMed Central

Fay, Allison; Meyer, Pablo; Dworkin, Jonathan

2010-01-01

The requirement of peptidoglycan synthesis for growth complicates the analysis of interactions between proteins involved in this pathway. In particular, the later steps that involve membrane-linked substrates have proven largely recalcitrant to in vivo analysis. Here we have taken advantage of the peptidoglycan synthesis that occurs during sporulation in Bacillus subtilis to examine the interactions between SpoVE, a non-essential, sporulation-specific homolog of the well-conserved and essential SEDS proteins, and SpoVD, a non-essential class B penicillin binding protein (PBP). We found that localization of SpoVD is dependent on SpoVE and that SpoVD protects SpoVE from in vivo proteolysis. Co-immunoprecipitations and Fluorescence Resonance Energy Transfer experiments indicated that SpoVE and SpoVD interact and co-affinity purification in E. coli demonstrated that this interaction is direct. Finally, we generated a functional protein consisting of a SpoVE-SpoVD fusion and found that a loss-of-function point mutation in either part of the fusion resulted in a loss of function of the entire fusion that was not complemented by a wild type protein. Thus, SpoVE has a direct and functional interaction with SpoVD and this conclusion will facilitate understanding the essential function SpoVE and related SEDS proteins such as FtsW and RodA play in bacterial growth and division. PMID:20417640

Specificity in cationic interaction with poly(N-isopropylacrylamide).

PubMed

Du, Hongbo; Wickramasinghe, Sumith Ranil; Qian, Xianghong

2013-05-02

Classical molecular dynamics (MD) simulations were conducted for PNIPAM in 1 M monovalent alkali chloride salt solutions as well as in 0.5 M divalent Mg(2+) and Ca(2+) chloride salt solutions. It was found that the strength for the direct alkali ion-amide O binding is strongly correlated with the size of the ionic radius. The smallest Li(+) ion binds strongest to amide O, and the largest Cs(+) ion has the weakest interaction with the amide bond. For the divalent Mg(2+) and Ca(2+) ions, their interactions with the amide bond are weak and appear to be mediated by the water molecules, particularly in the case of Mg(2+), resulting from their strong hydration. The direct binding between the cations and amide O requires partial desovlation of the ions that is energetically unfavorable for Mg(2+) and also to a great extent for Ca(2+). The higher cation charge makes the electrostatic interaction more favorable but the dehydration process less favorable. This competition between electrostatic interaction and the dehydration process largely dictates whether the direct binding between the cation and amide O is energetically preferred or not. For monovalent alkali ions, it is energetically preferred to bind directly with the amide O. Moreover, Li(+) ion is also found to associate strongly with the hydrophobic residues on PNIPAM.

Fatty Acid-binding Proteins Interact with Comparative Gene Identification-58 Linking Lipolysis with Lipid Ligand Shuttling*

PubMed Central

Hofer, Peter; Boeszoermenyi, Andras; Jaeger, Doris; Feiler, Ursula; Arthanari, Haribabu; Mayer, Nicole; Zehender, Fabian; Rechberger, Gerald; Oberer, Monika; Zimmermann, Robert; Lass, Achim; Haemmerle, Guenter; Breinbauer, Rolf; Zechner, Rudolf; Preiss-Landl, Karina

2015-01-01

The coordinated breakdown of intracellular triglyceride (TG) stores requires the exquisitely regulated interaction of lipolytic enzymes with regulatory, accessory, and scaffolding proteins. Together they form a dynamic multiprotein network designated as the “lipolysome.” Adipose triglyceride lipase (Atgl) catalyzes the initiating step of TG hydrolysis and requires comparative gene identification-58 (Cgi-58) as a potent activator of enzyme activity. Here, we identify adipocyte-type fatty acid-binding protein (A-Fabp) and other members of the fatty acid-binding protein (Fabp) family as interaction partners of Cgi-58. Co-immunoprecipitation, microscale thermophoresis, and solid phase assays proved direct protein/protein interaction between A-Fabp and Cgi-58. Using nuclear magnetic resonance titration experiments and site-directed mutagenesis, we located a potential contact region on A-Fabp. In functional terms, A-Fabp stimulates Atgl-catalyzed TG hydrolysis in a Cgi-58-dependent manner. Additionally, transcriptional transactivation assays with a luciferase reporter system revealed that Fabps enhance the ability of Atgl/Cgi-58-mediated lipolysis to induce the activity of peroxisome proliferator-activated receptors. Our studies identify Fabps as crucial structural and functional components of the lipolysome. PMID:25953897

Ebola Virus VP35 Interaction with Dynein LC8 Regulates Viral RNA Synthesis

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

Luthra, Priya; Jordan, David S.; Leung, Daisy W.

2015-03-04

Ebola virus VP35 inhibits alpha/beta interferon production and functions as a viral polymerase cofactor. Previously, the 8-kDa cytoplasmic dynein light chain (LC8) was demonstrated to interact with VP35, but the functional consequences were unclear. Here we demonstrate that the interaction is direct and of high affinity and that binding stabilizes the VP35 N-terminal oligomerization domain and enhances viral RNA synthesis. Mutational analysis demonstrates that VP35 interaction is required for the functional effects of LC8.

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

PubMed Central

Rahman, Masudur; Neff, David; Green, Nathaniel; Norton, Michael L.

2016-01-01

Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material. PMID:28335324

The CDM Superfamily Protein MBC Directs Myoblast Fusion through a Mechanism That Requires Phosphatidylinositol 3,4,5-Triphosphate Binding but Is Independent of Direct Interaction with DCrk▿§

PubMed Central

Balagopalan, Lakshmi; Chen, Mei-Hui; Geisbrecht, Erika R.; Abmayr, Susan M.

2006-01-01

myoblast city (mbc), a member of the CDM superfamily, is essential in the Drosophila melanogaster embryo for fusion of myoblasts into multinucleate fibers. Using germ line clones in which both maternal and zygotic contributions were eliminated and rescue of the zygotic loss-of-function phenotype, we established that mbc is required in the fusion-competent subset of myoblasts. Along with its close orthologs Dock180 and CED-5, MBC has an SH3 domain at its N terminus, conserved internal domains termed DHR1 and DHR2 (or “Docker”), and C-terminal proline-rich domains that associate with the adapter protein DCrk. The importance of these domains has been evaluated by the ability of MBC mutations and deletions to rescue the mbc loss-of-function muscle phenotype. We demonstrate that the SH3 and Docker domains are essential. Moreover, ethyl methanesulfonate-induced mutations that change amino acids within the MBC Docker domain to residues that are conserved in other CDM family members nevertheless eliminate MBC function in the embryo, which suggests that these sites may mediate interactions specific to Drosophila MBC. A functional requirement for the conserved DHR1 domain, which binds to phosphatidylinositol 3,4,5-triphosphate, implicates phosphoinositide signaling in myoblast fusion. Finally, the proline-rich C-terminal sites mediate strong interactions with DCrk, as expected. These sites are not required for MBC to rescue the muscle loss-of-function phenotype, however, which suggests that MBC's role in myoblast fusion can be carried out independently of direct DCrk binding. PMID:17030600

Arrestin Scaffolds NHERF1 to the P2Y12 Receptor to Regulate Receptor Internalization*

PubMed Central

Nisar, Shaista P.; Cunningham, Margaret; Saxena, Kunal; Pope, Robert J.; Kelly, Eamonn; Mundell, Stuart J.

2012-01-01

We have recently shown in a patient with mild bleeding that the PDZ-binding motif of the platelet G protein-coupled P2Y12 receptor (P2Y12R) is required for effective receptor traffic in human platelets. In this study we show for the first time that the PDZ motif-binding protein NHERF1 exerts a major role in potentiating G protein-coupled receptor (GPCR) internalization. NHERF1 interacts with the C-tail of the P2Y12R and unlike many other GPCRs, NHERF1 interaction is required for effective P2Y12R internalization. In vitro and prior to agonist stimulation P2Y12R/NHERF1 interaction requires the intact PDZ binding motif of this receptor. Interestingly on receptor stimulation NHERF1 no longer interacts directly with the receptor but instead binds to the receptor via the endocytic scaffolding protein arrestin. These findings suggest a novel model by which arrestin can serve as an adaptor to promote NHERF1 interaction with a GPCR to facilitate effective NHERF1-dependent receptor internalization. PMID:22610101

Arrestin scaffolds NHERF1 to the P2Y12 receptor to regulate receptor internalization.

PubMed

Nisar, Shaista P; Cunningham, Margaret; Saxena, Kunal; Pope, Robert J; Kelly, Eamonn; Mundell, Stuart J

2012-07-13

We have recently shown in a patient with mild bleeding that the PDZ-binding motif of the platelet G protein-coupled P2Y(12) receptor (P2Y(12)R) is required for effective receptor traffic in human platelets. In this study we show for the first time that the PDZ motif-binding protein NHERF1 exerts a major role in potentiating G protein-coupled receptor (GPCR) internalization. NHERF1 interacts with the C-tail of the P2Y(12)R and unlike many other GPCRs, NHERF1 interaction is required for effective P2Y(12)R internalization. In vitro and prior to agonist stimulation P2Y(12)R/NHERF1 interaction requires the intact PDZ binding motif of this receptor. Interestingly on receptor stimulation NHERF1 no longer interacts directly with the receptor but instead binds to the receptor via the endocytic scaffolding protein arrestin. These findings suggest a novel model by which arrestin can serve as an adaptor to promote NHERF1 interaction with a GPCR to facilitate effective NHERF1-dependent receptor internalization.

Development of a direct experimental test for any violation of the equivalence principle by the weak interaction

NASA Technical Reports Server (NTRS)

Parker, P. D. M.

1981-01-01

Violation of the equivalence principle by the weak interaction is tested. Any variation of the weak interaction coupling constant with gravitational potential, i.e., a spatial variation of the fundamental constants is investigated. The level of sensitivity required for such a measurement is estimated on the basis of the size of a change in the gravitational potential which is accessible. The alpha particle spectrum is analyzed, and the counting rate was improved by a factor of approximately 100.

Interactive real time flow simulations

NASA Technical Reports Server (NTRS)

Sadrehaghighi, I.; Tiwari, S. N.

1990-01-01

An interactive real time flow simulation technique is developed for an unsteady channel flow. A finite-volume algorithm in conjunction with a Runge-Kutta time stepping scheme was developed for two-dimensional Euler equations. A global time step was used to accelerate convergence of steady-state calculations. A raster image generation routine was developed for high speed image transmission which allows the user to have direct interaction with the solution development. In addition to theory and results, the hardware and software requirements are discussed.

DISCO interacting protein 2 determines direction of axon projection under the regulation of c-Jun N-terminal kinase in the Drosophila mushroom body

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

Nitta, Yohei; Brain Research Institute, Niigata University; Sugie, Atsushi

Precisely controlled axon guidance for complex neuronal wiring is essential for appropriate neuronal function. c-Jun N-terminal kinase (JNK) was found to play a role in axon guidance recently as well as in cell proliferation, protection and apoptosis. In spite of many genetic and molecular studies on these biological processes regulated by JNK, how JNK regulates axon guidance accurately has not been fully explained thus far. To address this question, we use the Drosophila mushroom body (MB) as a model since the α/β axons project in two distinct directions. Here we show that DISCO interacting protein 2 (DIP2) is required formore » the accurate direction of axonal guidance. DIP2 expression is under the regulation of Basket (Bsk), the Drosophila homologue of JNK. We additionally found that the Bsk/DIP2 pathway is independent from the AP-1 transcriptional factor complex pathway, which is directly activated by Bsk. In conclusion, our findings revealed DIP2 as a novel effector downstream of Bsk modulating the direction of axon projection. - Highlights: • DIP2 is required for accurate direction of axon guidance in Drosophila mushroom body. • DIP2 is a downstream of JNK in the axon guidance of Drosophila mushroom body neuron. • JNK/DIP2 pathway is independent from JNK/AP-1 transcriptional factor complex pathway.« less

Analysis of the Binding Moiety Mediating the Interaction between Monocarboxylate Transporters and Carbonic Anhydrase II*

PubMed Central

Noor, Sina Ibne; Dietz, Steffen; Heidtmann, Hella; Boone, Christopher D.; McKenna, Robert; Deitmer, Joachim W.; Becker, Holger M.

2015-01-01

Proton-coupled monocarboxylate transporters (MCTs) mediate the exchange of high energy metabolites like lactate between different cells and tissues. We have reported previously that carbonic anhydrase II augments transport activity of MCT1 and MCT4 by a noncatalytic mechanism, while leaving transport activity of MCT2 unaltered. In the present study, we combined electrophysiological measurements in Xenopus oocytes and pulldown experiments to analyze the direct interaction between carbonic anhydrase II (CAII) and MCT1, MCT2, and MCT4, respectively. Transport activity of MCT2-WT, which lacks a putative CAII-binding site, is not augmented by CAII. However, introduction of a CAII-binding site into the C terminus of MCT2 resulted in CAII-mediated facilitation of MCT2 transport activity. Interestingly, introduction of three glutamic acid residues alone was not sufficient to establish a direct interaction between MCT2 and CAII, but the cluster had to be arranged in a fashion that allowed access to the binding moiety in CAII. We further demonstrate that functional interaction between MCT4 and CAII requires direct binding of the enzyme to the acidic cluster 431EEE in the C terminus of MCT4 in a similar fashion as previously shown for binding of CAII to the cluster 489EEE in the C terminus of MCT1. In CAII, binding to MCT1 and MCT4 is mediated by a histidine residue at position 64. Taken together, our results suggest that facilitation of MCT transport activity by CAII requires direct binding between histidine 64 in CAII and a cluster of glutamic acid residues in the C terminus of the transporter that has to be positioned in surroundings that allow access to CAII. PMID:25561737

High-affinity DNA-binding Domains of Replication Protein A (RPA) Direct SMARCAL1-dependent Replication Fork Remodeling*

PubMed Central

Bhat, Kamakoti P.; Bétous, Rémy; Cortez, David

2015-01-01

SMARCAL1 catalyzes replication fork remodeling to maintain genome stability. It is recruited to replication forks via an interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells. In addition to directing its localization, RPA also activates SMARCAL1 on some fork substrates but inhibits it on others, thereby conferring substrate specificity to SMARCAL1 fork-remodeling reactions. We investigated the mechanism by which RPA regulates SMARCAL1. Our results indicate that although an interaction between SMARCAL1 and RPA is essential for SMARCAL1 activation, the location of the interacting surface on RPA is not. Counterintuitively, high-affinity DNA binding of RPA DNA-binding domain (DBD) A and DBD-B near the fork junction makes it easier for SMARCAL1 to remodel the fork, which requires removing RPA. We also found that RPA DBD-C and DBD-D are not required for SMARCAL1 regulation. Thus, the orientation of the high-affinity RPA DBDs at forks dictates SMARCAL1 substrate specificity. PMID:25552480

High-affinity DNA-binding domains of replication protein A (RPA) direct SMARCAL1-dependent replication fork remodeling.

PubMed

Bhat, Kamakoti P; Bétous, Rémy; Cortez, David

2015-02-13

SMARCAL1 catalyzes replication fork remodeling to maintain genome stability. It is recruited to replication forks via an interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells. In addition to directing its localization, RPA also activates SMARCAL1 on some fork substrates but inhibits it on others, thereby conferring substrate specificity to SMARCAL1 fork-remodeling reactions. We investigated the mechanism by which RPA regulates SMARCAL1. Our results indicate that although an interaction between SMARCAL1 and RPA is essential for SMARCAL1 activation, the location of the interacting surface on RPA is not. Counterintuitively, high-affinity DNA binding of RPA DNA-binding domain (DBD) A and DBD-B near the fork junction makes it easier for SMARCAL1 to remodel the fork, which requires removing RPA. We also found that RPA DBD-C and DBD-D are not required for SMARCAL1 regulation. Thus, the orientation of the high-affinity RPA DBDs at forks dictates SMARCAL1 substrate specificity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Tumour Suppressor Adenomatous Polyposis Coli (APC) localisation is regulated by both Kinesin-1 and Kinesin-2.

PubMed

Ruane, Peter T; Gumy, Laura F; Bola, Becky; Anderson, Beverley; Wozniak, Marcin J; Hoogenraad, Casper C; Allan, Victoria J

2016-06-07

Microtubules and their associated proteins (MAPs) underpin the polarity of specialised cells. Adenomatous polyposis coli (APC) is one such MAP with a multifunctional agenda that requires precise intracellular localisations. Although APC has been found to associate with kinesin-2 subfamily members, the exact mechanism for the peripheral localization of APC remains unclear. Here we show that the heavy chain of kinesin-1 directly interacts with the APC C-terminus, contributing to the peripheral localisation of APC in fibroblasts. In rat hippocampal neurons the kinesin-1 binding domain of APC is required for its axon tip enrichment. Moreover, we demonstrate that APC requires interactions with both kinesin-2 and kinesin-1 for this localisation. Underlining the importance of the kinesin-1 association, neurons expressing APC lacking kinesin-1-binding domain have shorter axons. The identification of this novel kinesin-1-APC interaction highlights the complexity and significance of APC localisation in neurons.

Plant Virus–Insect Vector Interactions: Current and Potential Future Research Directions

PubMed Central

Dietzgen, Ralf G.; Mann, Krin S.; Johnson, Karyn N.

2016-01-01

Acquisition and transmission by an insect vector is central to the infection cycle of the majority of plant pathogenic viruses. Plant viruses can interact with their insect host in a variety of ways including both non-persistent and circulative transmission; in some cases, the latter involves virus replication in cells of the insect host. Replicating viruses can also elicit both innate and specific defense responses in the insect host. A consistent feature is that the interaction of the virus with its insect host/vector requires specific molecular interactions between virus and host, commonly via proteins. Understanding the interactions between plant viruses and their insect host can underpin approaches to protect plants from infection by interfering with virus uptake and transmission. Here, we provide a perspective focused on identifying novel approaches and research directions to facilitate control of plant viruses by better understanding and targeting virus–insect molecular interactions. We also draw parallels with molecular interactions in insect vectors of animal viruses, and consider technical advances for their control that may be more broadly applicable to plant virus vectors. PMID:27834855

Plant Virus-Insect Vector Interactions: Current and Potential Future Research Directions.

PubMed

Dietzgen, Ralf G; Mann, Krin S; Johnson, Karyn N

2016-11-09

Acquisition and transmission by an insect vector is central to the infection cycle of the majority of plant pathogenic viruses. Plant viruses can interact with their insect host in a variety of ways including both non-persistent and circulative transmission; in some cases, the latter involves virus replication in cells of the insect host. Replicating viruses can also elicit both innate and specific defense responses in the insect host. A consistent feature is that the interaction of the virus with its insect host/vector requires specific molecular interactions between virus and host, commonly via proteins. Understanding the interactions between plant viruses and their insect host can underpin approaches to protect plants from infection by interfering with virus uptake and transmission. Here, we provide a perspective focused on identifying novel approaches and research directions to facilitate control of plant viruses by better understanding and targeting virus-insect molecular interactions. We also draw parallels with molecular interactions in insect vectors of animal viruses, and consider technical advances for their control that may be more broadly applicable to plant virus vectors.

Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

DOE PAGES

Filenko, Nina A.; Palets, Dmytro B.; Lyubchenko, Yuri L.

2012-01-01

Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their populationmore » was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.« less

Sociometric Indicators of Leadership: An Exploratory Analysis

DTIC Science & Technology

2018-01-01

streamline existing observational protocols and assessment methods . This research provides an initial test of sociometric badges in the context of the U.S...understand, the requirements of the mission. Traditional research and assessment methods focusing on leader and follower interactions require direct...based methods of social network analysis. Novel Measures of Leadership Building on these findings and earlier research , it is apparent that

Virtual Manufacturing (la Fabrication virtuelle)

DTIC Science & Technology

1998-05-01

with moving parts and subassemblies, • verification of product subcomponents and systems operations through kinematics studies, and • realism ...dimensions, parts moved in mechanism based directions, and realism of interaction is increased through use of sound, touch and other parameters. For the...direct converters from CAD systems. A simple cinematic package is also high on the requirement to be able to simulate motions as well as an interface to

A Spatial-frequency Method for Analyzing Antenna-to-Probe Interactions in Near-field Antenna Measurements.

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

Brock, Billy C.

The measurement of the radiation characteristics of an antenna on a near-field range requires that the antenna under test be located very close to the near-field probe. Although the direct coupling is utilized for characterizing the near field, this close proximity also presents the opportunity for significant undesired interactions (for example, reflections) to occur between the antenna and the near-field probe. When uncompensated, these additional interactions will introduce error into the measurement, increasing the uncertainty in the final gain pattern obtained through the near-field-to-far-field transformation. Quantifying this gain-uncertainty contribution requires quantifying the various additional interactions. A method incorporating spatial-frequency analysismore » is described which allows the dominant interaction contributions to be easily identified and quantified. In addition to identifying the additional antenna-to-probe interactions, the method also allows identification and quantification of interactions with other nearby objects within the measurement room. Because the method is a spatial-frequency method, wide-bandwidth data is not required, and it can be applied even when data is available at only a single temporal frequency. This feature ensures that the method can be applied to narrow-band antennas, where a similar time-domain analysis would not be possible. - 3 - - 4 -« less

Dynamic assessment of bridge deck performance considering realistic bridge-traffic interaction

DOT National Transportation Integrated Search

2017-09-01

Concrete bridge decks are directly exposed to daily traffic loads and may experience some surface cracking caused by excessive stress or fatigue accumulation, which requires repair or replacement. Among typical bridges in North America, bridge decks ...

Mechanical forces regulate the interactions of fibronectin and collagen I in extracellular matrix.

PubMed

Kubow, Kristopher E; Vukmirovic, Radmila; Zhe, Lin; Klotzsch, Enrico; Smith, Michael L; Gourdon, Delphine; Luna, Sheila; Vogel, Viola

2015-08-14

Despite the crucial role of extracellular matrix (ECM) in directing cell fate in healthy and diseased tissues--particularly in development, wound healing, tissue regeneration and cancer--the mechanisms that direct the assembly and regulate hierarchical architectures of ECM are poorly understood. Collagen I matrix assembly in vivo requires active fibronectin (Fn) fibrillogenesis by cells. Here we exploit Fn-FRET probes as mechanical strain sensors and demonstrate that collagen I fibres preferentially co-localize with more-relaxed Fn fibrils in the ECM of fibroblasts in cell culture. Fibre stretch-assay studies reveal that collagen I's Fn-binding domain is responsible for the mechano-regulated interaction. Furthermore, we show that Fn-collagen interactions are reciprocal: relaxed Fn fibrils act as multivalent templates for collagen assembly, but once assembled, collagen fibres shield Fn fibres from being stretched by cellular traction forces. Thus, in addition to the well-recognized, force-regulated, cell-matrix interactions, forces also tune the interactions between different structural ECM components.

Direct interaction of the bacteriophage SPP1 packaging ATPase with the portal protein.

PubMed

Oliveira, Leonor; Cuervo, Ana; Tavares, Paulo

2010-03-05

DNA packaging in tailed bacteriophages and other viruses requires assembly of a complex molecular machine at a specific vertex of the procapsid. This machine is composed of the portal protein that provides a tunnel for DNA entry, an ATPase that fuels DNA translocation (large terminase subunit), and most frequently, a small terminase subunit. Here we characterized the interaction between the terminase ATPase subunit of bacteriophage SPP1 (gp2) and the procapsid portal vertex. We found, by affinity pulldown assays with purified proteins, that gp2 interacts with the portal protein, gp6, independently of the terminase small subunit gp1, DNA, or ATP. The gp2-procapsid interaction via the portal protein depends on gp2 concentration and requires the presence of divalent cations. Competition experiments showed that isolated gp6 can only inhibit gp2-procapsid interactions and DNA packaging at gp6:procapsid molar ratios above 10-fold. Assays with gp6 carrying mutations in distinct regions of its structure that affect the portal-induced stimulation of ATPase and DNA packaging revealed that none of these mutations impedes gp2-gp6 binding. Our results demonstrate that the SPP1 packaging ATPase binds directly to the portal and that the interaction is stronger with the portal embedded in procapsids. Identification of mutations in gp6 that allow for assembly of the ATPase-portal complex but impair DNA packaging support an intricate cross-talk between the two proteins for activity of the DNA translocation motor.

Differential diagnosis and management of human-directed aggression in cats.

PubMed

Frank, Diane; Dehasse, Joel

2003-03-01

Human-directed aggression in cats should be evaluated as a multifactorial problem. It results from the combined actions of heredity, environment, learning, human social requirements (or needs), client interactions, lack of understanding of normal feline behavior, unrealistic client expectations, and lack of meeting the cat's basic ethologic needs. Managing human-directed aggression in cats encompasses the use of environmental modification, therapies, and, when and if needed, regulatory drugs so as to increase learning capabilities and adaptation and decrease danger to the human victims.

Gamma-ray momentum reconstruction from Compton electron trajectories by filtered back-projection

DOE PAGES

Haefner, A.; Gunter, D.; Plimley, B.; ...

2014-11-03

Gamma-ray imaging utilizing Compton scattering has traditionally relied on measuring coincident gamma-ray interactions to map directional information of the source distribution. This coincidence requirement makes it an inherently inefficient process. We present an approach to gamma-ray reconstruction from Compton scattering that requires only a single electron tracking detector, thus removing the coincidence requirement. From the Compton scattered electron momentum distribution, our algorithm analytically computes the incident photon's correlated direction and energy distributions. Because this method maps the source energy and location, it is useful in applications, where prior information about the source distribution is unknown. We demonstrate this method withmore » electron tracks measured in a scientific Si charge coupled device. While this method was demonstrated with electron tracks in a Si-based detector, it is applicable to any detector that can measure electron direction and energy, or equivalently the electron momentum. For example, it can increase the sensitivity to obtain energy and direction in gas-based systems that suffer from limited efficiency.« less

The Caenorhabditis elegans NF2/Merlin Molecule NFM-1 Nonautonomously Regulates Neuroblast Migration and Interacts Genetically with the Guidance Cue SLT-1/Slit.

PubMed

Josephson, Matthew P; Aliani, Rana; Norris, Megan L; Ochs, Matthew E; Gujar, Mahekta; Lundquist, Erik A

2017-02-01

During nervous system development, neurons and their progenitors migrate to their final destinations. In Caenorhabditis elegans, the bilateral Q neuroblasts and their descendants migrate long distances in opposite directions, despite being born in the same posterior region. QR on the right migrates anteriorly and generates the AQR neuron positioned near the head, and QL on the left migrates posteriorly, giving rise to the PQR neuron positioned near the tail. In a screen for genes required for AQR and PQR migration, we identified an allele of nfm-1, which encodes a molecule similar to vertebrate NF2/Merlin, an important tumor suppressor in humans. Mutations in NF2 lead to neurofibromatosis type II, characterized by benign tumors of glial tissues. Here we demonstrate that in C. elegans, nfm-1 is required for the ability of Q cells and their descendants to extend protrusions and to migrate, but is not required for direction of migration. Using a combination of mosaic analysis and cell-specific expression, we show that NFM-1 is required nonautonomously, possibly in muscles, to promote Q lineage migrations. We also show a genetic interaction between nfm-1 and the C. elegans Slit homolog slt-1, which encodes a conserved secreted guidance cue. Our results suggest that NFM-1 might be involved in the generation of an extracellular cue that promotes Q neuroblast protrusion and migration that acts with or in parallel to SLT-1 In vertebrates, NF2 and Slit2 interact in axon pathfinding, suggesting a conserved interaction of NF2 and Slit2 in regulating migratory events. Copyright © 2017 by the Genetics Society of America.

The Caenorhabditis elegans NF2/Merlin Molecule NFM-1 Nonautonomously Regulates Neuroblast Migration and Interacts Genetically with the Guidance Cue SLT-1/Slit

PubMed Central

Josephson, Matthew P.; Aliani, Rana; Norris, Megan L.; Ochs, Matthew E.; Gujar, Mahekta; Lundquist, Erik A.

2017-01-01

During nervous system development, neurons and their progenitors migrate to their final destinations. In Caenorhabditis elegans, the bilateral Q neuroblasts and their descendants migrate long distances in opposite directions, despite being born in the same posterior region. QR on the right migrates anteriorly and generates the AQR neuron positioned near the head, and QL on the left migrates posteriorly, giving rise to the PQR neuron positioned near the tail. In a screen for genes required for AQR and PQR migration, we identified an allele of nfm-1, which encodes a molecule similar to vertebrate NF2/Merlin, an important tumor suppressor in humans. Mutations in NF2 lead to neurofibromatosis type II, characterized by benign tumors of glial tissues. Here we demonstrate that in C. elegans, nfm-1 is required for the ability of Q cells and their descendants to extend protrusions and to migrate, but is not required for direction of migration. Using a combination of mosaic analysis and cell-specific expression, we show that NFM-1 is required nonautonomously, possibly in muscles, to promote Q lineage migrations. We also show a genetic interaction between nfm-1 and the C. elegans Slit homolog slt-1, which encodes a conserved secreted guidance cue. Our results suggest that NFM-1 might be involved in the generation of an extracellular cue that promotes Q neuroblast protrusion and migration that acts with or in parallel to SLT-1. In vertebrates, NF2 and Slit2 interact in axon pathfinding, suggesting a conserved interaction of NF2 and Slit2 in regulating migratory events. PMID:27913619

Separating direct and indirect effects of global change: a population dynamic modeling approach using readily available field data.

PubMed

Farrer, Emily C; Ashton, Isabel W; Knape, Jonas; Suding, Katharine N

2014-04-01

Two sources of complexity make predicting plant community response to global change particularly challenging. First, realistic global change scenarios involve multiple drivers of environmental change that can interact with one another to produce non-additive effects. Second, in addition to these direct effects, global change drivers can indirectly affect plants by modifying species interactions. In order to tackle both of these challenges, we propose a novel population modeling approach, requiring only measurements of abundance and climate over time. To demonstrate the applicability of this approach, we model population dynamics of eight abundant plant species in a multifactorial global change experiment in alpine tundra where we manipulated nitrogen, precipitation, and temperature over 7 years. We test whether indirect and interactive effects are important to population dynamics and whether explicitly incorporating species interactions can change predictions when models are forecast under future climate change scenarios. For three of the eight species, population dynamics were best explained by direct effect models, for one species neither direct nor indirect effects were important, and for the other four species indirect effects mattered. Overall, global change had negative effects on species population growth, although species responded to different global change drivers, and single-factor effects were slightly more common than interactive direct effects. When the fitted population dynamic models were extrapolated under changing climatic conditions to the end of the century, forecasts of community dynamics and diversity loss were largely similar using direct effect models that do not explicitly incorporate species interactions or best-fit models; however, inclusion of species interactions was important in refining the predictions for two of the species. The modeling approach proposed here is a powerful way of analyzing readily available datasets which should be added to our toolbox to tease apart complex drivers of global change. © 2013 John Wiley & Sons Ltd.

The human role in space: Technology, economics and optimization

NASA Technical Reports Server (NTRS)

Hall, S. B. (Editor)

1985-01-01

Man-machine interactions in space are explored in detail. The role and the degree of direct involvement of humans that will be required in future space missions are investigated. An attempt is made to establish valid criteria for allocating functional activities between humans and machines and to provide insight into the technological requirements, economics, and benefits of the human presence in space. Six basic categories of man-machine interactions are considered: manual, supported, augmented, teleoperated, supervised, and independent. Appendices are included which provide human capability data, project analyses, activity timeline profiles and data sheets for 37 generic activities, support equipment and human capabilities required in these activities, and cumulative costs as a function of activity for seven man-machine modes.

Status of the Planet Formation Imager (PFI) concept

NASA Astrophysics Data System (ADS)

Ireland, Michael J.; Monnier, John D.; Kraus, Stefan; Isella, Andrea; Minardi, Stefano; Petrov, Romain; ten Brummelaar, Theo; Young, John; Vasisht, Gautam; Mozurkewich, David; Rinehart, Stephen; Michael, Ernest A.; van Belle, Gerard; Woillez, Julien

2016-08-01

The Planet Formation Imager (PFI) project aims to image the period of planet assembly directly, resolving structures as small as a giant planet's Hill sphere. These images will be required in order to determine the key mechanisms for planet formation at the time when processes of grain growth, protoplanet assembly, magnetic fields, disk/planet dynamical interactions and complex radiative transfer all interact - making some planetary systems habitable and others inhospitable. We will present the overall vision for the PFI concept, focusing on the key technologies and requirements that are needed to achieve the science goals. Based on these key requirements, we will define a cost envelope range for the design and highlight where the largest uncertainties lie at this conceptual stage.

Sequence-dependent catalytic regulation of the SpoIIIE motor activity ensures directionality of DNA translocation.

PubMed

Chara, Osvaldo; Borges, Augusto; Milhiet, Pierre-Emmanuel; Nöllmann, Marcelo; Cattoni, Diego I

2018-03-27

Transport of cellular cargo by molecular motors requires directionality to ensure proper biological functioning. During sporulation in Bacillus subtilis, directionality of chromosome transport is mediated by the interaction between the membrane-bound DNA translocase SpoIIIE and specific octameric sequences (SRS). Whether SRS regulate directionality by recruiting and orienting SpoIIIE or by simply catalyzing its translocation activity is still unclear. By using atomic force microscopy and single-round fast kinetics translocation assays we determined the localization and dynamics of diffusing and translocating SpoIIIE complexes on DNA with or without SRS. Our findings combined with mathematical modelling revealed that SpoIIIE directionality is not regulated by protein recruitment to SRS but rather by a fine-tuned balance among the rates governing SpoIIIE-DNA interactions and the probability of starting translocation modulated by SRS. Additionally, we found that SpoIIIE can start translocation from non-specific DNA, providing an alternative active search mechanism for SRS located beyond the exploratory length defined by 1D diffusion. These findings are relevant in vivo in the context of chromosome transport through an open channel, where SpoIIIE can rapidly explore DNA while directionality is modulated by the probability of translocation initiation upon interaction with SRS versus non-specific DNA.

Inference of a Nonlinear Stochastic Model of the Cardiorespiratory Interaction

NASA Astrophysics Data System (ADS)

Smelyanskiy, V. N.; Luchinsky, D. G.; Stefanovska, A.; McClintock, P. V.

2005-03-01

We reconstruct a nonlinear stochastic model of the cardiorespiratory interaction in terms of a set of polynomial basis functions representing the nonlinear force governing system oscillations. The strength and direction of coupling and noise intensity are simultaneously inferred from a univariate blood pressure signal. Our new inference technique does not require extensive global optimization, and it is applicable to a wide range of complex dynamical systems subject to noise.

CbtA toxin of Escherichia coli inhibits cell division and cell elongation via direct and independent interactions with FtsZ and MreB.

PubMed

Heller, Danielle M; Tavag, Mrinalini; Hochschild, Ann

2017-09-01

The toxin components of toxin-antitoxin modules, found in bacterial plasmids, phages, and chromosomes, typically target a single macromolecule to interfere with an essential cellular process. An apparent exception is the chromosomally encoded toxin component of the E. coli CbtA/CbeA toxin-antitoxin module, which can inhibit both cell division and cell elongation. A small protein of only 124 amino acids, CbtA, was previously proposed to interact with both FtsZ, a tubulin homolog that is essential for cell division, and MreB, an actin homolog that is essential for cell elongation. However, whether or not the toxic effects of CbtA are due to direct interactions with these predicted targets is not known. Here, we genetically separate the effects of CbtA on cell elongation and cell division, showing that CbtA interacts directly and independently with FtsZ and MreB. Using complementary genetic approaches, we identify the functionally relevant target surfaces on FtsZ and MreB, revealing that in both cases, CbtA binds to surfaces involved in essential cytoskeletal filament architecture. We show further that each interaction contributes independently to CbtA-mediated toxicity and that disruption of both interactions is required to alleviate the observed toxicity. Although several other protein modulators are known to target FtsZ, the CbtA-interacting surface we identify represents a novel inhibitory target. Our findings establish CbtA as a dual function toxin that inhibits both cell division and cell elongation via direct and independent interactions with FtsZ and MreB.

CbtA toxin of Escherichia coli inhibits cell division and cell elongation via direct and independent interactions with FtsZ and MreB

PubMed Central

Heller, Danielle M.; Tavag, Mrinalini

2017-01-01

The toxin components of toxin-antitoxin modules, found in bacterial plasmids, phages, and chromosomes, typically target a single macromolecule to interfere with an essential cellular process. An apparent exception is the chromosomally encoded toxin component of the E. coli CbtA/CbeA toxin-antitoxin module, which can inhibit both cell division and cell elongation. A small protein of only 124 amino acids, CbtA, was previously proposed to interact with both FtsZ, a tubulin homolog that is essential for cell division, and MreB, an actin homolog that is essential for cell elongation. However, whether or not the toxic effects of CbtA are due to direct interactions with these predicted targets is not known. Here, we genetically separate the effects of CbtA on cell elongation and cell division, showing that CbtA interacts directly and independently with FtsZ and MreB. Using complementary genetic approaches, we identify the functionally relevant target surfaces on FtsZ and MreB, revealing that in both cases, CbtA binds to surfaces involved in essential cytoskeletal filament architecture. We show further that each interaction contributes independently to CbtA-mediated toxicity and that disruption of both interactions is required to alleviate the observed toxicity. Although several other protein modulators are known to target FtsZ, the CbtA-interacting surface we identify represents a novel inhibitory target. Our findings establish CbtA as a dual function toxin that inhibits both cell division and cell elongation via direct and independent interactions with FtsZ and MreB. PMID:28931012

How memory of direct animal interactions can lead to territorial pattern formation.

PubMed

Potts, Jonathan R; Lewis, Mark A

2016-05-01

Mechanistic home range analysis (MHRA) is a highly effective tool for understanding spacing patterns of animal populations. It has hitherto focused on populations where animals defend their territories by communicating indirectly, e.g. via scent marks. However, many animal populations defend their territories using direct interactions, such as ritualized aggression. To enable application of MHRA to such populations, we construct a model of direct territorial interactions, using linear stability analysis and energy methods to understand when territorial patterns may form. We show that spatial memory of past interactions is vital for pattern formation, as is memory of 'safe' places, where the animal has visited but not suffered recent territorial encounters. Additionally, the spatial range over which animals make decisions to move is key to understanding the size and shape of their resulting territories. Analysis using energy methods, on a simplified version of our system, shows that stability in the nonlinear system corresponds well to predictions of linear analysis. We also uncover a hysteresis in the process of territory formation, so that formation may depend crucially on initial space-use. Our analysis, in one dimension and two dimensions, provides mathematical groundwork required for extending MHRA to situations where territories are defended by direct encounters. © 2016 The Author(s).

Mapping protein-protein interactions using yeast two-hybrid assays.

PubMed

Mehla, Jitender; Caufield, J Harry; Uetz, Peter

2015-05-01

Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays. Array-based Y2H is commonly used to test a number of "prey" proteins for interactions with a single "bait" (target) protein or pool of proteins. The advantage of this approach is the direct identification of interacting protein pairs without further downstream experiments: The identity of the preys is known and does not require further confirmation. In contrast, constructing and screening a random prey library requires identification of individual prey clones and systematic retesting. Retesting is typically performed in an array format. © 2015 Cold Spring Harbor Laboratory Press.

Plant Endocytosis Requires the ER Membrane-Anchored Proteins VAP27-1 and VAP27-3.

PubMed

Stefano, Giovanni; Renna, Luciana; Wormsbaecher, Clarissa; Gamble, Jessie; Zienkiewicz, Krzysztof; Brandizzi, Federica

2018-05-22

Through yet-undefined mechanisms, the plant endoplasmic reticulum (ER) has a critical role in endocytosis. The plant ER establishes a close association with endosomes and contacts the plasma membrane (PM) at ER-PM contact sites (EPCSs) demarcated by the ER membrane-associated VAMP-associated-proteins (VAP). Here, we investigated two plant VAPs, VAP27-1 and VAP27-3, and found an interaction with clathrin and a requirement for the homeostasis of clathrin dynamics at endocytic membranes and endocytosis. We also demonstrated direct interaction of VAP27-proteins with phosphatidylinositol-phosphate lipids (PIPs) that populate endocytic membranes. These results support that, through interaction with PIPs, VAP27-proteins bridge the ER with endocytic membranes and maintain endocytic traffic, likely through their interaction with clathrin. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Dark matter spin determination with directional direct detection experiments

NASA Astrophysics Data System (ADS)

Catena, Riccardo; Conrad, Jan; Döring, Christian; Ferella, Alfredo Davide; Krauss, Martin B.

2018-01-01

If dark matter has spin 0, only two WIMP-nucleon interaction operators can arise as leading operators from the nonrelativistic reduction of renormalizable single-mediator models for dark matter-quark interactions. Based on this crucial observation, we show that about 100 signal events at next generation directional detection experiments can be enough to enable a 2 σ rejection of the spin 0 dark matter hypothesis in favor of alternative hypotheses where the dark matter particle has spin 1 /2 or 1. In this context, directional sensitivity is crucial since anisotropy patterns in the sphere of nuclear recoil directions depend on the spin of the dark matter particle. For comparison, about 100 signal events are expected in a CF4 detector operating at a pressure of 30 torr with an exposure of approximately 26,000 cubic-meter-detector days for WIMPs of 100 GeV mass and a WIMP-fluorine scattering cross section of 0.25 pb. Comparable exposures require an array of cubic meter time projection chamber detectors.

The Rice Resistance Protein Pair RGA4/RGA5 Recognizes the Magnaporthe oryzae Effectors AVR-Pia and AVR1-CO39 by Direct Binding[W][OA

PubMed Central

Cesari, Stella; Thilliez, Gaëtan; Ribot, Cécile; Chalvon, Véronique; Michel, Corinne; Jauneau, Alain; Rivas, Susana; Alaux, Ludovic; Kanzaki, Hiroyuki; Okuyama, Yudai; Morel, Jean-Benoit; Fournier, Elisabeth; Tharreau, Didier; Terauchi, Ryohei; Kroj, Thomas

2013-01-01

Resistance (R) proteins recognize pathogen avirulence (Avr) proteins by direct or indirect binding and are multidomain proteins generally carrying a nucleotide binding (NB) and a leucine-rich repeat (LRR) domain. Two NB-LRR protein-coding genes from rice (Oryza sativa), RGA4 and RGA5, were found to be required for the recognition of the Magnaporthe oryzae effector AVR1-CO39. RGA4 and RGA5 also mediate recognition of the unrelated M. oryzae effector AVR-Pia, indicating that the corresponding R proteins possess dual recognition specificity. For RGA5, two alternative transcripts, RGA5-A and RGA5-B, were identified. Genetic analysis showed that only RGA5-A confers resistance, while RGA5-B is inactive. Yeast two-hybrid, coimmunoprecipitation, and fluorescence resonance energy transfer–fluorescence lifetime imaging experiments revealed direct binding of AVR-Pia and AVR1-CO39 to RGA5-A, providing evidence for the recognition of multiple Avr proteins by direct binding to a single R protein. Direct binding seems to be required for resistance as an inactive AVR-Pia allele did not bind RGA5-A. A small Avr interaction domain with homology to the Avr recognition domain in the rice R protein Pik-1 was identified in the C terminus of RGA5-A. This reveals a mode of Avr protein recognition through direct binding to a novel, non-LRR interaction domain. PMID:23548743

Caenorhabditis elegans fibroblast growth factor receptor signaling can occur independently of the multi-substrate adaptor FRS2.

PubMed

Lo, Te-Wen; Bennett, Daniel C; Goodman, S Jay; Stern, Michael J

2010-06-01

The components of receptor tyrosine kinase signaling complexes help to define the specificity of the effects of their activation. The Caenorhabditis elegans fibroblast growth factor receptor (FGFR), EGL-15, regulates a number of processes, including sex myoblast (SM) migration guidance and fluid homeostasis, both of which require a Grb2/Sos/Ras cassette of signaling components. Here we show that SEM-5/Grb2 can bind directly to EGL-15 to mediate SM chemoattraction. A yeast two-hybrid screen identified SEM-5 as able to interact with the carboxy-terminal domain (CTD) of EGL-15, a domain that is specifically required for SM chemoattraction. This interaction requires the SEM-5 SH2-binding motifs present in the CTD (Y(1009) and Y(1087)), and these sites are required for the CTD role of EGL-15 in SM chemoattraction. SEM-5, but not the SEM-5 binding sites located in the CTD, is required for the fluid homeostasis function of EGL-15, indicating that SEM-5 can link to EGL-15 through an alternative mechanism. The multi-substrate adaptor protein FRS2 serves to link vertebrate FGFRs to Grb2. In C. elegans, an FRS2-like gene, rog-1, functions upstream of a Ras/MAPK pathway for oocyte maturation but is not required for EGL-15 function. Thus, unlike the vertebrate FGFRs, which require the multi-substrate adaptor FRS2 to recruit Grb2, EGL-15 can recruit SEM-5/Grb2 directly.

Interactions between human behaviour and ecological systems.

PubMed

Milner-Gulland, E J

2012-01-19

Research on the interactions between human behaviour and ecological systems tends to focus on the direct effects of human activities on ecosystems, such as biodiversity loss. There is also increasing research effort directed towards ecosystem services. However, interventions to control people's use of the environment alter the incentives that natural resource users face, and therefore their decisions about resource use. The indirect effects of conservation interventions on biodiversity, modulated through human decision-making, are poorly studied but are likely to be significant and potentially counterintuitive. This is particularly so where people are dependent on multiple natural resources for their livelihoods, when both poverty and biodiversity loss are acute. An inter-disciplinary approach is required to quantify these interactions, with an understanding of human decision-making at its core; otherwise, predictions about the impacts of conservation policies may be highly misleading.

Interactions between human behaviour and ecological systems

PubMed Central

Milner-Gulland, E. J.

2012-01-01

Research on the interactions between human behaviour and ecological systems tends to focus on the direct effects of human activities on ecosystems, such as biodiversity loss. There is also increasing research effort directed towards ecosystem services. However, interventions to control people's use of the environment alter the incentives that natural resource users face, and therefore their decisions about resource use. The indirect effects of conservation interventions on biodiversity, modulated through human decision-making, are poorly studied but are likely to be significant and potentially counterintuitive. This is particularly so where people are dependent on multiple natural resources for their livelihoods, when both poverty and biodiversity loss are acute. An inter-disciplinary approach is required to quantify these interactions, with an understanding of human decision-making at its core; otherwise, predictions about the impacts of conservation policies may be highly misleading. PMID:22144389

Man/Machine Interaction Dynamics And Performance (MMIDAP) capability

NASA Technical Reports Server (NTRS)

Frisch, Harold P.

1991-01-01

The creation of an ability to study interaction dynamics between a machine and its human operator can be approached from a myriad of directions. The Man/Machine Interaction Dynamics and Performance (MMIDAP) project seeks to create an ability to study the consequences of machine design alternatives relative to the performance of both machine and operator. The class of machines to which this study is directed includes those that require the intelligent physical exertions of a human operator. While Goddard's Flight Telerobotic's program was expected to be a major user, basic engineering design and biomedical applications reach far beyond telerobotics. Ongoing efforts are outlined of the GSFC and its University and small business collaborators to integrate both human performance and musculoskeletal data bases with analysis capabilities necessary to enable the study of dynamic actions, reactions, and performance of coupled machine/operator systems.

IGDS/TRAP Interface Program (ITIP). Software Design Document

NASA Technical Reports Server (NTRS)

Jefferys, Steve; Johnson, Wendell

1981-01-01

The preliminary design of the IGDS/TRAP Interface Program (ITIP) is described. The ITIP is implemented on the PDP 11/70 and interfaces directly with the Interactive Graphics Design System and the Data Management and Retrieval System. The program provides an efficient method for developing a network flow diagram. Performance requirements, operational rquirements, and design requirements are discussed along with sources and types of input and destination and types of output. Information processing functions and data base requirements are also covered.

Effect of interaction strength on robustness of controlling edge dynamics in complex networks

NASA Astrophysics Data System (ADS)

Pang, Shao-Peng; Hao, Fei

2018-05-01

Robustness plays a critical role in the controllability of complex networks to withstand failures and perturbations. Recent advances in the edge controllability show that the interaction strength among edges plays a more important role than network structure. Therefore, we focus on the effect of interaction strength on the robustness of edge controllability. Using three categories of all edges to quantify the robustness, we develop a universal framework to evaluate and analyze the robustness in complex networks with arbitrary structures and interaction strengths. Applying our framework to a large number of model and real-world networks, we find that the interaction strength is a dominant factor for the robustness in undirected networks. Meanwhile, the strongest robustness and the optimal edge controllability in undirected networks can be achieved simultaneously. Different from the case of undirected networks, the robustness in directed networks is determined jointly by the interaction strength and the network's degree distribution. Moreover, a stronger robustness is usually associated with a larger number of driver nodes required to maintain full control in directed networks. This prompts us to provide an optimization method by adjusting the interaction strength to optimize the robustness of edge controllability.

Effects of stimulus duration and vowel quality in cross-linguistic categorical perception of pitch directions

PubMed Central

Zhu, Yiqing; Wayland, Ratree

2017-01-01

We investigated categorical perception of rising and falling pitch contours by tonal and non-tonal listeners. Specifically, we determined minimum durations needed to perceive both contours and compared to those of production, how stimuli duration affects their perception, whether there is an intrinsic F0 effect, and how first language background, duration, directions of pitch and vowel quality interact with each other. Continua of fundamental frequency on different vowels with 9 duration values were created for identification and discrimination tasks. Less time is generally needed to effectively perceive a pitch direction than to produce it. Overall, tonal listeners’ perception is more categorical than non-tonal listeners. Stimuli duration plays a critical role for both groups, but tonal listeners showed a stronger duration effect, and may benefit more from the extra time in longer stimuli for context-coding, consistent with the multistore model of categorical perception. Within a certain range of semitones, tonal listeners also required shorter stimulus duration to perceive pitch direction changes than non-tonal listeners. Finally, vowel quality plays a limited role and only interacts with duration in perceiving falling pitch directions. These findings further our understanding on models of categorical perception, the relationship between speech perception and production, and the interaction between the perception of tones and vowel quality. PMID:28671991

Rhythm Patterns Interaction - Synchronization Behavior for Human-Robot Joint Action

PubMed Central

Mörtl, Alexander; Lorenz, Tamara; Hirche, Sandra

2014-01-01

Interactive behavior among humans is governed by the dynamics of movement synchronization in a variety of repetitive tasks. This requires the interaction partners to perform for example rhythmic limb swinging or even goal-directed arm movements. Inspired by that essential feature of human interaction, we present a novel concept and design methodology to synthesize goal-directed synchronization behavior for robotic agents in repetitive joint action tasks. The agents’ tasks are described by closed movement trajectories and interpreted as limit cycles, for which instantaneous phase variables are derived based on oscillator theory. Events segmenting the trajectories into multiple primitives are introduced as anchoring points for enhanced synchronization modes. Utilizing both continuous phases and discrete events in a unifying view, we design a continuous dynamical process synchronizing the derived modes. Inverse to the derivation of phases, we also address the generation of goal-directed movements from the behavioral dynamics. The developed concept is implemented to an anthropomorphic robot. For evaluation of the concept an experiment is designed and conducted in which the robot performs a prototypical pick-and-place task jointly with human partners. The effectiveness of the designed behavior is successfully evidenced by objective measures of phase and event synchronization. Feedback gathered from the participants of our exploratory study suggests a subjectively pleasant sense of interaction created by the interactive behavior. The results highlight potential applications of the synchronization concept both in motor coordination among robotic agents and in enhanced social interaction between humanoid agents and humans. PMID:24752212

The Tn7 transposition regulator TnsC interacts with the transposase subunit TnsB and target selector TnsD

PubMed Central

Choi, Ki Young; Spencer, Jeanelle M.; Craig, Nancy L.

2014-01-01

The excision of transposon Tn7 from a donor site and its insertion into its preferred target site, attachment site attTn7, is mediated by four Tn7-encoded transposition proteins: TnsA, TnsB, TnsC, and TnsD. Transposition requires the assembly of a nucleoprotein complex containing all four Tns proteins and the DNA substrates, the donor site containing Tn7, and the preferred target site attTn7. TnsA and TnsB together form the heteromeric Tn7 transposase, and TnsD is a target-selecting protein that binds specifically to attTn7. TnsC is the key regulator of transposition, interacting with both the TnsAB transposase and TnsD-attTn7. We show here that TnsC interacts directly with TnsB, and identify the specific region of TnsC involved in the TnsB–TnsC interaction during transposition. We also show that a TnsC mutant defective in interaction with TnsB is defective for Tn7 transposition both in vitro and in vivo. Tn7 displays cis-acting target immunity, which blocks Tn7 insertion into a target DNA that already contains Tn7. We provide evidence that the direct TnsB–TnsC interaction that we have identified also mediates cis-acting Tn7 target immunity. We also show that TnsC interacts directly with the target selector protein TnsD. PMID:24982178

Direction of information flow in large-scale resting-state networks is frequency-dependent.

PubMed

Hillebrand, Arjan; Tewarie, Prejaas; van Dellen, Edwin; Yu, Meichen; Carbo, Ellen W S; Douw, Linda; Gouw, Alida A; van Straaten, Elisabeth C W; Stam, Cornelis J

2016-04-05

Normal brain function requires interactions between spatially separated, and functionally specialized, macroscopic regions, yet the directionality of these interactions in large-scale functional networks is unknown. Magnetoencephalography was used to determine the directionality of these interactions, where directionality was inferred from time series of beamformer-reconstructed estimates of neuronal activation, using a recently proposed measure of phase transfer entropy. We observed well-organized posterior-to-anterior patterns of information flow in the higher-frequency bands (alpha1, alpha2, and beta band), dominated by regions in the visual cortex and posterior default mode network. Opposite patterns of anterior-to-posterior flow were found in the theta band, involving mainly regions in the frontal lobe that were sending information to a more distributed network. Many strong information senders in the theta band were also frequent receivers in the alpha2 band, and vice versa. Our results provide evidence that large-scale resting-state patterns of information flow in the human brain form frequency-dependent reentry loops that are dominated by flow from parieto-occipital cortex to integrative frontal areas in the higher-frequency bands, which is mirrored by a theta band anterior-to-posterior flow.

Homology-based modeling of the Erwinia amylovora type III secretion chaperone DspF used to identify amino acids required for virulence and interaction with the effector DspE.

PubMed

Triplett, Lindsay R; Wedemeyer, William J; Sundin, George W

2010-09-01

The structure of DspF, a type III secretion system (T3SS) chaperone required for virulence of the fruit tree pathogen Erwinia amylovora, was modeled based on predicted structural homology to characterized T3SS chaperones. This model guided the selection of 11 amino acid residues that were individually mutated to alanine via site-directed mutagenesis. Each mutant was assessed for its effect on virulence complementation, dimerization and interaction with the N-terminal chaperone-binding site of DspE. Four amino acid residues were identified that did not complement the virulence defect of a dspF knockout mutant, and three of these residues were required for interaction with the N-terminus of DspE. This study supports the significance of the predicted beta-sheet helix-binding groove in DspF chaperone function. Copyright 2010 Elsevier Masson SAS. All rights reserved.

Tumour Suppressor Adenomatous Polyposis Coli (APC) localisation is regulated by both Kinesin-1 and Kinesin-2

PubMed Central

Ruane, Peter T.; Gumy, Laura F.; Bola, Becky; Anderson, Beverley; Wozniak, Marcin J.; Hoogenraad, Casper C.; Allan, Victoria J.

2016-01-01

Microtubules and their associated proteins (MAPs) underpin the polarity of specialised cells. Adenomatous polyposis coli (APC) is one such MAP with a multifunctional agenda that requires precise intracellular localisations. Although APC has been found to associate with kinesin-2 subfamily members, the exact mechanism for the peripheral localization of APC remains unclear. Here we show that the heavy chain of kinesin-1 directly interacts with the APC C-terminus, contributing to the peripheral localisation of APC in fibroblasts. In rat hippocampal neurons the kinesin-1 binding domain of APC is required for its axon tip enrichment. Moreover, we demonstrate that APC requires interactions with both kinesin-2 and kinesin-1 for this localisation. Underlining the importance of the kinesin-1 association, neurons expressing APC lacking kinesin-1-binding domain have shorter axons. The identification of this novel kinesin-1-APC interaction highlights the complexity and significance of APC localisation in neurons. PMID:27272132

Pestivirus Npro Directly Interacts with Interferon Regulatory Factor 3 Monomer and Dimer

PubMed Central

Holthauzen, Luis Marcelo F.; Ruggli, Nicolas

2016-01-01

ABSTRACT Interferon regulatory factor 3 (IRF3) is a transcription factor involved in the activation of type I alpha/beta interferon (IFN-α/β) in response to viral infection. Upon viral infection, the IRF3 monomer is activated into a phosphorylated dimer, which induces the transcription of interferon genes in the nucleus. Viruses have evolved several ways to target IRF3 in order to subvert the innate immune response. Pestiviruses, such as classical swine fever virus (CSFV), target IRF3 for ubiquitination and subsequent proteasomal degradation. This is mediated by the viral protein Npro that interacts with IRF3, but the molecular details for this interaction are largely unknown. We used recombinant Npro and IRF3 proteins and show that Npro interacts with IRF3 directly without additional proteins and forms a soluble 1:1 complex. The full-length IRF3 but not merely either of the individual domains is required for this interaction. The interaction between Npro and IRF3 is not dependent on the activation state of IRF3, since Npro binds to a constitutively active form of IRF3 in the presence of its transcriptional coactivator, CREB-binding protein (CBP). The results indicate that the Npro-binding site on IRF3 encompasses a region that is unperturbed by the phosphorylation and subsequent activation of IRF3 and thus excludes the dimer interface and CBP-binding site. IMPORTANCE The pestivirus N-terminal protease, Npro, is essential for evading the host's immune system by facilitating the degradation of interferon regulatory factor 3 (IRF3). However, the nature of the Npro interaction with IRF3, including the IRF3 species (inactive monomer versus activated dimer) that Npro targets for degradation, is largely unknown. We show that classical swine fever virus Npro and porcine IRF3 directly interact in solution and that full-length IRF3 is required for interaction with Npro. Additionally, Npro interacts with a constitutively active form of IRF3 bound to its transcriptional cofactor, the CREB-binding protein. This is the first study to demonstrate that Npro is able to bind both inactive IRF3 monomer and activated IRF3 dimer and thus likely targets both IRF3 species for ubiquitination and proteasomal degradation. PMID:27334592

Neuropilin-1 interacts with the second branchial arch microenvironment to mediate chick neural crest cell dynamics

PubMed Central

McLennan, Rebecca; Kulesa, Paul M.

2011-01-01

Cranial neural crest cells (NCCs) require neuropilin signaling to reach and invade the branchial arches. Here, we use an in vivo chick model to investigate whether the neuropilin-1 knockdown phenotype is specific to the second branchial arch (ba2), changes in NCC behaviors and phenotypic consequences, and whether neuropilins work together to facilitate entry into and invasion of ba2. We find that cranial NCCs with reduced neuropilin-1 expression displayed shorter protrusions and decreased cell body and nuclear length-to-width ratios characteristic of a loss in polarity and motility, after specific interaction with ba2. Directed NCC migration was rescued by transplantation of transfected cells into rhombomere 4 of younger hosts. Lastly, reduction of neuropilin-2 expression by shRNA either solely or with reduction of neuropilin-1 expression did not lead to a stronger head phenotype. Thus, NCCs, independent of rhombomere origin, require neuropilin-1, but not neuropilin-2 to maintain polarity and directed migration into ba2. PMID:20503363

Nontranscriptional regulation of SYK by the coactivator OCA-B is required at multiple stages of B cell development.

PubMed

Siegel, Rachael; Kim, Unkyu; Patke, Alina; Yu, Xin; Ren, Xiaodi; Tarakhovsky, Alexander; Roeder, Robert G

2006-05-19

OCA-B was originally identified as a nuclear transcriptional coactivator that is essential for antigen-driven immune responses. The later identification of a membrane bound, myristoylated form of OCA-B suggested additional, unique functions in B cell signaling pathways. This study has shown that OCA-B also functions in the pre-B1-to-pre-B2 cell transition and, most surprisingly, that it directly interacts with SYK, a tyrosine kinase critical for pre-BCR and BCR signaling. This unprecedented type of interaction-a transcriptional coactivator with a signaling kinase-occurs in the cytoplasm and directly regulates SYK stability. This study indicates that OCA-B is required for pre-BCR and BCR signaling at multiple stages of B cell development through its nontranscriptional regulation of SYK. Combined with the deregulation of OCA-B target genes, this may help explain the multitude of defects observed in B cell development and immune responses of Oca-b-/- mice.

"My love-hate relationship": Ethical issues associated with nurses' interactions with industry.

PubMed

Grundy, Quinn

2014-08-01

Ethical issues associated with nurses' interactions with industry have implications for the safety, quality, and cost of healthcare. To date, little work has explored nurse-industry interactions and their associated ethical issues empirically. A phenomenological study was conducted to explore registered nurses' interactions with industry in clinical practice. Five registered nurses working in direct patient care were recruited and individual, in-depth interviews were conducted. The University's Committee on Human Research approved the study. Nurses frequently interacted with industry in their practice and felt ambivalent about these interactions. Nurses described systemic cuts to multiple "goods" central to nursing practice, including patient support, but paradoxically relied on industry resources to deliver these "goods." They relied on a particular conception of trust to navigate these interactions but were left to do so individually on the basis of their experience. Conflicts of interest arose as a result of multiple competing interests, and were frequently mediated through nurses' superiors. Nursing as a profession requires a guiding narrative to aid nurses in interpreting and navigating interactions with industry. A conception of trust that incorporates both the work of caring and attention to social justice could form the basis of these interactions, but would require that nursing take a much more critical stance toward marketing interactions. © The Author(s) 2013.

Ratchet Effects in Active Matter Systems

NASA Astrophysics Data System (ADS)

Reichhardt, C. J. Olson; Reichhardt, C.

2017-03-01

Ratchet effects can arise for single or collectively interacting Brownian particles on an asymmetric substrate when a net dc transport is produced by an externally applied ac driving force or by periodically flashing the substrate. Recently, a new class of active ratchet systems that do not require the application of external driving has been realized through the use of active matter; they are self-propelled units that can be biological or nonbiological in nature. When active materials such as swimming bacteria interact with an asymmetric substrate, a net dc directed motion can arise even without external driving, opening a wealth of possibilities such as sorting, cargo transport, or micromachine construction. We review the current status of active matter ratchets for swimming bacteria, cells, active colloids, and swarming models, focusing on the role of particle-substrate interactions. We describe ratchet reversals produced by collective effects and the use of active ratchets to transport passive particles. We discuss future directions including deformable substrates or particles, the role of different swimming modes, varied particle-particle interactions, and nondissipative effects.

P-MartCancer–Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets

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

Webb-Robertson, Bobbie-Jo M.; Bramer, Lisa M.; Jensen, Jeffrey L.

P-MartCancer is a new interactive web-based software environment that enables biomedical and biological scientists to perform in-depth analyses of global proteomics data without requiring direct interaction with the data or with statistical software. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access to multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium (CPTAC) at the peptide, gene and protein levels. P-MartCancer is deployed using Azure technologies (http://pmart.labworks.org/cptac.html), the web-service is alternativelymore » available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/) and many statistical functions can be utilized directly from an R package available on GitHub (https://github.com/pmartR).« less

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

Reichhardt, Cynthia Jane; Reichhardt, Charles

Ratchet effects can arise for single or collectively interacting Brownian particles on an asymmetric substrate when a net dc transport is produced by an externally applied ac driving force or by periodically flashing the substrate. Recently, a new class of active ratchet systems that do not require the application of external driving has been realized through the use of active matter; they are self-propelled units that can be biological or nonbiological in nature. When active materials such as swimming bacteria interact with an asymmetric substrate, a net dc directed motion can arise even without external driving, opening a wealth ofmore » possibilities such as sorting, cargo transport, or micromachine construction. We review the current status of active matter ratchets for swimming bacteria, cells, active colloids, and swarming models, focusing on the role of particle-substrate interactions. Here, we describe ratchet reversals produced by collective effects and the use of active ratchets to transport passive particles. We discuss future directions including deformable substrates or particles, the role of different swimming modes, varied particle–particle interactions, and nondissipative effects.« less

Direct detection signatures of self-interacting dark matter with a light mediator

DOE PAGES

Nobile, Eugenio Del; Kaplinghat, Manoj; Yu, Hai-Bo

2015-10-27

Self-interacting dark matter (SIDM) is a simple and well-motivated scenario that could explain long-standing puzzles in structure formation on small scales. If the required self-interaction arises through a light mediator (with mass ~ 10 MeV) in the dark sector, this new particle must be unstable to avoid overclosing the universe. The decay of the light mediator could happen due to a weak coupling of the hidden and visible sectors, providing new signatures for direct detection experiments. The SIDM nuclear recoil spectrum is more peaked towards low energies compared to the usual case of contact interactions, because the mediator mass ismore » comparable to the momentum transfer of nuclear recoils. We show that the SIDM signal could be distinguished from that of DM particles with contact interactions by considering the time-average energy spectrum in experiments employing different target materials, or the average and modulated spectra in a single experiment. Using current limits from LUX and SuperCDMS, we also derive strong bounds on the mixing parameter between hidden and visible sector.« less

The RSF1 histone-remodelling factor facilitates DNA double-strand break repair by recruiting centromeric and Fanconi Anaemia proteins.

PubMed

Pessina, Fabio; Lowndes, Noel F

2014-05-01

ATM is a central regulator of the cellular responses to DNA double-strand breaks (DSBs). Here we identify a biochemical interaction between ATM and RSF1 and we characterise the role of RSF1 in this response. The ATM-RSF1 interaction is dependent upon both DSBs and ATM kinase activity. Together with SNF2H/SMARCA5, RSF1 forms the RSF chromatin-remodelling complex. Although RSF1 is specific to the RSF complex, SNF2H/SMARCA5 is a catalytic subunit of several other chromatin-remodelling complexes. Although not required for checkpoint signalling, RSF1 is required for efficient repair of DSBs via both end-joining and homology-directed repair. Specifically, the ATM-dependent recruitment to sites of DSBs of the histone fold proteins CENPS/MHF1 and CENPX/MHF2, previously identified at centromeres, is RSF1-dependent. In turn these proteins recruit and regulate the mono-ubiquitination of the Fanconi Anaemia proteins FANCD2 and FANCI. We propose that by depositing CENPS/MHF1 and CENPX/MHF2, the RSF complex either directly or indirectly contributes to the reorganisation of chromatin around DSBs that is required for efficient DNA repair.

Multiple interactions amongst floral homeotic MADS box proteins.

PubMed Central

Davies, B; Egea-Cortines, M; de Andrade Silva, E; Saedler, H; Sommer, H

1996-01-01

Most known floral homeotic genes belong to the MADS box family and their products act in combination to specify floral organ identity by an unknown mechanism. We have used a yeast two-hybrid system to investigate the network of interactions between the Antirrhinum organ identity gene products. Selective heterodimerization is observed between MADS box factors. Exclusive interactions are detected between two factors, DEFICIENS (DEF) and GLOBOSA (GLO), previously known to heterodimerize and control development of petals and stamens. In contrast, a third factor, PLENA (PLE), which is required for reproductive organ development, can interact with the products of MADS box genes expressed at early, intermediate and late stages. We also demonstrate that heterodimerization of DEF and GLO requires the K box, a domain not found in non-plant MADS box factors, indicating that the plant MADS box factors may have different criteria for interaction. The association of PLENA and the temporally intermediate MADS box factors suggests that part of their function in mediating between the meristem and organ identity genes is accomplished through direct interaction. These data reveal an unexpectedly complex network of interactions between the factors controlling flower development and have implications for the determination of organ identity. Images PMID:8861961

A Course in Real-Time Embedded Software

ERIC Educational Resources Information Center

Archibald, J. K.; Fife, W. S.

2007-01-01

Embedded systems are increasingly pervasive, and the creation of reliable controlling software offers unique challenges. Embedded software must interact directly with hardware, it must respond to events in a time-critical fashion, and it typically employs concurrency to meet response time requirements. This paper describes an innovative course…

On the representation of cells in bone marrow pathology by a scalar field: propagation through serial sections, co-localization and spatial interaction analysis.

PubMed

Weis, Cleo-Aron; Grießmann, Benedict Walter; Scharff, Christoph; Detzner, Caecilia; Pfister, Eva; Marx, Alexander; Zoellner, Frank Gerrit

2015-09-02

Immunohistochemical analysis of cellular interactions in the bone marrow in situ is demanding, due to its heterogeneous cellular composition, the poor delineation and overlap of functional compartments and highly complex immunophenotypes of several cell populations (e.g. regulatory T-cells) that require immunohistochemical marker sets for unambiguous characterization. To overcome these difficulties, we herein present an approach to describe objects (e.g. cells, bone trabeculae) by a scalar field that can be propagated through registered images of serial histological sections. The transformation of objects within images (e.g. cells) to a scalar field was performed by convolution of the object's centroids with differently formed radial basis function (e.g. for direct or indirect spatial interaction). On the basis of such a scalar field, a summation field described distributed objects within an image. After image registration i) colocalization analysis could be performed on basis scalar field, which is propagated through registered images, and - due to the shape of the field - were barely prone to matching errors and morphological changes by different cutting levels; ii) furthermore, depending on the field shape the colocalization measurements could also quantify spatial interaction (e.g. direct or paracrine cellular contact); ii) the field-overlap, which represents the spatial distance, of different objects (e.g. two cells) could be calculated by the histogram intersection. The description of objects (e.g. cells, cell clusters, bone trabeculae etc.) as a field offers several possibilities: First, co-localization of different markers (e.g. by immunohistochemical staining) in serial sections can be performed in an automatic, objective and quantifiable way. In contrast to multicolour staining (e.g. 10-colour immunofluorescence) the financial and technical requirements are fairly minor. Second, the approach allows searching for different types of spatial interactions (e.g. direct and indirect cellular interaction) between objects by taking field shape into account (e.g. thin vs. broad). Third, by describing spatially distributed groups of objects as summation field, it gives cluster definition that relies rather on the bare object distance than on the modelled spatial cellular interaction.

From structure to function, via dynamics

NASA Astrophysics Data System (ADS)

Stetter, O.; Soriano, J.; Geisel, T.; Battaglia, D.

2013-01-01

Neurons in the brain are wired into a synaptic network that spans multiple scales, from local circuits within cortical columns to fiber tracts interconnecting distant areas. However, brain function require the dynamic control of inter-circuit interactions on time-scales faster than synaptic changes. In particular, strength and direction of causal influences between neural populations (described by the so-called directed functional connectivity) must be reconfigurable even when the underlying structural connectivity is fixed. Such directed functional influences can be quantified resorting to causal analysis of time-series based on tools like Granger Causality or Transfer Entropy. The ability to quickly reorganize inter-areal interactions is a chief requirement for performance in a changing natural environment. But how can manifold functional networks stem "on demand" from an essentially fixed structure? We explore the hypothesis that the self-organization of neuronal synchronous activity underlies the control of brain functional connectivity. Based on simulated and real recordings of critical neuronal cultures in vitro, as well as on mean-field and spiking network models of interacting brain areas, we have found that "function follows dynamics", rather than structure. Different dynamic states of a same structural network, characterized by different synchronization properties, are indeed associated to different functional digraphs (functional multiplicity). We also highlight the crucial role of dynamics in establishing a structure-to-function link, by showing that whenever different structural topologies lead to similar dynamical states, than the associated functional connectivities are also very similar (structural degeneracy).

The Red Light Receptor Phytochrome B Directly Enhances Substrate-E3 Ligase Interactions to Attenuate Ethylene Responses.

PubMed

Shi, Hui; Shen, Xing; Liu, Renlu; Xue, Chang; Wei, Ning; Deng, Xing Wang; Zhong, Shangwei

2016-12-05

Plants germinating under subterranean darkness assume skotomorphogenesis, a developmental program strengthened by ethylene in response to mechanical pressure of soil. Upon reaching the surface, light triggers a dramatic developmental transition termed de-etiolation that requires immediate termination of ethylene responses. Here, we report that light activation of photoreceptor phyB results in rapid degradation of EIN3, the master transcription factor in the ethylene signaling pathway. As a result, light rapidly and efficiently represses ethylene actions. Specifically, phyB directly interacts with EIN3 in a light-dependent manner and also physically associates with F box protein EBFs. The light-activated association of phyB, EIN3, and EBF1/EBF2 proteins stimulates robust EIN3 degradation by SCF EBF1/EBF2 E3 ligases. We reveal that phyB manipulates substrate-E3 ligase interactions in a light-dependent manner, thus directly controlling the stability of EIN3. Our findings illustrate a mechanistic model of how plants transduce light information to immediately turn off ethylene signaling for de-etiolation initiation. Copyright © 2016 Elsevier Inc. All rights reserved.

The AvrM Effector from Flax Rust Has a Structured C-Terminal Domain and Interacts Directly with the M Resistance Protein

PubMed Central

Catanzariti, Ann-Maree; Dodds, Peter N.; Ve, Thomas; Kobe, Bostjan; Ellis, Jeffrey G.; Staskawicz, Brian J.

2011-01-01

In plant immunity, recognition of pathogen effectors by plant resistance proteins leads to the activation of plant defenses and a localized cell death response. The AvrM effector from flax rust is a small secreted protein that is recognized by the M resistance protein in flax. Here, we investigate the mechanism of M–AvrM recognition and show that these two proteins directly interact in a yeast two-hybrid assay, and that this interaction correlates with the recognition specificity observed for each of the different AvrM variants. We further characterize this interaction by demonstrating that the C-terminal domain of AvrM is required for M-dependent cell death, and show that this domain also interacts with the M protein in yeast. We investigate the role of C-terminal differences among the different AvrM proteins for their involvement in this interaction and establish that M recognition is hindered by an additional 34 amino acids present at the C terminus of several AvrM variants. Structural characterization of recombinant AvrM-A protein revealed a globular C-terminal domain that dimerizes. PMID:19958138

Exploiting replication in distributed systems

NASA Technical Reports Server (NTRS)

Birman, Kenneth P.; Joseph, T. A.

1989-01-01

Techniques are examined for replicating data and execution in directly distributed systems: systems in which multiple processes interact directly with one another while continuously respecting constraints on their joint behavior. Directly distributed systems are often required to solve difficult problems, ranging from management of replicated data to dynamic reconfiguration in response to failures. It is shown that these problems reduce to more primitive, order-based consistency problems, which can be solved using primitives such as the reliable broadcast protocols. Moreover, given a system that implements reliable broadcast primitives, a flexible set of high-level tools can be provided for building a wide variety of directly distributed application programs.

Attractive noncovalent interactions in asymmetric catalysis: Links between enzymes and small molecule catalysts

PubMed Central

Knowles, Robert R.; Jacobsen, Eric N.

2010-01-01

Catalysis by neutral, organic, small molecules capable of binding and activating substrates solely via noncovalent interactions—particularly H-bonding—has emerged as an important approach in organocatalysis. The mechanisms by which such small molecule catalysts induce high enantioselectivity may be quite different from those used by catalysts that rely on covalent interactions with substrates. Attractive noncovalent interactions are weaker, less distance dependent, less directional, and more affected by entropy than covalent interactions. However, the conformational constraint required for high stereoinduction may be achieved, in principle, if multiple noncovalent attractive interactions are operating in concert. This perspective will outline some recent efforts to elucidate the cooperative mechanisms responsible for stereoinduction in highly enantioselective reactions promoted by noncovalent catalysts. PMID:20956302

Phytotechnology Technical and Regulatory Guidance and Decision Trees, Revised

DTIC Science & Technology

2009-02-01

upon planting . In other cases, it may require several seasons before the plant can interact with a contaminated zone at depth. Furthermore, it may...potential ecological exposures posed by the species planted need to be considered. The level of detail required is site specific and varies with the...to be assessed as well. However, the ecological exposure may not be directly from the consumption of the plant . Specifically, the U.S. Environmental

TRIC: Capturing the direct cellular targets of promoter‐bound transcriptional activators

PubMed Central

Dugan, Amanda; Pricer, Rachel; Katz, Micah

2016-01-01

Abstract Transcriptional activators coordinate the dynamic assembly of multiprotein coactivator complexes required for gene expression to occur. Here we combine the power of in vivo covalent chemical capture with p‐benzoyl‐L‐phenylalanine (Bpa), a genetically incorporated photo‐crosslinking amino acid, and chromatin immunoprecipitation (ChIP) to capture the direct protein interactions of the transcriptional activator VP16 with the general transcription factor TBP at the GAL1 promoter in live yeast. PMID:27213278

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.

The chaperone-histone partnership: for the greater good of histone traffic and chromatin plasticity.

PubMed

Hondele, Maria; Ladurner, Andreas G

2011-12-01

Histones are highly positively charged proteins that wrap our genome. Their surface properties also make them prone to nonspecific interactions and aggregation. A class of proteins known as histone chaperones is dedicated to safeguard histones by aiding their proper incorporation into nucleosomes. Histone chaperones facilitate ordered nucleosome assembly and disassembly reactions through the formation of semi-stable histone-chaperone intermediates without requiring ATP, but merely providing a complementary protein surface for histones to dynamically interact with. Recurrent 'chaperoning' mechanisms involve the masking of the histone's positive charge and the direct blocking of crucial histone surface sites, including those required for H3-H4 tetramerization or the binding of nucleosomal DNA. This shielding prevents histones from engaging in premature or unwanted interactions with nucleic acids and other cellular components. In this review, we analyze recent structural studies on chaperone-histone interactions and discuss the implications of this vital partnership for nucleosome assembly and disassembly pathways. Copyright © 2011 Elsevier Ltd. All rights reserved.

Random-field-induced disordering mechanism in a disordered ferromagnet: Between the Imry-Ma and the standard disordering mechanism

NASA Astrophysics Data System (ADS)

Andresen, Juan Carlos; Katzgraber, Helmut G.; Schechter, Moshe

2017-12-01

Random fields disorder Ising ferromagnets by aligning single spins in the direction of the random field in three space dimensions, or by flipping large ferromagnetic domains at dimensions two and below. While the former requires random fields of typical magnitude similar to the interaction strength, the latter Imry-Ma mechanism only requires infinitesimal random fields. Recently, it has been shown that for dilute anisotropic dipolar systems a third mechanism exists, where the ferromagnetic phase is disordered by finite-size glassy domains at a random field of finite magnitude that is considerably smaller than the typical interaction strength. Using large-scale Monte Carlo simulations and zero-temperature numerical approaches, we show that this mechanism applies to disordered ferromagnets with competing short-range ferromagnetic and antiferromagnetic interactions, suggesting its generality in ferromagnetic systems with competing interactions and an underlying spin-glass phase. A finite-size-scaling analysis of the magnetization distribution suggests that the transition might be first order.

Global constraints on vector-like WIMP effective interactions

DOE PAGES

Blennow, Mattias; Coloma, Pilar; Fernandez-Martinez, Enrique; ...

2016-04-07

In this work we combine information from relic abundance, direct detection, cosmic microwave background, positron fraction, gamma rays, and colliders to explore the existing constraints on couplings between Dark Matter and Standard Model constituents when no underlying model or correlation is assumed. For definiteness, we include independent vector-like effective interactions for each Standard Model fermion. Our results show that low Dark Matter masses below 20 GeV are disfavoured at the 3 σ  level with respect to higher masses, due to the tension between the relic abundance requirement and upper constraints on the Dark Matter couplings. Lastly, large couplings are typically onlymore » allowed in combinations which avoid effective couplings to the nuclei used in direct detection experiments.« less

Cryptochrome, Phytochrome, and Anthocyanin Production

PubMed Central

Mancinelli, Alberto L.; Rossi, Federica; Moroni, Anna

1991-01-01

Anthocyanin production in cabbage (Brassica oleracea L.) and tomato (Lycopersicon esculentum Mill.) seedlings exposed to prolonged irradiations was studied under conditions that allowed discrimination, within certain limits, between the contribution of cryptochrome and phytochrome in the photoregulation of the response. The results of the study provide confirming evidence for the involvement of cryptochrome and direct evidence for a significant contribution of cryptochrome to the fluence rate dependence of the response to blue. The results provide some preliminary, direct indication for an interaction between cryptochrome and phytochrome in the photoregulation of anthocyanin production in seedlings exposed to the prolonged irradiations required for a high level of expression of the response. The type and degree of interaction between the two photoreceptors vary significantly, depending on the species and experimental conditions. PMID:16668301

Infant Emotion Regulation: Relations to Bedtime Emotional Availability, Attachment Security, and Temperament

PubMed Central

Kim, Bo-Ram; Stifter, Cynthia A.; Philbrook, Lauren E.; Teti, Douglas M.

2014-01-01

The present study examines the influences of mothers’ emotional availability towards their infants during bedtime, infant attachment security, and interactions between bedtime parenting and attachment with infant temperamental negative affectivity, on infants’ emotion regulation strategy use at 12 and 18 months. Infants’ emotion regulation strategies were assessed during a frustration task that required infants to regulate their emotions in the absence of parental support. Whereas emotional availability was not directly related to infants’ emotion regulation strategies, infant attachment security had direct relations with infants’ orienting towards the environment and tension reduction behaviors. Both maternal emotional availability and security of the mother-infant attachment relationship interacted with infant temperamental negative affectivity to predict two strategies that were less adaptive in regulating frustration. PMID:24995668

Accurate formulas for interaction force and energy in frequency modulation force spectroscopy

NASA Astrophysics Data System (ADS)

Sader, John E.; Jarvis, Suzanne P.

2004-03-01

Frequency modulation atomic force microscopy utilizes the change in resonant frequency of a cantilever to detect variations in the interaction force between cantilever tip and sample. While a simple relation exists enabling the frequency shift to be determined for a given force law, the required complementary inverse relation does not exist for arbitrary oscillation amplitudes of the cantilever. In this letter we address this problem and present simple yet accurate formulas that enable the interaction force and energy to be determined directly from the measured frequency shift. These formulas are valid for any oscillation amplitude and interaction force, and are therefore of widespread applicability in frequency modulation dynamic force spectroscopy.

Distinct TERB1 Domains Regulate Different Protein Interactions in Meiotic Telomere Movement.

PubMed

Zhang, Jingjing; Tu, Zhaowei; Watanabe, Yoshinori; Shibuya, Hiroki

2017-11-14

Meiotic telomeres attach to the nuclear envelope (NE) and drive the chromosome movement required for the pairing of homologous chromosomes. The meiosis-specific telomere proteins TERB1, TERB2, and MAJIN are required to regulate these events, but their assembly processes are largely unknown. Here, we developed a germ-cell-specific knockout mouse of the canonical telomere-binding protein TRF1 and revealed an essential role for TRF1 in directing the assembly of TERB1-TERB2-MAJIN. Further, we identified a TERB2 binding (T2B) domain in TERB1 that is dispensable for the TRF1-TERB1 interaction but is essential for the subsequent TERB1-TERB2 interaction and therefore for telomere attachment to the NE. Meanwhile, cohesin recruitment at telomeres, which is required for efficient telomere movement, is mediated by the MYB-like domain of TERB1, but not by TERB2-MAJIN. Our results reveal distinct protein interactions through various domains of TERB1, which enable the sequential assembly of the meiotic telomere complex for their movements. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

New levels of language processing complexity and organization revealed by granger causation.

PubMed

Gow, David W; Caplan, David N

2012-01-01

Granger causation analysis of high spatiotemporal resolution reconstructions of brain activation offers a new window on the dynamic interactions between brain areas that support language processing. Premised on the observation that causes both precede and uniquely predict their effects, this approach provides an intuitive, model-free means of identifying directed causal interactions in the brain. It requires the analysis of all non-redundant potentially interacting signals, and has shown that even "early" processes such as speech perception involve interactions of many areas in a strikingly large network that extends well beyond traditional left hemisphere perisylvian cortex that play out over hundreds of milliseconds. In this paper we describe this technique and review several general findings that reframe the way we think about language processing and brain function in general. These include the extent and complexity of language processing networks, the central role of interactive processing dynamics, the role of processing hubs where the input from many distinct brain regions are integrated, and the degree to which task requirements and stimulus properties influence processing dynamics and inform our understanding of "language-specific" localized processes.

Direct Interaction between the WD40 Repeat Protein WDR-23 and SKN-1/Nrf Inhibits Binding to Target DNA

PubMed Central

Leung, Chi K.; Hasegawa, Koichi; Wang, Ying; Deonarine, Andrew; Tang, Lanlan; Miwa, Johji

2014-01-01

SKN-1/Nrf transcription factors activate cytoprotective genes in response to reactive small molecules and strongly influence stress resistance, longevity, and development. The molecular mechanisms of SKN-1/Nrf regulation are poorly defined. We previously identified the WD40 repeat protein WDR-23 as a repressor of Caenorhabditis elegans SKN-1 that functions with a ubiquitin ligase to presumably target the factor for degradation. However, SKN-1 activity and nuclear accumulation are not always correlated, suggesting that there could be additional regulatory mechanisms. Here, we integrate forward genetics and biochemistry to gain insights into how WDR-23 interacts with and regulates SKN-1. We provide evidence that WDR-23 preferentially regulates one of three SKN-1 variants through a direct interaction that is required for normal stress resistance and development. Homology modeling predicts that WDR-23 folds into a β-propeller, and we identify the top of this structure and four motifs at the termini of SKN-1c as essential for the interaction. Two of these SKN-1 motifs are highly conserved in human Nrf1 and Nrf2 and two directly interact with target DNA. Lastly, we demonstrate that WDR-23 can block the ability of SKN-1c to interact with DNA sequences of target promoters identifying a new mechanism of regulation that is independent of the ubiquitin proteasome system, which can become occupied with damaged proteins during stress. PMID:24912676

Interacting agricultural pests and their effect on crop yield: application of a Bayesian decision theory approach to the joint management of Bromus tectorum and Cephus cinctus.

PubMed

Keren, Ilai N; Menalled, Fabian D; Weaver, David K; Robison-Cox, James F

2015-01-01

Worldwide, the landscape homogeneity of extensive monocultures that characterizes conventional agriculture has resulted in the development of specialized and interacting multitrophic pest complexes. While integrated pest management emphasizes the need to consider the ecological context where multiple species coexist, management recommendations are often based on single-species tactics. This approach may not provide satisfactory solutions when confronted with the complex interactions occurring between organisms at the same or different trophic levels. Replacement of the single-species management model with more sophisticated, multi-species programs requires an understanding of the direct and indirect interactions occurring between the crop and all categories of pests. We evaluated a modeling framework to make multi-pest management decisions taking into account direct and indirect interactions among species belonging to different trophic levels. We adopted a Bayesian decision theory approach in combination with path analysis to evaluate interactions between Bromus tectorum (downy brome, cheatgrass) and Cephus cinctus (wheat stem sawfly) in wheat (Triticum aestivum) systems. We assessed their joint responses to weed management tactics, seeding rates, and cultivar tolerance to insect stem boring or competition. Our results indicated that C. cinctus oviposition behavior varied as a function of B. tectorum pressure. Crop responses were more readily explained by the joint effects of management tactics on both categories of pests and their interactions than just by the direct impact of any particular management scheme on yield. In accordance, a C. cinctus tolerant variety should be planted at a low seeding rate under high insect pressure. However as B. tectorum levels increase, the C. cinctus tolerant variety should be replaced by a competitive and drought tolerant cultivar at high seeding rates despite C. cinctus infestation. This study exemplifies the necessity of accounting for direct and indirect biological interactions occurring within agroecosystems and propagating this information from the statistical analysis stage to the management stage.

Pay modernisation and healthcare governance.

PubMed

Benton, David C

Policies interact and have direct and indirect consequences resulting in both short-term and longer-term effects on the working lives of professionals, the care they offer and the education needed by future generations of staff. This article explores how pay modernisation could result in benefits and risks for corporate, clinical and staff governance. It is argued that if pay modernisation as a major enabler of service redesign is to succeed then far greater understanding of how various policies interact and their potential consequences is required.

The cognitive impact of interactive design features for learning complex materials in medical education.

PubMed

Song, Hyuksoon S; Pusic, Martin; Nick, Michael W; Sarpel, Umut; Plass, Jan L; Kalet, Adina L

2014-02-01

To identify the most effective way for medical students to interact with a browser-based learning module on the symptoms and neurological underpinnings of stroke syndromes, this study manipulated the way in which subjects interacted with a graphical model of the brain and examined the impact of functional changes on learning outcomes. It was hypothesized that behavioral interactions that were behaviorally more engaging and which required deeper consideration of the model would result in heightened cognitive interaction and better learning than those whose manipulation required less deliberate behavioral and cognitive processing. One hundred forty four students were randomly assigned to four conditions whose model controls incorporated features that required different levels of behavioral and cognitive interaction: Movie (low behavioral/low cognitive, n = 40), Slider (high behavioral/low cognitive, n = 36), Click (low behavioral/high cognitive, n = 30), and Drag (high behavioral/high cognitive, n = 38). Analysis of Covariates (ANCOVA) showed that students who received the treatments associated with lower cognitive interactivity (Movie and Slider) performed better on a transfer task than those receiving the module associated with high cognitive interactivity (Click and Drag, partial eta squared = .03). In addition, the students in the high cognitive interactivity conditions spent significantly more time on the stroke locator activity than other conditions (partial eta squared = .36). The results suggest that interaction with controls that were tightly coupled with the model and whose manipulation required deliberate consideration of the model's features may have overtaxed subjects' cognitive resources. Cognitive effort that facilitated manipulation of content, though directed at the model, may have resulted in extraneous cognitive load, impeding subjects in recognizing the deeper, global relationships in the materials. Instructional designers must, therefore, keep in mind that the way in which functional affordances are integrated with the content can shape both behavioral and cognitive processing, and has significant cognitive load implications.

Calsyntenin-3 molecular architecture and interaction with neurexin 1α.

PubMed

Lu, Zhuoyang; Wang, Yun; Chen, Fang; Tong, Huimin; Reddy, M V V V Sekhar; Luo, Lin; Seshadrinathan, Suchithra; Zhang, Lei; Holthauzen, Luis Marcelo F; Craig, Ann Marie; Ren, Gang; Rudenko, Gabby

2014-12-12

Calsyntenin 3 (Cstn3 or Clstn3), a recently identified synaptic organizer, promotes the development of synapses. Cstn3 localizes to the postsynaptic membrane and triggers presynaptic differentiation. Calsyntenin members play an evolutionarily conserved role in memory and learning. Cstn3 was recently shown in cell-based assays to interact with neurexin 1α (n1α), a synaptic organizer that is implicated in neuropsychiatric disease. Interaction would permit Cstn3 and n1α to form a trans-synaptic complex and promote synaptic differentiation. However, it is contentious whether Cstn3 binds n1α directly. To understand the structure and function of Cstn3, we determined its architecture by electron microscopy and delineated the interaction between Cstn3 and n1α biochemically and biophysically. We show that Cstn3 ectodomains form monomers as well as tetramers that are stabilized by disulfide bonds and Ca(2+), and both are probably flexible in solution. We show further that the extracellular domains of Cstn3 and n1α interact directly and that both Cstn3 monomers and tetramers bind n1α with nanomolar affinity. The interaction is promoted by Ca(2+) and requires minimally the LNS domain of Cstn3. Furthermore, Cstn3 uses a fundamentally different mechanism to bind n1α compared with other neurexin partners, such as the synaptic organizer neuroligin 2, because Cstn3 does not strictly require the sixth LNS domain of n1α. Our structural data suggest how Cstn3 as a synaptic organizer on the postsynaptic membrane, particularly in tetrameric form, may assemble radially symmetric trans-synaptic bridges with the presynaptic synaptic organizer n1α to recruit and spatially organize proteins into networks essential for synaptic function. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Load emphasizes muscle effort minimization during selection of arm movement direction

PubMed Central

2012-01-01

Background Directional preferences during center-out horizontal shoulder-elbow movements were previously established for both the dominant and non-dominant arm with the use of a free-stroke drawing task that required random selection of movement directions. While the preferred directions were mirror-symmetrical in both arms, they were attributed to a tendency specific for the dominant arm to simplify control of interaction torque by actively accelerating one joint and producing largely passive motion at the other joint. No conclusive evidence has been obtained in support of muscle effort minimization as a contributing factor to the directional preferences. Here, we tested whether distal load changes directional preferences, making the influence of muscle effort minimization on the selection of movement direction more apparent. Methods The free-stroke drawing task was performed by the dominant and non-dominant arm with no load and with 0.454 kg load at the wrist. Motion of each arm was limited to rotation of the shoulder and elbow in the horizontal plane. Directional histograms of strokes produced by the fingertip were calculated to assess directional preferences in each arm and load condition. Possible causes for directional preferences were further investigated by studying optimization across directions of a number of cost functions. Results Preferences in both arms to move in the diagonal directions were revealed. The previously suggested tendency to actively accelerate one joint and produce passive motion at the other joint was supported in both arms and load conditions. However, the load increased the tendency to produce strokes in the transverse diagonal directions (perpendicular to the forearm orientation) in both arms. Increases in required muscle effort caused by the load suggested that the higher frequency of movements in the transverse directions represented increased influence of muscle effort minimization on the selection of movement direction. This interpretation was supported by cost function optimization results. Conclusions While without load, the contribution of muscle effort minimization was minor, and therefore, not apparent, the load revealed this contribution by enhancing it. Unlike control of interaction torque, the revealed tendency to minimize muscle effort was independent of arm dominance. PMID:23035925

Nanoribbon field-effect transistors as direct and label-free sensors of enzyme-substrate interactions

NASA Astrophysics Data System (ADS)

Mu, Luye; Droujinine, Ilia; Rajan, Nitin; Sawtelle, Sonya; Reed, Mark

2015-03-01

The ability to measure enzyme-substrate interactions is essential in areas such as diagnostics, treatment, and biochemical screens. Many enzymatic reactions alter the pH of its environment, suggesting of a simple and direct method for detection. We show the ability of Al2O3-coated Si nanoribbon field-effect transistor biosensors to sensitively measure various aspects of enzyme-substrate interactions through measuring the pH. Urea in phosphate buffered saline (PBS) and penicillinase in PBS and urine were measured to limits of <200 μM and 0.02 units/mL, respectively. We also show the ability to extract accurate kinetics from the interaction of acetylcholine and its esterase. Prior work on FET sensors has been limited by the use of surface functionalization, which not only alters enzyme-substrate affinity, but also makes enzyme activity quantification difficult. Our method involves direct detection of reactions in solution without requiring alteration to the reactants, allowing us to obtain repeatable results and sensitive limits of detection. This method is a simple, inexpensive, and effective platform for detection of enzymatic reactions, and can be readily generalized to many unrelated classes of reactants. This work was supported in part by U.S. Army Research Office and Air Force Research Laboratory.

Regulation of cargo transfer between ESCRT-0 and ESCRT-I complexes by flotillin-1 during endosomal sorting of ubiquitinated cargo

PubMed Central

Meister, M; Bänfer, S; Gärtner, U; Koskimies, J; Amaddii, M; Jacob, R; Tikkanen, R

2017-01-01

Ubiquitin-dependent sorting of membrane proteins in endosomes directs them to lysosomal degradation. In the case of receptors such as the epidermal growth factor receptor (EGFR), lysosomal degradation is important for the regulation of downstream signalling. Ubiquitinated proteins are recognised in endosomes by the endosomal sorting complexes required for transport (ESCRT) complexes, which sequentially interact with the ubiquitinated cargo. Although the role of each ESCRT complex in sorting is well established, it is not clear how the cargo is passed on from one ESCRT to the next. We here show that flotillin-1 is required for EGFR degradation, and that it interacts with the subunits of ESCRT-0 and -I complexes (hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs) and Tsg101). Flotillin-1 is required for cargo recognition and sorting by ESCRT-0/Hrs and for its interaction with Tsg101. In addition, flotillin-1 is also required for the sorting of human immunodeficiency virus 1 Gag polyprotein, which mimics ESCRT-0 complex during viral assembly. We propose that flotillin-1 functions in cargo transfer between ESCRT-0 and -I complexes. PMID:28581508

FANCG promotes formation of a newly identified protein complex containing BRCA2, FANCD2 and XRCC3.

PubMed

Wilson, J B; Yamamoto, K; Marriott, A S; Hussain, S; Sung, P; Hoatlin, M E; Mathew, C G; Takata, M; Thompson, L H; Kupfer, G M; Jones, N J

2008-06-12

Fanconi anemia (FA) is a human disorder characterized by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. Thirteen complementation groups and genes are identified, including BRCA2, which is defective in the FA-D1 group. Eight of the FA proteins, including FANCG, participate in a nuclear core complex that is required for the monoubiquitylation of FANCD2 and FANCI. FANCD2, like FANCD1/BRCA2, is not part of the core complex, and we previously showed direct BRCA2-FANCD2 interaction using yeast two-hybrid analysis. We now show in human and hamster cells that expression of FANCG protein, but not the other core complex proteins, is required for co-precipitation of BRCA2 and FANCD2. We also show that phosphorylation of FANCG serine 7 is required for its co-precipitation with BRCA2, XRCC3 and FANCD2, as well as the direct interaction of BRCA2-FANCD2. These results argue that FANCG has a role independent of the FA core complex, and we propose that phosphorylation of serine 7 is the signalling event required for forming a discrete complex comprising FANCD1/BRCA2-FANCD2-FANCG-XRCC3 (D1-D2-G-X3). Cells that fail to express either phospho-Ser7-FANCG, or full length BRCA2 protein, lack the interactions amongst the four component proteins. A role for D1-D2-G-X3 in homologous recombination repair (HRR) is supported by our finding that FANCG and the RAD51-paralog XRCC3 are epistatic for sensitivity to DNA crosslinking compounds in DT40 chicken cells. Our findings further define the intricate interface between FANC and HRR proteins in maintaining chromosome stability.

Evidenced-based review of clinical studies on periodontics.

PubMed

2009-08-01

Periodontal diseases have several implications for the practice of endodontics. First, advanced periodontitis often has direct implications for the long-term prognosis of the case and requires careful evaluation and coordinated treatment of both the periodontic and endodontic diseases. Second, the potential for functional interactions between odontogenic pathoses and marginal periodontitis requires careful collection of clinical observations and monitoring the outcome of various treatments. In this section, we provide an analysis of recent clinical studies in this area.

Man-systems requirements for the control of teleoperators in space

NASA Technical Reports Server (NTRS)

Shields, Nicholas L., Jr.

1988-01-01

The microgravity of the space environment has profound effects on humans and, consequently, on the design requirements for subsystems and components with which humans interact. There are changes in the anthropometry, vision, the perception of orientation, posture, and the ways in which we exert energy. The design requirements for proper human engineering must reflect each of the changes that results, and this is especially true in the exercise of control over remote and teleoperated systems where the operator is removed from any direct sense of control. The National Aeronautics and Space Administration has recently completed the first NASA-wide human factors standard for microgravity. The Man-Systems Integration Standard, NASA-STD-3000, contains considerable information on the appropriate design criteria for microgravity, and there is information that is useful in the design for teleoperated systems. There is not, however, a dedicated collection of data which pertains directly to the special cases of remote and robotic operations. The design considerations for human-system interaction in the control of remote systems in space are discussed, with brief details on the information to be found in the NASA-STD-3000, and arguments for a dedicated section within the Standard which deals with robotic, teleoperated and remote systems and the design requirements for effective human control of these systems in the space environment, and from the space environment.

Targeting and transport: How microtubules control focal adhesion dynamics

PubMed Central

Stehbens, Samantha

2012-01-01

Directional cell migration requires force generation that relies on the coordinated remodeling of interactions with the extracellular matrix (ECM), which is mediated by integrin-based focal adhesions (FAs). Normal FA turnover requires dynamic microtubules, and three members of the diverse group of microtubule plus-end-tracking proteins are principally involved in mediating microtubule interactions with FAs. Microtubules also alter the assembly state of FAs by modulating Rho GTPase signaling, and recent evidence suggests that microtubule-mediated clathrin-dependent and -independent endocytosis regulates FA dynamics. In addition, FA-associated microtubules may provide a polarized microtubule track for localized secretion of matrix metalloproteases (MMPs). Thus, different aspects of the molecular mechanisms by which microtubules control FA turnover in migrating cells are beginning to emerge. PMID:22908306

Antitumor triptycene analogs directly interact with isolated mitochondria to rapidly trigger markers of permeability transition.

PubMed

Perchellet, Elisabeth M; Wang, Yang; Lou, Kaiyan; Zhao, Huiping; Battina, Srinivas K; Hua, Duy H; Perchellet, Jean-Pierre H

2007-01-01

Substituted triptycenes (TT code number), which block nucleoside transport, macromolecule syntheses and DNA topoisomerase activities, induce cytochrome c release and apoptotic DNA fragmentation, inhibit the proliferation of drug-sensitive and -resistant tumor cells in the nM range in vitro and rapidly trigger the collapse of mitochondrial transmembrane potential in cell and cell-free systems. Because mitochondrial permeability transition (MPT) requires more than depolarization, antitumor TTs were tested for their ability to directly trigger specific markers of MPT in isolated mitochondria. Large amplitude swelling and Ca2+ release were assayed in isolated mitochondria to demonstrate TT-induced MPT. Antitumor TTs interact with isolated mitochondria in a concentration- and time-dependent manner to rapidly cause large amplitude swelling and Ca2+ release in relation with their antiproliferative activities in L1210, HL-60 and LL/2 tumor cells in vitro. The ability of 4-10 uM TT15, TT16 and TT24 to maximally induce mitochondrial swelling and Ca2+ release within 20 min is similar to that of classic MPT inducers, such as 5 microg/ml alamethicin, 200 microM atractyloside, 5 microM phenylarsine oxide, 100 microM arsenic trioxide and a 100 microM Ca2+ overload. TT15 requires a priming concentration of 20 microM Ca2+ to trigger mitochondrial swelling and Ca2+ release and these 0.1 microM ruthenium red-sensitive MPT events are abolished by 1 microM cyclosporin A, 2 mM ADP and 20 microM bongkrekic acid, which block components of the permeability transition pore (PTP), and by 50-100 microM of various ubiquinones, which interact with the quinone binding site of the PTP and raise the Ca2+ load required for PTP opening. Antitumor TTs that trigger MPT in isolated mitochondria might interact with components of the PTP to boost its Ca2+-sensitive transition from the closed to the open state and might be valuable to develop mitochondriotoxic drugs that directly activate early components of apoptosis.

Sapovirus Translation Requires an Interaction between VPg and the Cap Binding Protein eIF4E

PubMed Central

Hosmillo, Myra; Chaudhry, Yasmin; Kim, Deok-Song

2014-01-01

ABSTRACT Sapoviruses of the Caliciviridae family of small RNA viruses are emerging pathogens that cause gastroenteritis in humans and animals. Molecular studies on human sapovirus have been hampered due to the lack of a cell culture system. In contrast, porcine sapovirus (PSaV) can be grown in cell culture, making it a suitable model for understanding the infectious cycle of sapoviruses and the related enteric caliciviruses. Caliciviruses are known to use a novel mechanism of protein synthesis that relies on the interaction of cellular translation initiation factors with the virus genome-encoded viral protein genome (VPg) protein, which is covalently linked to the 5′ end of the viral genome. Using PSaV as a representative member of the Sapovirus genus, we characterized the role of the viral VPg protein in sapovirus translation. As observed for other caliciviruses, the PSaV genome was found to be covalently linked to VPg, and this linkage was required for the translation and the infectivity of viral RNA. The PSaV VPg protein was associated with the 4F subunit of the eukaryotic translation initiation factor (eIF4F) complex in infected cells and bound directly to the eIF4E protein. As has been previously demonstrated for feline calicivirus, a member of the Vesivirus genus, PSaV translation required eIF4E and the interaction between eIF4E and eIF4G. Overall, our study provides new insights into the novel mechanism of sapovirus translation, suggesting that sapovirus VPg can hijack the cellular translation initiation mechanism by recruiting the eIF4F complex through a direct eIF4E interaction. IMPORTANCE Sapoviruses, which are members of the Caliciviridae family, are one of the causative agents of viral gastroenteritis in humans. However, human sapovirus remains noncultivable in cell culture, hampering the ability to characterize the virus infectious cycle. Here, we show that the VPg protein from porcine sapovirus, the only cultivatable sapovirus, is essential for viral translation and functions via a direct interaction with the cellular translation initiation factor eIF4E. This work provides new insights into the novel protein-primed mechanism of calicivirus VPg-dependent translation initiation. PMID:25142584

Sapovirus translation requires an interaction between VPg and the cap binding protein eIF4E.

PubMed

Hosmillo, Myra; Chaudhry, Yasmin; Kim, Deok-Song; Goodfellow, Ian; Cho, Kyoung-Oh

2014-11-01

Sapoviruses of the Caliciviridae family of small RNA viruses are emerging pathogens that cause gastroenteritis in humans and animals. Molecular studies on human sapovirus have been hampered due to the lack of a cell culture system. In contrast, porcine sapovirus (PSaV) can be grown in cell culture, making it a suitable model for understanding the infectious cycle of sapoviruses and the related enteric caliciviruses. Caliciviruses are known to use a novel mechanism of protein synthesis that relies on the interaction of cellular translation initiation factors with the virus genome-encoded viral protein genome (VPg) protein, which is covalently linked to the 5' end of the viral genome. Using PSaV as a representative member of the Sapovirus genus, we characterized the role of the viral VPg protein in sapovirus translation. As observed for other caliciviruses, the PSaV genome was found to be covalently linked to VPg, and this linkage was required for the translation and the infectivity of viral RNA. The PSaV VPg protein was associated with the 4F subunit of the eukaryotic translation initiation factor (eIF4F) complex in infected cells and bound directly to the eIF4E protein. As has been previously demonstrated for feline calicivirus, a member of the Vesivirus genus, PSaV translation required eIF4E and the interaction between eIF4E and eIF4G. Overall, our study provides new insights into the novel mechanism of sapovirus translation, suggesting that sapovirus VPg can hijack the cellular translation initiation mechanism by recruiting the eIF4F complex through a direct eIF4E interaction. Sapoviruses, which are members of the Caliciviridae family, are one of the causative agents of viral gastroenteritis in humans. However, human sapovirus remains noncultivable in cell culture, hampering the ability to characterize the virus infectious cycle. Here, we show that the VPg protein from porcine sapovirus, the only cultivatable sapovirus, is essential for viral translation and functions via a direct interaction with the cellular translation initiation factor eIF4E. This work provides new insights into the novel protein-primed mechanism of calicivirus VPg-dependent translation initiation. Copyright © 2014 Hosmillo et al.

A study of modelling simplifications in ground vibration predictions for railway traffic at grade

NASA Astrophysics Data System (ADS)

Germonpré, M.; Degrande, G.; Lombaert, G.

2017-10-01

Accurate computational models are required to predict ground-borne vibration due to railway traffic. Such models generally require a substantial computational effort. Therefore, much research has focused on developing computationally efficient methods, by either exploiting the regularity of the problem geometry in the direction along the track or assuming a simplified track structure. This paper investigates the modelling errors caused by commonly made simplifications of the track geometry. A case study is presented investigating a ballasted track in an excavation. The soil underneath the ballast is stiffened by a lime treatment. First, periodic track models with different cross sections are analyzed, revealing that a prediction of the rail receptance only requires an accurate representation of the soil layering directly underneath the ballast. A much more detailed representation of the cross sectional geometry is required, however, to calculate vibration transfer from track to free field. Second, simplifications in the longitudinal track direction are investigated by comparing 2.5D and periodic track models. This comparison shows that the 2.5D model slightly overestimates the track stiffness, while the transfer functions between track and free field are well predicted. Using a 2.5D model to predict the response during a train passage leads to an overestimation of both train-track interaction forces and free field vibrations. A combined periodic/2.5D approach is therefore proposed in this paper. First, the dynamic axle loads are computed by solving the train-track interaction problem with a periodic model. Next, the vibration transfer to the free field is computed with a 2.5D model. This combined periodic/2.5D approach only introduces small modelling errors compared to an approach in which a periodic model is used in both steps, while significantly reducing the computational cost.

Direct Interactions Between Gli3, Wnt8b, and Fgfs Underlie Patterning of the Dorsal Telencephalon.

PubMed

Hasenpusch-Theil, Kerstin; Watson, Julia A; Theil, Thomas

2017-02-01

A key step in the development of the cerebral cortex is a patterning process, which subdivides the telencephalon into several molecularly distinct domains and is critical for cortical arealization. This process is dependent on a complex network of interactions between signaling molecules of the Fgf and Wnt gene families and the Gli3 transcription factor gene, but a better knowledge of the molecular basis of the interplay between these factors is required to gain a deeper understanding of the genetic circuitry underlying telencephalic patterning. Using DNA-binding and reporter gene assays, we here investigate the possibility that Gli3 and these signaling molecules interact by directly regulating each other's expression. We show that Fgf signaling is required for Wnt8b enhancer activity in the cortical hem, whereas Wnt/β-catenin signaling represses Fgf17 forebrain enhancer activity. In contrast, Fgf and Wnt/β-catenin signaling cooperate to regulate Gli3 expression. Taken together, these findings indicate that mutual interactions between Gli3, Wnt8b, and Fgf17 are crucial elements of the balance between these factors thereby conferring robustness to the patterning process. Hence, our study provides a framework for understanding the genetic circuitry underlying telencephalic patterning and how defects in this process can affect the formation of cortical areas. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Drosophila C-terminal binding protein, dCtBP is required for sensory organ prepattern and sharpens proneural transcriptional activity of the GATA factor Pnr.

PubMed

Biryukova, Inna; Heitzler, Pascal

2008-11-01

The peripheral nervous system is required for animals to detect and to relay environmental stimuli to central nervous system for the information processing. In Drosophila, the precise spatial and temporal expression of two proneural genes achaete (ac) and scute (sc), is necessary for development of the sensory organs. Here we present an evidence that the transcription co-repressor, dCtBP acts as a negative regulator of sensory organ prepattern. Loss of dCtBP function mutant exhibits ectopic sensory organs, while overexpression of dCtBP results in a dramatic loss of sensory organs. These phenotypes are correlated with mis-emerging of sensory organ precursors and perturbated expression of proneural transcription activator Ac. Mammalian CtBP-1 was identified via interaction with the consensus motif PXDLSX(K/R) of adenovirus E1A oncoprotein. We demonstrated that dCtBP binds directly to PLDLS motif of Drosophila Friend of GATA-1 protein, U-shaped and sharpens the adult sensory organ development. Moreover, we found that dCtBP mediates multivalent interaction with the GATA transcriptional activator Pannier and acts as a direct co-repressor of the Pannier-mediated activation of proneural genes. We demonstrated that Pannier genetically interacts with dCtBP-interacting protein HDAC1, suggesting that the dCtBP-dependent regulation of Pannier activity could utilize a repressive mechanism involving alteration of local chromatine structure.

Shape: A 3D Modeling Tool for Astrophysics.

PubMed

Steffen, Wolfgang; Koning, Nicholas; Wenger, Stephan; Morisset, Christophe; Magnor, Marcus

2011-04-01

We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type, and amount that is required for a reconstruction of an object's morphology. It is one of the first publicly available tools to apply interactive graphics to astrophysical modeling. The tool allows astrophysicists to provide a priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation. The tool has already been successfully used in a number of astrophysical research projects.

The Extensibility of an Interpreted Language Using Plugin Libraries

NASA Astrophysics Data System (ADS)

Herceg, Dorde; Radaković, Davorka

2011-09-01

Dynamic geometry software (DGS) are computer programs that allow one to create and manipulate geometrical drawings. They are mostly used in teaching and studying geometry. However, DGS can also be used to develop interactive drawings not directly related to geometry. Examples include teaching materials for numerical mathematics at secondary school and university levels, or interactive mathematical games for elementary school children. Such applications often surpass the intended purposes of the DGS and may require complicated programming on behalf of the user. In this paper we present a simple plug-in model which enables easy development and deployment of interactive GUI components for "Geometrijica", a DGS we are developing on Silverlight.

Collider study on the loop-induced dark matter mediation

NASA Astrophysics Data System (ADS)

Tsai, Yuhsin

2016-06-01

Collider experiments are one of the most promising ways to constrain Dark Matter (DM) interactions. For DM couplings involving light mediators, especially for the loop-mediated interactions, a meaningful interpretation of the results requires to go beyond effective field theory. In this note we discuss the study of the magnetic dipole interacting DM, focusing on a model with anarchic dark flavor structure. By including the momentum-dependent form factors that mediate the coupling - given by the Dark Penguin - in collider processes, we study bounds from monophoton, diphoton, and non-pointing photon searches at the LHC. We also compare our results to constraints from the direct detection experiments.

Demonstration of nonreciprocity in a microwave cavity optomechanical circuit

NASA Astrophysics Data System (ADS)

Peterson, Gabriel; Lecocq, Florent; Kotler, Shlomi; Cicak, Katarina; Simmonds, Raymond; Aumentado, Jose; Teufel, John

The ability to engineer nonreciprocal interactions is essential for many applications including quantum signal processing and quantum transduction. While attributes such as high efficiency and low added noise are always beneficial, for quantum applications these metrics are crucial. Here we present recent experimental results on a parametric, nonreciprocal microwave circuit based on the optomechanical interaction between a superconducting microwave resonator and a mechanically compliant vacuum gap capacitor. Unlike standard Faraday-based circulators, this parametric interaction does not require magnetic fields, and the direction of circulation can be controlled dynamically in situ. Looking forward, such devices could enable programmable, high-efficiency connections between disparate nodes of a quantum network.

Effect of ATP and 2-oxoglutarate on the in vitro interaction between the NifA GAF domain and the GlnB protein of Azospirillum brasilense

PubMed Central

Sotomaior, P.; Araújo, L.M.; Nishikawa, C.Y.; Huergo, L.F.; Monteiro, R.A.; Pedrosa, F.O.; Chubatsu, L.S.; Souza, E.M.

2012-01-01

Azospirillum brasilense is a diazotroph that associates with important agricultural crops and thus has potential to be a nitrogen biofertilizer. The A. brasilense transcription regulator NifA, which seems to be constitutively expressed, activates the transcription of nitrogen fixation genes. It has been suggested that the nitrogen status-signaling protein GlnB regulates NifA activity by direct interaction with the NifA N-terminal GAF domain, preventing the inhibitory effect of this domain under conditions of nitrogen fixation. In the present study, we show that an N-terminal truncated form of NifA no longer required GlnB for activity and lost regulation by ammonium. On the other hand, in trans co-expression of the N-terminal GAF domain inhibited the N-truncated protein in response to fixed nitrogen levels. We also used pull-down assays to show in vitro interaction between the purified N-terminal GAF domain of NifA and the GlnB protein. The results showed that A. brasilense GlnB interacts directly with the NifA N-terminal domain and this interaction is dependent on the presence of ATP and 2-oxoglutarate. PMID:22983183

Effect of ATP and 2-oxoglutarate on the in vitro interaction between the NifA GAF domain and the GlnB protein of Azospirillum brasilense.

PubMed

Sotomaior, P; Araújo, L M; Nishikawa, C Y; Huergo, L F; Monteiro, R A; Pedrosa, F O; Chubatsu, L S; Souza, E M

2012-12-01

Azospirillum brasilense is a diazotroph that associates with important agricultural crops and thus has potential to be a nitrogen biofertilizer. The A. brasilense transcription regulator NifA, which seems to be constitutively expressed, activates the transcription of nitrogen fixation genes. It has been suggested that the nitrogen status-signaling protein GlnB regulates NifA activity by direct interaction with the NifA N-terminal GAF domain, preventing the inhibitory effect of this domain under conditions of nitrogen fixation. In the present study, we show that an N-terminal truncated form of NifA no longer required GlnB for activity and lost regulation by ammonium. On the other hand, in trans co-expression of the N-terminal GAF domain inhibited the N-truncated protein in response to fixed nitrogen levels. We also used pull-down assays to show in vitro interaction between the purified N-terminal GAF domain of NifA and the GlnB protein. The results showed that A. brasilense GlnB interacts directly with the NifA N-terminal domain and this interaction is dependent on the presence of ATP and 2-oxoglutarate.

Norovirus translation requires an interaction between the C Terminus of the genome-linked viral protein VPg and eukaryotic translation initiation factor 4G.

PubMed

Chung, Liliane; Bailey, Dalan; Leen, Eoin N; Emmott, Edward P; Chaudhry, Yasmin; Roberts, Lisa O; Curry, Stephen; Locker, Nicolas; Goodfellow, Ian G

2014-08-01

Viruses have evolved a variety of mechanisms to usurp the host cell translation machinery to enable translation of the viral genome in the presence of high levels of cellular mRNAs. Noroviruses, a major cause of gastroenteritis in man, have evolved a mechanism that relies on the interaction of translation initiation factors with the virus-encoded VPg protein covalently linked to the 5' end of the viral RNA. To further characterize this novel mechanism of translation initiation, we have used proteomics to identify the components of the norovirus translation initiation factor complex. This approach revealed that VPg binds directly to the eIF4F complex, with a high affinity interaction occurring between VPg and eIF4G. Mutational analyses indicated that the C-terminal region of VPg is important for the VPg-eIF4G interaction; viruses with mutations that alter or disrupt this interaction are debilitated or non-viable. Our results shed new light on the unusual mechanisms of protein-directed translation initiation. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Interactions between dorsal and ventral streams for controlling skilled grasp

PubMed Central

van Polanen, Vonne; Davare, Marco

2015-01-01

The two visual systems hypothesis suggests processing of visual information into two distinct routes in the brain: a dorsal stream for the control of actions and a ventral stream for the identification of objects. Recently, increasing evidence has shown that the dorsal and ventral streams are not strictly independent, but do interact with each other. In this paper, we argue that the interactions between dorsal and ventral streams are important for controlling complex object-oriented hand movements, especially skilled grasp. Anatomical studies have reported the existence of direct connections between dorsal and ventral stream areas. These physiological interconnections appear to be gradually more active as the precision demands of the grasp become higher. It is hypothesised that the dorsal stream needs to retrieve detailed information about object identity, stored in ventral stream areas, when the object properties require complex fine-tuning of the grasp. In turn, the ventral stream might receive up to date grasp-related information from dorsal stream areas to refine the object internal representation. Future research will provide direct evidence for which specific areas of the two streams interact, the timing of their interactions and in which behavioural context they occur. PMID:26169317

SAD-3, a Putative Helicase Required for Meiotic Silencing by Unpaired DNA, Interacts with Other Components of the Silencing Machinery

PubMed Central

Hammond, Thomas M.; Xiao, Hua; Boone, Erin C.; Perdue, Tony D.; Pukkila, Patricia J.; Shiu, Patrick K. T.

2011-01-01

In Neurospora crassa, genes lacking a pairing partner during meiosis are suppressed by a process known as meiotic silencing by unpaired DNA (MSUD). To identify novel MSUD components, we have developed a high-throughput reverse-genetic screen for use with the N. crassa knockout library. Here we describe the screening method and the characterization of a gene (sad-3) subsequently discovered. SAD-3 is a putative helicase required for MSUD and sexual spore production. It exists in a complex with other known MSUD proteins in the perinuclear region, a center for meiotic silencing activity. Orthologs of SAD-3 include Schizosaccharomyces pombe Hrr1, a helicase required for RNAi-induced heterochromatin formation. Both SAD-3 and Hrr1 interact with an RNA-directed RNA polymerase and an Argonaute, suggesting that certain aspects of silencing complex formation may be conserved between the two fungal species. PMID:22384347

Ratchet Effects in Active Matter Systems

DOE PAGES

Reichhardt, Cynthia Jane; Reichhardt, Charles

2016-12-21

Ratchet effects can arise for single or collectively interacting Brownian particles on an asymmetric substrate when a net dc transport is produced by an externally applied ac driving force or by periodically flashing the substrate. Recently, a new class of active ratchet systems that do not require the application of external driving has been realized through the use of active matter; they are self-propelled units that can be biological or nonbiological in nature. When active materials such as swimming bacteria interact with an asymmetric substrate, a net dc directed motion can arise even without external driving, opening a wealth ofmore » possibilities such as sorting, cargo transport, or micromachine construction. We review the current status of active matter ratchets for swimming bacteria, cells, active colloids, and swarming models, focusing on the role of particle-substrate interactions. Here, we describe ratchet reversals produced by collective effects and the use of active ratchets to transport passive particles. We discuss future directions including deformable substrates or particles, the role of different swimming modes, varied particle–particle interactions, and nondissipative effects.« less

Huntingtin interacting protein 1 (HIP1) regulates clathrin assembly through direct binding to the regulatory region of the clathrin light chain.

PubMed

Legendre-Guillemin, Valerie; Metzler, Martina; Lemaire, Jean-Francois; Philie, Jacynthe; Gan, Lu; Hayden, Michael R; McPherson, Peter S

2005-02-18

Huntingtin interacting protein 1 (HIP1) is a component of clathrin coats. We previously demonstrated that HIP1 promotes clathrin assembly through its central helical domain, which binds directly to clathrin light chains (CLCs). To better understand the relationship between CLC binding and clathrin assembly we sought to dissect this interaction. Using C-terminal deletion constructs of the HIP1 helical domain, we identified a region between residues 450 and 456 that is required for CLC binding. Within this region, point mutations showed the importance of residues Leu-451, Leu-452, and Arg-453. Mutants that fail to bind CLC are unable to promote clathrin assembly in vitro but still mediate HIP1 homodimerization and heterodimerization with the family member HIP12/HIP1R. Moreover, HIP1 binding to CLC is necessary for HIP1 targeting to clathrin-coated pits and clathrin-coated vesicles. Interestingly, HIP1 binds to a highly conserved region of CLC previously demonstrated to regulate clathrin assembly. These results suggest a role for HIP1/CLC interactions in the regulation of clathrin assembly.

Implications of the Social Web Environment for User Story Education

ERIC Educational Resources Information Center

Fancott, Terrill; Kamthan, Pankaj; Shahmir, Nazlie

2012-01-01

In recent years, user stories have emerged in academia, as well as industry, as a notable approach for expressing user requirements of interactive software systems that are developed using agile methodologies. There are social aspects inherent to software development, in general, and user stories, in particular. This paper presents directions and…

Manipulating 3D-Printed and Paper Models Enhances Student Understanding of Viral Replication

ERIC Educational Resources Information Center

Couper, Lisa; Johannes, Kristen; Powers, Jackie; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Understanding key concepts in molecular biology requires reasoning about molecular processes that are not directly observable and, as such, presents a challenge to students and teachers. We ask whether novel interactive physical models and activities can help students understand key processes in viral replication. Our 3D tangible models are…

Striking the Right Balance: Fusion Centers and Privacy

DTIC Science & Technology

2010-09-01

LAPD Los Angeles Police Department MDPD Miami-Dade Police Department MOU Memorandum of Understanding NCISP...Stanley, the Los Angeles Police Department issued a department directive requiring officers to report 65 behaviors, including “innocuous, clearly...Virginia State Police for refusing to provide requested information concerning the agency’s interaction with the Department of

The global regulator of pathogenesis PnCon7 positively regulates Tox3 effector gene expression through direct interaction in the wheat pathogen Parastagonospora nodorum.

PubMed

Lin, Shao-Yu; Chooi, Yit-Heng; Solomon, Peter S

2018-05-03

To investigate effector gene regulation in the wheat pathogenic fungus Parastagonospora nodorum, the promoter and expression of Tox3 was characterised through a series of complementary approaches. Promoter deletion and DNase I footprinting experiments identified a 25 bp region in the Tox3 promoter as being required for transcription. Subsequent yeast one-hybrid analysis using the DNA sequence as bait identified that interacting partner as the C2H2 zinc finger transcription factor PnCon7, a putative master regulator of pathogenesis. Silencing of PnCon7 resulted in the down-regulation of Tox3 demonstrating that the transcription factor has a positive regulatory role on gene expression. Analysis of Tox3 expression in the PnCon7 silenced strains revealed a strong correlation with PnCon7 transcript levels, supportive of a direct regulatory role. Subsequent pathogenicity assays using PnCon7-silenced isolates revealed that the transcription factor was required for Tox3-mediated disease. The expression of two other necrotrophic effectors (ToxA and Tox1) was also affected but in a non-dose dependent manner suggesting that the regulatory role of PnCon7 on these genes was indirect. Collectively, these data have advanced our fundamental understanding of the Con7 master regulator of pathogenesis by demonstrating its positive regulatory role on the Tox3 effector in P. nodorum through direct interaction. This article is protected by copyright. All rights reserved. © 2018 John Wiley & Sons Ltd.

T7 replisome directly overcomes DNA damage

NASA Astrophysics Data System (ADS)

Sun, Bo; Pandey, Manjula; Inman, James T.; Yang, Yi; Kashlev, Mikhail; Patel, Smita S.; Wang, Michelle D.

2015-12-01

Cells and viruses possess several known `restart' pathways to overcome lesions during DNA replication. However, these `bypass' pathways leave a gap in replicated DNA or require recruitment of accessory proteins, resulting in significant delays to fork movement or even cell division arrest. Using single-molecule and ensemble methods, we demonstrate that the bacteriophage T7 replisome is able to directly replicate through a leading-strand cyclobutane pyrimidine dimer (CPD) lesion. We show that when a replisome encounters the lesion, a substantial fraction of DNA polymerase (DNAP) and helicase stay together at the lesion, the replisome does not dissociate and the helicase does not move forward on its own. The DNAP is able to directly replicate through the lesion by working in conjunction with helicase through specific helicase-DNAP interactions. These observations suggest that the T7 replisome is fundamentally permissive of DNA lesions via pathways that do not require fork adjustment or replisome reassembly.

Ligand requirements for involvement of PKCε in synergistic analgesic interactions between spinal μ and δ opioid receptors.

PubMed

Schuster, D J; Metcalf, M D; Kitto, K F; Messing, R O; Fairbanks, C A; Wilcox, G L

2015-01-01

We recently found that PKCε was required for spinal analgesic synergy between two GPCRs, δ opioid receptors and α2 A adrenoceptors, co-located in the same cellular subpopulation. We sought to determine if co-delivery of μ and δ opioid receptor agonists would similarly result in synergy requiring PKCε. Combinations of μ and δ opioid receptor agonists were co-administered intrathecally by direct lumbar puncture to PKCε-wild-type (PKCε-WT) and -knockout (PKCε-KO) mice. Antinociception was assessed using the hot-water tail-flick assay. Drug interactions were evaluated by isobolographic analysis. All agonists produced comparable antinociception in both PKCε-WT and PKCε-KO mice. Of 19 agonist combinations that produced analgesic synergy, only 3 required PKCε for a synergistic interaction. In these three combinations, one of the agonists was morphine, although not all combinations involving morphine required PKCε. Morphine + deltorphin II and morphine + deltorphin I required PKCε for synergy, whereas a similar combination, morphine + deltorphin, did not. Additionally, morphine + oxymorphindole required PKCε for synergy, whereas a similar combination, morphine + oxycodindole, did not. We discovered biased agonism for a specific signalling pathway at the level of spinally co-delivered opioid agonists. As the bias is only revealed by an appropriate ligand combination and cannot be accounted for by a single drug, it is likely that the receptors these agonists act on are interacting with each other. Our results support the existence of μ and δ opioid receptor heteromers at the spinal level in vivo. This article is part of a themed section on Opioids: New Pathways to Functional Selectivity. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue-2. © 2014 The British Pharmacological Society.

The RSF1 Histone-Remodelling Factor Facilitates DNA Double-Strand Break Repair by Recruiting Centromeric and Fanconi Anaemia Proteins

PubMed Central

Pessina, Fabio; Lowndes, Noel F.

2014-01-01

ATM is a central regulator of the cellular responses to DNA double-strand breaks (DSBs). Here we identify a biochemical interaction between ATM and RSF1 and we characterise the role of RSF1 in this response. The ATM–RSF1 interaction is dependent upon both DSBs and ATM kinase activity. Together with SNF2H/SMARCA5, RSF1 forms the RSF chromatin-remodelling complex. Although RSF1 is specific to the RSF complex, SNF2H/SMARCA5 is a catalytic subunit of several other chromatin-remodelling complexes. Although not required for checkpoint signalling, RSF1 is required for efficient repair of DSBs via both end-joining and homology-directed repair. Specifically, the ATM-dependent recruitment to sites of DSBs of the histone fold proteins CENPS/MHF1 and CENPX/MHF2, previously identified at centromeres, is RSF1-dependent. In turn these proteins recruit and regulate the mono-ubiquitination of the Fanconi Anaemia proteins FANCD2 and FANCI. We propose that by depositing CENPS/MHF1 and CENPX/MHF2, the RSF complex either directly or indirectly contributes to the reorganisation of chromatin around DSBs that is required for efficient DNA repair. PMID:24800743

Characterization of Type Three Secretion System Translocator Interactions with Phospholipid Membranes.

PubMed

Adam, Philip R; Barta, Michael L; Dickenson, Nicholas E

2017-01-01

In vitro characterization of type III secretion system (T3SS) translocator proteins has proven challenging due to complex purification schemes and their hydrophobic nature that often requires detergents to provide protein solubility and stability. Here, we provide experimental details for several techniques that overcome these hurdles, allowing for the direct characterization of the Shigella translocator protein IpaB with respect to phospholipid membrane interaction. The techniques specifically discussed in this chapter include membrane interaction/liposome flotation, liposome sensitive fluorescence quenching, and protein-mediated liposome disruption assays. These assays have provided valuable insight into the role of IpaB in T3SS-mediated phospholipid membrane interactions by Shigella and should readily extend to other members of this important class of proteins.

Infant emotion regulation: relations to bedtime emotional availability, attachment security, and temperament.

PubMed

Kim, Bo-Ram; Stifter, Cynthia A; Philbrook, Lauren E; Teti, Douglas M

2014-11-01

The present study examines the influences of mothers' emotional availability toward their infants during bedtime, infant attachment security, and interactions between bedtime parenting and attachment with infant temperamental negative affectivity, on infants' emotion regulation strategy use at 12 and 18 months. Infants' emotion regulation strategies were assessed during a frustration task that required infants to regulate their emotions in the absence of parental support. Whereas emotional availability was not directly related to infants' emotion regulation strategies, infant attachment security had direct relations with infants' orienting toward the environment and tension reduction behaviors. Both maternal emotional availability and security of the mother-infant attachment relationship interacted with infant temperamental negative affectivity to predict two strategies that were less adaptive in regulating frustration. Copyright © 2014 Elsevier Inc. All rights reserved.

Functional responses and scaling in predator-prey interactions of marine fishes: contemporary issues and emerging concepts.

PubMed

Hunsicker, Mary E; Ciannelli, Lorenzo; Bailey, Kevin M; Buckel, Jeffrey A; Wilson White, J; Link, Jason S; Essington, Timothy E; Gaichas, Sarah; Anderson, Todd W; Brodeur, Richard D; Chan, Kung-Sik; Chen, Kun; Englund, Göran; Frank, Kenneth T; Freitas, Vânia; Hixon, Mark A; Hurst, Thomas; Johnson, Darren W; Kitchell, James F; Reese, Doug; Rose, George A; Sjodin, Henrik; Sydeman, William J; van der Veer, Henk W; Vollset, Knut; Zador, Stephani

2011-12-01

Predator-prey interactions are a primary structuring force vital to the resilience of marine communities and sustainability of the world's oceans. Human influences on marine ecosystems mediate changes in species interactions. This generality is evinced by the cascading effects of overharvesting top predators on the structure and function of marine ecosystems. It follows that ecological forecasting, ecosystem management, and marine spatial planning require a better understanding of food web relationships. Characterising and scaling predator-prey interactions for use in tactical and strategic tools (i.e. multi-species management and ecosystem models) are paramount in this effort. Here, we explore what issues are involved and must be considered to advance the use of predator-prey theory in the context of marine fisheries science. We address pertinent contemporary ecological issues including (1) the approaches and complexities of evaluating predator responses in marine systems; (2) the 'scaling up' of predator-prey interactions to the population, community, and ecosystem level; (3) the role of predator-prey theory in contemporary fisheries and ecosystem modelling approaches; and (4) directions for the future. Our intent is to point out needed research directions that will improve our understanding of predator-prey interactions in the context of the sustainable marine fisheries and ecosystem management. 2011 Blackwell Publishing Ltd/CNRS.

The FANCJ/MutLα interaction is required for correction of the cross-link response in FA-J cells

PubMed Central

Peng, Min; Litman, Rachel; Xie, Jenny; Sharma, Sudha; Brosh, Robert M; Cantor, Sharon B

2007-01-01

FANCJ also called BACH1/BRIP1 was first linked to hereditary breast cancer through its direct interaction with BRCA1. FANCJ was also recently identified as a Fanconi anemia (FA) gene product, establishing FANCJ as an essential tumor suppressor. Similar to other FA cells, FANCJ-null (FA-J) cells accumulate 4N DNA content in response to DNA interstrand crosslinks (ICLs). This accumulation is corrected by reintroduction of wild-type FANCJ. Here, we show that FANCJ interacts with the mismatch repair complex MutLα, composed of PMS2 and MLH1. Specifically, FANCJ directly interacts with MLH1 independent of BRCA1, through its helicase domain. Genetic studies reveal that FANCJ helicase activity and MLH1 binding, but not BRCA1 binding, are essential to correct the FA-J cells' ICL-induced 4N DNA accumulation and sensitivity to ICLs. These results suggest that the FANCJ/MutLα interaction, but not FANCJ/BRCA1 interaction, is essential for establishment of a normal ICL-induced response. The functional role of the FANCJ/MutLα complex demonstrates a novel link between FA and MMR, and predicts a broader role for FANCJ in DNA damage signaling independent of BRCA1. PMID:17581638

Recognition of the Xenopus ribosomal core promoter by the transcription factor xUBF involves multiple HMG box domains and leads to an xUBF interdomain interaction.

PubMed

Leblanc, B; Read, C; Moss, T

1993-02-01

The interaction of the ribosomal transcription factor xUBF with the RNA polymerase I core promoter of Xenopus laevis has been studied both at the DNA and protein levels. It is shown that a single xUBF-DNA complex forms over the 40S initiation site (+1) and involves at least the DNA sequences between -20 and +60 bp. DNA sequences upstream of +10 and downstream of +18 are each sufficient to direct complex formation independently. HMG box 1 of xUBF independently recognizes the sequences -20 to -1 and +1 to +22 and the addition of the N-terminal dimerization domain to HMG box 1 stabilizes its interaction with these sequences approximately 10-fold. HMG boxes 2/3 interact with the DNA downstream of +22 and can independently position xUBF across the initiation site. The C-terminal segment of xUBF, HMG boxes 4, 5 or the acidic domain, directly or indirectly interact with HMG box 1, making the core promoter sequences between -11 and -15 hypersensitive to DNase. This interaction also requires the DNA sequences between +17 and +32, i.e. the HMG box 2/3 binding site. The data suggest extensive folding of the core promoter within the xUBF complex.

Design and Integration of a Three Degrees-of-Freedom Robotic Vehicle with Control Moment Gyro for the Autonomous Multi-Agent Physically Interacting Spacecraft (AMPHIS) Testbed

DTIC Science & Technology

2006-09-01

required directional control for each thruster due to their high precision and equivalent power and computer interface requirements to those for the...Universal Serial Bus) ports, LPT (Line Printing Terminal) and KVM (Keyboard-Video- Mouse) interfaces. Additionally, power is supplied to the computer through...of the IDE cable to the Prometheus Development Kit ACC-IDEEXT. Connect a small drive power connector from the desktop ATX power supply to the ACC

Optical resonance-enhanced absorption-based near-field immunochip biosensor for allergen detection.

PubMed

Maier, Irene; Morgan, Michael R A; Lindner, Wolfgang; Pittner, Fritz

2008-04-15

An optical immunochip biosensor has been developed as a rapid method for allergen detection in complex food matrixes, and its application evaluated for the detection of the egg white allergens, ovalbumin and ovomucoid. The optical near-field phenomenon underlying the basic principle of the sensor design is called resonance-enhanced absorption (REA), which utilizes gold nanoparticles (Au NPs) as signal transducers in a highly sensitive interferometric setup. Using this approach, a novel, simple, and rapid colorimetric solid-phase immunoassay on a planar chip substrate was realized in direct and sandwich assay formats, with a detection system that does not require any instrumentation for readout. Semiquantitative immunochemical responses are directly visible to the naked eye of the analyst. The biosensor shows concentration-dependent color development by capturing antibody-functionalized Au NPs on allergen-coated chips and has a detection limit of 1 ng/mL. To establish a rapid method, we took advantage of the physicochemical microenvironment of the Au NP-antibody bioconjugate to be bound directly over an interacting poly(styrene-methyl methacrylate) interlayer by an immobilized antigen. In the direct assay format, a coating time with allergen of only 5 min under "soft" nondenaturing conditions was sufficient for accurate reproducibility and sensitivity. In conclusion, the REA-based immunochip sensor is easy to fabricate, is reproducible and selective in its performance, has minimal technical requirements, and will enable high-throughput screening of affinity binding interactions in technological and medical applications.

The Mini-Chromosome Maintenance (Mcm) Complexes Interact with DNA Polymerase α-Primase and Stimulate Its Ability to Synthesize RNA Primers

PubMed Central

You, Zhiying; De Falco, Mariarosaria; Kamada, Katsuhiko; Pisani, Francesca M.; Masai, Hisao

2013-01-01

The Mini-chromosome maintenance (Mcm) proteins are essential as central components for the DNA unwinding machinery during eukaryotic DNA replication. DNA primase activity is required at the DNA replication fork to synthesize short RNA primers for DNA chain elongation on the lagging strand. Although direct physical and functional interactions between helicase and primase have been known in many prokaryotic and viral systems, potential interactions between helicase and primase have not been explored in eukaryotes. Using purified Mcm and DNA primase complexes, a direct physical interaction is detected in pull-down assays between the Mcm2∼7 complex and the hetero-dimeric DNA primase composed of the p48 and p58 subunits. The Mcm4/6/7 complex co-sediments with the primase and the DNA polymerase α-primase complex in glycerol gradient centrifugation and forms a Mcm4/6/7-primase-DNA ternary complex in gel-shift assays. Both the Mcm4/6/7 and Mcm2∼7 complexes stimulate RNA primer synthesis by DNA primase in vitro. However, primase inhibits the Mcm4/6/7 helicase activity and this inhibition is abolished by the addition of competitor DNA. In contrast, the ATP hydrolysis activity of Mcm4/6/7 complex is not affected by primase. Mcm and primase proteins mutually stimulate their DNA-binding activities. Our findings indicate that a direct physical interaction between primase and Mcm proteins may facilitate priming reaction by the former protein, suggesting that efficient DNA synthesis through helicase-primase interactions may be conserved in eukaryotic chromosomes. PMID:23977294

Prefrontal-hippocampal interactions for spatial navigation.

PubMed

Ito, Hiroshi T

2018-04-01

Animals have the ability to navigate to a desired location by making use of information about environmental landmarks and their own movements. While decades of neuroscience research have identified neurons in the hippocampus and parahippocampal structures that represent an animal's position in space, it is still largely unclear how an animal can choose the next movement direction to reach a desired goal. As the goal destination is typically located somewhere outside of the range of sensory perception, the animal is required to rely on the internal metric of space to estimate the direction and distance of the destination to plan a next action. Therefore, the hippocampal spatial map should interact with action-planning systems in other cortical regions. In accordance with this idea, several recent studies have indicated the importance of functional interactions between the hippocampus and the prefrontal cortex for goal-directed navigation. In this paper, I will review these studies and discuss how an animal can estimate its future positions correspond to a next movement. Investigation of the navigation problem may further provide general insights into internal models of the brain for action planning. Copyright © 2017 Elsevier Ireland Ltd and Japan Neuroscience Society. All rights reserved.

Direct interaction of microtubule- and actin-based transport motors

NASA Technical Reports Server (NTRS)

Huang, J. D.; Brady, S. T.; Richards, B. W.; Stenolen, D.; Resau, J. H.; Copeland, N. G.; Jenkins, N. A.

1999-01-01

The microtubule network is thought to be used for long-range transport of cellular components in animal cells whereas the actin network is proposed to be used for short-range transport, although the mechanism(s) by which this transport is coordinated is poorly understood. For example, in sea urchins long-range Ca2+-regulated transport of exocytotic vesicles requires a microtubule-based motor, whereas an actin-based motor is used for short-range transport. In neurons, microtubule-based kinesin motor proteins are used for long-range vesicular transport but microtubules do not extend into the neuronal termini, where actin filaments form the cytoskeletal framework, and kinesins are rapidly degraded upon their arrival in neuronal termini, indicating that vesicles may have to be transferred from microtubules to actin tracks to reach their final destination. Here we show that an actin-based vesicle-transport motor, MyoVA, can interact directly with a microtubule-based transport motor, KhcU. As would be expected if these complexes were functional, they also contain kinesin light chains and the localization of MyoVA and KhcU overlaps in the cell. These results indicate that cellular transport is, in part, coordinated through the direct interaction of different motor molecules.

Accelerating progress in Artificial General Intelligence: Choosing a benchmark for natural world interaction

NASA Astrophysics Data System (ADS)

Rohrer, Brandon

2010-12-01

Measuring progress in the field of Artificial General Intelligence (AGI) can be difficult without commonly accepted methods of evaluation. An AGI benchmark would allow evaluation and comparison of the many computational intelligence algorithms that have been developed. In this paper I propose that a benchmark for natural world interaction would possess seven key characteristics: fitness, breadth, specificity, low cost, simplicity, range, and task focus. I also outline two benchmark examples that meet most of these criteria. In the first, the direction task, a human coach directs a machine to perform a novel task in an unfamiliar environment. The direction task is extremely broad, but may be idealistic. In the second, the AGI battery, AGI candidates are evaluated based on their performance on a collection of more specific tasks. The AGI battery is designed to be appropriate to the capabilities of currently existing systems. Both the direction task and the AGI battery would require further definition before implementing. The paper concludes with a description of a task that might be included in the AGI battery: the search and retrieve task.

Learning from epidemiological, clinical, and immunological studies on Mycobacterium africanum for improving current understanding of host-pathogen interactions, and for the development and evaluation of diagnostics, host-directed therapies, and vaccines for tuberculosis.

PubMed

Zumla, Alimuddin; Otchere, Isaac Darko; Mensah, Gloria Ivy; Asante-Poku, Adwoa; Gehre, Florian; Maeurer, Markus; Bates, Matthew; Mwaba, Peter; Ntoumi, Francine; Yeboah-Manu, Dorothy

2017-03-01

Mycobacterium africanum comprises two phylogenetic lineages within the Mycobacterium tuberculosis complex (MTBC). M. africanum was first described and isolated in 1968 from the sputum of a Senegalese patient with pulmonary tuberculosis (TB) and it has been identified increasingly as an important cause of human TB, particularly prevalent in West Africa. The restricted geographical distribution of M. africanum, in contrast to the widespread global distribution of other species of MTBC, requires explanation. Available data indicate that M. africanum may also have important differences in transmission, pathogenesis, and host-pathogen interactions, which could affect the evaluation of new TB intervention tools (diagnostics and vaccines)-those currently in use and those under development. The unequal geographical distribution and spread of MTBC species means that individual research findings from one country or region cannot be generalized across the continent. Thus, generalizing data from previous and ongoing research studies on MTBC may be inaccurate and inappropriate. A major rethink is required regarding the design and structure of future clinical trials of new interventions. The West, Central, East, and Southern African EDCTP Networks of Excellence provide opportunities to take forward these pan-Africa studies. More investments into molecular, epidemiological, clinical, diagnostic, and immunological studies across the African continent are required to enable further understanding of host-M. africanum interactions, leading to the development of more specific diagnostics, biomarkers, host-directed therapies, and vaccines for TB. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Discover the pythagorean theorem using interactive multimedia learning

NASA Astrophysics Data System (ADS)

Adhitama, I.; Sujadi, I.; Pramudya, I.

2018-04-01

In learning process students are required to play an active role in learning. They do not just accept the concept directly from teachers, but also build their own knowledge so that the learning process becomes more meaningful. Based on the observation, when learning Pythagorean theorem, students got difficulty on determining hypotenuse. One of the solution to solve this problem is using an interactive multimedia learning. This article aims to discuss the interactive multimedia as learning media for students. This was a Research and Development (R&D) by using ADDIE model of development. The results obtained was multimedia which was developed proper for students as learning media. Besides, on Phytagorian theorem learning activity we also compare Discovery Learning (DL) model with interactive multimedia and DL without interactive multimedia, and obtained that DL with interactive gave positive effect better than DL without interactive multimedia. It was also obtainde that interactive multimedia can attract and increase the interest ot the students on learning math. Therefore, the use of interactive multimedia on DL procees can improve student learning achievement.

Gain in Transcriptional Activity by Primate-specific Coevolution of Melanoma Antigen-A11 and Its Interaction Site in Androgen Receptor*

PubMed Central

Liu, Qiang; Su, Shifeng; Blackwelder, Amanda J.; Minges, John T.; Wilson, Elizabeth M.

2011-01-01

Male sex development and growth occur in response to high affinity androgen binding to the androgen receptor (AR). In contrast to complete amino acid sequence conservation in the AR DNA and ligand binding domains among mammals, a primate-specific difference in the AR NH2-terminal region that regulates the NH2- and carboxyl-terminal (N/C) interaction enables direct binding to melanoma antigen-A11 (MAGE-11), an AR coregulator that is also primate-specific. Human, mouse, and rat AR share the same NH2-terminal 23FQNLF27 sequence that mediates the androgen-dependent N/C interaction. However, the mouse and rat AR FXXLF motif is flanked by Ala33 that evolved to Val33 in primates. Human AR Val33 was required to interact directly with MAGE-11 and for the inhibitory effect of the AR N/C interaction on activation function 2 that was relieved by MAGE-11. The functional importance of MAGE-11 was indicated by decreased human AR regulation of an androgen-dependent endogenous gene using lentivirus short hairpin RNAs and by the greater transcriptional strength of human compared with mouse AR. MAGE-11 increased progesterone and glucocorticoid receptor activity independently of binding an FXXLF motif by interacting with p300 and p160 coactivators. We conclude that the coevolution of the AR NH2-terminal sequence and MAGE-11 expression among primates provides increased regulatory control over activation domain dominance. Primate-specific expression of MAGE-11 results in greater steroid receptor transcriptional activity through direct interactions with the human AR FXXLF motif region and indirectly through steroid receptor-associated p300 and p160 coactivators. PMID:21730049

A minimally invasive optical trapping system to understand cellular interactions at onset of an immune response

PubMed Central

Glass, David G.; McAlinden, Niall; Millington, Owain R.

2017-01-01

T-cells and antigen presenting cells are an essential part of the adaptive immune response system and how they interact is crucial in how the body effectively fights infection or responds to vaccines. Much of the experimental work studying interaction forces between cells has looked at the average properties of bulk samples of cells or applied microscopy to image the dynamic contact between these cells. In this paper we present a novel optical trapping technique for interrogating the force of this interaction and measuring relative interaction forces at the single-cell level. A triple-spot optical trap is used to directly manipulate the cells of interest without introducing foreign bodies such as beads to the system. The optical trap is used to directly control the initiation of cell-cell contact and, subsequently to terminate the interaction at a defined time point. The laser beam power required to separate immune cell pairs is determined and correlates with the force applied by the optical trap. As proof of concept, the antigen-specific increase in interaction force between a dendritic cell and a specific T-cell is demonstrated. Furthermore, it is demonstrated that this interaction force is completely abrogated when T-cell signalling is blocked. As a result the potential of using optical trapping to interrogate cellular interactions at the single cell level without the need to introduce foreign bodies such as beads is clearly demonstrated. PMID:29220398

Direct interaction with an assistive robot for individuals with chronic stroke.

PubMed

Kmetz, Brandon; Markham, Heather; Brewer, Bambi R

2011-01-01

Many robotic systems have been developed to provide assistance to individuals with disabilities. Most of these systems require the individual to interact with the robot via a joystick or keypad, though some utilize techniques such as speech recognition or selection of objects with a laser pointer. In this paper, we describe a prototype system using a novel method of interaction with an assistive robot. A touch-sensitive skin enables the user to directly guide a robotic arm to a desired position. When the skin is released, the robot remains fixed in position. The target population for this system is individuals with hemiparesis due to chronic stroke. The system can be used as a substitute for the paretic arm and hand in bimanual tasks such as holding a jar while removing the lid. This paper describes the hardware and software of the prototype system, which includes a robotic arm, the touch-sensitive skin, a hook-style prehensor, and weight compensation and speech recognition software.

Tiam1 interaction with the PAR complex promotes talin-mediated Rac1 activation during polarized cell migration

PubMed Central

Wang, Shujie; Watanabe, Takashi; Matsuzawa, Kenji; Katsumi, Akira; Kakeno, Mai; Matsui, Toshinori; Ye, Feng; Sato, Kazuhide; Murase, Kiyoko; Sugiyama, Ikuko; Kimura, Kazushi; Mizoguchi, Akira; Ginsberg, Mark H.; Collard, John G.

2012-01-01

Migrating cells acquire front-rear polarity with a leading edge and a trailing tail for directional movement. The Rac exchange factor Tiam1 participates in polarized cell migration with the PAR complex of PAR3, PAR6, and atypical protein kinase C. However, it remains largely unknown how Tiam1 is regulated and contributes to the establishment of polarity in migrating cells. We show here that Tiam1 interacts directly with talin, which binds and activates integrins to mediate their signaling. Tiam1 accumulated at adhesions in a manner dependent on talin and the PAR complex. The interactions of talin with Tiam1 and the PAR complex were required for adhesion-induced Rac1 activation, cell spreading, and migration toward integrin substrates. Furthermore, Tiam1 acted with talin to regulate adhesion turnover. Thus, we propose that Tiam1, with the PAR complex, binds to integrins through talin and, together with the PAR complex, thereby regulates Rac1 activity and adhesion turnover for polarized migration. PMID:23071154

Sorting nexin 9 recruits clathrin heavy chain to the mitotic spindle for chromosome alignment and segregation.

PubMed

Ma, Maggie P C; Robinson, Phillip J; Chircop, Megan

2013-01-01

Sorting nexin 9 (SNX9) and clathrin heavy chain (CHC) each have roles in mitosis during metaphase. Since the two proteins directly interact for their other cellular function in endocytosis we investigated whether they also interact for metaphase and operate on the same pathway. We report that SNX9 and CHC functionally interact during metaphase in a specific molecular pathway that contributes to stabilization of mitotic spindle kinetochore (K)-fibres for chromosome alignment and segregation. This function is independent of their endocytic role. SNX9 residues in the clathrin-binding low complexity domain are required for CHC association and for targeting both CHC and transforming acidic coiled-coil protein 3 (TACC3) to the mitotic spindle. Mutation of these sites to serine increases the metaphase plate width, indicating inefficient chromosome congression. Therefore SNX9 and CHC function in the same molecular pathway for chromosome alignment and segregation, which is dependent on their direct association.

Sorting Nexin 9 Recruits Clathrin Heavy Chain to the Mitotic Spindle for Chromosome Alignment and Segregation

PubMed Central

Ma, Maggie P. C.; Robinson, Phillip J.; Chircop, Megan

2013-01-01

Sorting nexin 9 (SNX9) and clathrin heavy chain (CHC) each have roles in mitosis during metaphase. Since the two proteins directly interact for their other cellular function in endocytosis we investigated whether they also interact for metaphase and operate on the same pathway. We report that SNX9 and CHC functionally interact during metaphase in a specific molecular pathway that contributes to stabilization of mitotic spindle kinetochore (K)-fibres for chromosome alignment and segregation. This function is independent of their endocytic role. SNX9 residues in the clathrin-binding low complexity domain are required for CHC association and for targeting both CHC and transforming acidic coiled-coil protein 3 (TACC3) to the mitotic spindle. Mutation of these sites to serine increases the metaphase plate width, indicating inefficient chromosome congression. Therefore SNX9 and CHC function in the same molecular pathway for chromosome alignment and segregation, which is dependent on their direct association. PMID:23861900

Direct optical measurement of the on-shot incoherent focal spot and intensity contrast on the OMEGA EP laser

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

Dorrer, C.; Consentino, A.; Irwin, D.

Characterizing the prepulse temporal contrast of optical pulses is required to understand their interaction with matter. Light with relatively low intensity can interact with the target before the main high-intensity pulse. Estimating the intensity contrast, instead of the spatially averaged power contrast, is important to understand intensity-dependent laser–matter interactions. A direct optical approach to determining the on-shot intensity of the incoherent pedestal on an aberrated high-intensity laser system is presented. The spatially resolved focal spot of the incoherent pedestal preceding the main coherent pulse and the intensity contrast are calculated using experimental data. Furthermore, this technique is experimentally validated onmore » one of the chirped pulse amplification beamlines of the OMEGA EP Laser System. The intensity contrast of a 1-kJ, 10-ps laser pulse is shown to be ~10× higher than the power contrast because of the larger spatial extent of the incoherent focal spot relative to the coherent focal spot.« less

Direct optical measurement of the on-shot incoherent focal spot and intensity contrast on the OMEGA EP laser

DOE PAGES

Dorrer, C.; Consentino, A.; Irwin, D.

2016-05-18

Characterizing the prepulse temporal contrast of optical pulses is required to understand their interaction with matter. Light with relatively low intensity can interact with the target before the main high-intensity pulse. Estimating the intensity contrast, instead of the spatially averaged power contrast, is important to understand intensity-dependent laser–matter interactions. A direct optical approach to determining the on-shot intensity of the incoherent pedestal on an aberrated high-intensity laser system is presented. The spatially resolved focal spot of the incoherent pedestal preceding the main coherent pulse and the intensity contrast are calculated using experimental data. Furthermore, this technique is experimentally validated onmore » one of the chirped pulse amplification beamlines of the OMEGA EP Laser System. The intensity contrast of a 1-kJ, 10-ps laser pulse is shown to be ~10× higher than the power contrast because of the larger spatial extent of the incoherent focal spot relative to the coherent focal spot.« less

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

Limiting parental interaction during vocal development affects acoustic call structure in marmoset monkeys

PubMed Central

2018-01-01

Human vocal development is dependent on learning by imitation through social feedback between infants and caregivers. Recent studies have revealed that vocal development is also influenced by parental feedback in marmoset monkeys, suggesting vocal learning mechanisms in nonhuman primates. Marmoset infants that experience more contingent vocal feedback than their littermates develop vocalizations more rapidly, and infant marmosets with limited parental interaction exhibit immature vocal behavior beyond infancy. However, it is yet unclear whether direct parental interaction is an obligate requirement for proper vocal development because all monkeys in the aforementioned studies were able to produce the adult call repertoire after infancy. Using quantitative measures to compare distinct call parameters and vocal sequence structure, we show that social interaction has a direct impact not only on the maturation of the vocal behavior but also on acoustic call structures during vocal development. Monkeys with limited parental interaction during development show systematic differences in call entropy, a measure for maturity, compared with their normally raised siblings. In addition, different call types were occasionally uttered in motif-like sequences similar to those exhibited by vocal learners, such as birds and humans, in early vocal development. These results indicate that a lack of parental interaction leads to long-term disturbances in the acoustic structure of marmoset vocalizations, suggesting an imperative role for social interaction in proper primate vocal development. PMID:29651461

Chromatin loops as allosteric modulators of enhancer-promoter interactions.

PubMed

Doyle, Boryana; Fudenberg, Geoffrey; Imakaev, Maxim; Mirny, Leonid A

2014-10-01

The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site.

Limiting parental interaction during vocal development affects acoustic call structure in marmoset monkeys.

PubMed

Gultekin, Yasemin B; Hage, Steffen R

2018-04-01

Human vocal development is dependent on learning by imitation through social feedback between infants and caregivers. Recent studies have revealed that vocal development is also influenced by parental feedback in marmoset monkeys, suggesting vocal learning mechanisms in nonhuman primates. Marmoset infants that experience more contingent vocal feedback than their littermates develop vocalizations more rapidly, and infant marmosets with limited parental interaction exhibit immature vocal behavior beyond infancy. However, it is yet unclear whether direct parental interaction is an obligate requirement for proper vocal development because all monkeys in the aforementioned studies were able to produce the adult call repertoire after infancy. Using quantitative measures to compare distinct call parameters and vocal sequence structure, we show that social interaction has a direct impact not only on the maturation of the vocal behavior but also on acoustic call structures during vocal development. Monkeys with limited parental interaction during development show systematic differences in call entropy, a measure for maturity, compared with their normally raised siblings. In addition, different call types were occasionally uttered in motif-like sequences similar to those exhibited by vocal learners, such as birds and humans, in early vocal development. These results indicate that a lack of parental interaction leads to long-term disturbances in the acoustic structure of marmoset vocalizations, suggesting an imperative role for social interaction in proper primate vocal development.

Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions

PubMed Central

Shklarsh, Adi; Ariel, Gil; Schneidman, Elad; Ben-Jacob, Eshel

2011-01-01

Collective navigation and swarming have been studied in animal groups, such as fish schools, bird flocks, bacteria, and slime molds. Computer modeling has shown that collective behavior of simple agents can result from simple interactions between the agents, which include short range repulsion, intermediate range alignment, and long range attraction. Here we study collective navigation of bacteria-inspired smart agents in complex terrains, with adaptive interactions that depend on performance. More specifically, each agent adjusts its interactions with the other agents according to its local environment – by decreasing the peers' influence while navigating in a beneficial direction, and increasing it otherwise. We show that inclusion of such performance dependent adaptable interactions significantly improves the collective swarming performance, leading to highly efficient navigation, especially in complex terrains. Notably, to afford such adaptable interactions, each modeled agent requires only simple computational capabilities with short-term memory, which can easily be implemented in simple swarming robots. PMID:21980274

Smart swarms of bacteria-inspired agents with performance adaptable interactions.

PubMed

Shklarsh, Adi; Ariel, Gil; Schneidman, Elad; Ben-Jacob, Eshel

2011-09-01

Collective navigation and swarming have been studied in animal groups, such as fish schools, bird flocks, bacteria, and slime molds. Computer modeling has shown that collective behavior of simple agents can result from simple interactions between the agents, which include short range repulsion, intermediate range alignment, and long range attraction. Here we study collective navigation of bacteria-inspired smart agents in complex terrains, with adaptive interactions that depend on performance. More specifically, each agent adjusts its interactions with the other agents according to its local environment--by decreasing the peers' influence while navigating in a beneficial direction, and increasing it otherwise. We show that inclusion of such performance dependent adaptable interactions significantly improves the collective swarming performance, leading to highly efficient navigation, especially in complex terrains. Notably, to afford such adaptable interactions, each modeled agent requires only simple computational capabilities with short-term memory, which can easily be implemented in simple swarming robots.

Non-covalent Interactions with SUMO and Ubiquitin Orchestrate Distinct Functions of the SLX4 Complex in Genome Maintenance

PubMed Central

Ouyang, Jian; Garner, Elizabeth; Hallet, Alexander; Nguyen, Hai Dang; Rickman, Kimberly A.; Gill, Grace; Smogorzewska, Agata; Zou, Lee

2014-01-01

SLX4, a coordinator of multiple DNA structure-specific endonucleases, is important for several DNA repair pathways. Non-covalent interactions of SLX4 with ubiquitin are required for localizing SLX4 to DNA-interstrand crosslinks (ICLs), yet how SLX4 is targeted to other functional contexts remains unclear. Here, we show that SLX4 binds SUMO-2/3 chains via SUMO-interacting motifs (SIMs). The SIMs of SLX4 are dispensable for ICL repair, but important for processing CPT-induced replication intermediates, suppressing fragile site instability, and localizing SLX4 to ALT telomeres. The localization of SLX4 to laser-induced DNA damage also requires the SIMs, as well as DNA-end resection, UBC9 and MDC1. Furthermore, the SUMO binding of SLX4 enhances its interaction with specific DNA-damage sensors or telomere-binding proteins, including RPA, MRE11-RAD50-NBS1 and TRF2. Thus, the interactions of SLX4 with SUMO and ubiquitin increase its affinity for factors recognizing different DNA lesions or telomeres, helping to direct the SLX4 complex in distinct functional contexts. PMID:25533185

Complex of Fas-associated Factor 1 (FAF1) with Valosin-containing Protein (VCP)-Npl4-Ufd1 and Polyubiquitinated Proteins Promotes Endoplasmic Reticulum-associated Degradation (ERAD)*

PubMed Central

Lee, Jae-Jin; Park, Joon Kyu; Jeong, Jaeho; Jeon, Hyesung; Yoon, Jong-Bok; Kim, Eunice EunKyeong; Lee, Kong-Joo

2013-01-01

Fas-associated factor 1 (FAF1) is a ubiquitin receptor containing multiple ubiquitin-related domains including ubiquitin-associated (UBA), ubiquitin-like (UBL) 1, UBL2, and ubiquitin regulatory X (UBX). We previously showed that N-terminal UBA domain recognizes Lys48-ubiquitin linkage to recruit polyubiquitinated proteins and that a C-terminal UBX domain interacts with valosin-containing protein (VCP). This study shows that FAF1 interacts only with VCP complexed with Npl4-Ufd1 heterodimer, a requirement for the recruitment of polyubiquitinated proteins to UBA domain. Intriguingly, VCP association to C-terminal UBX domain regulates ubiquitin binding to N-terminal UBA domain without direct interaction between UBA and UBX domains. These interactions are well characterized by structural and biochemical analysis. VCP-Npl4-Ufd1 complex is known as the machinery required for endoplasmic reticulum-associated degradation. We demonstrate here that FAF1 binds to VCP-Npl4-Ufd1 complex via UBX domain and polyubiquitinated proteins via UBA domain to promote endoplasmic reticulum-associated degradation. PMID:23293021

Structure and function of the interacting domains of Spire and Fmn-family formins.

PubMed

Vizcarra, Christina L; Kreutz, Barry; Rodal, Avital A; Toms, Angela V; Lu, Jun; Zheng, Wei; Quinlan, Margot E; Eck, Michael J

2011-07-19

Evidence for cooperation between actin nucleators is growing. The WH2-containing nucleator Spire and the formin Cappuccino interact directly, and both are essential for assembly of an actin mesh during Drosophila oogenesis. Their interaction requires the kinase noncatalytic C-lobe domain (KIND) domain of Spire and the C-terminal tail of the formin. Here we describe the crystal structure of the KIND domain of human Spir1 alone and in complex with the tail of Fmn2, a mammalian ortholog of Cappuccino. The KIND domain is structurally similar to the C-lobe of protein kinases. The Fmn2 tail is coordinated in an acidic cleft at the base of the domain that appears to have evolved via deletion of a helix from the canonical kinase fold. Our functional analysis of Cappuccino reveals an unexpected requirement for its tail in actin assembly. In addition, we find that the KIND/tail interaction blocks nucleation by Cappuccino and promotes its displacement from filament barbed ends providing insight into possible modes of cooperation between Spire and Cappuccino.

Gene environment interaction studies in depression and suicidal behavior: An update.

PubMed

Mandelli, Laura; Serretti, Alessandro

2013-12-01

Increasing evidence supports the involvement of both heritable and environmental risk factors in major depression (MD) and suicidal behavior (SB). Studies investigating gene-environment interaction (G × E) may be useful for elucidating the role of biological mechanisms in the risk for mental disorders. In the present paper, we review the literature regarding the interaction between genes modulating brain functions and stressful life events in the etiology of MD and SB and discuss their potential added benefit compared to genetic studies only. Within the context of G × E investigation, thus far, only a few reliable results have been obtained, although some genes have consistently shown interactive effects with environmental risk in MD and, to a lesser extent, in SB. Further investigation is required to disentangle the direct and mediated effects that are common or specific to MD and SB. Since traditional G × E studies overall suffer from important methodological limitations, further effort is required to develop novel methodological strategies with an interdisciplinary approach. Copyright © 2013 Elsevier Ltd. All rights reserved.

FAM21 directs SNX27–retromer cargoes to the plasma membrane by preventing transport to the Golgi apparatus

PubMed Central

Lee, Seongju; Chang, Jaerak; Blackstone, Craig

2016-01-01

The endosomal network maintains cellular homeostasis by sorting, recycling and degrading endocytosed cargoes. Retromer organizes the endosomal sorting pathway in conjunction with various sorting nexin (SNX) proteins. The SNX27–retromer complex has recently been identified as a major endosomal hub that regulates endosome-to-plasma membrane recycling by preventing lysosomal entry of cargoes. Here, we show that SNX27 directly interacts with FAM21, which also binds retromer, within the Wiskott–Aldrich syndrome protein and SCAR homologue (WASH) complex. This interaction is required for the precise localization of SNX27 at an endosomal subdomain as well as for recycling of SNX27-retromer cargoes. Furthermore, FAM21 prevents cargo transport to the Golgi apparatus by controlling levels of phosphatidylinositol 4-phosphate, which facilitates cargo dissociation at the Golgi. Together, our results demonstrate that the SNX27–retromer–WASH complex directs cargoes to the plasma membrane by blocking their transport to lysosomes and the Golgi. PMID:26956659

FAM21 directs SNX27-retromer cargoes to the plasma membrane by preventing transport to the Golgi apparatus.

PubMed

Lee, Seongju; Chang, Jaerak; Blackstone, Craig

2016-03-09

The endosomal network maintains cellular homeostasis by sorting, recycling and degrading endocytosed cargoes. Retromer organizes the endosomal sorting pathway in conjunction with various sorting nexin (SNX) proteins. The SNX27-retromer complex has recently been identified as a major endosomal hub that regulates endosome-to-plasma membrane recycling by preventing lysosomal entry of cargoes. Here, we show that SNX27 directly interacts with FAM21, which also binds retromer, within the Wiskott-Aldrich syndrome protein and SCAR homologue (WASH) complex. This interaction is required for the precise localization of SNX27 at an endosomal subdomain as well as for recycling of SNX27-retromer cargoes. Furthermore, FAM21 prevents cargo transport to the Golgi apparatus by controlling levels of phosphatidylinositol 4-phosphate, which facilitates cargo dissociation at the Golgi. Together, our results demonstrate that the SNX27-retromer-WASH complex directs cargoes to the plasma membrane by blocking their transport to lysosomes and the Golgi.

Preconditions for Sustainable Changes in Didactics Applying Self-Directed Learning in the General Education School

ERIC Educational Resources Information Center

Kazlauskiene, Ausra; Gaucaite, Ramute; Poceviciene, Rasa

2016-01-01

Implementation of the result-oriented (self-)education paradigm in the general education school requires sustainable changes in didactics not only on the strategic document plane but also in educational practice. However, its implementation in practice is complicated. The success of the interaction between theory and practice largely depends on…

Design and Development of an Identity Management System: The Minnesota State College-Southeast Technical Case Study

ERIC Educational Resources Information Center

Elhindi, Mohamed A.

2010-01-01

Historically, managing access to information systems (ISs) required direct interaction with a limited number of users. Increasingly, managing access involves handling an increased numbers of internal and external students, faculty, and staff as well as partners such as workforce development centers, the U.S. Department of Education, and the…

Student Engagement with Assessment and Feedback: Some Lessons from Short-Answer Free-Text E-Assessment Questions

ERIC Educational Resources Information Center

Jordan, Sally

2012-01-01

Students were observed directly, in a usability laboratory, and indirectly, by means of an extensive evaluation of responses, as they attempted interactive computer-marked assessment questions that required free-text responses of up to 20 words and as they amended their responses after receiving feedback. This provided more general insight into…

Microprocessor-Controlled Laser Balancing System

NASA Technical Reports Server (NTRS)

Demuth, R. S.

1985-01-01

Material removed by laser action as part tested for balance. Directed by microprocessor, laser fires appropriate amount of pulses in correct locations to remove necessary amount of material. Operator and microprocessor software interact through video screen and keypad; no programing skills or unprompted system-control decisions required. System provides complete and accurate balancing in single load-and-spinup cycle.

Factors Associated with Choice of Web or Print Intervention Materials in the Healthy Directions 2 Study

ERIC Educational Resources Information Center

Greaney, Mary L.; Puleo, Elaine; Bennett, Gary G.; Haines, Jess; Viswanath, K.; Gillman, Matthew W.; Sprunck-Harrild, Kim; Coeling, Molly; Rusinak, Donna; Emmons, Karen M.

2014-01-01

Background: Many U.S. adults have multiple behavioral risk factors, and effective, scalable interventions are needed to promote population-level health. In the health care setting, interventions are often provided in print, although accessible to nearly everyone, are brief (e.g., pamphlets), are not interactive, and can require some logistics…

Serine Phosphorylation of HIV-1 Vpu and Its Binding to Tetherin Regulates Interaction with Clathrin Adaptors

PubMed Central

Sumner, Jonathan C.; Pickering, Suzanne; Neil, Stuart J. D.

2015-01-01

HIV-1 Vpu prevents incorporation of tetherin (BST2/ CD317) into budding virions and targets it for ESCRT-dependent endosomal degradation via a clathrin-dependent process. This requires a variant acidic dileucine-sorting motif (ExxxLV) in Vpu. Structural studies demonstrate that recombinant Vpu/tetherin fusions can form a ternary complex with the clathrin adaptor AP-1. However, open questions still exist about Vpu’s mechanism of action. Particularly, whether endosomal degradation and the recruitment of the E3 ubiquitin ligase SCFβTRCP1/2 to a conserved phosphorylated binding site, DSGNES, are required for antagonism. Re-evaluation of the phenotype of Vpu phosphorylation mutants and naturally occurring allelic variants reveals that the requirement for the Vpu phosphoserine motif in tetherin antagonism is dissociable from SCFβTRCP1/2 and ESCRT-dependent tetherin degradation. Vpu phospho-mutants phenocopy ExxxLV mutants, and can be rescued by direct clathrin interaction in the absence of SCFβTRCP1/2 recruitment. Moreover, we demonstrate physical interaction between Vpu and AP-1 or AP-2 in cells. This requires Vpu/tetherin transmembrane domain interactions as well as the ExxxLV motif. Importantly, it also requires the Vpu phosphoserine motif and adjacent acidic residues. Taken together these data explain the discordance between the role of SCFβTRCP1/2 and Vpu phosphorylation in tetherin antagonism, and indicate that phosphorylation of Vpu in Vpu/tetherin complexes regulates promiscuous recruitment of adaptors, implicating clathrin-dependent sorting as an essential first step in tetherin antagonism. PMID:26317613

A Dual Interaction Between the 5'- and 3'-Ends of the Melon Necrotic Spot Virus (MNSV) RNA Genome Is Required for Efficient Cap-Independent Translation.

PubMed

Miras, Manuel; Rodríguez-Hernández, Ana M; Romero-López, Cristina; Berzal-Herranz, Alfredo; Colchero, Jaime; Aranda, Miguel A; Truniger, Verónica

2018-01-01

In eukaryotes, the formation of a 5'-cap and 3'-poly(A) dependent protein-protein bridge is required for translation of its mRNAs. In contrast, several plant virus RNA genomes lack both of these mRNA features, but instead have a 3'-CITE (for cap-independent translation enhancer), a RNA element present in their 3'-untranslated region that recruits translation initiation factors and is able to control its cap-independent translation. For several 3'-CITEs, direct RNA-RNA long-distance interactions based on sequence complementarity between the 5'- and 3'-ends are required for efficient translation, as they bring the translation initiation factors bound to the 3'-CITE to the 5'-end. For the carmovirus melon necrotic spot virus (MNSV), a 3'-CITE has been identified, and the presence of its 5'-end in cis has been shown to be required for its activity. Here, we analyze the secondary structure of the 5'-end of the MNSV RNA genome and identify two highly conserved nucleotide sequence stretches that are complementary to the apical loop of its 3'-CITE. In in vivo cap-independent translation assays with mutant constructs, by disrupting and restoring sequence complementarity, we show that the interaction between the 3'-CITE and at least one complementary sequence in the 5'-end is essential for virus RNA translation, although efficient virus translation and multiplication requires both connections. The complementary sequence stretches are invariant in all MNSV isolates, suggesting that the dual 5'-3' RNA:RNA interactions are required for optimal MNSV cap-independent translation and multiplication.

Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails.

PubMed

Benleulmi, Mohamed S; Matysiak, Julien; Robert, Xavier; Miskey, Csaba; Mauro, Eric; Lapaillerie, Delphine; Lesbats, Paul; Chaignepain, Stéphane; Henriquez, Daniel R; Calmels, Christina; Oladosu, Oyindamola; Thierry, Eloïse; Leon, Oscar; Lavigne, Marc; Andreola, Marie-Line; Delelis, Olivier; Ivics, Zoltán; Ruff, Marc; Gouet, Patrice; Parissi, Vincent

2017-11-28

Stable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein-protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process. We show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy. Collectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin.

Collider study on the loop-induced dark matter mediation

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

Tsai, Yuhsin, E-mail: yhtsai@umd.edu

2016-06-21

Collider experiments are one of the most promising ways to constrain Dark Matter (DM) interactions. For DM couplings involving light mediators, especially for the loop-mediated interactions, a meaningful interpretation of the results requires to go beyond effective field theory. In this note we discuss the study of the magnetic dipole interacting DM, focusing on a model with anarchic dark flavor structure. By including the momentum-dependent form factors that mediate the coupling – given by the Dark Penguin – in collider processes, we study bounds from monophoton, diphoton, and non-pointing photon searches at the LHC. We also compare our results tomore » constraints from the direct detection experiments.« less

A Planar-Fluorescence Imaging Technique for Studying Droplet-Turbulence Interactions in Vaporizing Sprays

NASA Technical Reports Server (NTRS)

Santavicca, Dom A.; Coy, E.

1990-01-01

Droplet turbulence interactions directly affect the vaporization and dispersion of droplets in liquid sprays and therefore play a major role in fuel oxidizer mixing in liquid fueled combustion systems. Proper characterization of droplet turbulence interactions in vaporizing sprays require measurement of droplet size velocity and size temperature correlations. A planar, fluorescence imaging technique is described which is being developed for simultaneously measuring the size, velocity, and temperature of individual droplets in vaporizing sprays. Preliminary droplet size velocity correlation measurements made with this technique are presented. These measurements are also compared to and show very good agreement with measurements made in the same spray using a phase Doppler particle analyzer.

Noncovalent interaction-assisted drug delivery system with highly efficient uptake and release of paclitaxel for anticancer therapy.

PubMed

Wei, Yuping; Ma, Liang; Zhang, Liang; Xu, Xia

2017-01-01

An effective drug delivery system requires efficient drug uptake and release inside cancer cells. Here, we report a novel drug delivery system, in which paclitaxel (PTX) interacts with a novel cell penetrating peptide (CPP) through noncovalent interaction designed based on molecular simulations. This CPP/PTX complex confers high efficiency in delivering PTX into cancer cells not by endocytosis but by an energy-independent pathway. Once inside cells, the noncovalent interaction between PTX and the CPP may allow fast release of PTX within cells due to the direct translocation of CPP/PTX. This drug delivery system exhibits strong capacity for inhibition of tumor growth and offers a new avenue for the development of advanced drug delivery systems for anticancer therapy.

Anticoagulant management in the cardiovascular setting.

PubMed

Verheugt, Freek W A

2012-02-01

Vitamin K antagonists have been used as oral anticoagulants (OACs) for over five decades, yet their use in real-world practice is problematic primarily because of their narrow therapeutic window, exacerbated by extensive food and drug interactions, necessitating regular coagulation monitoring and dose adjustment. Around half of patients receiving warfarin are within the therapeutic range, exposing them to the dangers of under-anticoagulation (i.e. thrombosis formation) or over-anticoagulation (i.e. bleeding). A new generation of OACs with improved pharmacology promises to revolutionize antithrombotic management. Rivaroxaban, apixaban (both oral direct Factor Xa inhibitors) and dabigatran (a direct thrombin inhibitor) all exhibit predictable anticoagulant responses and few drug-drug interactions and do not require routine coagulation monitoring. © 2011 The Author Fundamental and Clinical Pharmacology © 2011 Société Française de Pharmacologie et de Thérapeutique.

Direct activation of RIP3/MLKL-dependent necrosis by herpes simplex virus 1 (HSV-1) protein ICP6 triggers host antiviral defense

PubMed Central

Wang, Xing; Li, Yun; Liu, Shan; Yu, Xiaoliang; Li, Lin; Shi, Cuilin; He, Wenhui; Li, Jun; Xu, Lei; Hu, Zhilin; Yu, Lu; Yang, Zhongxu; Chen, Qin; Ge, Lin; Zhang, Zili; Zhou, Biqi; Jiang, Xuejun; Chen, She; He, Sudan

2014-01-01

The receptor-interacting kinase-3 (RIP3) and its downstream substrate mixed lineage kinase domain-like protein (MLKL) have emerged as the key cellular components in programmed necrotic cell death. Receptors for the cytokines of tumor necrosis factor (TNF) family and Toll-like receptors (TLR) 3 and 4 are able to activate RIP3 through receptor-interacting kinase-1 and Toll/IL-1 receptor domain-containing adapter inducing IFN-β, respectively. This form of cell death has been implicated in the host-defense system. However, the molecular mechanisms that drive the activation of RIP3 by a variety of pathogens, other than the above-mentioned receptors, are largely unknown. Here, we report that human herpes simplex virus 1 (HSV-1) infection triggers RIP3-dependent necrosis. This process requires MLKL but is independent of TNF receptor, TLR3, cylindromatosis, and host RIP homotypic interaction motif-containing protein DNA-dependent activator of IFN regulatory factor. After HSV-1 infection, the viral ribonucleotide reductase large subunit (ICP6) interacts with RIP3. The formation of the ICP6–RIP3 complex requires the RHIM domains of both proteins. An HSV-1 ICP6 deletion mutant failed to cause effective necrosis of HSV-1–infected cells. Furthermore, ectopic expression of ICP6, but not RHIM mutant ICP6, directly activated RIP3/MLKL-mediated necrosis. Mice lacking RIP3 exhibited severely impaired control of HSV-1 replication and pathogenesis. Therefore, this study reveals a previously uncharacterized host antipathogen mechanism. PMID:25316792

Chloroplastic protein NRIP1 mediates innate immune receptor recognition of a viral effector

PubMed Central

Caplan, Jeffrey L.; Mamillapalli, Padmavathi; Burch-Smith, Tessa M.; Czymmek, Kirk; Dinesh-Kumar, S.P.

2008-01-01

Summary Plant innate immunity relies on the recognition of pathogen effector molecules by nucleotide-binding-leucine-rich repeat (NB-LRR) immune receptor families. Previously we have shown the N immune receptor, a member of TIR-NB-LRR family, indirectly recognizes the 50-kDa helicase (p50) domain of Tobacco mosaic virus (TMV) through its TIR domain. We have identified an N receptor-interacting protein, NRIP1, that directly interacts with both N's TIR domain and p50. NRIP1 is a functional rhodanese sulfurtransferase and is required for N to provide complete resistance to TMV. Interestingly, NRIP1 that normally localizes to the chloroplasts is recruited to the cytoplasm and nucleus by the p50 effector. As a consequence, NRIP1 interacts with N only in the presence of the p50 effector. Our findings show that a chloroplastic protein is intimately involved in pathogen recognition. We propose that N's activation requires a pre-recognition complex containing the p50 effector and NRIP1. PMID:18267075

Bacterial actin MreB assembles in complex with cell shape protein RodZ.

PubMed

van den Ent, Fusinita; Johnson, Christopher M; Persons, Logan; de Boer, Piet; Löwe, Jan

2010-03-17

Bacterial actin homologue MreB is required for cell shape maintenance in most non-spherical bacteria, where it assembles into helical structures just underneath the cytoplasmic membrane. Proper assembly of the actin cytoskeleton requires RodZ, a conserved, bitopic membrane protein that colocalises to MreB and is essential for cell shape determination. Here, we present the first crystal structure of bacterial actin engaged with a natural partner and provide a clear functional significance of the interaction. We show that the cytoplasmic helix-turn-helix motif of Thermotoga maritima RodZ directly interacts with monomeric as well as filamentous MreB and present the crystal structure of the complex. In vitro and in vivo analyses of mutant T. maritima and Escherichia coli RodZ validate the structure and reveal the importance of the MreB-RodZ interaction in the ability of cells to propagate as rods. Furthermore, the results elucidate how the bacterial actin cytoskeleton might be anchored to the membrane to help constrain peptidoglycan synthesis in the periplasm.

The Role of the Human Mirror Neuron System in Supporting Communication in a Digital World.

PubMed

Dickerson, Kelly; Gerhardstein, Peter; Moser, Alecia

2017-01-01

Humans use both verbal and non-verbal communication to interact with others and their environment and increasingly these interactions are occurring in a digital medium. Whether live or digital, learning to communicate requires overcoming the correspondence problem: There is no direct mapping, or correspondence between perceived and self-produced signals. Reconciliation of the differences between perceived and produced actions, including linguistic actions, is difficult and requires integration across multiple modalities and neuro-cognitive networks. Recent work on the neural substrates of social learning suggests that there may be a common mechanism underlying the perception-production cycle for verbal and non-verbal communication. The purpose of this paper is to review evidence supporting the link between verbal and non-verbal communications, and to extend the hMNS literature by proposing that recent advances in communication technology, which at times have had deleterious effects on behavioral and perceptual performance, may disrupt the success of the hMNS in supporting social interactions because these technologies are virtual and spatiotemporal distributed nature.

Combined administration of antibiotics and direct oral anticoagulants: a renewed indication for laboratory monitoring?

PubMed

Lippi, Giuseppe; Favaloro, Emmanuel J; Mattiuzzi, Camilla

2014-10-01

The recent development and marketing of novel direct oral anticoagulants (DOACs) represents a paradigm shift in the management of patients requiring long-term anticoagulation. The advantages of these compounds over traditional therapy with vitamin K antagonists include a reportedly lower risk of severe hemorrhages and the limited need for laboratory measurements. However, there are several scenarios in which testing should be applied. The potential for drug-to-drug interaction is one plausible but currently underrecognized indication for laboratory assessment of the anticoagulant effect of DOACs. In particular, substantial concern has been raised during Phase I studies regarding the potential interaction of these drugs with some antibiotics, especially those that interplay with permeability glycoprotein (P-gp) and cytochrome 3A4 (CYP3A4). A specific electronic search on clinical trials published so far confirms that clarithromycin and rifampicin significantly impair the bioavailability of dabigatran, whereas clarithromycin, erythromycin, fluconazole, and ketoconazole alter the metabolism of rivaroxaban in vivo. Because of their more recent development, no published data were found for apixaban and edoxaban, or for potential interactions of DOACs with other and widely used antibiotics. It is noteworthy, however, that an online resource based on Food and Drug Administration and social media information, reports several hemorrhagic and thrombotic events in patients simultaneously taking dabigatran and some commonly used antibiotics such as amoxicillin, cephalosporin, and metronidazole. According to these reports, the administration of antibiotics in patients undergoing therapy with DOACs would seem to require accurate evaluation as to whether dose adjustments (personalized or antibiotic class driven) of the anticoagulant drug may be advisable. This might be facilitated by direct laboratory assessments of their anticoagulant effect ex vivo. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Site-directed fluorescence labeling reveals a revised N-terminal membrane topology and functional periplasmic residues in the Escherichia coli cell division protein FtsK.

PubMed

Berezuk, Alison M; Goodyear, Mara; Khursigara, Cezar M

2014-08-22

In Escherichia coli, FtsK is a large integral membrane protein that coordinates chromosome segregation and cell division. The N-terminal domain of FtsK (FtsKN) is essential for division, and the C terminus (FtsKC) is a well characterized DNA translocase. Although the function of FtsKN is unknown, it is suggested that FtsK acts as a checkpoint to ensure DNA is properly segregated before septation. This may occur through modulation of protein interactions between FtsKN and other division proteins in both the periplasm and cytoplasm; thus, a clear understanding of how FtsKN is positioned in the membrane is required to characterize these interactions. The membrane topology of FtsKN was initially determined using site-directed reporter fusions; however, questions regarding this topology persist. Here, we report a revised membrane topology generated by site-directed fluorescence labeling. The revised topology confirms the presence of four transmembrane segments and reveals a newly identified periplasmic loop between the third and fourth transmembrane domains. Within this loop, four residues were identified that, when mutated, resulted in the appearance of cellular voids. High resolution transmission electron microscopy of these voids showed asymmetric division of the cytoplasm in the absence of outer membrane invagination or visible cell wall ingrowth. This uncoupling reveals a novel role for FtsK in linking cell envelope septation events and yields further evidence for FtsK as a critical checkpoint of cell division. The revised topology of FtsKN also provides an important platform for future studies on essential interactions required for this process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

The kinetochore proteins CENP-E and CENP-F directly and specifically interact with distinct BUB mitotic checkpoint Ser/Thr kinases.

PubMed

Ciossani, Giuseppe; Overlack, Katharina; Petrovic, Arsen; Huis In 't Veld, Pim J; Koerner, Carolin; Wohlgemuth, Sabine; Maffini, Stefano; Musacchio, Andrea

2018-05-10

The segregation of chromosomes during cell division relies on the function of the kinetochores, protein complexes that physically connect chromosomes with microtubules of the spindle. The metazoan proteins, centromere protein E (CENP-E) and CENP-F, are components of a fibrous layer of mitotic kinetochores named the corona. Several of their features suggest that CENP-E and CENP-F are paralogs: they are very large (comprising approximately 2700 and 3200 residues, respectively), contain abundant predicted coiled-coil structures, are C-terminally prenylated, and are endowed with microtubule-binding sites at their termini. Moreover, CENP-E contains an ATP-hydrolyzing motor domain that promotes microtubule plus end-directed motion. Here, we show that both CENP-E and CENP-F are recruited to mitotic kinetochores independently of the main corona constituent, the Rod-Zwilch-ZW10 (RZZ) complex. We identified specific interactions of CENP-F and CENP-E with budding uninhibited by benzimidazole 1 (BUB1) and BUB1-related (BUBR1) mitotic checkpoint Ser/Thr kinases, respectively, paralogous proteins involved in mitotic checkpoint control and chromosome alignment. Whereas BUBR1 was dispensable for kinetochore localization of CENP-E, BUB1 was stringently required for CENP-F localization. Through biochemical reconstitution, we demonstrated that the CENP-E-BUBR1 and CENP-F-BUB1 interactions are direct and require similar determinants, a dimeric coiled-coil in CENP-E or CENP-F and a kinase domain in BUBR1 or BUB1. Our findings are consistent with the existence of structurally similar BUB1-CENP-F and BUBR1-CENP-E complexes, supporting the notion that CENP-E and CENP-F are evolutionarily related. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

ISS Mini AERCam Radio Frequency (RF) Coverage Analysis Using iCAT Development Tool

NASA Technical Reports Server (NTRS)

Bolen, Steve; Vazquez, Luis; Sham, Catherine; Fredrickson, Steven; Fink, Patrick; Cox, Jan; Phan, Chau; Panneton, Robert

2003-01-01

The long-term goals of the National Aeronautics and Space Administration's (NASA's) Human Exploration and Development of Space (HEDS) enterprise may require the development of autonomous free-flier (FF) robotic devices to operate within the vicinity of low-Earth orbiting spacecraft to supplement human extravehicular activities (EVAs) in space. Future missions could require external visual inspection of the spacecraft that would be difficult, or dangerous, for humans to perform. Under some circumstance, it may be necessary to employ an un-tethered communications link between the FF and the users. The interactive coverage analysis tool (ICAT) is a software tool that has been developed to perform critical analysis of the communications link performance for a FF operating in the vicinity of the International Space Station (ISS) external environment. The tool allows users to interactively change multiple parameters of the communications link parameters to efficiently perform systems engineering trades on network performance. These trades can be directly translated into design and requirements specifications. This tool significantly reduces the development time in determining a communications network topology by allowing multiple parameters to be changed, and the results of link coverage to be statistically characterized and plotted interactively.

The Use of Arabidopsis to Study Interactions between Parasitic Angiosperms and Their Plant Hosts

PubMed Central

Goldwasser, Y.; Westwood, J. H.; Yoder, J. I.

2002-01-01

Parasitic plants invade host plants in order to rob them of water, minerals and nutrients. The consequences to the infected hosts can be debilitating and some of the world's most pernicious agricultural weeds are parasitic. Parasitic genera of the Scrophulariaceae and Orobanchaceae directly invade roots of neighboring plants via underground structures called haustoria. The mechanisms by which these parasites identify and associate with host plants present unsurpassed opportunities for studying chemical signaling in plant-plant interactions. Seeds of some parasites require specific host factors for efficient germination, thereby insuring the availability of an appropriate host root prior to germination. A second set of signal molecules is required to induce haustorium development and the beginning of heterotrophy. Later stages in parasitism also require the presence of host factors, although these have not yet been well characterized. Arabidopsis is being used as a model host plant to identify genetic loci associated with stimulating parasite germination, haustorium development, and parasite support. Arabidopsis is also being employed to explore how host plants respond to parasite attack. Current methodologies and recent findings in Arabidopsis – parasitic plant interactions will be discussed. PMID:22303205

Radiant energy required for infrared neural stimulation

DOE PAGES

Tan, Xiaodong; Rajguru, Suhrud; Young, Hunter; ...

2015-08-25

Infrared neural stimulation (INS) has been proposed as an alternative method to electrical stimulation because of its spatial selective stimulation. Independent of the mechanism for INS, to translate the method into a device it is important to determine the energy for stimulation required at the target structure. Custom-designed, flat and angle polished fibers, were used to deliver the photons. By rotating the angle polished fibers, the orientation of the radiation beam in the cochlea could be changed. INS-evoked compound action potentials and single unit responses in the central nucleus of the inferior colliculus (ICC) were recorded. X-ray computed tomography wasmore » used to determine the orientation of the optical fiber. Maximum responses were observed when the radiation beam was directed towards the spiral ganglion neurons (SGNs), whereas little responses were seen when the beam was directed towards the basilar membrane. The radiant exposure required at the SGNs to evoke compound action potentials (CAPs) or ICC responses was on average 18.9 ± 12.2 or 10.3 ± 4.9 mJ/cm 2, respectively. For cochlear INS it has been debated whether the radiation directly stimulates the SGNs or evokes a photoacoustic effect. The results support the view that a direct interaction between neurons and radiation dominates the response to INS.« less

Radiant energy required for infrared neural stimulation

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

Tan, Xiaodong; Rajguru, Suhrud; Young, Hunter

Infrared neural stimulation (INS) has been proposed as an alternative method to electrical stimulation because of its spatial selective stimulation. Independent of the mechanism for INS, to translate the method into a device it is important to determine the energy for stimulation required at the target structure. Custom-designed, flat and angle polished fibers, were used to deliver the photons. By rotating the angle polished fibers, the orientation of the radiation beam in the cochlea could be changed. INS-evoked compound action potentials and single unit responses in the central nucleus of the inferior colliculus (ICC) were recorded. X-ray computed tomography wasmore » used to determine the orientation of the optical fiber. Maximum responses were observed when the radiation beam was directed towards the spiral ganglion neurons (SGNs), whereas little responses were seen when the beam was directed towards the basilar membrane. The radiant exposure required at the SGNs to evoke compound action potentials (CAPs) or ICC responses was on average 18.9 ± 12.2 or 10.3 ± 4.9 mJ/cm 2, respectively. For cochlear INS it has been debated whether the radiation directly stimulates the SGNs or evokes a photoacoustic effect. The results support the view that a direct interaction between neurons and radiation dominates the response to INS.« less

Laser Teeth Bleaching: Evaluation of Eventual Side Effects on Enamel and the Pulp and the Efficiency In Vitro and In Vivo

PubMed Central

De Moor, Roeland Jozef Gentil; Meire, Maarten August; De Coster, Peter Jozef

2015-01-01

Light and heat increase the reactivity of hydrogen peroxide. There is no evidence that light activation (power bleaching with high-intensity light) results in a more effective bleaching with a longer lasting effect with high concentrated hydrogen peroxide bleaching gels. Laser light differs from conventional light as it requires a laser-target interaction. The interaction takes place in the first instance in the bleaching gel. The second interaction has to be induced in the tooth, more specifically in the dentine. There is evidence that interaction exists with the bleaching gel: photothermal, photocatalytical, and photochemical interactions are described. The reactivity of the gel is increased by adding photocatalyst of photosensitizers. Direct and effective photobleaching, that is, a direct interaction with the colour molecules in the dentine, however, is only possible with the argon (488 and 415 nm) and KTP laser (532 nm). A number of risks have been described such as heat generation. Nd:YAG and especially high power diode lasers present a risk with intrapulpal temperature elevation up to 22°C. Hypersensitivity is regularly encountered, being it of temporary occurrence except for a number of diode wavelengths and the Nd:YAG. The tooth surface remains intact after laser bleaching. At present, KTP laser is the most efficient dental bleaching wavelength. PMID:25874258

Interactions of the Human LIP5 Regulatory Protein with Endosomal Sorting Complexes Required for Transport*♦

PubMed Central

Skalicky, Jack J.; Arii, Jun; Wenzel, Dawn M.; Stubblefield, William-May B.; Katsuyama, Angela; Uter, Nathan T.; Bajorek, Monika; Myszka, David G.; Sundquist, Wesley I.

2012-01-01

The endosomal sorting complex required for transport (ESCRT) pathway remodels membranes during multivesicular body biogenesis, the abscission stage of cytokinesis, and enveloped virus budding. The ESCRT-III and VPS4 ATPase complexes catalyze the membrane fission events associated with these processes, and the LIP5 protein helps regulate their interactions by binding directly to a subset of ESCRT-III proteins and to VPS4. We have investigated the biochemical and structural basis for different LIP5-ligand interactions and show that the first microtubule-interacting and trafficking (MIT) module of the tandem LIP5 MIT domain binds CHMP1B (and other ESCRT-III proteins) through canonical type 1 MIT-interacting motif (MIM1) interactions. In contrast, the second LIP5 MIT module binds with unusually high affinity to a novel MIM element within the ESCRT-III protein CHMP5. A solution structure of the relevant LIP5-CHMP5 complex reveals that CHMP5 helices 5 and 6 and adjacent linkers form an amphipathic “leucine collar” that wraps almost completely around the second LIP5 MIT module but makes only limited contacts with the first MIT module. LIP5 binds MIM1-containing ESCRT-III proteins and CHMP5 and VPS4 ligands independently in vitro, but these interactions are coupled within cells because formation of stable VPS4 complexes with both LIP5 and CHMP5 requires LIP5 to bind both a MIM1-containing ESCRT-III protein and CHMP5. Our studies thus reveal how the tandem MIT domain of LIP5 binds different types of ESCRT-III proteins, promoting assembly of active VPS4 enzymes on the polymeric ESCRT-III substrate. PMID:23105106

Interaction and interdependent packaging of tegument protein UL11 and glycoprotein e of herpes simplex virus.

PubMed

Han, Jun; Chadha, Pooja; Meckes, David G; Baird, Nicholas L; Wills, John W

2011-09-01

The UL11 tegument protein of herpes simplex virus plays a critical role in the secondary envelopment; however, the mechanistic details remain elusive. Here, we report a new function of UL11 in the budding process in which it directs efficient acquisition of glycoprotein E (gE) via a direct interaction. In vitro binding assays showed that the interaction required only the first 28, membrane-proximal residues of the cytoplasmic tail of gE, and the C-terminal 26 residues of UL11. A second, weaker binding site was also found in the N-terminal half of UL11. The significance of the gE-UL11 interaction was subsequently investigated with viral deletion mutants. In the absence of the gE tail, virion packaging of UL11, but not other tegument proteins such as VP22 and VP16, was reduced by at least 80%. Reciprocally, wild-type gE packaging was also drastically reduced by about 87% in the absence of UL11, and this defect could be rescued in trans by expressing U(L)11 at the U(L)35 locus. Surprisingly, a mutant that lacks the C-terminal gE-binding site of UL11 packaged nearly normal amounts of gE despite its strong interaction with the gE tail in vitro, indicating that the interaction with the UL11 N terminus may be important. Mutagenesis studies of the UL11 N terminus revealed that the association of UL11 with membrane was not required for this function. In contrast, the UL11 acidic cluster motif was found to be critical for gE packaging and was not replaceable with foreign acidic clusters. Together, these results highlight an important role of UL11 in the acquisition of glycoprotein-enriched lipid bilayers, and the findings may also have important implications for the role of UL11 in gE-mediated cell-to-cell spread.

A pollen-specific calmodulin-binding protein, NPG1, interacts with putative pectate lyases.

PubMed

Shin, Sung-Bong; Golovkin, Maxim; Reddy, Anireddy S N

2014-06-12

Previous genetic studies have revealed that a pollen-specific calmodulin-binding protein, No Pollen Germination 1 (NPG1), is required for pollen germination. However, its mode of action is unknown. Here we report direct interaction of NPG1 with pectate lyase-like proteins (PLLs). A truncated form of AtNPG1 lacking the N-terminal tetratricopeptide repeat 1 (TPR1) failed to interact with PLLs, suggesting that it is essential for NPG1 interaction with PLLs. Localization studies with AtNPG1 fused to a fluorescent reporter driven by its native promoter revealed its presence in the cytosol and cell wall of the pollen grain and the growing pollen tube of plasmolyzed pollen. Together, our data suggest that the function of NPG1 in regulating pollen germination is mediated through its interaction with PLLs, which may modify the pollen cell wall and regulate pollen tube emergence and growth.

Dual-Color Click Beetle Luciferase Heteroprotein Fragment Complementation Assays

PubMed Central

Villalobos, Victor; Naik, Snehal; Bruinsma, Monique; Dothager, Robin S.; Pan, Mei-Hsiu; Samrakandi, Mustapha; Moss, Britney; Elhammali, Adnan; Piwnica-Worms, David

2010-01-01

Summary Understanding the functional complexity of protein interactions requires mapping biomolecular complexes within the cellular environment over biologically-relevant time scales. Herein we describe a novel set of reversible, multicolored heteroprotein complementation fragments based on various firefly and click beetle luciferases that utilize the same substrate, D-luciferin. Luciferase heteroprotein fragment complementation systems enabled dual-color quantification of two discreet pairs of interacting proteins simultaneously or two distinct proteins interacting with a third shared protein in live cells. Using real-time analysis of click beetle green and click beetle red luciferase heteroprotein fragment complementation applied to β-TrCP, an E3-ligase common to the regulation of both β-catenin and IκBα, GSK3β was identified as a novel candidate kinase regulating IκBα processing. These dual-color protein interaction switches may enable directed dynamic analysis of a variety of protein interactions in living cells. PMID:20851351

Teaching Programming by Emphasizing Self-Direction: How Did Students React to the Active Role Required of Them?

ERIC Educational Resources Information Center

Isomottonen, Ville; Tirronen, Ville

2013-01-01

Lecturing is known to be a controversial form of teaching. With massed classrooms, in particular, it tends to constrain the active participation of students. One of the remedies applied to programming education is to use technology that can vitalize interaction in the classroom, while another is to base teaching increasingly on programming…

Space and energy conservation housing prototype unit development

NASA Technical Reports Server (NTRS)

Sunshine, D. R.

1975-01-01

Construction plans are discussed for a house which will demonstrate the application of advanced technology to minimize energy requirements and to help direct further development in home construction by defining the interaction of integrated energy and water systems with building configuration and construction materials. Housing unit designs are provided and procedures for the analysis of a variety of housing strategies are developed.

The Effects of Interactive Storybook Reading with Preschoolers Who Are Deaf and Hard-of-Hearing

ERIC Educational Resources Information Center

Trussell, Jessica W.; Dunagan, Janna; Kane, Joy; Cascioli, Toni

2017-01-01

Vocabulary is a consistent predictor of reading achievement for deaf and hard-of-hearing (DHH) children. DHH children tend to have a smaller vocabulary knowledge base than their hearing peers and require direct instruction in this area. There are no evidence-based vocabulary instruction strategies for this population. One reason for the lack of an…

An Rgd Sequence in the P2y2 Receptor Interacts with αVβ3 Integrins and Is Required for Go-Mediated Signal Transduction

PubMed Central

Erb, Laurie; Liu, Jun; Ockerhausen, Jonathan; Kong, Qiongman; Garrad, Richard C.; Griffin, Korey; Neal, Chris; Krugh, Brent; Santiago-Pérez, Laura I.; González, Fernando A.; Gresham, Hattie D.; Turner, John T.; Weisman, Gary A.

2001-01-01

The P2Y2 nucleotide receptor (P2Y2R) contains the integrin-binding domain arginine-glycine-aspartic acid (RGD) in its first extracellular loop, raising the possibility that this G protein–coupled receptor interacts directly with an integrin. Binding of a peptide corresponding to the first extracellular loop of the P2Y2R to K562 erythroleukemia cells was inhibited by antibodies against αVβ3/β5 integrins and the integrin-associated thrombospondin receptor, CD47. Immunofluorescence of cells transfected with epitope-tagged P2Y2Rs indicated that αV integrins colocalized 10-fold better with the wild-type P2Y2R than with a mutant P2Y2R in which the RGD sequence was replaced with RGE. Compared with the wild-type P2Y2R, the RGE mutant required 1,000-fold higher agonist concentrations to phosphorylate focal adhesion kinase, activate extracellular signal–regulated kinases, and initiate the PLC-dependent mobilization of intracellular Ca2+. Furthermore, an anti-αV integrin antibody partially inhibited these signaling events mediated by the wild-type P2Y2R. Pertussis toxin, an inhibitor of Gi/o proteins, partially inhibited Ca2+ mobilization mediated by the wild-type P2Y2R, but not by the RGE mutant, suggesting that the RGD sequence is required for P2Y2R-mediated activation of Go, but not Gq. Since CD47 has been shown to associate directly with Gi/o family proteins, these results suggest that interactions between P2Y2Rs, integrins, and CD47 may be important for coupling the P2Y2R to Go. PMID:11331301

Spindle pole body-anchored Kar3 drives the nucleus along microtubules from another nucleus in preparation for nuclear fusion during yeast karyogamy.

PubMed

Gibeaux, Romain; Politi, Antonio Z; Nédélec, François; Antony, Claude; Knop, Michael

2013-02-01

Nuclear migration during yeast karyogamy, termed nuclear congression, is required to initiate nuclear fusion. Congression involves a specific regulation of the microtubule minus end-directed kinesin-14 motor Kar3 and a rearrangement of the cytoplasmic microtubule attachment sites at the spindle pole bodies (SPBs). However, how these elements interact to produce the forces necessary for nuclear migration is less clear. We used electron tomography, molecular genetics, quantitative imaging, and first principles modeling to investigate how cytoplasmic microtubules are organized during nuclear congression. We found that Kar3, with the help of its light chain, Cik1, is anchored during mating to the SPB component Spc72 that also serves as a nucleator and anchor for microtubules via their minus ends. Moreover, we show that no direct microtubule-microtubule interactions are required for nuclear migration. Instead, SPB-anchored Kar3 exerts the necessary pulling forces laterally on microtubules emanating from the SPB of the mating partner nucleus. Therefore, a twofold symmetrical application of the core principle that drives nuclear migration in higher cells is used in yeast to drive nuclei toward each other before nuclear fusion.

Spindle pole body-anchored Kar3 drives the nucleus along microtubules from another nucleus in preparation for nuclear fusion during yeast karyogamy

PubMed Central

Gibeaux, Romain; Politi, Antonio Z.; Nédélec, François; Antony, Claude; Knop, Michael

2013-01-01

Nuclear migration during yeast karyogamy, termed nuclear congression, is required to initiate nuclear fusion. Congression involves a specific regulation of the microtubule minus end-directed kinesin-14 motor Kar3 and a rearrangement of the cytoplasmic microtubule attachment sites at the spindle pole bodies (SPBs). However, how these elements interact to produce the forces necessary for nuclear migration is less clear. We used electron tomography, molecular genetics, quantitative imaging, and first principles modeling to investigate how cytoplasmic microtubules are organized during nuclear congression. We found that Kar3, with the help of its light chain, Cik1, is anchored during mating to the SPB component Spc72 that also serves as a nucleator and anchor for microtubules via their minus ends. Moreover, we show that no direct microtubule–microtubule interactions are required for nuclear migration. Instead, SPB-anchored Kar3 exerts the necessary pulling forces laterally on microtubules emanating from the SPB of the mating partner nucleus. Therefore, a twofold symmetrical application of the core principle that drives nuclear migration in higher cells is used in yeast to drive nuclei toward each other before nuclear fusion. PMID:23388829

Activation of IKKalpha and IKKbeta through their fusion with HTLV-I tax protein.

PubMed

Xiao, G; Sun, S C

2000-10-26

Human T-cell leukemia virus type I (HTLV-I) Tax protein persistently stimulates the activity of IkappaB kinase (IKK), resulting in constitutive activation of the transcription factor NF-kappaB. Tax activation of IKK requires physical interaction of this viral protein with the IKK regulatory subunit, IKKgamma. The Tax/IKKgamma interaction allows Tax to engage the IKK catalytic subunits, IKKalpha and IKKbeta, although it remains unclear whether this linker function of IKKgamma is sufficient for supporting the Tax-specific IKK activation. To address this question, we have examined the sequences of IKKgamma required for modulating the Tax/IKK signaling. We demonstrate that when fused to Tax, a small N-terminal fragment of IKKgamma, containing its minimal IKKalpha/beta-binding domain, is sufficient for bringing Tax to and activating the IKK catalytic subunits. Disruption of the IKKalpha/beta-binding activity of this domain abolishes its function in modulating the Tax/IKK signaling. We further demonstrate that direct fusion of Tax to IKKalpha and IKKbeta leads to activation of these kinases. These findings suggest that the IKKgamma-directed Tax/IKK association serves as a molecular trigger for IKK activation.

Recognition and Blocking of Innate Immunity Cells by Candida albicans Chitin ▿ †

PubMed Central

Mora-Montes, Héctor M.; Netea, Mihai G.; Ferwerda, Gerben; Lenardon, Megan D.; Brown, Gordon D.; Mistry, Anita R.; Kullberg, Bart Jan; O'Callaghan, Chris A.; Sheth, Chirag C.; Odds, Frank C.; Brown, Alistair J. P.; Munro, Carol A.; Gow, Neil A. R.

2011-01-01

Chitin is a skeletal cell wall polysaccharide of the inner cell wall of fungal pathogens. As yet, little about its role during fungus-host immune cell interactions is known. We show here that ultrapurified chitin from Candida albicans cell walls did not stimulate cytokine production directly but blocked the recognition of C. albicans by human peripheral blood mononuclear cells (PBMCs) and murine macrophages, leading to significant reductions in cytokine production. Chitin did not affect the induction of cytokines stimulated by bacterial cells or lipopolysaccharide (LPS), indicating that blocking was not due to steric masking of specific receptors. Toll-like receptor 2 (TLR2), TLR4, and Mincle (the macrophage-inducible C-type lectin) were not required for interactions with chitin. Dectin-1 was required for immune blocking but did not bind chitin directly. Cytokine stimulation was significantly reduced upon stimulation of PBMCs with heat-killed chitin-deficient C. albicans cells but not with live cells. Therefore, chitin is normally not exposed to cells of the innate immune system but is capable of influencing immune recognition by blocking dectin-1-mediated engagement with fungal cell walls. PMID:21357722

Protein Kinase A Modulates Transforming Growth Factor-β Signaling through a Direct Interaction with Smad4 Protein*

PubMed Central

Yang, Huibin; Li, Gangyong; Wu, Jing-Jiang; Wang, Lidong; Uhler, Michael; Simeone, Diane M.

2013-01-01

Transforming growth factor β (TGFβ) signaling normally functions to regulate embryonic development and cellular homeostasis. It is increasingly recognized that TGFβ signaling is regulated by cross-talk with other signaling pathways. We previously reported that TGFβ activates protein kinase A (PKA) independent of cAMP through an interaction of an activated Smad3-Smad4 complex and the regulatory subunit of the PKA holoenzyme (PKA-R). Here we define the interaction domains of Smad4 and PKA-R and the functional consequences of this interaction. Using a series of Smad4 and PKA-R truncation mutants, we identified amino acids 290–300 of the Smad4 linker region as critical for the specific interaction of Smad4 and PKA-R. Co-immunoprecipitation assays showed that the B cAMP binding domain of PKA-R was sufficient for interaction with Smad4. Targeting of B domain regions conserved among all PKA-R isoforms and exposed on the molecular surface demonstrated that amino acids 281–285 and 320–329 were required for complex formation with Smad4. Interactions of these specific regions of Smad4 and PKA-R were necessary for TGFβ-mediated increases in PKA activity, CREB (cAMP-response element-binding protein) phosphorylation, induction of p21, and growth inhibition. Moreover, this Smad4-PKA interaction was required for TGFβ-induced epithelial mesenchymal transition, invasion of pancreatic tumor cells, and regulation of tumor growth in vivo. PMID:23362281

TRICCS: A proposed teleoperator/robot integrated command and control system for space applications

NASA Technical Reports Server (NTRS)

Will, R. W.

1985-01-01

Robotic systems will play an increasingly important role in space operations. An integrated command and control system based on the requirements of space-related applications and incorporating features necessary for the evolution of advanced goal-directed robotic systems is described. These features include: interaction with a world model or domain knowledge base, sensor feedback, multiple-arm capability and concurrent operations. The system makes maximum use of manual interaction at all levels for debug, monitoring, and operational reliability. It is shown that the robotic command and control system may most advantageously be implemented as packages and tasks in Ada.

SAR by Oxime-Containing Peptide Libraries: Application to Tsg101 Ligand Optimization

PubMed Central

Liu, Fa; Stephen, Andrew G.; Waheed, Abdul A.; Aman, M. Javad; Freed, Eric O.; Fisher, Robert J.; Burke, Terrence R.

2008-01-01

HIV-1 viral assembly requires a direct interaction between a Pro-Thr-Ala-Pro (“PTAP”) motif in the viral protein Gag-p6 and the cellular endosomal sorting factor Tsg101. In an effort to develop competitive inhibitors of this interaction, an SAR study was conducted based on the application of post solid-phase oxime formation involving the sequential insertion of aminooxy-containing residues within a nonamer parent peptide followed by reaction with libraries of aldehydes. Approximately 15–20-fold enhancement in binding affinity was achieved by this approach. PMID:18655064

Cell division requires a direct link between microtubule-bound RacGAP and Anillin in the contractile ring.

PubMed

Gregory, Stephen L; Ebrahimi, Saman; Milverton, Joanne; Jones, Whitney M; Bejsovec, Amy; Saint, Robert

2008-01-08

The mitotic microtubule array plays two primary roles in cell division. It acts as a scaffold for the congression and separation of chromosomes, and it specifies and maintains the contractile-ring position. The current model for initiation of Drosophila and mammalian cytokinesis [1-5] postulates that equatorial localization of a RhoGEF (Pbl/Ect2) by a microtubule-associated motor protein complex creates a band of activated RhoA [6], which subsequently recruits contractile-ring components such as actin, myosin, and Anillin [1-3]. Equatorial microtubules are essential for continued constriction, but how they interact with the contractile apparatus is unknown. Here, we report the first direct molecular link between the microtubule spindle and the actomyosin contractile ring. We find that the spindle-associated component, RacGAP50C, which specifies the site of cleavage [1-5], interacts directly with Anillin, an actin and myosin binding protein found in the contractile ring [7-10]. Both proteins depend on this interaction for their localization. In the absence of Anillin, the spindle-associated RacGAP loses its association with the equatorial cortex, and cytokinesis fails. These results account for the long-observed dependence of cytokinesis on the continual presence of microtubules at the cortex.

Comparing reactive and memory-one strategies of direct reciprocity

NASA Astrophysics Data System (ADS)

Baek, Seung Ki; Jeong, Hyeong-Chai; Hilbe, Christian; Nowak, Martin A.

2016-05-01

Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player’s previous move, and memory-one strategies, which take into account the own and the co-player’s previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation.

Comparing reactive and memory-one strategies of direct reciprocity

PubMed Central

Baek, Seung Ki; Jeong, Hyeong-Chai; Hilbe, Christian; Nowak, Martin A.

2016-01-01

Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player’s previous move, and memory-one strategies, which take into account the own and the co-player’s previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation. PMID:27161141

Identification of a domain within human TAF(I)48, a subunit of Selectivity Factor 1, that interacts with helix 2 of TBP.

PubMed

Xu, Shuping; Hori, Roderick T

2004-09-01

RNA polymerase I transcription in human cells requires Selectivity Factor 1, a multisubunit complex composed of the TATA-box-binding protein (TBP) and three TBP-associated factors (TAFs) called TAF(I)48, TAF(I)63 and TAF(I)110. Each of the Selectivity Factor 1 subunits binds directly to the other three components, but these interactions have not been characterized. This study is the initial identification and analysis of a TBP-binding domain within a Selectivity Factor 1 TAF. The interaction between human TBP and human TAF(I)48 was initially examined using the yeast two-hybrid assay, and a TBP-binding domain was identified in the carboxyl-terminus of human (h)TAF(I)48. Consistent with this result, the hTAF(I)48 carboxyl-terminus was able to bind directly to TBP in protein-protein interaction assays. When mutations were introduced into the hTAF(I)48 carboxyl-terminus, we identified changes in uncharged and positive residues that affect its interaction with TBP. By examining TBP mutants, residues within and adjacent to helix 2 of TBP, previously demonstrated to interact with subunits of other TBP-containing complexes [Transcription Factor IID (TFIID) and TFIIIB] were also found to diminish its affinity for the carboxyl-terminus of hTAF(I)48. The regions of hTAF(I)48 and TBP that interact are compared to those identified within other complexes containing TBP.

Dark matter directionality revisited with a high pressure xenon gas detector

DOE PAGES

Mohlabeng, Gopolang; Kong, Kyoungchul; Li, Jin; ...

2015-07-20

An observation of the anisotropy of dark matter interactions in a direction-sensitive detector would provide decisive evidence for the discovery of galactic dark matter. Directional information would also provide a crucial input to understanding its distribution in the local Universe. Most of the existing directional dark matter detectors utilize particle tracking methods in a low-pressure gas time projection chamber. These low pressure detectors require excessively large volumes in order to be competitive in the search for physics beyond the current limit. In order to avoid these volume limitations, we consider a novel proposal, which exploits a columnar recombination effect inmore » a high-pressure gas time projection chamber. The ratio of scintillation to ionization signals observed in the detector carries the angular information of the particle interactions. In this paper, we investigate the sensitivity of a future directional detector focused on the proposed high-pressure Xenon gas time projection chamber. We study the prospect of detecting an anisotropy in the dark matter velocity distribution. We find that tens of events are needed to exclude an isotropic distribution of dark matter interactions at 95% confidence level in the most optimistic case with head-to-tail information. However, one needs at least 10-20 times more events without head-to-tail information for light dark matter below ~50 GeV. For an intermediate mass range, we find it challenging to observe an anisotropy of the dark matter distribution. Our results also show that the directional information significantly improves precision measurements of dark matter mass and the elastic scattering cross section for a heavy dark matter.« less

Distinct self-interaction domains promote Multi Sex Combs accumulation in and formation of the Drosophila histone locus body

PubMed Central

Terzo, Esteban A.; Lyons, Shawn M.; Poulton, John S.; Temple, Brenda R. S.; Marzluff, William F.; Duronio, Robert J.

2015-01-01

Nuclear bodies (NBs) are structures that concentrate proteins, RNAs, and ribonucleoproteins that perform functions essential to gene expression. How NBs assemble is not well understood. We studied the Drosophila histone locus body (HLB), a NB that concentrates factors required for histone mRNA biosynthesis at the replication-dependent histone gene locus. We coupled biochemical analysis with confocal imaging of both fixed and live tissues to demonstrate that the Drosophila Multi Sex Combs (Mxc) protein contains multiple domains necessary for HLB assembly. An important feature of this assembly process is the self-interaction of Mxc via two conserved N-terminal domains: a LisH domain and a novel self-interaction facilitator (SIF) domain immediately downstream of the LisH domain. Molecular modeling suggests that the LisH and SIF domains directly interact, and mutation of either the LisH or the SIF domain severely impairs Mxc function in vivo, resulting in reduced histone mRNA accumulation. A region of Mxc between amino acids 721 and 1481 is also necessary for HLB assembly independent of the LisH and SIF domains. Finally, the C-terminal 195 amino acids of Mxc are required for recruiting FLASH, an essential histone mRNA-processing factor, to the HLB. We conclude that multiple domains of the Mxc protein promote HLB assembly in order to concentrate factors required for histone mRNA biosynthesis. PMID:25694448

Direct contact with perivascular tumor cells enhances integrin αvβ3 signaling and migration of endothelial cells

PubMed Central

Burgett, Monica E.; Lathia, Justin D.; Roth, Patrick; Nowacki, Amy S.; Galileo, Deni S.; Pugacheva, Elena; Huang, Ping; Vasanji, Amit; Li, Meizhang; Byzova, Tatiana; Mikkelsen, Tom; Bao, Shideng; Rich, Jeremy N.; Weller, Michael; Gladson, Candece L.

2016-01-01

The secretion of soluble pro-angiogenic factors by tumor cells and stromal cells in the perivascular niche promotes the aggressive angiogenesis that is typical of glioblastoma (GBM). Here, we show that angiogenesis also can be promoted by a direct interaction between brain tumor cells, including tumor cells with cancer stem-like properties (CSCs), and endothelial cells (ECs). As shown in vitro, this direct interaction is mediated by binding of integrin αvβ3 expressed on ECs to the RGD-peptide in L1CAM expressed on CSCs. It promotes both EC network formation and enhances directed migration toward basic fibroblast growth factor. Activation of αvβ3 and bone marrow tyrosine kinase on chromosome X (BMX) is required for migration stimulated by direct binding but not for migration stimulated by soluble factors. RGD-peptide treatment of mice with established intracerebral GBM xenografts significantly reduced the percentage of Sox2-positive tumor cells and CSCs in close proximity to ECs, decreased integrin αvβ3 and BMX activation and p130CAS phosphorylation in the ECs, and reduced the vessel surface area. These results reveal a previously unrecognized aspect of the regulation of angiogenesis in GBM that can impact therapeutic anti-angiogenic targeting. PMID:27270311

Cadherin-2 Is Required Cell Autonomously for Collective Migration of Facial Branchiomotor Neurons.

PubMed

Rebman, Jane K; Kirchoff, Kathryn E; Walsh, Gregory S

2016-01-01

Collective migration depends on cell-cell interactions between neighbors that contribute to their overall directionality, yet the mechanisms that control the coordinated migration of neurons remains to be elucidated. During hindbrain development, facial branchiomotor neurons (FBMNs) undergo a stereotypic tangential caudal migration from their place of birth in rhombomere (r)4 to their final location in r6/7. FBMNs engage in collective cell migration that depends on neuron-to-neuron interactions to facilitate caudal directionality. Here, we demonstrate that Cadherin-2-mediated neuron-to-neuron adhesion is necessary for directional and collective migration of FBMNs. We generated stable transgenic zebrafish expressing dominant-negative Cadherin-2 (Cdh2ΔEC) driven by the islet1 promoter. Cell-autonomous inactivation of Cadherin-2 function led to non-directional migration of FBMNs and a defect in caudal tangential migration. Additionally, mosaic analysis revealed that Cdh2ΔEC-expressing FBMNs are not influenced to migrate caudally by neighboring wild-type FBMNs due to a defect in collective cell migration. Taken together, our data suggest that Cadherin-2 plays an essential cell-autonomous role in mediating the collective migration of FBMNs.

Tetratricopeptide-motif-mediated interaction of FANCG with recombination proteins XRCC3 and BRCA2.

PubMed

Hussain, Shobbir; Wilson, James B; Blom, Eric; Thompson, Larry H; Sung, Patrick; Gordon, Susan M; Kupfer, Gary M; Joenje, Hans; Mathew, Christopher G; Jones, Nigel J

2006-05-10

Fanconi anaemia is an inherited chromosomal instability disorder characterised by cellular sensitivity to DNA interstrand crosslinkers, bone-marrow failure and a high risk of cancer. Eleven FA genes have been identified, one of which, FANCD1, is the breast cancer susceptibility gene BRCA2. At least eight FA proteins form a nuclear core complex required for monoubiquitination of FANCD2. The BRCA2/FANCD1 protein is connected to the FA pathway by interactions with the FANCG and FANCD2 proteins, both of which co-localise with the RAD51 recombinase, which is regulated by BRCA2. These connections raise the question of whether any of the FANC proteins of the core complex might also participate in other complexes involved in homologous recombination repair. We therefore tested known FA proteins for direct interaction with RAD51 and its paralogs XRCC2 and XRCC3. FANCG was found to interact with XRCC3, and this interaction was disrupted by the FA-G patient derived mutation L71P. FANCG was co-immunoprecipitated with both XRCC3 and BRCA2 from extracts of human and hamster cells. The FANCG-XRCC3 and FANCG-BRCA2 interactions did not require the presence of other FA proteins from the core complex, suggesting that FANCG also participates in a DNA repair complex that is downstream and independent of FANCD2 monoubiquitination. Additionally, XRCC3 and BRCA2 proteins co-precipitate in both human and hamster cells and this interaction requires FANCG. The FANCG protein contains multiple tetratricopeptide repeat motifs (TPRs), which function as scaffolds to mediate protein-protein interactions. Mutation of one or more of these motifs disrupted all of the known interactions of FANCG. We propose that FANCG, in addition to stabilising the FA core complex, may have a role in building multiprotein complexes that facilitate homologous recombination repair.

The interaction of spacecraft high voltage power systems with the space plasma environment

NASA Technical Reports Server (NTRS)

Domitz, S.; Grier, N. T.

1974-01-01

The development of spacecraft with electrical loads that require high voltage power is discussed. The high voltage solar array has been considered for supplying d.c. power directly to high voltage loads such as ion thrusters and communication tubes without intermediate power processing. Space power stations for transferring solar power to earth are being studied in the 40 kilovolt, multikilowatt regime. Analytical and experimental studies have determined that with the advent of high voltage power, new problems will arise through the interaction of the high voltage surfaces with the charged particle environment of space. The interactive environment has been identified and duplicated to some extent in simulation facilities at NASA-Lewis Research Center and at several contractor locations.

Quantum liquid droplets in a mixture of Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Cabrera, C. R.; Tanzi, L.; Sanz, J.; Naylor, B.; Thomas, P.; Cheiney, P.; Tarruell, L.

2018-01-01

Quantum droplets are small clusters of atoms self-bound by the balance of attractive and repulsive forces. Here, we report on the observation of droplets solely stabilized by contact interactions in a mixture of two Bose-Einstein condensates. We demonstrate that they are several orders of magnitude more dilute than liquid helium by directly measuring their size and density via in situ imaging. We show that the droplets are stablized against collapse by quantum fluctuations and that they require a minimum atom number to be stable. Below that number, quantum pressure drives a liquid-to-gas transition that we map out as a function of interaction strength. These ultradilute isotropic liquids remain weakly interacting and constitute an ideal platform to benchmark quantum many-body theories.

Interaction between dorsal and ventral processing streams: where, when and how?

PubMed

Cloutman, Lauren L

2013-11-01

The execution of complex visual, auditory, and linguistic behaviors requires a dynamic interplay between spatial ('where/how') and non-spatial ('what') information processed along the dorsal and ventral processing streams. However, while it is acknowledged that there must be some degree of interaction between the two processing networks, how they interact, both anatomically and functionally, is a question which remains little explored. The current review examines the anatomical, temporal, and behavioral evidence regarding three potential models of dual stream interaction: (1) computations along the two pathways proceed independently and in parallel, reintegrating within shared target brain regions; (2) processing along the separate pathways is modulated by the existence of recurrent feedback loops; and (3) information is transferred directly between the two pathways at multiple stages and locations along their trajectories. Copyright © 2012 Elsevier Inc. All rights reserved.

Sound-turbulence interaction in transonic boundary layers

NASA Astrophysics Data System (ADS)

Lelostec, Ludovic; Scalo, Carlo; Lele, Sanjiva

2014-11-01

Acoustic wave scattering in a transonic boundary layer is investigated through a novel approach. Instead of simulating directly the interaction of an incoming oblique acoustic wave with a turbulent boundary layer, suitable Dirichlet conditions are imposed at the wall to reproduce only the reflected wave resulting from the interaction of the incident wave with the boundary layer. The method is first validated using the laminar boundary layer profiles in a parallel flow approximation. For this scattering problem an exact inviscid solution can be found in the frequency domain which requires numerical solution of an ODE. The Dirichlet conditions are imposed in a high-fidelity unstructured compressible flow solver for Large Eddy Simulation (LES), CharLESx. The acoustic field of the reflected wave is then solved and the interaction between the boundary layer and sound scattering can be studied.

Exploring Gigabyte Datasets in Real Time: Architectures, Interfaces and Time-Critical Design

NASA Technical Reports Server (NTRS)

Bryson, Steve; Gerald-Yamasaki, Michael (Technical Monitor)

1998-01-01

Architectures and Interfaces: The implications of real-time interaction on software architecture design: decoupling of interaction/graphics and computation into asynchronous processes. The performance requirements of graphics and computation for interaction. Time management in such an architecture. Examples of how visualization algorithms must be modified for high performance. Brief survey of interaction techniques and design, including direct manipulation and manipulation via widgets. talk discusses how human factors considerations drove the design and implementation of the virtual wind tunnel. Time-Critical Design: A survey of time-critical techniques for both computation and rendering. Emphasis on the assignment of a time budget to both the overall visualization environment and to each individual visualization technique in the environment. The estimation of the benefit and cost of an individual technique. Examples of the modification of visualization algorithms to allow time-critical control.

Structural and Functional Characterization of the Interaction of Snapin with the Dopamine Transporter: Differential Modulation of Psychostimulant Actions.

PubMed

Erdozain, Amaia M; De Gois, Stéphanie; Bernard, Véronique; Gorgievski, Victor; Pietrancosta, Nicolas; Dumas, Sylvie; Macedo, Carlos E; Vanhoutte, Peter; Ortega, Jorge E; Meana, J Javier; Tzavara, Eleni T; Vialou, Vincent; Giros, Bruno

2018-04-01

The importance of dopamine (DA) neurotransmission is emphasized by its direct implication in several neurological and psychiatric disorders. The DA transporter (DAT), target of psychostimulant drugs, is the key protein that regulates spatial and temporal activity of DA in the synaptic cleft via the rapid reuptake of DA into the presynaptic terminal. There is strong evidence suggesting that DAT-interacting proteins may have a role in its function and regulation. Performing a two-hybrid screening, we identified snapin, a SNARE-associated protein implicated in synaptic transmission, as a new binding partner of the carboxyl terminal of DAT. Our data show that snapin is a direct partner and regulator of DAT. First, we determined the domains required for this interaction in both proteins and characterized the DAT-snapin interface by generating a 3D model. Using different approaches, we demonstrated that (i) snapin is expressed in vivo in dopaminergic neurons along with DAT; (ii) both proteins colocalize in cultured cells and brain and, (iii) DAT and snapin are present in the same protein complex. Moreover, by functional studies we showed that snapin produces a significant decrease in DAT uptake activity. Finally, snapin downregulation in mice produces an increase in DAT levels and transport activity, hence increasing DA concentration and locomotor response to amphetamine. In conclusion, snapin/DAT interaction represents a direct link between exocytotic and reuptake mechanisms and is a potential target for DA transmission modulation.

Interaction of toluene with two-color asymmetric laser fields: Controlling the directional emission of molecular hydrogen fragments

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

Kaziannis, S.; Kotsina, N.; Kosmidis, C.

The interaction of toluene with strong asymmetric two-color laser irradiation of 40 fs duration is studied by means of Time of flight mass spectrometry. Highly energetic H{sub 2}{sup +} and H{sub 3}{sup +} fragment ions are produced through an isomerization process taking place within transient multiply charged parent ions. Comparative study of deuterium labeled toluene isotopes enables the discrimination between molecular hydrogen fragments formed exclusively within the CH{sub 3}- part from those that require hydrogen atom exchange between the former and the phenyl moiety. It is demonstrated that by manipulating the relative phase of the ω/2ω field components the selectivemore » ionization of oriented toluene molecules can be used as a tool to control the directional emission of the H{sub 2}{sup +}, H{sub 3}{sup +} species.« less

Feedback repression is required for mammalian circadian clock function.

PubMed

Sato, Trey K; Yamada, Rikuhiro G; Ukai, Hideki; Baggs, Julie E; Miraglia, Loren J; Kobayashi, Tetsuya J; Welsh, David K; Kay, Steve A; Ueda, Hiroki R; Hogenesch, John B

2006-03-01

Direct evidence for the requirement of transcriptional feedback repression in circadian clock function has been elusive. Here, we developed a molecular genetic screen in mammalian cells to identify mutants of the circadian transcriptional activators CLOCK and BMAL1, which were uncoupled from CRYPTOCHROME (CRY)-mediated transcriptional repression. Notably, mutations in the PER-ARNT-SIM domain of CLOCK and the C terminus of BMAL1 resulted in synergistic insensitivity through reduced physical interactions with CRY. Coexpression of these mutant proteins in cultured fibroblasts caused arrhythmic phenotypes in population and single-cell assays. These data demonstrate that CRY-mediated repression of the CLOCK/BMAL1 complex activity is required for maintenance of circadian rhythmicity and provide formal proof that transcriptional feedback is required for mammalian clock function.

Effective atomic numbers of some tissue substitutes by different methods: A comparative study.

PubMed

Singh, Vishwanath P; Badiger, N M

2014-01-01

Effective atomic numbers of some human organ tissue substitutes such as polyethylene terephthalate, red articulation wax, paraffin 1, paraffin 2, bolus, pitch, polyphenylene sulfide, polysulfone, polyvinylchloride, and modeling clay have been calculated by four different methods like Auto-Zeff, direct, interpolation, and power law. It was found that the effective atomic numbers computed by Auto-Zeff, direct and interpolation methods were in good agreement for intermediate energy region (0.1 MeV < E < 5 MeV) where the Compton interaction dominates. A large difference in effective atomic numbers by direct method and Auto-Zeff was observed in photo-electric and pair-production regions. Effective atomic numbers computed by power law were found to be close to direct method in photo-electric absorption region. The Auto-Zeff, direct and interpolation methods were found to be in good agreement for computation of effective atomic numbers in intermediate energy region (100 keV < E < 10 MeV). The direct method was found to be appropriate method for computation of effective atomic numbers in photo-electric region (10 keV < E < 100 keV). The tissue equivalence of the tissue substitutes is possible to represent by any method for computation of effective atomic number mentioned in the present study. An accurate estimation of Rayleigh scattering is required to eliminate effect of molecular, chemical, or crystalline environment of the atom for estimation of gamma interaction parameters.

Effective atomic numbers of some tissue substitutes by different methods: A comparative study

PubMed Central

Singh, Vishwanath P.; Badiger, N. M.

2014-01-01

Effective atomic numbers of some human organ tissue substitutes such as polyethylene terephthalate, red articulation wax, paraffin 1, paraffin 2, bolus, pitch, polyphenylene sulfide, polysulfone, polyvinylchloride, and modeling clay have been calculated by four different methods like Auto-Zeff, direct, interpolation, and power law. It was found that the effective atomic numbers computed by Auto-Zeff, direct and interpolation methods were in good agreement for intermediate energy region (0.1 MeV < E < 5 MeV) where the Compton interaction dominates. A large difference in effective atomic numbers by direct method and Auto-Zeff was observed in photo-electric and pair-production regions. Effective atomic numbers computed by power law were found to be close to direct method in photo-electric absorption region. The Auto-Zeff, direct and interpolation methods were found to be in good agreement for computation of effective atomic numbers in intermediate energy region (100 keV < E < 10 MeV). The direct method was found to be appropriate method for computation of effective atomic numbers in photo-electric region (10 keV < E < 100 keV). The tissue equivalence of the tissue substitutes is possible to represent by any method for computation of effective atomic number mentioned in the present study. An accurate estimation of Rayleigh scattering is required to eliminate effect of molecular, chemical, or crystalline environment of the atom for estimation of gamma interaction parameters. PMID:24600169

CD4/CD8/Dendritic cell complexes in the spleen: CD8+ T cells can directly bind CD4+ T cells and modulate their response

PubMed Central

Barinov, Aleksandr; Galgano, Alessia; Krenn, Gerald; Tanchot, Corinne; Vasseur, Florence

2017-01-01

CD4+ T cell help to CD8+ T cell responses requires that CD4+ and CD8+ T cells interact with the same antigen presenting dendritic cell (Ag+DC), but it remains controversial whether helper signals are delivered indirectly through a licensed DC and/or involve direct CD4+/CD8+ T cell contacts and/or the formation of ternary complexes. We here describe the first in vivo imaging of the intact spleen, aiming to evaluate the first interactions between antigen-specific CD4+, CD8+ T cells and Ag+DCs. We show that in contrast to CD4+ T cells which form transient contacts with Ag+DC, CD8+ T cells form immediate stable contacts and activate the Ag+DC, acquire fragments of the DC membranes by trogocytosis, leading to their acquisition of some of the DC properties. They express MHC class II, and become able to present the specific Marilyn peptide to naïve Marilyn CD4+ T cells, inducing their extensive division. In vivo, these CD8+ T cells form direct stable contacts with motile naïve CD4+ T cells, recruiting them to Ag+DC binding and to the formation of ternary complexes, where CD4+ and CD8+ T cells interact with the DC and with one another. The presence of CD8+ T cells during in vivo immune responses leads to the early activation and up-regulation of multiple functions by CD4+ T lymphocytes. Thus, while CD4+ T cell help is important to CD8+ T cell responses, CD8+ T cells can interact directly with naïve CD4+ T cells impacting their recruitment and differentiation. PMID:28686740

Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression.

PubMed

Danno, Hiroki; Michiue, Tatsuo; Hitachi, Keisuke; Yukita, Akira; Ishiura, Shoichi; Asashima, Makoto

2008-04-08

The neural-related genes Sox2, Pax6, Otx2, and Rax have been associated with severe ocular malformations such as anophthalmia and microphthalmia, but it remains unclear as to how these genes are linked functionally. We analyzed the upstream signaling of Xenopus Rax (also known as Rx1) and identified the Otx2 and Sox2 proteins as direct upstream regulators of Rax. We revealed that endogenous Otx2 and Sox2 proteins bound to the conserved noncoding sequence (CNS1) located approximately 2 kb upstream of the Rax promoter. This sequence is conserved among vertebrates and is required for potent transcriptional activity. Reporter assays showed that Otx2 and Sox2 synergistically activated transcription via CNS1. Furthermore, the Otx2 and Sox2 proteins physically interacted with each other, and this interaction was affected by the Sox2-missense mutations identified in these ocular disorders. These results demonstrate that the direct interaction and interdependence between the Otx2 and Sox2 proteins coordinate Rax expression in eye development, providing molecular linkages among the genes responsible for ocular malformation.

Learning Bridge: Curricular Integration of Didactic and Experiential Education

PubMed Central

Arendt, Cassandra S.; Cawley, Pauline; Buhler, Amber V.; Elbarbry, Fawzy; Roberts, Sigrid C.

2010-01-01

Objectives To assess the impact of a program to integrate introductory pharmacy practice experiences with pharmaceutical science topics by promoting active learning, self-directed learning skills, and critical-thinking skills. Design The Learning Bridge, a curriculum program, was created to better integrate the material first-year (P1) students learned in pharmaceutical science courses into their introductory pharmacy practice experiences. Four Learning Bridge assignments required students to interact with their preceptors and answer questions relating to the pharmaceutical science material concurrently covered in their didactic courses. Assessment Surveys of students and preceptors were conducted to measure the effectiveness of the Learning Bridge process. Feedback indicated the Learning Bridge promoted students' interaction with their preceptors as well as development of active learning, self-directed learning, and critical-thinking skills. Students also indicated that the Learning Bridge assignments increased their learning, knowledge of drug information, and comprehension of relevant data in package inserts. Conclusion The Learning Bridge process integrated the didactic and experiential components of the curriculum, enhancing student learning in both areas, and offered students educational opportunities to interact more with their preceptors. PMID:20498741

Autistic traits and positive psychotic experiences modulate the association of psychopathic tendencies with theory of mind in opposite directions.

PubMed

Gillespie, Steven M; Mitchell, Ian J; Abu-Akel, Ahmad M

2017-07-25

Various clinical disorders, including psychopathy, and autism and schizophrenia spectrum disorders, have been linked with impairments in Theory of Mind (ToM). However, although these conditions can co-occur in the same individual, the effect of their inter-play on ToM abilities has not been investigated. Here we assessed ToM abilities in 55 healthy adults while performing a naturalistic ToM task, requiring participants to watch a short film and judge the actors' mental states. The results reveal for the first time that autistic traits and positive psychotic experiences interact with psychopathic tendencies in opposite directions to predict ToM performance-the interaction of psychopathic tendencies with autism traits was associated with a decrement in performance, whereas the interaction of psychopathic tendencies and positive psychotic experiences was associated with improved performance. These effects were specific to cognitive rather than affective ToM. These results underscore the importance of the simultaneous assessment of these dimensions within clinical settings. Future research in these clinical populations may benefit by taking into account such individual differences.

Regulation of exocytosis by the exocyst subunit Sec6 and the SM protein Sec1.

PubMed

Morgera, Francesca; Sallah, Margaret R; Dubuke, Michelle L; Gandhi, Pallavi; Brewer, Daniel N; Carr, Chavela M; Munson, Mary

2012-01-01

Trafficking of protein and lipid cargo through the secretory pathway in eukaryotic cells is mediated by membrane-bound vesicles. Secretory vesicle targeting and fusion require a conserved multisubunit protein complex termed the exocyst, which has been implicated in specific tethering of vesicles to sites of polarized exocytosis. The exocyst is directly involved in regulating soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor (SNARE) complexes and membrane fusion through interactions between the Sec6 subunit and the plasma membrane SNARE protein Sec9. Here we show another facet of Sec6 function-it directly binds Sec1, another SNARE regulator, but of the Sec1/Munc18 family. The Sec6-Sec1 interaction is exclusive of Sec6-Sec9 but compatible with Sec6-exocyst assembly. In contrast, the Sec6-exocyst interaction is incompatible with Sec6-Sec9. Therefore, upon vesicle arrival, Sec6 is proposed to release Sec9 in favor of Sec6-exocyst assembly and to simultaneously recruit Sec1 to sites of secretion for coordinated SNARE complex formation and membrane fusion.

Physical interaction of the activator protein-1 factors c-Fos and c-Jun with Cbfa1 for collagenase-3 promoter activation

NASA Technical Reports Server (NTRS)

D'Alonzo, Richard C.; Selvamurugan, Nagarajan; Karsenty, Gerard; Partridge, Nicola C.

2002-01-01

Previously, we determined that the activator protein-1 (AP-1)-binding site and the runt domain (RD)-binding site and their binding proteins, c-Fos.c-Jun and Cbfa, regulate the collagenase-3 promoter in parathyroid hormone-treated and differentiating osteoblasts. Here we show that Cbfa1 and c-Fos.c-Jun appear to cooperatively bind the RD- and AP-1-binding sites and form ternary structures in vitro. Both in vitro and in vivo co-immunoprecipitation and yeast two-hybrid studies further demonstrate interaction between Cbfa1 with c-Fos and c-Jun in the absence of phosphorylation and without binding to DNA. Additionally, only the runt domain of Cbfa1 was required for interaction with c-Jun and c-Fos. In mammalian cells, overexpression of Cbfa1 enhanced c-Jun activation of AP-1-binding site promoter activity, demonstrating functional interaction. Finally, insertion of base pairs that disrupted the helical phasing between the AP-1- and RD-binding sites also inhibited collagenase-3 promoter activation. Thus, we provide direct evidence that Cbfa1 and c-Fos.c-Jun physically interact and cooperatively bind the AP-1- and RD-binding sites in the collagenase-3 promoter. Moreover, the AP-1- and RD-binding sites appear to be organized in a specific required helical arrangement that facilitates transcription factor interaction and enables promoter activation.

Direct interaction between the tobacco mosaic virus helicase domain and the ATP-bound resistance protein, N factor during the hypersensitive response in tobacco plants.

PubMed

Ueda, Hirokazu; Yamaguchi, Yube; Sano, Hiroshi

2006-05-01

Plants cope with pathogens with distinct mechanisms. One example is a gene-for-gene system, in which plants recognize the pathogen molecule by specified protein(s), this being called the R factor. However, mechanisms of interaction between proteins from the host and the pathogen are not completely understood. Here, we analyzed the mode of interaction between the N factor, a tobacco R factor, and the helicase domain (p50) of tobacco mosaic virus (TMV). To this end, domain dissected proteins were prepared and subjected to Agroinfiltration into intact leaves, followed by yeast two hybrid and pull-down assays. The results pointed to three novel features. First, the N factor was found to directly bind to the p50 of TMV, second, ATP was pre-requisite for this interaction, with formation of an ATP/N factor complex, and third, the N factor was shown to possess ATPase activity, which is enhanced by the p50. Moreover, we found that intra- and/or inter-molecular interactions take place in the N factor molecule. This interaction required ATP, and was disrupted by the p50. Based on these results, we propose a following model for the TMV recognition mechanism in tobacco plants. The N factor forms a complex with ATP, to which the helicase domain interacts, and enhances ATP hydrolysis. The resulting ADP/N factor complex then changes its conformation, thereby facilitating further interaction with the down-stream signaling factor(s). This model is consistent with the idea of 'protein machine'.

A protein interaction map for cell polarity development

PubMed Central

Drees, Becky L.; Sundin, Bryan; Brazeau, Elizabeth; Caviston, Juliane P.; Chen, Guang-Chao; Guo, Wei; Kozminski, Keith G.; Lau, Michelle W.; Moskow, John J.; Tong, Amy; Schenkman, Laura R.; McKenzie, Amos; Brennwald, Patrick; Longtine, Mark; Bi, Erfei; Chan, Clarence; Novick, Peter; Boone, Charles; Pringle, John R.; Davis, Trisha N.; Fields, Stanley; Drubin, David G.

2001-01-01

Many genes required for cell polarity development in budding yeast have been identified and arranged into a functional hierarchy. Core elements of the hierarchy are widely conserved, underlying cell polarity development in diverse eukaryotes. To enumerate more fully the protein–protein interactions that mediate cell polarity development, and to uncover novel mechanisms that coordinate the numerous events involved, we carried out a large-scale two-hybrid experiment. 68 Gal4 DNA binding domain fusions of yeast proteins associated with the actin cytoskeleton, septins, the secretory apparatus, and Rho-type GTPases were used to screen an array of yeast transformants that express ∼90% of the predicted Saccharomyces cerevisiae open reading frames as Gal4 activation domain fusions. 191 protein–protein interactions were detected, of which 128 had not been described previously. 44 interactions implicated 20 previously uncharacterized proteins in cell polarity development. Further insights into possible roles of 13 of these proteins were revealed by their multiple two-hybrid interactions and by subcellular localization. Included in the interaction network were associations of Cdc42 and Rho1 pathways with proteins involved in exocytosis, septin organization, actin assembly, microtubule organization, autophagy, cytokinesis, and cell wall synthesis. Other interactions suggested direct connections between Rho1- and Cdc42-regulated pathways; the secretory apparatus and regulators of polarity establishment; actin assembly and the morphogenesis checkpoint; and the exocytic and endocytic machinery. In total, a network of interactions that provide an integrated response of signaling proteins, the cytoskeleton, and organelles to the spatial cues that direct polarity development was revealed. PMID:11489916

Molecular level in silico studies for oncology. Direct models review

NASA Astrophysics Data System (ADS)

Psakhie, S. G.; Tsukanov, A. A.

2017-09-01

The combination of therapy and diagnostics in one process "theranostics" is a trend in a modern medicine, especially in oncology. Such an approach requires development and usage of multifunctional hybrid nanoparticles with a hierarchical structure. Numerical methods and mathematical models play a significant role in the design of the hierarchical nanoparticles and allow looking inside the nanoscale mechanisms of agent-cell interactions. The current position of in silico approach in biomedicine and oncology is discussed. The review of the molecular level in silico studies in oncology, which are using the direct models, is presented.

Model for the computation of self-motion in biological systems

NASA Technical Reports Server (NTRS)

Perrone, John A.

1992-01-01

A technique is presented by which direction- and speed-tuned cells, such as those commonly found in the middle temporal region of the primate brain, can be utilized to analyze the patterns of retinal image motion that are generated during observer movement through the environment. The developed model determines heading by finding the peak response in a population of detectors or neurons each tuned to a particular heading direction. It is suggested that a complex interaction of multiple cell networks is required for the solution of the self-motion problem in the primate brain.

An algorithm for automatic reduction of complex signal flow graphs

NASA Technical Reports Server (NTRS)

Young, K. R.; Hoberock, L. L.; Thompson, J. G.

1976-01-01

A computer algorithm is developed that provides efficient means to compute transmittances directly from a signal flow graph or a block diagram. Signal flow graphs are cast as directed graphs described by adjacency matrices. Nonsearch computation, designed for compilers without symbolic capability, is used to identify all arcs that are members of simple cycles for use with Mason's gain formula. The routine does not require the visual acumen of an interpreter to reduce the topology of the graph, and it is particularly useful for analyzing control systems described for computer analyses by means of interactive graphics.

Directional biases reveal utilization of arm's biomechanical properties for optimization of motor behavior.

PubMed

Goble, Jacob A; Zhang, Yanxin; Shimansky, Yury; Sharma, Siddharth; Dounskaia, Natalia V

2007-09-01

Strategies used by the CNS to optimize arm movements in terms of speed, accuracy, and resistance to fatigue remain largely unknown. A hypothesis is studied that the CNS exploits biomechanical properties of multijoint limbs to increase efficiency of movement control. To test this notion, a novel free-stroke drawing task was used that instructs subjects to make straight strokes in as many different directions as possible in the horizontal plane through rotations of the elbow and shoulder joints. Despite explicit instructions to distribute strokes uniformly, subjects showed biases to move in specific directions. These biases were associated with a tendency to perform movements that included active motion at one joint and largely passive motion at the other joint, revealing a tendency to minimize intervention of muscle torque for regulation of the effect of interaction torque. Other biomechanical factors, such as inertial resistance and kinematic manipulability, were unable to adequately account for these significant biases. Also, minimizations of jerk, muscle torque change, and sum of squared muscle torque were analyzed; however, these cost functions failed to explain the observed directional biases. Collectively, these results suggest that knowledge of biomechanical cost functions regarding interaction torque (IT) regulation is available to the control system. This knowledge may be used to evaluate potential movements and to select movement of "low cost." The preference to reduce active regulation of interaction torque suggests that, in addition to muscle energy, the criterion for movement cost may include neural activity required for movement control.

A sophisticated cad tool for the creation of complex models for electromagnetic interaction analysis

NASA Astrophysics Data System (ADS)

Dion, Marc; Kashyap, Satish; Louie, Aloisius

1991-06-01

This report describes the essential features of the MS-DOS version of DIDEC-DREO, an interactive program for creating wire grid, surface patch, and cell models of complex structures for electromagnetic interaction analysis. It uses the device-independent graphics library DIGRAF and the graphics kernel system HALO, and can be executed on systems with various graphics devices. Complicated structures can be created by direct alphanumeric keyboard entry, digitization of blueprints, conversion form existing geometric structure files, and merging of simple geometric shapes. A completed DIDEC geometric file may then be converted to the format required for input to a variety of time domain and frequency domain electromagnetic interaction codes. This report gives a detailed description of the program DIDEC-DREO, its installation, and its theoretical background. Each available interactive command is described. The associated program HEDRON which generates simple geometric shapes, and other programs that extract the current amplitude data from electromagnetic interaction code outputs, are also discussed.

Novel interactions of CAPS (Ca2+-dependent activator protein for secretion) with the three neuronal SNARE proteins required for vesicle fusion.

PubMed

Daily, Neil J; Boswell, Kristin L; James, Declan J; Martin, Thomas F J

2010-11-12

CAPS (aka CADPS) is required for optimal vesicle exocytosis in neurons and endocrine cells where it functions to prime the exocytic machinery for Ca(2+)-triggered fusion. Fusion is mediated by trans complexes of the SNARE proteins VAMP-2, syntaxin-1, and SNAP-25 that bridge vesicle and plasma membrane. CAPS promotes SNARE complex formation on liposomes, but the SNARE binding properties of CAPS are unknown. The current work revealed that CAPS exhibits high affinity binding to syntaxin-1 and SNAP-25 and moderate affinity binding to VAMP-2. CAPS binding is specific for a subset of exocytic SNARE protein isoforms and requires membrane integration of the SNARE proteins. SNARE protein binding by CAPS is novel and mediated by interactions with the SNARE motifs in the three proteins. The C-terminal site for CAPS binding on syntaxin-1 does not overlap the Munc18-1 binding site and both proteins can co-reside on membrane-integrated syntaxin-1. As expected for a C-terminal binding site on syntaxin-1, CAPS stimulates SNARE-dependent liposome fusion with N-terminal truncated syntaxin-1 but exhibits impaired activity with C-terminal syntaxin-1 mutants. Overall the results suggest that SNARE complex formation promoted by CAPS may be mediated by direct interactions of CAPS with each of the three SNARE proteins required for vesicle exocytosis.

Novel Interactions of CAPS (Ca2+-dependent Activator Protein for Secretion) with the Three Neuronal SNARE Proteins Required for Vesicle Fusion*

PubMed Central

Daily, Neil J.; Boswell, Kristin L.; James, Declan J.; Martin, Thomas F. J.

2010-01-01

CAPS (aka CADPS) is required for optimal vesicle exocytosis in neurons and endocrine cells where it functions to prime the exocytic machinery for Ca2+-triggered fusion. Fusion is mediated by trans complexes of the SNARE proteins VAMP-2, syntaxin-1, and SNAP-25 that bridge vesicle and plasma membrane. CAPS promotes SNARE complex formation on liposomes, but the SNARE binding properties of CAPS are unknown. The current work revealed that CAPS exhibits high affinity binding to syntaxin-1 and SNAP-25 and moderate affinity binding to VAMP-2. CAPS binding is specific for a subset of exocytic SNARE protein isoforms and requires membrane integration of the SNARE proteins. SNARE protein binding by CAPS is novel and mediated by interactions with the SNARE motifs in the three proteins. The C-terminal site for CAPS binding on syntaxin-1 does not overlap the Munc18-1 binding site and both proteins can co-reside on membrane-integrated syntaxin-1. As expected for a C-terminal binding site on syntaxin-1, CAPS stimulates SNARE-dependent liposome fusion with N-terminal truncated syntaxin-1 but exhibits impaired activity with C-terminal syntaxin-1 mutants. Overall the results suggest that SNARE complex formation promoted by CAPS may be mediated by direct interactions of CAPS with each of the three SNARE proteins required for vesicle exocytosis. PMID:20826818

The Transcription Elongation Factor CA150 Interacts with RNA Polymerase II and the Pre-mRNA Splicing Factor SF1

PubMed Central

Goldstrohm, Aaron C.; Albrecht, Todd R.; Suñé, Carles; Bedford, Mark T.; Garcia-Blanco, Mariano A.

2001-01-01

CA150 represses RNA polymerase II (RNAPII) transcription by inhibiting the elongation of transcripts. The FF repeat domains of CA150 bind directly to the phosphorylated carboxyl-terminal domain of the largest subunit of RNAPII. We determined that this interaction is required for efficient CA150-mediated repression of transcription from the α4-integrin promoter. Additional functional determinants, namely, the WW1 and WW2 domains of CA150, were also required for efficient repression. A protein that interacted directly with CA150 WW1 and WW2 was identified as the splicing-transcription factor SF1. Previous studies have demonstrated a role for SF1 in transcription repression, and we found that binding of the CA150 WW1 and WW2 domains to SF1 correlated exactly with the functional contribution of these domains for repression. The binding specificity of the CA150 WW domains was found to be unique in comparison to known classes of WW domains. Furthermore, the CA150 binding site, within the carboxyl-terminal half of SF1, contains a novel type of proline-rich motif that may be recognized by the CA150 WW1 and WW2 domains. These results support a model for the recruitment of CA150 to repress transcription elongation. In this model, CA150 binds to the phosphorylated CTD of elongating RNAPII and SF1 targets the nascent transcript. PMID:11604498

The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1.

PubMed

Goldstrohm, A C; Albrecht, T R; Suñé, C; Bedford, M T; Garcia-Blanco, M A

2001-11-01

CA150 represses RNA polymerase II (RNAPII) transcription by inhibiting the elongation of transcripts. The FF repeat domains of CA150 bind directly to the phosphorylated carboxyl-terminal domain of the largest subunit of RNAPII. We determined that this interaction is required for efficient CA150-mediated repression of transcription from the alpha(4)-integrin promoter. Additional functional determinants, namely, the WW1 and WW2 domains of CA150, were also required for efficient repression. A protein that interacted directly with CA150 WW1 and WW2 was identified as the splicing-transcription factor SF1. Previous studies have demonstrated a role for SF1 in transcription repression, and we found that binding of the CA150 WW1 and WW2 domains to SF1 correlated exactly with the functional contribution of these domains for repression. The binding specificity of the CA150 WW domains was found to be unique in comparison to known classes of WW domains. Furthermore, the CA150 binding site, within the carboxyl-terminal half of SF1, contains a novel type of proline-rich motif that may be recognized by the CA150 WW1 and WW2 domains. These results support a model for the recruitment of CA150 to repress transcription elongation. In this model, CA150 binds to the phosphorylated CTD of elongating RNAPII and SF1 targets the nascent transcript.

The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

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

Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.

XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localize in nuclear foci. The co-localization was observed in mid- to late-S-phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain protein markers of both stalled replication forks andmore » telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains, but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S-phase that is at least in part carried out coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.« less

Simulation studies of reconstruction of hadron shower direction in INO ICAL detector

NASA Astrophysics Data System (ADS)

Devi, M. M.; Dighe, A.; Indumathi, D.; Lakshmi, S. M.

2018-03-01

The proposed Iron Calorimeter (ICAL) at India-based Neutrino Observatory (INO) will be a 50 kt magnetised iron detector for the detection of atmospheric neutrinos. The atmospheric neutrinos interact via both charged current (CC) and neutral current (NC) interactions with the target iron to produce the detectable final state particles. While CC νμ (bar nuμ) leave a muon track and a hadron shower in the detector, the NC will leave only a hadron shower apart from the secondary invisible neutrino. A GEANT4 based simulation studies to reconstruct hadron showers in CC and NC, using two techniques namely the Orientation Matrix Method (OMM) and the Raw Hit Method (RHM) are presented here. While OMM requires information about the interaction vertex obtained from muon track reconstruction, RHM requires only the shower hit positions and timings and no vertex information and hence can be used for NC events as well. Hadrons from neutrino events generated with NUANCE neutrino generator are analysed. For hadrons in the energy range 0.5-15 GeV produced in CC νμ and bar nuμ interactions, a Δθ'h resolution of around 19o-9o (around 20.5o-12o) is obtained in the |cosθ'h|=[0.8, 1] bin with OMM (RHM). For NC events in the same true energy and direction bins, Δθ'h resolution varies from around 20.5o-13o, from RHM only. OMM (RHM) gives a resolution of about 55o-20o (38o-14o) for the angle between the muon and the hadron shower, βμ h', in the [E'had;cos θ'h] range [0.5-15 GeV; [0.8,1.0

Type I γ Phosphatidylinositol Phosphate 5-Kinase i5 Controls the Ubiquitination and Degradation of the Tumor Suppressor Mitogen-inducible Gene 6*

PubMed Central

Sun, Ming; Cai, Jinyang; Anderson, Richard A.; Sun, Yue

2016-01-01

Mitogen-inducible gene 6 (Mig6) is a tumor suppressor, and the disruption of Mig6 expression is associated with cancer development. Mig6 directly interacts with epidermal growth factor receptor (EGFR) to suppress the activation and downstream signaling of EGFR. Therefore, loss of Mig6 enhances EGFR-mediated signaling and promotes EGFR-dependent carcinogenesis. The molecular mechanism modulating Mig6 expression in cancer remains unclear. Here we demonstrate that type I γ phosphatidylinositol phosphate 5-kinase i5 (PIPKIγi5), an enzyme producing phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), stabilizes Mig6 expression. Knockdown of PIPKIγi5 leads to the loss of Mig6 expression, which dramatically enhances and prolongs EGFR-mediated cell signaling. Loss of PIPKIγi5 significantly promotes Mig6 protein degradation via proteasomes, but it does not affect the Mig6 mRNA level. PIPKIγi5 directly interacts with the E3 ubiquitin ligase neuronal precursor cell-expressed developmentally down-regulated 4-1 (NEDD4-1). The C-terminal domain of PIPKIγi5 and the WW1 and WW2 domains of NEDD4-1 are required for their interaction. The C2 domain of NEDD4-1 is required for its interaction with PtdIns(4,5)P2. By binding with NEDD4-1 and producing PtdIns(4,5)P2, PIPKIγi5 perturbs NEDD4-1-mediated Mig6 ubiquitination and the subsequent proteasomal degradation. Thus, loss of NEDD4-1 can rescue Mig6 expression in PIPKIγi5 knockdown cells. In this way, PIPKIγi5, NEDD4-1, and Mig6 form a novel molecular nexus that controls EGFR activation and downstream signaling. PMID:27557663

Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay.

PubMed

Hudry, Bruno; Viala, Séverine; Graba, Yacine; Merabet, Samir

2011-01-28

Protein interactions control the regulatory networks underlying developmental processes. The understanding of developmental complexity will, therefore, require the characterization of protein interactions within their proper environment. The bimolecular fluorescence complementation (BiFC) technology offers this possibility as it enables the direct visualization of protein interactions in living cells. However, its potential has rarely been applied in embryos of animal model organisms and was only performed under transient protein expression levels. Using a Hox protein partnership as a test case, we investigated the suitability of BiFC for the study of protein interactions in the living Drosophila embryo. Importantly, all BiFC parameters were established with constructs that were stably expressed under the control of endogenous promoters. Under these physiological conditions, we showed that BiFC is specific and sensitive enough to analyse dynamic protein interactions. We next used BiFC in a candidate interaction screen, which led to the identification of several Hox protein partners. Our results establish the general suitability of BiFC for revealing and studying protein interactions in their physiological context during the rapid course of Drosophila embryonic development.

Structured Parent-Child Observations Predict Development of Conduct Problems: the Importance of Parental Negative Attention in Child-Directed Play.

PubMed

Fleming, Andrew P; McMahon, Robert J; King, Kevin M

2017-04-01

Structured observations of parent-child interactions are commonly used in research and clinical settings, but require additional empirical support. The current study examined the capacity of child-directed play, parent-directed play, and parent-directed chore interaction analogs to uniquely predict the development of conduct problems across a 6-year follow-up period. Parent-child observations were collected from 338 families from high-risk neighborhoods during the summer following the child's first-grade year. Participating children were 49.2 % female, 54.4 % white, and 45.6 % black, and had an average age of 7.52 years at the first assessment. Conduct problems were assessed via parent report and teacher report at five assessment points between first grade and seventh grade. Latent growth curve modeling was used to analyze predictors of conduct problem trajectory across this 6-year follow-up period. When race, sex, socioeconomic status, and maternal depressive symptoms were controlled, parental negative attention during child-directed play predicted higher levels of parent-reported conduct problems concurrently and after a 6-year follow-up period. Parental negative attention during child-directed play also predicted higher teacher-reported conduct problems 6 years later. Findings support the use of child-directed play and parent-directed chore analogs in predicting longitudinal development of conduct problems. The presence of parental negative attention during child-directed play appears to be an especially important predictor of greater conduct problems over time and across multiple domains. Additionally, the potential importance of task-incongruent behavior is proposed for further study.

Long-range population dynamics of anatomically defined neocortical networks

PubMed Central

Chen, Jerry L; Voigt, Fabian F; Javadzadeh, Mitra; Krueppel, Roland; Helmchen, Fritjof

2016-01-01

The coordination of activity across neocortical areas is essential for mammalian brain function. Understanding this process requires simultaneous functional measurements across the cortex. In order to dissociate direct cortico-cortical interactions from other sources of neuronal correlations, it is furthermore desirable to target cross-areal recordings to neuronal subpopulations that anatomically project between areas. Here, we combined anatomical tracers with a novel multi-area two-photon microscope to perform simultaneous calcium imaging across mouse primary (S1) and secondary (S2) somatosensory whisker cortex during texture discrimination behavior, specifically identifying feedforward and feedback neurons. We find that coordination of S1-S2 activity increases during motor behaviors such as goal-directed whisking and licking. This effect was not specific to identified feedforward and feedback neurons. However, these mutually projecting neurons especially participated in inter-areal coordination when motor behavior was paired with whisker-texture touches, suggesting that direct S1-S2 interactions are sensory-dependent. Our results demonstrate specific functional coordination of anatomically-identified projection neurons across sensory cortices. DOI: http://dx.doi.org/10.7554/eLife.14679.001 PMID:27218452

Three Dimensional Projection Environment for Molecular Design and Surgical Simulation

DTIC Science & Technology

2011-08-01

bypasses the cumbersome meshing process . The deformation model is only comprised of mass nodes, which are generated by sampling the object volume before...force should minimize the penetration volume, the haptic feedback force is derived directly. Additionally, a post- processing technique is developed to...render distinct physi-cal tissue properties across different interaction areas. The proposed approach does not require any pre- processing and is

A method for experimental modal separation

NASA Technical Reports Server (NTRS)

Hallauer, W. L., Jr.

1977-01-01

A method is described for the numerical simulation of multiple-shaker modal survey testing using simulated experimental data to optimize the shaker force-amplitude distribution for the purpose of isolating individual modes of vibration. Inertia, damping, stiffness, and model data are stored on magnetic disks, available by direct access to the interactive FORTRAN programs which perform all computations required by this relative force amplitude distribution method.

Molecular imaging of drug-modulated protein-protein interactions in living subjects.

PubMed

Paulmurugan, Ramasamy; Massoud, Tarik F; Huang, Jing; Gambhir, Sanjiv S

2004-03-15

Networks of protein interactions mediate cellular responses to environmental stimuli and direct the execution of many different cellular functional pathways. Small molecules synthesized within cells or recruited from the external environment mediate many protein interactions. The study of small molecule-mediated interactions of proteins is important to understand abnormal signal transduction pathways in cancer and in drug development and validation. In this study, we used split synthetic renilla luciferase (hRLUC) protein fragment-assisted complementation to evaluate heterodimerization of the human proteins FRB and FKBP12 mediated by the small molecule rapamycin. The concentration of rapamycin required for efficient dimerization and that of its competitive binder ascomycin required for dimerization inhibition were studied in cell lines. The system was dually modulated in cell culture at the transcription level, by controlling nuclear factor kappaB promoter/enhancer elements using tumor necrosis factor alpha, and at the interaction level, by controlling the concentration of the dimerizer rapamycin. The rapamycin-mediated dimerization of FRB and FKBP12 also was studied in living mice by locating, quantifying, and timing the hRLUC complementation-based bioluminescence imaging signal using a cooled charged coupled device camera. This split reporter system can be used to efficiently screen small molecule drugs that modulate protein-protein interactions and also to assess drugs in living animals. Both are essential steps in the preclinical evaluation of candidate pharmaceutical agents targeting protein-protein interactions, including signaling pathways in cancer cells.

Postural Coordination during Socio-motor Improvisation

PubMed Central

Gueugnon, Mathieu; Salesse, Robin N.; Coste, Alexandre; Zhao, Zhong; Bardy, Benoît G.; Marin, Ludovic

2016-01-01

Human interaction often relies on socio-motor improvisation. Creating unprepared movements during social interaction is not a random process but relies on rules of synchronization. These situations do not only involve people to be coordinated, but also require the adjustment of their posture in order to maintain balance and support movements. The present study investigated posture in such a context. More precisely, we first evaluated the impact of amplitude and complexity of arm movements on posture in solo situation. Then, we assessed the impact of interpersonal coordination on posture using the mirror game in which dyads performed improvised and synchronized movements (i.e., duo situation). Posture was measured through ankle-hip coordination in medio-lateral and antero-posterior directions (ML and AP respectively). Our results revealed the spontaneous emergence of in-phase pattern in ML direction and antiphase pattern in AP direction for solo and duo situations. These two patterns respectively refer to the simultaneous flexion/extension of the ankles and the hips in the same or opposite direction. It suggests different functional roles of postural coordination patterns in each direction, with in-phase supporting task performance in ML (dynamical stability) and antiphase supporting postural control in AP (mechanical stability). Although amplitude of movement did not influence posture, movement complexity disturbed postural stability in both directions. Conversely, interpersonal coordination promoted postural stability in ML but not in AP direction. These results are discussed in terms of the difference in coupling strength between ankle-hip coordination and interpersonal coordination. PMID:27547193

Postural Coordination during Socio-motor Improvisation.

PubMed

Gueugnon, Mathieu; Salesse, Robin N; Coste, Alexandre; Zhao, Zhong; Bardy, Benoît G; Marin, Ludovic

2016-01-01

Human interaction often relies on socio-motor improvisation. Creating unprepared movements during social interaction is not a random process but relies on rules of synchronization. These situations do not only involve people to be coordinated, but also require the adjustment of their posture in order to maintain balance and support movements. The present study investigated posture in such a context. More precisely, we first evaluated the impact of amplitude and complexity of arm movements on posture in solo situation. Then, we assessed the impact of interpersonal coordination on posture using the mirror game in which dyads performed improvised and synchronized movements (i.e., duo situation). Posture was measured through ankle-hip coordination in medio-lateral and antero-posterior directions (ML and AP respectively). Our results revealed the spontaneous emergence of in-phase pattern in ML direction and antiphase pattern in AP direction for solo and duo situations. These two patterns respectively refer to the simultaneous flexion/extension of the ankles and the hips in the same or opposite direction. It suggests different functional roles of postural coordination patterns in each direction, with in-phase supporting task performance in ML (dynamical stability) and antiphase supporting postural control in AP (mechanical stability). Although amplitude of movement did not influence posture, movement complexity disturbed postural stability in both directions. Conversely, interpersonal coordination promoted postural stability in ML but not in AP direction. These results are discussed in terms of the difference in coupling strength between ankle-hip coordination and interpersonal coordination.

Targeted knockout in Physcomitrella reveals direct actions of phytochrome in the cytoplasm.

PubMed

Mittmann, Franz; Brücker, Gerhard; Zeidler, Mathias; Repp, Alexander; Abts, Thomas; Hartmann, Elmar; Hughes, Jon

2004-09-21

The plant photoreceptor phytochrome plays an important role in the nucleus as a regulator of transcription. Numerous studies imply, however, that phytochromes in both higher and lower plants mediate physiological reactions within the cytoplasm. In particular, the tip cells of moss protonemal filaments use phytochrome to sense light direction, requiring a signaling system that transmits the directional information directly to the microfilaments that direct tip growth. In this work we describe four canonical phytochrome genes in the model moss species Physcomitrella patens, each of which was successfully targeted via homologous recombination and the distinct physiological functions of each gene product thereby identified. One homolog in particular mediates positive phototropism, polarotropism, and chloroplast movement in polarized light. This photoreceptor thus interacts with a cytoplasmic signal/response system. This is our first step in elucidating the cytoplasmic signaling function of phytochrome at the molecular level.

All Tapped Out: Touchscreen Interactivity and Young Children’s Word Learning

PubMed Central

Russo-Johnson, Colleen; Troseth, Georgene; Duncan, Charlotte; Mesghina, Almaz

2017-01-01

Touchscreen devices differ from passive screen media in promoting physical interaction with events on the screen. Two studies examined how young children’s screen-directed actions related to self-regulation (Study 1) and word learning (Study 2). In Study 1, 30 2-year-old children’s tapping behaviors during game play were related to their self-regulation, measured using Carlson’s snack task: girls and children with high self-regulation tapped significantly less during instruction portions of an app (including object labeling events) than did boys and children with low self-regulation. Older preschoolers (N = 47, aged 4–6 years) tapped significantly less during instruction than 2-year-olds did. Study 2 explored whether the particular way in which 170 children (2–4 years of age) interacted with a touchscreen app affected their learning of novel object labels. Conditions in which children tapped or dragged a named object to move it across the screen required different amounts of effort and focus, compared to a non-interactive (watching) condition. Age by sex interactions revealed a particular benefit of dragging (a motorically challenging behavior) for preschool girls’ learning compared to that of boys, especially for girls older than age 2. Boys benefited more from watching than dragging. Children from low socioeconomic status families learned more object names when dragging objects versus tapping them, possibly because tapping is a prepotent response that does not require thoughtful attention. Parents and industry experts should consider age, sex, self-regulation, and the physical requirements of children’s engagement with touchscreens when designing and using educational content. PMID:28446895

The Ustilago maydis Effector Pep1 Suppresses Plant Immunity by Inhibition of Host Peroxidase Activity

PubMed Central

Zechmann, Bernd; Hillmer, Morten; Doehlemann, Gunther

2012-01-01

The corn smut Ustilago maydis establishes a biotrophic interaction with its host plant maize. This interaction requires efficient suppression of plant immune responses, which is attributed to secreted effector proteins. Previously we identified Pep1 (Protein essential during penetration-1) as a secreted effector with an essential role for U. maydis virulence. pep1 deletion mutants induce strong defense responses leading to an early block in pathogenic development of the fungus. Using cytological and functional assays we show that Pep1 functions as an inhibitor of plant peroxidases. At sites of Δpep1 mutant penetrations, H2O2 strongly accumulated in the cell walls, coinciding with a transcriptional induction of the secreted maize peroxidase POX12. Pep1 protein effectively inhibited the peroxidase driven oxidative burst and thereby suppresses the early immune responses of maize. Moreover, Pep1 directly inhibits peroxidases in vitro in a concentration-dependent manner. Using fluorescence complementation assays, we observed a direct interaction of Pep1 and the maize peroxidase POX12 in vivo. Functional relevance of this interaction was demonstrated by partial complementation of the Δpep1 mutant defect by virus induced gene silencing of maize POX12. We conclude that Pep1 acts as a potent suppressor of early plant defenses by inhibition of peroxidase activity. Thus, it represents a novel strategy for establishing a biotrophic interaction. PMID:22589719

Atomic and molecular physics in the gas phase

NASA Astrophysics Data System (ADS)

Toburen, L. H.

1990-09-01

The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years there has been a great deal of progress in our understanding of these interactions; much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged particle interactions with atomic and molecular targets.

Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex.

PubMed

Hiraga, Shin-Ichiro; Alvino, Gina M; Chang, Fujung; Lian, Hui-Yong; Sridhar, Akila; Kubota, Takashi; Brewer, Bonita J; Weinreich, Michael; Raghuraman, M K; Donaldson, Anne D

2014-02-15

Initiation of eukaryotic DNA replication requires phosphorylation of the MCM complex by Dbf4-dependent kinase (DDK), composed of Cdc7 kinase and its activator, Dbf4. We report here that budding yeast Rif1 (Rap1-interacting factor 1) controls DNA replication genome-wide and describe how Rif1 opposes DDK function by directing Protein Phosphatase 1 (PP1)-mediated dephosphorylation of the MCM complex. Deleting RIF1 partially compensates for the limited DDK activity in a cdc7-1 mutant strain by allowing increased, premature phosphorylation of Mcm4. PP1 interaction motifs within the Rif1 N-terminal domain are critical for its repressive effect on replication. We confirm that Rif1 interacts with PP1 and that PP1 prevents premature Mcm4 phosphorylation. Remarkably, our results suggest that replication repression by Rif1 is itself also DDK-regulated through phosphorylation near the PP1-interacting motifs. Based on our findings, we propose that Rif1 is a novel PP1 substrate targeting subunit that counteracts DDK-mediated phosphorylation during replication. Fission yeast and mammalian Rif1 proteins have also been implicated in regulating DNA replication. Since PP1 interaction sites are evolutionarily conserved within the Rif1 sequence, it is likely that replication control by Rif1 through PP1 is a conserved mechanism.

Helicopter noise prediction - The current status and future direction

NASA Technical Reports Server (NTRS)

Brentner, Kenneth S.; Farassat, F.

1992-01-01

The paper takes stock of the progress, assesses the current prediction capabilities, and forecasts the direction of future helicopter noise prediction research. The acoustic analogy approach, specifically, theories based on the Ffowcs Williams-Hawkings equations, are the most widely used for deterministic noise sources. Thickness and loading noise can be routinely predicted given good plane motion and blade loading inputs. Blade-vortex interaction noise can also be predicted well with measured input data, but prediction of airloads with the high spatial and temporal resolution required for BVI is still difficult. Current semiempirical broadband noise predictions are useful and reasonably accurate. New prediction methods based on a Kirchhoff formula and direct computation appear to be very promising, but are currently very demanding computationally.

Direct Ca2+-dependent Heterophilic Interaction between Desmosomal Cadherins, Desmoglein and Desmocollin, Contributes to Cell–Cell Adhesion

PubMed Central

Chitaev, Nikolai A.; Troyanovsky, Sergey M.

1997-01-01

Human fibrosarcoma cells, HT-1080, feature extensive adherens junctions, lack mature desmosomes, and express a single known desmosomal protein, Desmoglein 2 (Dsg2). Transfection of these cells with bovine Desmocollin 1a (Dsc1a) caused dramatic changes in the subcellular distribution of endogenous Dsg2. Both cadherins clustered in the areas of the adherens junctions, whereas only a minor portion of Dsg2 was seen in these areas in the parental cells. Deletion mapping showed that intact extracellular cadherin-like repeats of Dsc1a (Arg1-Thr170) are required for the translocation of Dsg2. Deletion of the intracellular C-domain that mediates the interaction of Dsc1a with plakoglobin, or the CSI region that is involved in the binding to desmoplakin, had no effect. Coimmunoprecipitation experiments of cell lysates stably expressing Dsc1a with anti-Dsc or -Dsg antibodies demonstrate that the desmosomal cadherins, Dsg2 and Dsc1a, are involved in a direct Ca2+-dependent interaction. This conclusion was further supported by the results of solid phase binding experiments. These showed that the Dsc1a fragment containing cadherin-like repeats 1 and 2 binds directly to the extracellular portion of Dsg in a Ca2+-dependent manner. The contribution of the Dsg/ Dsc interaction to cell–cell adhesion was tested by coculturing HT-1080 cells expressing Dsc1a with HT-1080 cells lacking Dsc but expressing myc-tagged plakoglobin (MPg). In the latter cells, MPg and the endogenous Dsg form stable complexes. The observed specific coimmunoprecipitation of MPg by anti-Dsc antibodies in coculture indicates that an intercellular interaction between Dsc1 and Dsg is involved in cell–cell adhesion. PMID:9214392

Interactive, technology-enhanced self-regulated learning tools in healthcare education: a literature review.

PubMed

Petty, Julia

2013-01-01

Learning technology is increasingly being implemented for programmes of blended learning within nurse education. With a growing emphasis on self-directed study particularly in post-basic education, there is a need for learners to be guided in their learning away from practice and limited classroom time. Technology-enabled (TE) tools which engage learners actively can play a part in this. The effectiveness and value of interactive TE learning strategies within healthcare is the focus of this paper. To identify literature that explores the effectiveness of interactive, TE tools on knowledge acquisition and learner satisfaction within healthcare with a view to evaluating their use for post-basic nurse education. A Literature Review was performed focusing on papers exploring the comparative value and perceived benefit of TE tools compared to traditional modes of learning within healthcare. The Databases identified as most suitable due to their relevance to healthcare were accessed through EBSCOhost. Primary, Boolean and advanced searches on key terms were undertaken. Inclusion and exclusion criteria were applied which resulted in a final selection of 11 studies for critique. Analysis of the literature found that knowledge acquisition in most cases was enhanced and measured learner satisfaction was generally positive for interactive, self-regulated TE tools. However, TE education may not suit all learners and this is critiqued in the light of the identified limitations. Interactive self regulation and/or testing can be a valuable learning strategy that can be incorporated into self-directed programmes of study for post-registration learners. Whilst acknowledging the learning styles not suited to such tools, the concurrent use of self-directed TE tools with those learning strategies necessitating a more social presence can work together to support enhancement of knowledge required to deliver rationale for nursing practice. Copyright © 2012 Elsevier Ltd. All rights reserved.

Invasive non-native plants have a greater effect on neighbouring natives than other non-natives.

PubMed

Kuebbing, Sara E; Nuñez, Martin A

2016-09-12

Human activity is creating a global footprint by changing the climate, altering habitats and reshuffling the distribution of species. The movement of species around the globe has led to the naturalization and accumulation of multiple non-native species within ecosystems, which is frequently associated with habitat disturbance and changing environmental conditions. However, interactions among species will also influence community composition, but little is known about the full range of direct and indirect interactions among native and non-native species. Here, we show through a meta-analysis of 1,215 pairwise plant interactions between 274 vascular plant species in 21 major habitat types that interactions between non-native plants are asymmetrical with interactions between non-native and native plants. Non-native plants were always bad neighbours, but the negative effect of non-natives on natives was around two times greater than the effect of non-natives on other non-natives. In contrast, the performance of non-native plants was five times higher in the presence of a neighbouring native plant species than in the presence of a neighbouring non-native plant species. Together, these results demonstrate that invaded plant communities may accumulate additional non-native species even if direct interactions between non-natives species are negative. Put another way, invasions may be more likely to lead to more invasions, requiring more active management of ecosystems by promoting native species restoration to undermine invasive positive feedback and to assist native species recovery in invaded ecosystems.

Type IV pilins regulate their own expression via direct intramembrane interactions with the sensor kinase PilS.

PubMed

Kilmury, Sara L N; Burrows, Lori L

2016-05-24

Type IV pili are important virulence factors for many pathogens, including Pseudomonas aeruginosa Transcription of the major pilin gene-pilA-is controlled by the PilS-PilR two-component system in response to unknown signals. The absence of a periplasmic sensing domain suggested that PilS may sense an intramembrane signal, possibly PilA. We suggest that direct interactions between PilA and PilS in the inner membrane reduce pilA transcription when PilA levels are high. Overexpression in trans of PilA proteins with diverse and/or truncated C termini decreased native pilA transcription, suggesting that the highly conserved N terminus of PilA was the regulatory signal. Point mutations in PilA or PilS that disrupted their interaction prevented autoregulation of pilA transcription. A subset of PilA point mutants retained the ability to interact with PilS but could no longer decrease pilA transcription, suggesting that interaction between the pilin and sensor kinase is necessary but not sufficient for pilA autoregulation. Furthermore, PilS's phosphatase motif was required for the autoregulation of pilA transcription, suggesting that under conditions where PilA is abundant, the PilA-PilS interaction promotes PilR dephosphorylation and thus down-regulation of further pilA transcription. These data reveal a clever bacterial inventory control strategy in which the major subunit of an important P. aeruginosa virulence factor controls its own expression.

Computer simulations suggest direct and stable tip to tip interaction between the outer membrane channel TolC and the isolated docking domain of the multidrug RND efflux transporter AcrB.

PubMed

Schmidt, Thomas H; Raunest, Martin; Fischer, Nadine; Reith, Dirk; Kandt, Christian

2016-07-01

One way by which bacteria achieve antibiotics resistance is preventing drug access to its target molecule for example through an overproduction of multi-drug efflux pumps of the resistance nodulation division (RND) protein super family of which AcrAB-TolC in Escherichia coli is a prominent example. Although representing one of the best studied efflux systems, the question of how AcrB and TolC interact is still unclear as the available experimental data suggest that either both proteins interact in a tip to tip manner or do not interact at all but are instead connected by a hexamer of AcrA molecules. Addressing the question of TolC-AcrB interaction, we performed a series of 100 ns - 1 µs-molecular dynamics simulations of membrane-embedded TolC in presence of the isolated AcrB docking domain (AcrB(DD)). In 5/6 simulations we observe direct TolC-AcrB(DD) interaction that is only stable on the simulated time scale when both proteins engage in a tip to tip manner. At the same time we find TolC opening and closing freely on extracellular side while remaining closed at the inner periplasmic bottleneck region, suggesting that either the simulated time is too short or additional components are required to unlock TolC. Copyright © 2016 Elsevier B.V. All rights reserved.

Recruitment of Mcm10 to Sites of Replication Initiation Requires Direct Binding to the Minichromosome Maintenance (MCM) Complex*

PubMed Central

Douglas, Max E.

2016-01-01

Mcm10 is required for the initiation of eukaryotic DNA replication and contributes in some unknown way to the activation of the Cdc45-MCM-GINS (CMG) helicase. How Mcm10 is localized to sites of replication initiation is unclear, as current models indicate that direct binding to minichromosome maintenance (MCM) plays a role, but the details and functional importance of this interaction have not been determined. Here, we show that purified Mcm10 can bind both DNA-bound double hexamers and soluble single hexamers of MCM. The binding of Mcm10 to MCM requires the Mcm10 C terminus. Moreover, the binding site for Mcm10 on MCM includes the Mcm2 and Mcm6 subunits and overlaps that for the loading factor Cdt1. Whether Mcm10 recruitment to replication origins depends on CMG helicase assembly has been unclear. We show that Mcm10 recruitment occurs via two modes: low affinity recruitment in the absence of CMG assembly (“G1-like”) and high affinity recruitment when CMG assembly takes place (“S-phase-like”). Mcm10 that cannot bind directly to MCM is defective in both modes of recruitment and is unable to support DNA replication. These findings indicate that Mcm10 is localized to replication initiation sites by directly binding MCM through the Mcm10 C terminus. PMID:26719337

Drosophila parthenogenesis: A tool to decipher centrosomal vs acentrosomal spindle assembly pathways

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

Riparbelli, Maria Giovanna; Callaini, Giuliano

2008-04-15

Development of unfertilized eggs in the parthenogenetic strain K23-O-im of Drosophila mercatorum requires the stochastic interactions of self-assembled centrosomes with the female chromatin. In a portion of the unfertilized eggs that do not assemble centrosomes, microtubules organize a bipolar anastral mitotic spindle around the chromatin like the one formed during the first female meiosis, suggesting that similar pathways may be operative. In the cytoplasm of eggs in which centrosomes do form, monastral and biastral spindles are found. Analysis by laser scanning confocal microscopy suggests that these spindles are derived from the stochastic interaction of astral microtubules directly with kinetochore regionsmore » or indirectly with kinetochore microtubules. Our findings are consistent with the idea that mitotic spindle assembly requires both acentrosomal and centrosomal pathways, strengthening the hypothesis that astral microtubules can dictate the organization of the spindle by capturing kinetochore microtubules.« less

Inequity aversion and the evolution of cooperation

NASA Astrophysics Data System (ADS)

Ahmed, Asrar; Karlapalem, Kamalakar

2014-02-01

Evolution of cooperation is a widely studied problem in biology, social science, economics, and artificial intelligence. Most of the existing approaches that explain cooperation rely on some notion of direct or indirect reciprocity. These reciprocity based models assume agents recognize their partner and know their previous interactions, which requires advanced cognitive abilities. In this paper we are interested in developing a model that produces cooperation without requiring any explicit memory of previous game plays. Our model is based on the notion of inequity aversion, a concept introduced within behavioral economics, whereby individuals care about payoff equality in outcomes. Here we explore the effect of using income inequality to guide partner selection and interaction. We study our model by considering both the well-mixed and the spatially structured population and present the conditions under which cooperation becomes dominant. Our results support the hypothesis that inequity aversion promotes cooperative relationship among nonkin.

Inequity aversion and the evolution of cooperation.

PubMed

Ahmed, Asrar; Karlapalem, Kamalakar

2014-02-01

Evolution of cooperation is a widely studied problem in biology, social science, economics, and artificial intelligence. Most of the existing approaches that explain cooperation rely on some notion of direct or indirect reciprocity. These reciprocity based models assume agents recognize their partner and know their previous interactions, which requires advanced cognitive abilities. In this paper we are interested in developing a model that produces cooperation without requiring any explicit memory of previous game plays. Our model is based on the notion of inequity aversion, a concept introduced within behavioral economics, whereby individuals care about payoff equality in outcomes. Here we explore the effect of using income inequality to guide partner selection and interaction. We study our model by considering both the well-mixed and the spatially structured population and present the conditions under which cooperation becomes dominant. Our results support the hypothesis that inequity aversion promotes cooperative relationship among nonkin.

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.

PubMed

Chen, Chun-Kan; Blanco, Mario; Jackson, Constanza; Aznauryan, Erik; Ollikainen, Noah; Surka, Christine; Chow, Amy; Cerase, Andrea; McDonel, Patrick; Guttman, Mitchell

2016-10-28

The Xist long noncoding RNA orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the three-dimensional (3D) structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here, we show that Xist directly interacts with the Lamin B receptor, an integral component of the nuclear lamina, and that this interaction is required for Xist-mediated silencing by recruiting the inactive X to the nuclear lamina and by doing so enables Xist to spread to actively transcribed genes across the X. Our results demonstrate that lamina recruitment changes the 3D structure of DNA, enabling Xist and its silencing proteins to spread across the X to silence transcription. Copyright © 2016, American Association for the Advancement of Science.

Is transcranial direct current stimulation a potential method for improving response inhibition?☆

PubMed Central

Kwon, Yong Hyun; Kwon, Jung Won

2013-01-01

Inhibitory control of movement in motor learning requires the ability to suppress an inappropriate action, a skill needed to stop a planned or ongoing motor response in response to changes in a variety of environments. This study used a stop-signal task to determine whether transcranial direct-current stimulation over the pre-supplementary motor area alters the reaction time in motor inhibition. Forty healthy subjects were recruited for this study and were randomly assigned to either the transcranial direct-current stimulation condition or a sham-transcranial direct-current stimulation condition. All subjects consecutively performed the stop-signal task before, during, and after the delivery of anodal transcranial direct-current stimulation over the pre-supplementary motor area (pre-transcranial direct-current stimulation phase, transcranial direct-current stimulation phase, and post-transcranial direct-current stimulation phase). Compared to the sham condition, there were significant reductions in the stop-signal processing times during and after transcranial direct-current stimulation, and change times were significantly greater in the transcranial direct-current stimulation condition. There was no significant change in go processing-times during or after transcranial direct-current stimulation in either condition. Anodal transcranial direct-current stimulation was feasibly coupled to an interactive improvement in inhibitory control. This coupling led to a decrease in the stop-signal process time required for the appropriate responses between motor execution and inhibition. However, there was no transcranial direct-current stimulation effect on the no-signal reaction time during the stop-signal task. Transcranial direct-current stimulation can adjust certain behaviors, and it could be a useful clinical intervention for patients who have difficulties with response inhibition. PMID:25206399

Is transcranial direct current stimulation a potential method for improving response inhibition?

PubMed

Kwon, Yong Hyun; Kwon, Jung Won

2013-04-15

Inhibitory control of movement in motor learning requires the ability to suppress an inappropriate action, a skill needed to stop a planned or ongoing motor response in response to changes in a variety of environments. This study used a stop-signal task to determine whether transcranial direct-current stimulation over the pre-supplementary motor area alters the reaction time in motor inhibition. Forty healthy subjects were recruited for this study and were randomly assigned to either the transcranial direct-current stimulation condition or a sham-transcranial direct-current stimulation condition. All subjects consecutively performed the stop-signal task before, during, and after the delivery of anodal transcranial direct-current stimulation over the pre-supplementary motor area (pre-transcranial direct-current stimulation phase, transcranial direct-current stimulation phase, and post-transcranial direct-current stimulation phase). Compared to the sham condition, there were significant reductions in the stop-signal processing times during and after transcranial direct-current stimulation, and change times were significantly greater in the transcranial direct-current stimulation condition. There was no significant change in go processing-times during or after transcranial direct-current stimulation in either condition. Anodal transcranial direct-current stimulation was feasibly coupled to an interactive improvement in inhibitory control. This coupling led to a decrease in the stop-signal process time required for the appropriate responses between motor execution and inhibition. However, there was no transcranial direct-current stimulation effect on the no-signal reaction time during the stop-signal task. Transcranial direct-current stimulation can adjust certain behaviors, and it could be a useful clinical intervention for patients who have difficulties with response inhibition.

Running with the Red Queen: the role of biotic conflicts in evolution

PubMed Central

Brockhurst, Michael A.; Chapman, Tracey; King, Kayla C.; Mank, Judith E.; Paterson, Steve; Hurst, Gregory D. D.

2014-01-01

What are the causes of natural selection? Over 40 years ago, Van Valen proposed the Red Queen hypothesis, which emphasized the primacy of biotic conflict over abiotic forces in driving selection. Species must continually evolve to survive in the face of their evolving enemies, yet on average their fitness remains unchanged. We define three modes of Red Queen coevolution to unify both fluctuating and directional selection within the Red Queen framework. Empirical evidence from natural interspecific antagonisms provides support for each of these modes of coevolution and suggests that they often operate simultaneously. We argue that understanding the evolutionary forces associated with interspecific interactions requires incorporation of a community framework, in which new interactions occur frequently. During their early phases, these newly established interactions are likely to drive fast evolution of both parties. We further argue that a more complete synthesis of Red Queen forces requires incorporation of the evolutionary conflicts within species that arise from sexual reproduction. Reciprocally, taking the Red Queen's perspective advances our understanding of the evolution of these intraspecific conflicts. PMID:25355473

Estimating Development Cost of an Interactive Website Based Cancer Screening Promotion Program

PubMed Central

Lairson, David R.; Chung, Tong Han; Smith, Lisa G.; Springston, Jeffrey K.; Champion, Victoria L.

2015-01-01

Objectives The aim of this study was to estimate the initial development costs for an innovative talk show format tailored intervention delivered via the interactive web, for increasing cancer screening in women 50 to 75 who were non-adherent to screening guidelines for colorectal cancer and/or breast cancer. Methods The cost of the intervention development was estimated from a societal perspective. Micro costing methods plus vendor contract costs were used to estimate cost. Staff logs were used to track personnel time. Non-personnel costs include all additional resources used to produce the intervention. Results Development cost of the interactive web based intervention was $.39 million, of which 77% was direct cost. About 98% of the cost was incurred in personnel time cost, contract cost and overhead cost. Conclusions The new web-based disease prevention medium required substantial investment in health promotion and media specialist time. The development cost was primarily driven by the high level of human capital required. The cost of intervention development is important information for assessing and planning future public and private investments in web-based health promotion interventions. PMID:25749548

Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1.

PubMed

Harrison, Joseph S; Cornett, Evan M; Goldfarb, Dennis; DaRosa, Paul A; Li, Zimeng M; Yan, Feng; Dickson, Bradley M; Guo, Angela H; Cantu, Daniel V; Kaustov, Lilia; Brown, Peter J; Arrowsmith, Cheryl H; Erie, Dorothy A; Major, Michael B; Klevit, Rachel E; Krajewski, Krzysztof; Kuhlman, Brian; Strahl, Brian D; Rothbart, Scott B

2016-09-06

The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. HeDNA recognition activates UHRF1 ubiquitylation towards multiple lysines on the H3 tail adjacent to the UHRF1 histone-binding site. Collectively, our studies are the first demonstrations of a DNA-protein interaction and an epigenetic modification directly regulating E3 ubiquitin ligase activity. They also define an orchestrated epigenetic control mechanism involving modifications both to histones and DNA that facilitate UHRF1 chromatin targeting, H3 ubiquitylation, and DNA methylation inheritance.

Harnessing cell–biomaterial interactions for osteochondral tissue regeneration.

PubMed

Kim, Kyobum; Yoon, Diana M; Mikos, Antonios; Kasper, F Kurtis

2012-01-01

Articular cartilage that is damaged or diseased often requires surgical intervention to repair the tissue; therefore, tissue engineering strategies have been developed to aid in cartilage regeneration. Tissue engineering approaches often require the integration of cells, biomaterials, and growth factors to direct and support tissue formation. A variety of cell types have been isolated from adipose, bone marrow, muscle, and skin tissue to promote cartilage regeneration. The interaction of cells with each other and with their surrounding environment has been shown to play a key role in cartilage engineering. In tissue engineering approaches, biomaterials are commonly used to provide an initial framework for cell recruitment and proliferation and tissue formation. Modifications of the properties of biomaterials, such as creating sites for cell binding, altering their physicochemical characteristics, and regulating the delivery of growth factors, can have a significant influence on chondrogenesis. Overall, the goal is to completely restore healthy cartilage within an articular cartilage defect. This chapter aims to provide information about the importance of cell–biomaterial interactions for the chondrogenic differentiation of various cell populations that can eventually produce functional cartilage matrix that is indicative of healthy cartilage tissue.

Field driven magnetic racetrack memory accompanied with the interfacial Dzyaloshinskii-Moriya interaction

NASA Astrophysics Data System (ADS)

Kim, June-Seo; Lee, Hyeon-Jun; Hong, Jung-Il; You, Chun-Yeol

2018-06-01

The in-plane magnetic field pulse driven domain wall motion on a perpendicularly magnetized nanowire is numerically investigated by performing micromagnetic simulations and magnetic domain wall dynamics are evaluated analytically with one-dimensional collective coordinate models including the interfacial Dzyaloshinskii-Moriya interaction. With the action of the precession torque, the chirality and the magnetic field direction dependent displacements of the magnetic domain walls are clearly observed. In order to move Bloch type and Neel type domain walls, a longitudinal and a transverse in-plane magnetic field pulse are required, respectively. The domain wall type (Bloch or Neel) can easily be determined by the dynamic motion of the domain walls under the applied pulse fields. By applying a temporally asymmetric in-plane field pulse and successive notches in the perpendicularly magnetized nanowire strip line with a proper interval, the concept of racetrack memory based on the synchronous displacements of the chirality dependent multiple domain walls is verified to be feasible. Requirement of multiple domain walls with homogeneous chirality is achieved with the help of Dzyaloshinskii-Moriya interaction.

Aub and Ago3 are recruited to nuage through two mechanisms to form a ping-pong complex assembled by Krimper

PubMed Central

Webster, Alexandre; Li, Sisi; Hur, Junho K.; Wachsmuth, Malte; Bois, Justin S.; Perkins, Edward M.; Patel, Dinshaw J.; Aravin, Alexei A.

2015-01-01

In Drosophila, two Piwi proteins, Aubergine (Aub) and Argonaute-3 (Ago3) localize to perinuclear ‘nuage’ granules and use guide piRNAs to target and destroy transposable element transcripts. We find that Aub and Ago3 are recruited to nuage by two different mechanisms. Aub requires a piRNA guide for nuage recruitment, indicating that its localization depends on recognition of RNA targets. Ago3 is recruited to nuage independently of a piRNA cargo and relies on interaction with Krimper, a stable component of nuage that is able to aggregate in the absence of other nuage proteins. We show that Krimper interacts directly with Aub and Ago3 to coordinate the assembly of the ping-pong piRNA processing (4P) complex. Symmetrical dimethylated arginines are required for Aub to interact with Krimper, but are dispensable for Ago3 to bind Krimper. Our study reveals a multi-step process responsible for the assembly and function of nuage complexes in piRNA-guided transposon repression. PMID:26295961

Itk tyrosine kinase substrate docking is mediated by a nonclassical SH2 domain surface of PLCgamma1.

PubMed

Min, Lie; Joseph, Raji E; Fulton, D Bruce; Andreotti, Amy H

2009-12-15

Interleukin-2 tyrosine kinase (Itk) is a Tec family tyrosine kinase that mediates signaling processes after T cell receptor engagement. Activation of Itk requires recruitment to the membrane via its pleckstrin homology domain, phosphorylation of Itk by the Src kinase, Lck, and binding of Itk to the SLP-76/LAT adapter complex. After activation, Itk phosphorylates and activates phospholipase C-gamma1 (PLC-gamma1), leading to production of two second messengers, DAG and IP(3). We have previously shown that phosphorylation of PLC-gamma1 by Itk requires a direct, phosphotyrosine-independent interaction between the Src homology 2 (SH2) domain of PLC-gamma1 and the kinase domain of Itk. We now define this docking interface using a combination of mutagenesis and NMR spectroscopy and show that disruption of the Itk/PLCgamma1 docking interaction attenuates T cell signaling. The binding surface on PLCgamma1 that mediates recognition by Itk highlights a nonclassical binding activity of the well-studied SH2 domain providing further evidence that SH2 domains participate in important signaling interactions beyond recognition of phosphotyrosine.

Comparison of thyroid segmentation techniques for 3D ultrasound

NASA Astrophysics Data System (ADS)

Wunderling, T.; Golla, B.; Poudel, P.; Arens, C.; Friebe, M.; Hansen, C.

2017-02-01

The segmentation of the thyroid in ultrasound images is a field of active research. The thyroid is a gland of the endocrine system and regulates several body functions. Measuring the volume of the thyroid is regular practice of diagnosing pathological changes. In this work, we compare three approaches for semi-automatic thyroid segmentation in freehand-tracked three-dimensional ultrasound images. The approaches are based on level set, graph cut and feature classification. For validation, sixteen 3D ultrasound records were created with ground truth segmentations, which we make publicly available. The properties analyzed are the Dice coefficient when compared against the ground truth reference and the effort of required interaction. Our results show that in terms of Dice coefficient, all algorithms perform similarly. For interaction, however, each algorithm has advantages over the other. The graph cut-based approach gives the practitioner direct influence on the final segmentation. Level set and feature classifier require less interaction, but offer less control over the result. All three compared methods show promising results for future work and provide several possible extensions.

Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

PubMed Central

Dunipace, Leslie; Ozdemir, Anil; Stathopoulos, Angelike

2011-01-01

It has been shown in several organisms that multiple cis-regulatory modules (CRMs) of a gene locus can be active concurrently to support similar spatiotemporal expression. To understand the functional importance of such seemingly redundant CRMs, we examined two CRMs from the Drosophila snail gene locus, which are both active in the ventral region of pre-gastrulation embryos. By performing a deletion series in a ∼25 kb DNA rescue construct using BAC recombineering and site-directed transgenesis, we demonstrate that the two CRMs are not redundant. The distal CRM is absolutely required for viability, whereas the proximal CRM is required only under extreme conditions such as high temperature. Consistent with their distinct requirements, the CRMs support distinct expression patterns: the proximal CRM exhibits an expanded expression domain relative to endogenous snail, whereas the distal CRM exhibits almost complete overlap with snail except at the anterior-most pole. We further show that the distal CRM normally limits the increased expression domain of the proximal CRM and that the proximal CRM serves as a `damper' for the expression levels driven by the distal CRM. Thus, the two CRMs interact in cis in a non-additive fashion and these interactions may be important for fine-tuning the domains and levels of gene expression. PMID:21813571

NuMA-microtubule interactions are critical for spindle orientation and the morphogenesis of diverse epidermal structures

PubMed Central

Seldin, Lindsey; Muroyama, Andrew; Lechler, Terry

2016-01-01

Mitotic spindle orientation is used to generate cell fate diversity and drive proper tissue morphogenesis. A complex of NuMA and dynein/dynactin is required for robust spindle orientation in a number of cell types. Previous research proposed that cortical dynein/dynactin was sufficient to generate forces on astral microtubules (MTs) to orient the spindle, with NuMA acting as a passive tether. In this study, we demonstrate that dynein/dynactin is insufficient for spindle orientation establishment in keratinocytes and that NuMA’s MT-binding domain, which targets MT tips, is also required. Loss of NuMA-MT interactions in skin caused defects in spindle orientation and epidermal differentiation, leading to neonatal lethality. In addition, we show that NuMA-MT interactions are also required in adult mice for hair follicle morphogenesis and spindle orientation within the transit-amplifying cells of the matrix. Loss of spindle orientation in matrix cells results in defective differentiation of matrix-derived lineages. Our results reveal an additional and direct function of NuMA during mitotic spindle positioning, as well as a reiterative use of spindle orientation in the skin to build diverse structures. DOI: http://dx.doi.org/10.7554/eLife.12504.001 PMID:26765568

Interaction matters: A perceived social partner alters the neural processing of human speech.

PubMed

Rice, Katherine; Redcay, Elizabeth

2016-04-01

Mounting evidence suggests that social interaction changes how communicative behaviors (e.g., spoken language, gaze) are processed, but the precise neural bases by which social-interactive context may alter communication remain unknown. Various perspectives suggest that live interactions are more rewarding, more attention-grabbing, or require increased mentalizing-thinking about the thoughts of others. Dissociating between these possibilities is difficult because most extant neuroimaging paradigms examining social interaction have not directly compared live paradigms to conventional "offline" (or recorded) paradigms. We developed a novel fMRI paradigm to assess whether and how an interactive context changes the processing of speech matched in content and vocal characteristics. Participants listened to short vignettes--which contained no reference to people or mental states--believing that some vignettes were prerecorded and that others were presented over a real-time audio-feed by a live social partner. In actuality, all speech was prerecorded. Simply believing that speech was live increased activation in each participant's own mentalizing regions, defined using a functional localizer. Contrasting live to recorded speech did not reveal significant differences in attention or reward regions. Further, higher levels of autistic-like traits were associated with altered neural specialization for live interaction. These results suggest that humans engage in ongoing mentalizing about social partners, even when such mentalizing is not explicitly required, illustrating how social context shapes social cognition. Understanding communication in social context has important implications for typical and atypical social processing, especially for disorders like autism where social difficulties are more acute in live interaction. Copyright © 2015 Elsevier Inc. All rights reserved.

ORNL Direct Purchase Information System (DPIS) user's manual. [For PDP-10

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

Grubb, J.W.; Lovin, J.K.; Smith, M.B.

1980-08-01

The ORNL Management Information System (MIS) Direct Purchase Information System (DPIS) is an on-line interactive system of computer programs. The system can provide a manager with commitment and delivery schedule information on current direct purchase requisitions. The commitment data accounts for the orders that have been placed and those requisitions yet to be placed with a vendor. Information can be summarized at many different levels, and individuals can quickly determine the status of their requisitions. DPIS contains data only on active outside direct purchases, but has the capability to access historical data. It provides sufficient flexibility to be used tomore » answer many questions pertinent to the status of these direct purchases and their obligating costs. Even an inexperienced computer user should have little difficulty in learning to use DPIS. The User Module prompts the user on what type of response it is expecting. If the user has doubts as to the response, or if the meaning of the response is not clear, the module will give a detailed list of the options available at that level. The user has control of what data are to be considered, how they are to be grouped, and what format the output will take. As the user selects the options available at a given level, the module proceeds to the next lower level until sufficient input has been supplied to provide the requested information. A major benefit of this interactive, user-oriented system is that the manager can specify the information requirements and does not have to spend time going through a great deal of other data to locate what is needed. Because it is interactive, a search can begin at a summary level and then resort to a more detailed level if needed. DPIS allows the user direct control for selecting the type of commitment data, output, funds, and direct purchase.« less

Sticking to cellulose: exploiting Arabidopsis seed coat mucilage to understand cellulose biosynthesis and cell wall polysaccharide interactions.

PubMed

Griffiths, Jonathan S; North, Helen M

2017-05-01

The cell wall defines the shape of cells and ultimately plant architecture. It provides mechanical resistance to osmotic pressure while still being malleable and allowing cells to grow and divide. These properties are determined by the different components of the wall and the interactions between them. The major components of the cell wall are the polysaccharides cellulose, hemicellulose and pectin. Cellulose biosynthesis has been extensively studied in Arabidopsis hypocotyls, and more recently in the mucilage-producing epidermal cells of the seed coat. The latter has emerged as an excellent system to study cellulose biosynthesis and the interactions between cellulose and other cell wall polymers. Here we review some of the major advances in our understanding of cellulose biosynthesis in the seed coat, and how mucilage has aided our understanding of the interactions between cellulose and other cell wall components required for wall cohesion. Recently, 10 genes involved in cellulose or hemicellulose biosynthesis in mucilage have been identified. These discoveries have helped to demonstrate that xylan side-chains on rhamnogalacturonan I act to link this pectin directly to cellulose. We also examine other factors that, either directly or indirectly, influence cellulose organization or crystallization in mucilage. © 2017 INRA. New Phytologist © 2017 New Phytologist Trust.

Helicobacter pylori induces activation of human peripheral γδ+ T lymphocytes.

PubMed

Romi, Benedetta; Soldaini, Elisabetta; Pancotto, Laura; Castellino, Flora; Del Giudice, Giuseppe; Schiavetti, Francesca

2011-04-29

Helicobacter pylori is a gram-negative bacterium that causes gastric and duodenal diseases in humans. Despite a robust antibody and cellular immune response, H. pylori infection persists chronically. To understand if and how H. pylori could modulate T cell activation, in the present study we investigated in vitro the interaction between H. pylori and human T lymphocytes freshly isolated from peripheral blood of H. pylori-negative donors. A direct interaction of live, but not killed bacteria with purified CD3+ T lymphocytes was observed by microscopy and confirmed by flow cytometry. Live H. pylori activated CD3+ T lymphocytes and predominantly γδ+ T cells bearing the TCR chain Vδ2. Upon interaction with H. pylori, these cells up-regulated the activation molecule CD69 and produced cytokines (such as TNFα, IFNγ) and chemokines (such as MIP-1β, RANTES) in a non-antigen-specific manner. This activation required viable H. pylori and was not exhibited by other gram-negative bacteria. The cytotoxin-associated antigen-A (CagA), was at least partially responsible of this activation. Our results suggest that H. pylori can directly interact with T cells and modulate the response of γδ+ T cells, thereby favouring an inflammatory environment which can contribute to the chronic persistence of the bacteria and eventually to the gastric pathology.

Direct Interaction between Scaffolding Proteins RACK1 and 14-3-3ζ Regulates Brain-derived Neurotrophic Factor (BDNF) Transcription*

PubMed Central

Neasta, Jérémie; Kiely, Patrick A.; He, Dao-Yao; Adams, David R.; O'Connor, Rosemary; Ron, Dorit

2012-01-01

RACK1 is a scaffolding protein that spatially and temporally regulates numerous signaling cascades. We previously found that activation of the cAMP signaling pathway induces the translocation of RACK1 to the nucleus. We further showed that nuclear RACK1 is required to promote the transcription of the brain-derived neurotrophic factor (BDNF). Here, we set out to elucidate the mechanism underlying cAMP-dependent RACK1 nuclear translocation and BDNF transcription. We identified the scaffolding protein 14-3-3ζ as a direct binding partner of RACK1. Moreover, we found that 14-3-3ζ was necessary for the cAMP-dependent translocation of RACK1 to the nucleus. We further observed that the disruption of RACK1/14-3-3ζ interaction with a peptide derived from the RACK1/14-3-3ζ binding site or shRNA-mediated 14-3-3ζ knockdown inhibited cAMP induction of BDNF transcription. Together, these data reveal that the function of nuclear RACK1 is mediated through its interaction with 14-3-3ζ. As RACK1 and 14-3-3ζ are two multifunctional scaffolding proteins that coordinate a wide variety of signaling events, their interaction is likely to regulate other essential cellular functions. PMID:22069327

Direct interaction of the Golgi V-ATPase a-subunit isoform with PI(4)P drives localization of Golgi V-ATPases in yeast.

PubMed

Banerjee, Subhrajit; Kane, Patricia M

2017-09-15

Luminal pH and phosphoinositide content are fundamental features of organelle identity. Vacuolar H + -ATPases (V-ATPases) drive organelle acidification in all eukaryotes, and membrane-bound a-subunit isoforms of the V-ATPase are implicated in organelle-specific targeting and regulation. Earlier work demonstrated that the endolysosomal lipid PI(3,5)P 2 activates V-ATPases containing the vacuolar a-subunit isoform in Saccharomyces cerevisiae Here we demonstrate that PI(4)P, the predominant Golgi phosphatidylinositol (PI) species, directly interacts with the cytosolic amino terminal (NT) domain of the yeast Golgi V-ATPase a-isoform Stv1. Lysine-84 of Stv1NT is essential for interaction with PI(4)P in vitro and in vivo, and interaction with PI(4)P is required for efficient localization of Stv1-containing V-ATPases. The cytosolic NT domain of the human V-ATPase a2 isoform specifically interacts with PI(4)P in vitro, consistent with its Golgi localization and function. We propose that NT domains of V o a-subunit isoforms interact specifically with PI lipids in their organelles of residence. These interactions can transmit organelle-specific targeting or regulation information to V-ATPases. © 2017 Banerjee and Kane. 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).

Adapting GOMS to Model Human-Robot Interaction

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

Drury, Jill; Scholtz, Jean; Kieras, David

2007-03-09

Human-robot interaction (HRI) has been maturing in tandem with robots’ commercial success. In the last few years HRI researchers have been adopting—and sometimes adapting—human-computer interaction (HCI) evaluation techniques to assess the efficiency and intuitiveness of HRI designs. For example, Adams (2005) used Goal Directed Task Analysis to determine the interaction needs of officers from the Nashville Metro Police Bomb Squad. Scholtz et al. (2004) used Endsley’s (1988) Situation Awareness Global Assessment Technique to determine robotic vehicle supervisors’ awareness of when vehicles were in trouble and thus required closer monitoring or intervention. Yanco and Drury (2004) employed usability testing to determinemore » (among other things) how well a search-andrescue interface supported use by first responders. One set of HCI tools that has so far seen little exploration in the HRI domain, however, is the class of modeling and evaluation techniques known as formal methods.« less

Maslinic acid promotes autophagy by disrupting the interaction between Bcl2 and Beclin1 in rat pheochromocytoma PC12 cells

PubMed Central

Dong, Xiaoli; Zhang, Jiaxiao; Zhou, Zhilin; Ye, Zhennan; Chen, Jiahao; Yuan, Jifan; Cao, Fengjun; Wang, Xuanbin; Liu, Wenchao; Yu, Wenxuan; Li, Xiaohua

2017-01-01

Maslinic acid (2α, 3β-dihydroxyolean-12-en-28-oic acid, MA) was isolated from natural plants and showed anti-cancer activity in rat Pheochromocytoma PC12 cells in our previous studies. We now discover that MA disrupts the interaction between Bcl2 and autophagy scaffold protein Beclin1 in the above cell line, leading to the up-regulation of autophagy. We investigated the effect of MA on the interaction between Bcl2 and Beclin1 by biochemical and biophysical methods in combination with autophagy characterization in the above cell line. Our results suggest that MA may serve as an autophagy activator by directly blocking the Bcl2-Beclin1 interaction to release free Beclin1 required for the recruitment of autophagy positive regulators, implying MA may exert its anti-cancer activity by regulating autophagy. PMID:29088805

Bridging a gap between continuum-QCD and ab initio predictions of hadron observables

DOE PAGES

Binosi, Daniele; Chang, Lei; Papavassiliou, Joannis; ...

2015-03-01

Within contemporary hadron physics there are two common methods for determining the momentum- dependence of the interaction between quarks: the top-down approach, which works toward an ab initiocomputation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD’s gauge sector coincides with that required in order to describe ground-state hadron observables usingmore » a nonperturbative truncation of QCD’s Dyson–Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.« less

A mammalian germ cell-specific RNA-binding protein interacts with ubiquitously expressed proteins involved in splice site selection

NASA Astrophysics Data System (ADS)

Elliott, David J.; Bourgeois, Cyril F.; Klink, Albrecht; Stévenin, James; Cooke, Howard J.

2000-05-01

RNA-binding motif (RBM) genes are found on all mammalian Y chromosomes and are implicated in spermatogenesis. Within human germ cells, RBM protein shows a similar nuclear distribution to components of the pre-mRNA splicing machinery. To address the function of RBM, we have used protein-protein interaction assays to test for possible physical interactions between these proteins. We find that RBM protein directly interacts with members of the SR family of splicing factors and, in addition, strongly interacts with itself. We have mapped the protein domains responsible for mediating these interactions and expressed the mouse RBM interaction region as a bacterial fusion protein. This fusion protein can pull-down several functionally active SR protein species from cell extracts. Depletion and add-back experiments indicate that these SR proteins are the only splicing factors bound by RBM which are required for the splicing of a panel of pre-mRNAs. Our results suggest that RBM protein is an evolutionarily conserved mammalian splicing regulator which operates as a germ cell-specific cofactor for more ubiquitously expressed pre-mRNA splicing activators.

Coordinated vigilance provides evidence for direct reciprocity in coral reef fishes.

PubMed

Brandl, Simon J; Bellwood, David R

2015-09-25

Reciprocity is frequently assumed to require complex cognitive abilities. Therefore, it has been argued that reciprocity may be restricted to animals that can meet these demands. Here, we provide evidence for the potential presence of direct reciprocity in teleost fishes. We demonstrate that in pairs of coral reef rabbitfishes (f. Siganidae), one fish frequently assumes an upright vigilance position in the water column, while the partner forages in small crevices in the reef substratum. Both behaviours are strongly coordinated and partners regularly alternate their positions, resulting in a balanced distribution of foraging activity. Compared to solitary individuals, fishes in pairs exhibit longer vigilance bouts, suggesting that the help provided to the partner is costly. In turn, fishes in pairs take more consecutive bites and penetrate deeper into crevices than solitary individuals, suggesting that the safety provided by a vigilant partner may outweigh initial costs by increasing foraging efficiency. Thus, the described system appears to meet all of the requirements for direct reciprocity. We argue that the nature of rabbitfish pairs provides favourable conditions for the establishment of direct reciprocity, as continuous interaction with the same partner, simultaneous needs, interdependence, and communication relax the cognitive demands of reciprocal cooperation.

DHU1 negatively regulates UV-B signaling via its direct interaction with COP1 and RUP1.

PubMed

Kim, Sang-Hoon; Kim, Hani; Chung, Sunglan; Lee, Jae-Hoon

2017-09-16

Although DWD HYPERSENSITIVE TO UV-B 1 (DHU1) is reported to be a negative regulator in UV-B mediated cellular responses, its detailed role in UV-B signaling is still elusive. To further understand the action mechanism of DHU1 in UV-B response, physical and genetic interactions of DHU1 with various UV-B signaling components were investigated. Yeast two hybrid assay results suggested that DHU1 directly interacts with COP1 and RUP1, implying a functional connection with both COP1 and RUP1. In spite of the physical association between DHU1 and COP1, loss of DHU1 did not affect protein stability of COP1. Epistatic analysis showed that the functional loss of both DHU1 and UVR8 leads to alleviation of UV-B hypersensitivity displayed in dhu1-1. Moreover, phenotypic studies with dhu1-1 cop1-6 and dhu1-1 hy5-215 revealed that COP1 and HY5 are epistatic to DHU1, indicating that UV-B hypersensitivity of dhu1-1 requires both COP1 and HY5. In the case of dhu1-1 rup1-1, UV-B responsiveness was similar to that of both dhu1-1 and rup1-1, implying that DHU1 and RUP1 are required for each other's function. Collectively, these results show that the role of DHU1 as a negative regulator in UV-B response may be derived from its direct interaction with COP1 by sequestering COP1 from the active UVR8-COP1 complex, resulting in a decrease in the COP1 population that positively participates in UV-B signaling together with UVR8. Furthermore, this inhibitory role of DHU1 in UV-B signaling is likely to be functionally connected to RUP1. This study will serve as a platform to further understand more detailed action mechanism of DHU1 in UV-B response and DHU1-mediated core UV-B signaling in Arabidopsis. Copyright © 2017 Elsevier Inc. All rights reserved.

Planar polarity pathway and Nance-Horan syndrome-like 1b have essential cell-autonomous functions in neuronal migration.

PubMed

Walsh, Gregory S; Grant, Paul K; Morgan, John A; Moens, Cecilia B

2011-07-01

Components of the planar cell polarity (PCP) pathway are required for the caudal tangential migration of facial branchiomotor (FBM) neurons, but how PCP signaling regulates this migration is not understood. In a forward genetic screen, we identified a new gene, nhsl1b, required for FBM neuron migration. nhsl1b encodes a WAVE-homology domain-containing protein related to human Nance-Horan syndrome (NHS) protein and Drosophila GUK-holder (Gukh), which have been shown to interact with components of the WAVE regulatory complex that controls cytoskeletal dynamics and with the polarity protein Scribble, respectively. Nhsl1b localizes to FBM neuron membrane protrusions and interacts physically and genetically with Scrib to control FBM neuron migration. Using chimeric analysis, we show that FBM neurons have two modes of migration: one involving interactions between the neurons and their planar-polarized environment, and an alternative, collective mode involving interactions between the neurons themselves. We demonstrate that the first mode of migration requires the cell-autonomous functions of Nhsl1b and the PCP components Scrib and Vangl2 in addition to the non-autonomous functions of Scrib and Vangl2, which serve to polarize the epithelial cells in the environment of the migrating neurons. These results define a role for Nhsl1b as a neuronal effector of PCP signaling and indicate that proper FBM neuron migration is directly controlled by PCP signaling between the epithelium and the migrating neurons.

Planar polarity pathway and Nance-Horan syndrome-like 1b have essential cell-autonomous functions in neuronal migration

PubMed Central

Walsh, Gregory S.; Grant, Paul K.; Morgan, John A.; Moens, Cecilia B.

2011-01-01

Components of the planar cell polarity (PCP) pathway are required for the caudal tangential migration of facial branchiomotor (FBM) neurons, but how PCP signaling regulates this migration is not understood. In a forward genetic screen, we identified a new gene, nhsl1b, required for FBM neuron migration. nhsl1b encodes a WAVE-homology domain-containing protein related to human Nance-Horan syndrome (NHS) protein and Drosophila GUK-holder (Gukh), which have been shown to interact with components of the WAVE regulatory complex that controls cytoskeletal dynamics and with the polarity protein Scribble, respectively. Nhsl1b localizes to FBM neuron membrane protrusions and interacts physically and genetically with Scrib to control FBM neuron migration. Using chimeric analysis, we show that FBM neurons have two modes of migration: one involving interactions between the neurons and their planar-polarized environment, and an alternative, collective mode involving interactions between the neurons themselves. We demonstrate that the first mode of migration requires the cell-autonomous functions of Nhsl1b and the PCP components Scrib and Vangl2 in addition to the non-autonomous functions of Scrib and Vangl2, which serve to polarize the epithelial cells in the environment of the migrating neurons. These results define a role for Nhsl1b as a neuronal effector of PCP signaling and indicate that proper FBM neuron migration is directly controlled by PCP signaling between the epithelium and the migrating neurons. PMID:21693519

The Chromatin Remodeling Factor SMARCB1 Forms a Complex with Human Cytomegalovirus Proteins UL114 and UL44

PubMed Central

Ranneberg-Nilsen, Toril; Rollag, Halvor; Slettebakk, Ragnhild; Backe, Paul Hoff; Olsen, Øyvind; Luna, Luisa; Bjørås, Magnar

2012-01-01

Background Human cytomegalovirus (HCMV) uracil DNA glycosylase, UL114, is required for efficient viral DNA replication. Presumably, UL114 functions as a structural partner to other factors of the DNA-replication machinery and not as a DNA repair protein. UL114 binds UL44 (HCMV processivity factor) and UL54 (HCMV-DNA-polymerase). In the present study we have searched for cellular partners of UL114. Methodology/Principal Findings In a yeast two-hybrid screen SMARCB1, a factor of the SWI/SNF chromatin remodeling complex, was found to be an interacting partner of UL114. This interaction was confirmed in vitro by co-immunoprecipitation and pull-down. Immunofluorescence microscopy revealed that SMARCB1 along with BRG-1, BAF170 and BAF155, which are the core SWI/SNF components required for efficient chromatin remodeling, were present in virus replication foci 24–48 hours post infection (hpi). Furthermore a direct interaction was also demonstrated for SMARCB1 and UL44. Conclusions/Significance The core SWI/SNF factors required for efficient chromatin remodeling are present in the HCMV replication foci throughout infection. The proteins UL44 and UL114 interact with SMARCB1 and may participate in the recruitment of the SWI/SNF complex to the chromatinized virus DNA. Thus, the presence of the SWI/SNF chromatin remodeling complex in replication foci and its association with UL114 and with UL44 might imply its involvement in different DNA transactions. PMID:22479537

Core Problem: Does the CV Parent Body Magnetization require differentiation?

NASA Astrophysics Data System (ADS)

O'Brien, T.; Tarduno, J. A.; Smirnov, A. V.

2016-12-01

Evidence for the presence of past dynamos from magnetic studies of meteorites can provide key information on the nature and evolution of parent bodies. However, the suggestion of a past core dynamo for the CV parent body based on the study of the Allende meteorite has led to a paradox: a core dynamo requires differentiation, evidence for which is missing in the meteorite record. The key parameter used to distinguish core dynamo versus external field mechanisms is absolute field paleointensity, with high values (>>1 μT) favoring the former. Here we explore the fundamental requirements for absolute field intensity measurement in the Allende meteorite: single domain grains that are non-interacting. Magnetic hysteresis and directional data define strong magnetic interactions, negating a standard interpretation of paleointensity measurements in terms of absolute paleofield values. The Allende low field magnetic susceptibility is dominated by magnetite and FeNi grains, whereas the magnetic remanence is carried by an iron sulfide whose remanence-carrying capacity increases with laboratory cycling at constant field values, indicating reordering. The iron sulfide and FeNi grains are in close proximity, providing mineralogical context for interactions. We interpret the magnetization of Allende to record the intense early solar wind with metal-sulfide interactions amplifying the field, giving the false impression of a higher field value in some prior studies. An undifferentiated CV parent body is thus compatible with Allende's magnetization. Early solar wind magnetization should be the null hypothesis for evaluating the source of magnetization for chondrites and other meteorites.

Training direct care staff to increase positive interactions with individuals with developmental disabilities.

PubMed

Zoder-Martell, Kimberly A; Dufrene, Brad A; Tingstrom, Daniel H; Olmi, D Joe; Jordan, Sara S; Biskie, Erika M; Sherman, Julie C

2014-09-01

This study tested the effects of direct training on direct care staff's initiation of positive interactions with individuals with developmental disabilities who resided in an intermediate care facility. Participants included four direct care staff and their residents. Direct training included real-time prompts delivered via a one-way radio, and data were collected for immediate and sustained increases in rates of direct care staff's positive interactions. Additionally, this study evaluated the link between increased rates of positive interactions and concomitant decreases in residents' challenging behaviors. A multiple baseline design across participants was used and results indicated that all direct care staff increased their rates of positive interactions during direct training. Moreover, all but one participant continued to engage residents in positive interactions at levels above the criterion during the maintenance phase and follow-up phases. The direct care staff member who did not initially meet the criterion improved to adequate levels following one brief performance feedback session. With regard to residents' challenging behaviors, across phases, residents engaged in low levels of challenging behaviors making those results difficult to evaluate. However, improvements in residents' rate of positive interactions were noted. Copyright © 2014 Elsevier Ltd. All rights reserved.

Midwives' motivation for continuing education.

PubMed

Laszlo, H; Strettle, R J

1996-10-01

This study examined midwives' motivations for continuing their education by conducting a survey amongst a sample population of midwives, employed in 4 Health Authorities in the North West of England. The survey was carried out using a questionnaire which asked midwives to indicate the 'importance' of a series of requirements of continuing education. Of 120 midwives who received the questionnaire, 83 (69%) replied. Motivational factors included: learning for professional and personal development; fulfilling legal or statutory practice requirement, or as a social activity. The results showed that motivation for continuing education was strongest in relation to professional competence and an innate desire for knowledge. Where personal development was achieved, the emphasis was to promote professional advancement rather than social interaction. Less emphasis was placed on fulfilling the legal requirements for practice. The strongest motivators were learning orientated, which suggests that the subjects were self-directed to fulfil their needs, based on a desire to learn, this being less dependent on external motivators, which may be activated by statutory or employer requirements. Social interaction was seen as the least important aspect, although subjects found it beneficial to meet colleagues from other areas and felt that they learnt from exchanging views about various clinical practices.

The Air Force Interactive Meteorological System: A Research Tool for Satellite Meteorology

DTIC Science & Technology

1992-12-02

NFARnet itself is a subnet to the global computer network INTERNET that links nearly all U.S. government research facilities and universi- ties along...required input to a generalized mathematical solution to the satellite/earth coordinate transform used for earth location of GOES sensor data. A direct...capability also exists to convert absolute coordinates to relative coordinates for transformations associated with gridded fields. 3. Spatial objective

Molecular Mechanisms for Synaptic Modification in the Visual Cortex: Interaction between Theory and Experiment

DTIC Science & Technology

1989-02-03

known that the large majority of neurons in layers Ill, IV and VI receive direct monosynaptic input from the lateral geniculate nucleus (Toyama et al...1974; Ferster and Lindstrom, 1983; Martin, 1987). The receptive fields of lateral geniculate nucleus (LGN) neurons resemble those of retinal ganglion...the lateral geniculate nucleus only. The second stage of the theoretical analysis requires that relevant intracortical connections be incorporated

A Comparative Study of GDSS (Group Decision Support System) Use: Empirical Evidence and Model Design

DTIC Science & Technology

1987-09-01

G D SS ............................................... 67 APPENDIX A: ENERGY INTERNATIONAL CASE ...................... 69 APPENDIX B: QUESTIONNAIRE...the impact of many of the disadvantages. C. DESIRABLE CHARACTERISTICS OF A GDSS The designer of a GDSS must consider the major functional requirements...592]. Alter has stated that interaction with the GDSS is not the most important aspect of the system. Instead, designers should direct their energies

Pictorial communication: Pictures and the synthetic universe

NASA Technical Reports Server (NTRS)

Ellis, Stephen R.

1989-01-01

Principles for the design of dynamic spatial instruments for communicating quantitative information to viewers are considered through a brief review of the history of pictorial communication. Pictorial communication is seen to have two directions: (1) from the picture to the viewer; and (2) from the viewer to the picture. Optimization of the design of interactive instruments using pictorial formats requires an understanding of the manipulative, perceptual, and cognitive limitations of human viewers.

Casein Kinase 2 Reverses Tail-Independent Inhibition of Kinesin-1

NASA Astrophysics Data System (ADS)

Xu, Jing; Shu, Zhanyong; Anand, Preetha; Reddy, Babu; Cermelli, Silvia; Whisenant, Thomas; King, Stephen; Bardwell, Lee; Huang, Lan; Gross, Steven

2011-03-01

Kinesin-1 is a plus-end microtubule-based molecular motor, and defects in kinesin transport are linked to diseases including neurodegeneration. Kinesin can auto-inhibit via a direct head-tail interaction, but is believed to be active otherwise. In contrast, this study uncovers a fast but reversible inhibition distinct from the canonical auto-inhibition pathway. The majority of the initially active kinesin (full-length or tail-less) loses its ability to bind/interact with microtubule, and Casein Kinase 2 (CK2) reverses this inactivation (up to 4-fold) without altering kinesin's single motor properties. Motor phosphorylation is not required for this CK2 -mediated kinesin activation. In cultured mammalian cells, knockdown of CK2 level, but not kinase activity, was sufficient to decrease the force required to stall lipid droplet transport, consistent with a reduction in the number of active motors. We propose that CK2 forms a positive regulating complex with the motor. This study provides the first direct evidence of a protein kinase positively regulating kinesin-transport, and uncovers a pathway whereby inactive cargo-bound kinesin can be activated. This work is supported by NIGMS grants GM64624 and GM079156 to SPG, GM-74830 to LH, NIH grants GM76516 and GM60366 to LB, and AHA grant 825278F to JX.

Direct-Acting Oral Anticoagulants: Practical Considerations for Emergency Medicine Physicians

PubMed Central

Peacock, W. Frank; Rafique, Zubaid; Singer, Adam J.

2016-01-01

Nonvalvular atrial fibrillation- (NVAF-) related stroke and venous thromboembolism (VTE) are cardiovascular diseases associated with significant morbidity and economic burden. The historical standard treatment of VTE has been the administration of parenteral heparinoid until oral warfarin therapy attains a therapeutic international normalized ratio. Warfarin has been the most common medication for stroke prevention in NVAF. Warfarin use is complicated by a narrow therapeutic window, unpredictable dose response, numerous food and drug interactions, and requirements for frequent monitoring. To overcome these disadvantages, direct-acting oral anticoagulants (DOACs)—dabigatran, rivaroxaban, apixaban, and edoxaban—have been developed for the prevention of stroke or systemic embolic events (SEE) in patients with NVAF and for the treatment of VTE. Advantages of DOACs include predictable pharmacokinetics, few drug-drug interactions, and low monitoring requirements. In clinical studies, DOACs are noninferior to warfarin for the prevention of NVAF-related stroke and the treatment and prevention of VTE as well as postoperative knee and hip surgery VTE prophylaxis, with decreased bleeding risks. This review addresses the practical considerations for the emergency physician in DOAC use, including dosing recommendations, laboratory monitoring, anticoagulation reversal, and cost-effectiveness. The challenges of DOACs, such as the lack of specific laboratory measurements and antidotes, are also discussed. PMID:27293895

Applications of nuclear reactor power systems to electric propulsion missions.

NASA Technical Reports Server (NTRS)

Schaupp, R. W.; Sawyer, C. D.

1971-01-01

The performance of nuclear electric propulsion systems (NEP) has been evaluated for a wide variety of missions in an attempt to establish the commonality of NEP system requirements. Emphasis was given to those requirements and system characteristics that serve as guidelines for current technology development programs. Various interactions and tradeoffs between NEP system and mission parameters are described. The results show that the most significant factors in selecting NEP system size are launch mode (direct or spiral escape) and, to a weaker extent, launch vehicle capability. Other factors such as mission, payload, and thrust time constraints, have little influence, thus allowing one NEP system to be used for many missions. The results indicated that a 100 kWe NEP would be suitable for most direct escape missions and a 250 kWe NEP system would be suitable for more demanding missions that use the spiral escape mode.

The juxtamembrane domain of the E-cadherin cytoplasmic tail contributes to its interaction with Myosin VI

PubMed Central

Mangold, Sabine; Norwood, Suzanne J.; Yap, Alpha S.; Collins, Brett M.

2012-01-01

We recently identified the atypical myosin, Myosin VI, as a component of epithelial cell-cell junctions that interacts with E-cadherin. Recombinant proteins bearing the cargo-binding domain of Myosin VI (Myo VI-CBD) or the cytoplasmic tail of E-cadherin can interact directly with one another. In this report we further investigate the molecular requirements of the interaction between Myo VI-CBD and E-cadherin combining truncation mutation analysis with in vitro binding assays. We report that a short (28 amino acid) juxtamembrane region of the cadherin cytoplasmic tail is sufficient to bind Myo VI-CBD. However, central regions of the cadherin tail adjacent to the juxtamembrane sequence also display binding activity for Myo VI-CBD. It is therefore possible that the cadherin tail bears two binding sites for Myosin VI, or an extended binding site that includes the juxtamembrane region. Nevertheless, our biochemical data highlight the capacity for the juxtamembrane region to interact with functionally-significant cytoplasmic proteins. PMID:23007415

Multi-Axis Force Sensor for Human-Robot Interaction Sensing in a Rehabilitation Robotic Device.

PubMed

Grosu, Victor; Grosu, Svetlana; Vanderborght, Bram; Lefeber, Dirk; Rodriguez-Guerrero, Carlos

2017-06-05

Human-robot interaction sensing is a compulsory feature in modern robotic systems where direct contact or close collaboration is desired. Rehabilitation and assistive robotics are fields where interaction forces are required for both safety and increased control performance of the device with a more comfortable experience for the user. In order to provide an efficient interaction feedback between the user and rehabilitation device, high performance sensing units are demanded. This work introduces a novel design of a multi-axis force sensor dedicated for measuring pelvis interaction forces in a rehabilitation exoskeleton device. The sensor is conceived such that it has different sensitivity characteristics for the three axes of interest having also movable parts in order to allow free rotations and limit crosstalk errors. Integrated sensor electronics make it easy to acquire and process data for a real-time distributed system architecture. Two of the developed sensors are integrated and tested in a complex gait rehabilitation device for safe and compliant control.

Directional Charge Separation in Isolated Organic Semiconductor Crystalline Nanowires

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

Barnes, Michael; Labastide, Joelle; Bond-Thompson, Hilary

2017-03-01

In the conventional view of organic photovoltaics (OPV), localized electronic excitations (excitons) formed in the active layer are transported by random 3D diffusion to an interface where charge separation and extraction take place. Because radiative de-excitation is usually strongly allowed in organic semiconductors, efficient charge separation requires high exciton mobility, with much of the diffusive motion ‘wasted’ in directions that don’t result in an interface encounter. Our research efforts are focused on ways to enforce a preferred directionality in energy and/or charge transport using ordered crystalline nanowires in which the intermolecular interactions that facilitate transport along, for example, the pi-stackingmore » axis, can be made several orders of magnitude stronger than those in a transverse direction. The results presented in our recent work (Nature Communications) is a first step towards realizing the goal of directional control of both energy transport and charge separation, where excitons shared between adjacent molecules dissociate exclusively along the pi-stacking direction.« less

Rotenone Activates Phagocyte NADPH Oxidase through Binding to Its Membrane Subunit gp91phox

PubMed Central

Zhou, Hui; Zhang, Feng; Chen, Shih-heng; Zhang, Dan; Wilson, Belinda; Hong, Jau-shyong; Gao, Hui-Ming

2011-01-01

Rotenone, a widely used pesticide, reproduces Parkinsonism in rodents and associates with increased risk for Parkinson’s disease. We previously reported rotenone increased superoxide production through stimulating microglial phagocyte NADPH oxidase (PHOX). The present study identified a novel mechanism by which rotenone activates PHOX. Ligand-binding assay revealed that rotenone directly bound to membrane gp91phox, the catalytic subunit of PHOX; such binding was inhibited by diphenyleneiodonium, a PHOX inhibitor with a binding site on gp91phox. Functional studies showed both membrane and cytosolic subunits were required for rotenone-induced superoxide production in cell-free systems, intact phagocytes, and COS7 cells transfected with membrane subunits (gp91phox/p22phox) and cytosolic subunits (p67phox and p47phox). Rotenone-elicited extracellular superoxide release in p47phox-deficient macrophages suggested rotenone enabled to activate PHOX through a p47phox-independent mechanism. Increased membrane translocation of p67phox, elevated binding of p67phox to rotenone-treated membrane fractions, and co-immunoprecipitation of p67phox and gp91phox in rotenone-treated wild-type and p47phox-deficient macrophages indicated p67phox played a critical role in rotenone-induced PHOX activation via its direct interaction with gp91phox. Rac1, a Rho-like small GTPase, enhanced p67phox-gp91phox interaction; Rac1 inhibition decreased rotenone-elicited superoxide release. In conclusion, rotenone directly interacted with gp91phox; such an interaction triggered membrane translocation of p67phox, leading to PHOX activation and superoxide production. PMID:22094225

Peptide library synthesis on spectrally encoded beads for multiplexed protein/peptide bioassays

NASA Astrophysics Data System (ADS)

Nguyen, Huy Q.; Brower, Kara; Harink, Björn; Baxter, Brian; Thorn, Kurt S.; Fordyce, Polly M.

2017-02-01

Protein-peptide interactions are essential for cellular responses. Despite their importance, these interactions remain largely uncharacterized due to experimental challenges associated with their measurement. Current techniques (e.g. surface plasmon resonance, fluorescence polarization, and isothermal calorimetry) either require large amounts of purified material or direct fluorescent labeling, making high-throughput measurements laborious and expensive. In this report, we present a new technology for measuring antibody-peptide interactions in vitro that leverages spectrally encoded beads for biological multiplexing. Specific peptide sequences are synthesized directly on encoded beads with a 1:1 relationship between peptide sequence and embedded code, thereby making it possible to track many peptide sequences throughout the course of an experiment within a single small volume. We demonstrate the potential of these bead-bound peptide libraries by: (1) creating a set of 46 peptides composed of 3 commonly used epitope tags (myc, FLAG, and HA) and single amino-acid scanning mutants; (2) incubating with a mixture of fluorescently-labeled antimyc, anti-FLAG, and anti-HA antibodies; and (3) imaging these bead-bound libraries to simultaneously identify the embedded spectral code (and thus the sequence of the associated peptide) and quantify the amount of each antibody bound. To our knowledge, these data demonstrate the first customized peptide library synthesized directly on spectrally encoded beads. While the implementation of the technology provided here is a high-affinity antibody/protein interaction with a small code space, we believe this platform can be broadly applicable to any range of peptide screening applications, with the capability to multiplex into libraries of hundreds to thousands of peptides in a single assay.

Direct Interaction of CaVβ with Actin Up-regulates L-type Calcium Currents in HL-1 Cardiomyocytes*

PubMed Central

Stölting, Gabriel; de Oliveira, Regina Campos; Guzman, Raul E.; Miranda-Laferte, Erick; Conrad, Rachel; Jordan, Nadine; Schmidt, Silke; Hendriks, Johnny; Gensch, Thomas; Hidalgo, Patricia

2015-01-01

Expression of the β-subunit (CaVβ) is required for normal function of cardiac L-type calcium channels, and its up-regulation is associated with heart failure. CaVβ binds to the α1 pore-forming subunit of L-type channels and augments calcium current density by facilitating channel opening and increasing the number of channels in the plasma membrane, by a poorly understood mechanism. Actin, a key component of the intracellular trafficking machinery, interacts with Src homology 3 domains in different proteins. Although CaVβ encompasses a highly conserved Src homology 3 domain, association with actin has not yet been explored. Here, using co-sedimentation assays and FRET experiments, we uncover a direct interaction between CaVβ and actin filaments. Consistently, single-molecule localization analysis reveals streaklike structures composed by CaVβ2 that distribute over several micrometers along actin filaments in HL-1 cardiomyocytes. Overexpression of CaVβ2-N3 in HL-1 cells induces an increase in L-type current without altering voltage-dependent activation, thus reflecting an increased number of channels in the plasma membrane. CaVβ mediated L-type up-regulation, and CaVβ-actin association is prevented by disruption of the actin cytoskeleton with cytochalasin D. Our study reveals for the first time an interacting partner of CaVβ that is directly involved in vesicular trafficking. We propose a model in which CaVβ promotes anterograde trafficking of the L-type channels by anchoring them to actin filaments in their itinerary to the plasma membrane. PMID:25533460

Deep-Subwavelength Resolving and Manipulating of Hidden Chirality in Achiral Nanostructures.

PubMed

Zu, Shuai; Han, Tianyang; Jiang, Meiling; Lin, Feng; Zhu, Xing; Fang, Zheyu

2018-04-24

The chiral state of light plays a vital role in light-matter interactions and the consequent revolution of nanophotonic devices and advanced modern chiroptics. As the light-matter interaction goes into the nano- and quantum world, numerous chiroptical technologies and quantum devices require precise knowledge of chiral electromagnetic modes and chiral radiative local density of states (LDOS) distributions in detail, which directly determine the chiral light-matter interaction for applications such as chiral light detection and emission. With classical optical techniques failing to directly measure the chiral radiative LDOS, deep-subwavelength imaging and control of circular polarization (CP) light associated phenomena are introduced into the agenda. Here, we simultaneously reveal the hidden chiral electromagnetic mode and acquire its chiral radiative LDOS distribution of a single symmetric nanostructure at the deep-subwavelength scale by using CP-resolved cathodoluminescence (CL) microscopy. The chirality of the symmetric nanostructure under normally incident light excitation, resulting from the interference between the symmetric and antisymmetric modes of the V-shaped nanoantenna, is hidden in the near field with a giant chiral distribution (∼99%) at the arm-ends, which enables the circularly polarized CL emission from the radiative LDOS hot-spot and the following active helicity control at the deep-subwavelength scale. The proposed V-shaped nanostructure as a functional unit is further applied to the helicity-dependent binary encoding and the two-dimensional display applications. The proposed physical principle and experimental configuration can promote the future chiral characterization and manipulation at the deep-subwavelength scale and provide direct guidelines for the optimization of chiral light-matter interactions for future quantum studies.

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

Directional Collective Cell Migration Emerges as a Property of Cell Interactions

PubMed Central

Woods, Mae L.; Carmona-Fontaine, Carlos; Barnes, Chris P.; Couzin, Iain D.; Mayor, Roberto; Page, Karen M.

2014-01-01

Collective cell migration is a fundamental process, occurring during embryogenesis and cancer metastasis. Neural crest cells exhibit such coordinated migration, where aberrant motion can lead to fatality or dysfunction of the embryo. Migration involves at least two complementary mechanisms: contact inhibition of locomotion (a repulsive interaction corresponding to a directional change of migration upon contact with a reciprocating cell), and co-attraction (a mutual chemoattraction mechanism). Here, we develop and employ a parameterized discrete element model of neural crest cells, to investigate how these mechanisms contribute to long-range directional migration during development. Motion is characterized using a coherence parameter and the time taken to reach, collectively, a target location. The simulated cell group is shown to switch from a diffusive to a persistent state as the response-rate to co-attraction is increased. Furthermore, the model predicts that when co-attraction is inhibited, neural crest cells can migrate into restrictive regions. Indeed, inhibition of co-attraction in vivo and in vitro leads to cell invasion into restrictive areas, confirming the prediction of the model. This suggests that the interplay between the complementary mechanisms may contribute to guidance of the neural crest. We conclude that directional migration is a system property and does not require action of external chemoattractants. PMID:25181349

Identification of Direct Protein Targets of Small Molecules

PubMed Central

2010-01-01

Small-molecule target identification is a vital and daunting task for the chemical biology community as well as for researchers interested in applying the power of chemical genetics to impact biology and medicine. To overcome this “target ID” bottleneck, new technologies are being developed that analyze protein–drug interactions, such as drug affinity responsive target stability (DARTS), which aims to discover the direct binding targets (and off targets) of small molecules on a proteome scale without requiring chemical modification of the compound. Here, we review the DARTS method, discuss why it works, and provide new perspectives for future development in this area. PMID:21077692

Gaussian Processes for Data-Efficient Learning in Robotics and Control.

PubMed

Deisenroth, Marc Peter; Fox, Dieter; Rasmussen, Carl Edward

2015-02-01

Autonomous learning has been a promising direction in control and robotics for more than a decade since data-driven learning allows to reduce the amount of engineering knowledge, which is otherwise required. However, autonomous reinforcement learning (RL) approaches typically require many interactions with the system to learn controllers, which is a practical limitation in real systems, such as robots, where many interactions can be impractical and time consuming. To address this problem, current learning approaches typically require task-specific knowledge in form of expert demonstrations, realistic simulators, pre-shaped policies, or specific knowledge about the underlying dynamics. In this paper, we follow a different approach and speed up learning by extracting more information from data. In particular, we learn a probabilistic, non-parametric Gaussian process transition model of the system. By explicitly incorporating model uncertainty into long-term planning and controller learning our approach reduces the effects of model errors, a key problem in model-based learning. Compared to state-of-the art RL our model-based policy search method achieves an unprecedented speed of learning. We demonstrate its applicability to autonomous learning in real robot and control tasks.

Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis.

PubMed

Pham, Phuong; Seitz, Erica M; Saveliev, Sergei; Shen, Xuan; Woodgate, Roger; Cox, Michael M; Goodman, Myron F

2002-08-20

SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD'(2)C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are "nonfilamentous". That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3' primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3' filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis.

Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis

PubMed Central

Pham, Phuong; Seitz, Erica M.; Saveliev, Sergei; Shen, Xuan; Woodgate, Roger; Cox, Michael M.; Goodman, Myron F.

2002-01-01

SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD′2C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are “nonfilamentous”. That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3′ primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3′ filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis. PMID:12177433

Dual chromatin recognition by the histone deacetylase complex HCHC is required for proper DNA methylation in Neurospora crassa

PubMed Central

Honda, Shinji; Bicocca, Vincent T.; Gessaman, Jordan D.; Rountree, Michael R.; Yokoyama, Ayumi; Yu, Eun Y.; Selker, Jeanne M. L.; Selker, Eric U.

2016-01-01

DNA methylation, heterochromatin protein 1 (HP1), histone H3 lysine 9 (H3K9) methylation, histone deacetylation, and highly repeated sequences are prototypical heterochromatic features, but their interrelationships are not fully understood. Prior work showed that H3K9 methylation directs DNA methylation and histone deacetylation via HP1 in Neurospora crassa and that the histone deacetylase complex HCHC is required for proper DNA methylation. The complex consists of the chromodomain proteins HP1 and chromodomain protein 2 (CDP-2), the histone deacetylase HDA-1, and the AT-hook motif protein CDP-2/HDA-1–associated protein (CHAP). We show that the complex is required for proper chromosome segregation, dissect its function, and characterize interactions among its components. Our analyses revealed the existence of an HP1-based DNA methylation pathway independent of its chromodomain. The pathway partially depends on CHAP but not on the CDP-2 chromodomain. CDP-2 serves as a bridge between the recognition of H3K9 trimethylation (H3K9me3) by HP1 and the histone deacetylase activity of HDA-1. CHAP is also critical for HDA-1 localization to heterochromatin. Specifically, the CHAP zinc finger interacts directly with the HDA-1 argonaute-binding protein 2 (Arb2) domain, and the CHAP AT-hook motifs recognize heterochromatic regions by binding to AT-rich DNA. Our data shed light on the interrelationships among the prototypical heterochromatic features and support a model in which dual recognition by the HP1 chromodomain and the CHAP AT-hooks are required for proper heterochromatin formation. PMID:27681634

Calcium Regulates Molecular Interactions of Otoferlin with Soluble NSF Attachment Protein Receptor (SNARE) Proteins Required for Hair Cell Exocytosis*

PubMed Central

Ramakrishnan, Neeliyath A.; Drescher, Marian J.; Morley, Barbara J.; Kelley, Philip M.; Drescher, Dennis G.

2014-01-01

Mutations in otoferlin, a C2 domain-containing ferlin family protein, cause non-syndromic hearing loss in humans (DFNB9 deafness). Furthermore, transmitter secretion of cochlear inner hair cells is compromised in mice lacking otoferlin. In the present study, we show that the C2F domain of otoferlin directly binds calcium (KD = 267 μm) with diminished binding in a pachanga (D1767G) C2F mouse mutation. Calcium was found to differentially regulate binding of otoferlin C2 domains to target SNARE (t-SNARE) proteins and phospholipids. C2D–F domains interact with the syntaxin-1 t-SNARE motif with maximum binding within the range of 20–50 μm Ca2+. At 20 μm Ca2+, the dissociation rate was substantially lower, indicating increased binding (KD = ∼10−9) compared with 0 μm Ca2+ (KD = ∼10−8), suggesting a calcium-mediated stabilization of the C2 domain·t-SNARE complex. C2A and C2B interactions with t-SNAREs were insensitive to calcium. The C2F domain directly binds the t-SNARE SNAP-25 maximally at 100 μm and with reduction at 0 μm Ca2+, a pattern repeated for C2F domain interactions with phosphatidylinositol 4,5-bisphosphate. In contrast, C2F did not bind the vesicle SNARE protein synaptobrevin-1 (VAMP-1). Moreover, an antibody targeting otoferlin immunoprecipitated syntaxin-1 and SNAP-25 but not synaptobrevin-1. As opposed to an increase in binding with increased calcium, interactions between otoferlin C2F domain and intramolecular C2 domains occurred in the absence of calcium, consistent with intra-C2 domain interactions forming a “closed” tertiary structure at low calcium that “opens” as calcium increases. These results suggest a direct role for otoferlin in exocytosis and modulation of calcium-dependent membrane fusion. PMID:24478316

Comparing species interaction networks along environmental gradients.

PubMed

Pellissier, Loïc; Albouy, Camille; Bascompte, Jordi; Farwig, Nina; Graham, Catherine; Loreau, Michel; Maglianesi, Maria Alejandra; Melián, Carlos J; Pitteloud, Camille; Roslin, Tomas; Rohr, Rudolf; Saavedra, Serguei; Thuiller, Wilfried; Woodward, Guy; Zimmermann, Niklaus E; Gravel, Dominique

2018-05-01

Knowledge of species composition and their interactions, in the form of interaction networks, is required to understand processes shaping their distribution over time and space. As such, comparing ecological networks along environmental gradients represents a promising new research avenue to understand the organization of life. Variation in the position and intensity of links within networks along environmental gradients may be driven by turnover in species composition, by variation in species abundances and by abiotic influences on species interactions. While investigating changes in species composition has a long tradition, so far only a limited number of studies have examined changes in species interactions between networks, often with differing approaches. Here, we review studies investigating variation in network structures along environmental gradients, highlighting how methodological decisions about standardization can influence their conclusions. Due to their complexity, variation among ecological networks is frequently studied using properties that summarize the distribution or topology of interactions such as number of links, connectance, or modularity. These properties can either be compared directly or using a procedure of standardization. While measures of network structure can be directly related to changes along environmental gradients, standardization is frequently used to facilitate interpretation of variation in network properties by controlling for some co-variables, or via null models. Null models allow comparing the deviation of empirical networks from random expectations and are expected to provide a more mechanistic understanding of the factors shaping ecological networks when they are coupled with functional traits. As an illustration, we compare approaches to quantify the role of trait matching in driving the structure of plant-hummingbird mutualistic networks, i.e. a direct comparison, standardized by null models and hypothesis-based metaweb. Overall, our analysis warns against a comparison of studies that rely on distinct forms of standardization, as they are likely to highlight different signals. Fostering a better understanding of the analytical tools available and the signal they detect will help produce deeper insights into how and why ecological networks vary along environmental gradients. © 2017 Cambridge Philosophical Society.

Independent signaling by Drosophila insulin receptor for axon guidance and growth.

PubMed

Li, Caroline R; Guo, Dongyu; Pick, Leslie

2013-01-01

The Drosophila insulin receptor (DInR) regulates a diverse array of biological processes including growth, axon guidance, and sugar homeostasis. Growth regulation by DInR is mediated by Chico, the Drosophila homolog of vertebrate insulin receptor substrate proteins IRS1-4. In contrast, DInR regulation of photoreceptor axon guidance in the developing visual system is mediated by the SH2-SH3 domain adaptor protein Dreadlocks (Dock). In vitro studies by others identified five NPXY motifs, one in the juxtamembrane region and four in the signaling C-terminal tail (C-tail), important for interaction with Chico. Here we used yeast two-hybrid assays to identify regions in the DInR C-tail that interact with Dock. These Dock binding sites were in separate portions of the C-tail from the previously identified Chico binding sites. To test whether these sites are required for growth or axon guidance in whole animals, a panel of DInR proteins, in which the putative Chico and Dock interaction sites had been mutated individually or in combination, were tested for their ability to rescue viability, growth and axon guidance defects of dinr mutant flies. Sites required for viability were identified. Unexpectedly, mutation of both putative Dock binding sites, either individually or in combination, did not lead to defects in photoreceptor axon guidance. Thus, either sites also required for viability are necessary for DInR function in axon guidance and/or there is redundancy built into the DInR/Dock interaction such that Dock is able to interact with multiple regions of DInR. We also found that simultaneous mutation of all five NPXY motifs implicated in Chico interaction drastically decreased growth in both male and female adult flies. These animals resembled chico mutants, supporting the notion that DInR interacts directly with Chico in vivo to control body size. Mutation of these five NPXY motifs did not affect photoreceptor axon guidance, segregating the roles of DInR in the processes of growth and axon guidance.

Unlocking data: federated identity with LSDMA and dCache

NASA Astrophysics Data System (ADS)

Millar, AP; Behrmann, G.; Bernardt, C.; Fuhrmann, P.; Hardt, M.; Hayrapetyan, A.; Litvintsev, D.; Mkrtchyan, T.; Rossi, A.; Schwank, K.

2015-12-01

X.509, the dominant identity system from grid computing, has proved unpopular for many user communities. More popular alternatives generally assume the user is interacting via their web-browser. Such alternatives allow a user to authenticate with many services with the same credentials (user-name and password). They also allow users from different organisations form collaborations quickly and simply. Scientists generally require that their custom analysis software has direct access to the data. Such direct access is not currently supported by alternatives to X.509, as they require the use of a web-browser. Various approaches to solve this issue are being investigated as part of the Large Scale Data Management and Analysis (LSDMA) project, a German funded national R&D project. These involve dynamic credential translation (creating an X.509 credential) to allow backwards compatibility in addition to direct SAML- and OpenID Connect-based authentication. We present a summary of the current state of art and the current status of the federated identity work funded by the LSDMA project along with the future road map.

Human DHEA sulfation requires direct interaction between PAPS synthase 2 and DHEA sulfotransferase SULT2A1.

PubMed

Mueller, Jonathan W; Idkowiak, Jan; Gesteira, Tarsis F; Vallet, Cecilia; Hardman, Rebecca; van den Boom, Johannes; Dhir, Vivek; Knauer, Shirley K; Rosta, Edina; Arlt, Wiebke

2018-06-22

The high-energy sulfate donor 3'-phosphoadenosine-5'-phosphosulfate (PAPS), generated by human PAPS synthase isoforms PAPSS1 and PAPSS2, is required for all human sulfation pathways. Sulfotransferase SULT2A1 uses PAPS for sulfation of the androgen precursor dehydroepiandrosterone (DHEA), thereby reducing downstream activation of DHEA to active androgens. Human PAPSS2 mutations manifest with undetectable DHEA sulfate, androgen excess, and metabolic disease, suggesting that ubiquitous PAPSS1 cannot compensate for deficient PAPSS2 in supporting DHEA sulfation. In knockdown studies in human adrenocortical NCI-H295R1 cells, we found that PAPSS2, but not PAPSS1, is required for efficient DHEA sulfation. Specific APS kinase activity, the rate-limiting step in PAPS biosynthesis, did not differ between PAPSS1 and PAPSS2. Co-expression of cytoplasmic SULT2A1 with a cytoplasmic PAPSS2 variant supported DHEA sulfation more efficiently than co-expression with nuclear PAPSS2 or nuclear/cytosolic PAPSS1. Proximity ligation assays revealed protein-protein interactions between SULT2A1 and PAPSS2 and, to a lesser extent, PAPSS1. Molecular docking studies showed a putative binding site for SULT2A1 within the PAPSS2 APS kinase domain. Energy-dependent scoring of docking solutions identified the interaction as specific for the PAPSS2 and SULT2A1 isoforms. These findings elucidate the mechanistic basis for the selective requirement for PAPSS2 in human DHEA sulfation. © 2018 Mueller et al.

Direct evidence for dominant bond-directional interactions in a honeycomb lattice iridate Na 2IrO 3

DOE PAGES

Hwan Chun, Sae; Kim, Jong-Woo; Kim, Jungho; ...

2015-05-11

We show that heisenberg interactions are ubiquitous in magnetic materials and play a central role in modelling and designing quantum magnets. Bond-directional interactions offer a novel alternative to Heisenberg exchange and provide the building blocks of the Kitaev model, which has a quantum spin liquid as its exact ground state. Honeycomb iridates, A 2IrO 3 (A = Na, Li), offer potential realizations of the Kitaev magnetic exchange coupling, and their reported magnetic behaviour may be interpreted within the Kitaev framework. However, the extent of their relevance to the Kitaev model remains unclear, as evidence for bond-directional interactions has so farmore » been indirect. Here we present direct evidence for dominant bond-directional interactions in antiferromagnetic Na 2IrO 3 and show that they lead to strong magnetic frustration. Diffuse magnetic X-ray scattering reveals broken spin-rotational symmetry even above the Néel temperature, with the three spin components exhibiting short-range correlations along distinct crystallographic directions. Lastly, this spin- and real-space entanglement directly uncovers the bond-directional nature of these interactions, thus providing a direct connection between honeycomb iridates and Kitaev physics.« less

Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors.

PubMed

Wallqvist, Anders; Memišević, Vesna; Zavaljevski, Nela; Pieper, Rembert; Rajagopala, Seesandra V; Kwon, Keehwan; Yu, Chenggang; Hoover, Timothy A; Reifman, Jaques

2015-12-29

Francisella tularensis is a select bio-threat agent and one of the most virulent intracellular pathogens known, requiring just a few organisms to establish an infection. Although several virulence factors are known, we lack an understanding of virulence factors that act through host-pathogen protein interactions to promote infection. To address these issues in the highly infectious F. tularensis subsp. tularensis Schu S4 strain, we deployed a combined in silico, in vitro, and in vivo analysis to identify virulence factors and their interactions with host proteins to characterize bacterial infection mechanisms. We initially used comparative genomics and literature to identify and select a set of 49 putative and known virulence factors for analysis. Each protein was then subjected to proteome-scale yeast two-hybrid (Y2H) screens with human and murine cDNA libraries to identify potential host-pathogen protein-protein interactions. Based on the bacterial protein interaction profile with both hosts, we selected seven novel putative virulence factors for mutant construction and animal validation experiments. We were able to create five transposon insertion mutants and used them in an intranasal BALB/c mouse challenge model to establish 50 % lethal dose estimates. Three of these, ΔFTT0482c, ΔFTT1538c, and ΔFTT1597, showed attenuation in lethality and can thus be considered novel F. tularensis virulence factors. The analysis of the accompanying Y2H data identified intracellular protein trafficking between the early endosome to the late endosome as an important component in virulence attenuation for these virulence factors. Furthermore, we also used the Y2H data to investigate host protein binding of two known virulence factors, showing that direct protein binding was a component in the modulation of the inflammatory response via activation of mitogen-activated protein kinases and in the oxidative stress response. Direct interactions with specific host proteins and the ability to influence interactions among host proteins are important components for F. tularensis to avoid host-cell defense mechanisms and successfully establish an infection. Although direct host-pathogen protein-protein binding is only one aspect of Francisella virulence, it is a critical component in directly manipulating and interfering with cellular processes in the host cell.

Direct Ubiquitin Independent Recognition and Degradation of a Folded Protein by the Eukaryotic Proteasomes-Origin of Intrinsic Degradation Signals

PubMed Central

Singh Gautam, Amit Kumar; Balakrishnan, Satish; Venkatraman, Prasanna

2012-01-01

Eukaryotic 26S proteasomes are structurally organized to recognize, unfold and degrade globular proteins. However, all existing model substrates of the 26S proteasome in addition to ubiquitin or adaptor proteins require unstructured regions in the form of fusion tags for efficient degradation. We report for the first time that purified 26S proteasome can directly recognize and degrade apomyoglobin, a globular protein, in the absence of ubiquitin, extrinsic degradation tags or adaptor proteins. Despite a high affinity interaction, absence of a ligand and presence of only helices/loops that follow the degradation signal, apomyoglobin is degraded slowly by the proteasome. A short floppy F-helix exposed upon ligand removal and in conformational equilibrium with a disordered structure is mandatory for recognition and initiation of degradation. Holomyoglobin, in which the helix is buried, is neither recognized nor degraded. Exposure of the floppy F-helix seems to sensitize the proteasome and primes the substrate for degradation. Using peptide panning and competition experiments we speculate that initial encounters through the floppy helix and additional strong interactions with N-terminal helices anchors apomyoglobin to the proteasome. Stabilizing helical structure in the floppy F-helix slows down degradation. Destabilization of adjacent helices accelerates degradation. Unfolding seems to follow the mechanism of helix unraveling rather than global unfolding. Our findings while confirming the requirement for unstructured regions in degradation offers the following new insights: a) origin and identification of an intrinsic degradation signal in the substrate, b) identification of sequences in the native substrate that are likely to be responsible for direct interactions with the proteasome, and c) identification of critical rate limiting steps like exposure of the intrinsic degron and destabilization of an unfolding intermediate that are presumably catalyzed by the ATPases. Apomyoglobin emerges as a new model substrate to further explore the role of ATPases and protein structure in proteasomal degradation PMID:22506054

Phosphorylation regulates the Star-PAP-PIPKIα interaction and directs specificity toward mRNA targets

PubMed Central

Mohan, Nimmy; AP, Sudheesh; Francis, Nimmy; Anderson, Richard; Laishram, Rakesh S.

2015-01-01

Star-PAP is a nuclear non-canonical poly(A) polymerase (PAP) that shows specificity toward mRNA targets. Star-PAP activity is stimulated by lipid messenger phosphatidyl inositol 4,5 bisphoshate (PI4,5P2) and is regulated by the associated Type I phosphatidylinositol-4-phosphate 5-kinase that synthesizes PI4,5P2 as well as protein kinases. These associated kinases act as coactivators of Star-PAP that regulates its activity and specificity toward mRNAs, yet the mechanism of control of these interactions are not defined. We identified a phosphorylated residue (serine 6, S6) on Star-PAP in the zinc finger region, the domain required for PIPKIα interaction. We show that S6 is phosphorylated by CKIα within the nucleus which is required for Star-PAP nuclear retention and interaction with PIPKIα. Unlike the CKIα mediated phosphorylation at the catalytic domain, Star-PAP S6 phosphorylation is insensitive to oxidative stress suggesting a signal mediated regulation of CKIα activity. S6 phosphorylation together with coactivator PIPKIα controlled select subset of Star-PAP target messages by regulating Star-PAP-mRNA association. Our results establish a novel role for phosphorylation in determining Star-PAP target mRNA specificity and regulation of 3′-end processing. PMID:26138484

Direct Interaction of Jak1 and v-Abl Is Required for v-Abl-Induced Activation of STATs and Proliferation

PubMed Central

Danial, Nika N.; Losman, Julie A.; Lu, Tianhong; Yip, Natalie; Krishnan, Kartik; Krolewski, John; Goff, Stephen P.; Wang, Jean Y. J.; Rothman, Paul B.

1998-01-01

In Abelson murine leukemia virus (A-MuLV)-transformed cells, members of the Janus kinase (Jak) family of non-receptor tyrosine kinases and the signal transducers and activators of transcription (STAT) family of signaling proteins are constitutively activated. In these cells, the v-Abl oncoprotein and the Jak proteins physically associate. To define the molecular mechanism of constitutive Jak-STAT signaling in these cells, the functional significance of the v-Abl–Jak association was examined. Mapping the Jak1 interaction domain in v-Abl demonstrates that amino acids 858 to 1080 within the carboxyl-terminal region of v-Abl bind Jak1 through a direct interaction. A mutant of v-Abl lacking this region exhibits a significant defect in Jak1 binding in vivo, fails to activate Jak1 and STAT proteins, and does not support either the proliferation or the survival of BAF/3 cells in the absence of cytokine. Cells expressing this v-Abl mutant show extended latency and decreased frequency in generating tumors in nude mice. In addition, inducible expression of a kinase-inactive mutant of Jak1 protein inhibits the ability of v-Abl to activate STATs and to induce cytokine-independent proliferation, indicating that an active Jak1 is required for these v-Abl-induced signaling pathways in vivo. We propose that Jak1 is a mediator of v-Abl-induced STAT activation and v-Abl induced proliferation in BAF/3 cells, and may be important for efficient transformation of immature B cells by the v-abl oncogene. PMID:9774693

Tangible Landscape: Cognitively Grasping the Flow of Water

NASA Astrophysics Data System (ADS)

Harmon, B. A.; Petrasova, A.; Petras, V.; Mitasova, H.; Meentemeyer, R. K.

2016-06-01

Complex spatial forms like topography can be challenging to understand, much less intentionally shape, given the heavy cognitive load of visualizing and manipulating 3D form. Spatiotemporal processes like the flow of water over a landscape are even more challenging to understand and intentionally direct as they are dependent upon their context and require the simulation of forces like gravity and momentum. This cognitive work can be offloaded onto computers through 3D geospatial modeling, analysis, and simulation. Interacting with computers, however, can also be challenging, often requiring training and highly abstract thinking. Tangible computing - an emerging paradigm of human-computer interaction in which data is physically manifested so that users can feel it and directly manipulate it - aims to offload this added cognitive work onto the body. We have designed Tangible Landscape, a tangible interface powered by an open source geographic information system (GRASS GIS), so that users can naturally shape topography and interact with simulated processes with their hands in order to make observations, generate and test hypotheses, and make inferences about scientific phenomena in a rapid, iterative process. Conceptually Tangible Landscape couples a malleable physical model with a digital model of a landscape through a continuous cycle of 3D scanning, geospatial modeling, and projection. We ran a flow modeling experiment to test whether tangible interfaces like this can effectively enhance spatial performance by offloading cognitive processes onto computers and our bodies. We used hydrological simulations and statistics to quantitatively assess spatial performance. We found that Tangible Landscape enhanced 3D spatial performance and helped users understand water flow.

Cooperative control theory and integrated flight and propulsion control

NASA Technical Reports Server (NTRS)

Schmidt, David K.; Schierman, John D.

1995-01-01

The major contribution of this research was the exposition of the fact that airframe and engine interactions could be present, and their effects could include loss of stability and performance of the control systems. Also, the significance of two directional, as opposed to one-directional, coupling was identified and explained. A multivariable stability and performance analysis methodology was developed, and applied to several candidate aircraft configurations. In these example evaluations, the significance of these interactions was underscored. Also exposed was the fact that with interactions present along with some integrated control approaches, the engine command/limiting logic (which represents an important nonlinear component of the engine control system) can impact closed-loop airframe/engine system stability. Finally, a brief investigation of control-law synthesis techniques appropriate for the class of systems was pursued, and it was determined that multivariable techniques, including model-following formulations of LQG and/or H infinity methods, showed promise. However, for practical reasons, decentralized control architectures are preferred, which is an architecture incompatible with these synthesis methods. The major contributions of the second phase of the grant was the development of conditions under which no decentralized controller could achieve closed loop system requirements on stability and/or performance. Sought were conditions that depended only on properties of the plant and the requirement, and independent of any particular control law or synthesis approach. Therefore, they could be applied a priori, before synthesis of a candidate control law. Under this grant, such conditions were found regarding stability, and encouraging initial results were obtained regarding performance.

Bi-directional exchange of membrane components occurs during co-culture of mesenchymal stem cells and nucleus pulposus cells.

PubMed

Strassburg, Sandra; Hodson, Nigel W; Hill, Patrick I; Richardson, Stephen M; Hoyland, Judith A

2012-01-01

Mesenchymal stem cell (MSC)-based therapies have been proposed as novel treatments for intervertebral disc (IVD) degeneration. We have previously demonstrated that when MSCs are co-cultured with nucleus pulposus (NP) cells with direct cell-cell contact, they differentiate along the NP lineage and simultaneously stimulate the degenerate NP cell population to regain a normal (non-degenerate) phenotype, an effect which requires cell-cell communication. However, the mechanisms by which NP cells and MSCs interact in this system are currently unclear. Thus, in this study we investigated a range of potential mechanisms for exchange of cellular components or information that may direct these changes, including cell fusion, gap-junctional communication and exchange of membrane components by direct transfer or via microvesicle formation. Flow cytometry of fluorescently labeled MSCs and NP cells revealed evidence of some cell fusion and formation of gapjunctions, although at the three timepoints studied these phenomena were detectable only in a small proportion of cells. While these mechanisms may play a role in cell-cell communication, the data suggests they are not the predominant mechanism of interaction. However, flow cytometry of fluorescently dual-labeled cells showed that extensive bi-directional transfer of membrane components is operational during direct co-culture of MSCs and NP cells. Furthermore, there was also evidence for secretion and internalization of membrane-bound microvesicles by both cell types. Thus, this study highlights bi-directional intercellular transfer of membrane components as a possible mechanism of cellular communication between MSC and NP cells.

Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression

PubMed Central

Danno, Hiroki; Michiue, Tatsuo; Hitachi, Keisuke; Yukita, Akira; Ishiura, Shoichi; Asashima, Makoto

2008-01-01

The neural-related genes Sox2, Pax6, Otx2, and Rax have been associated with severe ocular malformations such as anophthalmia and microphthalmia, but it remains unclear as to how these genes are linked functionally. We analyzed the upstream signaling of Xenopus Rax (also known as Rx1) and identified the Otx2 and Sox2 proteins as direct upstream regulators of Rax. We revealed that endogenous Otx2 and Sox2 proteins bound to the conserved noncoding sequence (CNS1) located ≈2 kb upstream of the Rax promoter. This sequence is conserved among vertebrates and is required for potent transcriptional activity. Reporter assays showed that Otx2 and Sox2 synergistically activated transcription via CNS1. Furthermore, the Otx2 and Sox2 proteins physically interacted with each other, and this interaction was affected by the Sox2-missense mutations identified in these ocular disorders. These results demonstrate that the direct interaction and interdependence between the Otx2 and Sox2 proteins coordinate Rax expression in eye development, providing molecular linkages among the genes responsible for ocular malformation. PMID:18385377

Direct TFIIA-TFIID Protein Contacts Drive Budding Yeast Ribosomal Protein Gene Transcription*

PubMed Central

Layer, Justin H.; Weil, P. Anthony

2013-01-01

We have previously shown that yeast TFIID provides coactivator function on the promoters of ribosomal protein-encoding genes (RPGs) by making direct contact with the transactivator repressor activator protein 1 (Rap1). Further, our structural studies of assemblies generated with purified Rap1, TFIID, and TFIIA on RPG enhancer-promoter DNA indicate that Rap1-TFIID interaction induces dramatic conformational rearrangements of enhancer-promoter DNA and TFIID-bound TFIIA. These data indicate a previously unknown yet critical role for yeast TFIIA in the integration of activator-TFIID contacts with promoter conformation and downstream preinitiation complex formation and/or function. Here we describe the use of systematic mutagenesis to define how specific TFIIA contacts contribute to these processes. We have verified that TFIIA is required for RPG transcription in vivo and in vitro, consistent with the existence of a critical Rap1-TFIIA-TFIID interaction network. We also identified essential points of contact for TFIIA and Rap1 within the Rap1 binding domain of the Taf4 subunit of TFIID. These data suggest a mechanism for how interactions between TFIID, TFIIA, and Rap1 contribute to the high rate of transcription initiation seen on RPGs in vivo. PMID:23814059

A CAF-1–PCNA-Mediated Chromatin Assembly Pathway Triggered by Sensing DNA Damage

PubMed Central

Moggs, Jonathan G.; Grandi, Paola; Quivy, Jean-Pierre; Jónsson, Zophonías O.; Hübscher, Ulrich; Becker, Peter B.; Almouzni, Geneviève

2000-01-01

Sensing DNA damage is crucial for the maintenance of genomic integrity and cell cycle progression. The participation of chromatin in these events is becoming of increasing interest. We show that the presence of single-strand breaks and gaps, formed either directly or during DNA damage processing, can trigger the propagation of nucleosomal arrays. This nucleosome assembly pathway involves the histone chaperone chromatin assembly factor 1 (CAF-1). The largest subunit (p150) of this factor interacts directly with proliferating cell nuclear antigen (PCNA), and critical regions for this interaction on both proteins have been mapped. To isolate proteins specifically recruited during DNA repair, damaged DNA linked to magnetic beads was used. The binding of both PCNA and CAF-1 to this damaged DNA was dependent on the number of DNA lesions and required ATP. Chromatin assembly linked to the repair of single-strand breaks was disrupted by depletion of PCNA from a cell-free system. This defect was rescued by complementation with recombinant PCNA, arguing for role of PCNA in mediating chromatin assembly linked to DNA repair. We discuss the importance of the PCNA–CAF-1 interaction in the context of DNA damage processing and checkpoint control. PMID:10648606

The relative importance of rapid evolution for plant-microbe interactions depends on ecological context.

PubMed

Terhorst, Casey P; Lennon, Jay T; Lau, Jennifer A

2014-06-22

Evolution can occur on ecological time-scales, affecting community and ecosystem processes. However, the importance of evolutionary change relative to ecological processes remains largely unknown. Here, we analyse data from a long-term experiment in which we allowed plant populations to evolve for three generations in dry or wet soils and used a reciprocal transplant to compare the ecological effect of drought and the effect of plant evolutionary responses to drought on soil microbial communities and nutrient availability. Plants that evolved under drought tended to support higher bacterial and fungal richness, and increased fungal : bacterial ratios in the soil. Overall, the magnitudes of ecological and evolutionary effects on microbial communities were similar; however, the strength and direction of these effects depended on the context in which they were measured. For example, plants that evolved in dry environments increased bacterial abundance in dry contemporary environments, but decreased bacterial abundance in wet contemporary environments. Our results suggest that interactions between recent evolutionary history and ecological context affect both the direction and magnitude of plant effects on soil microbes. Consequently, an eco-evolutionary perspective is required to fully understand plant-microbe interactions.

Wild bees enhance honey bees’ pollination of hybrid sunflower

PubMed Central

Greenleaf, Sarah S.; Kremen, Claire

2006-01-01

Pollinators are required for producing 15–30% of the human food supply, and farmers rely on managed honey bees throughout the world to provide these services. Yet honey bees are not always the most efficient pollinators of all crops and are declining in various parts of the world. Crop pollination shortages are becoming increasingly common. We found that behavioral interactions between wild and honey bees increase the pollination efficiency of honey bees on hybrid sunflower up to 5-fold, effectively doubling honey bee pollination services on the average field. These indirect contributions caused by interspecific interactions between wild and honey bees were more than five times more important than the contributions wild bees make to sunflower pollination directly. Both proximity to natural habitat and crop planting practices were significantly correlated with pollination services provided directly and indirectly by wild bees. Our results suggest that conserving wild habitat at the landscape scale and altering selected farm management techniques could increase hybrid sunflower production. These findings also demonstrate the economic importance of interspecific interactions for ecosystem services and suggest that protecting wild bee populations can help buffer the human food supply from honey bee shortages. PMID:16940358

Wild bees enhance honey bees' pollination of hybrid sunflower.

PubMed

Greenleaf, Sarah S; Kremen, Claire

2006-09-12

Pollinators are required for producing 15-30% of the human food supply, and farmers rely on managed honey bees throughout the world to provide these services. Yet honey bees are not always the most efficient pollinators of all crops and are declining in various parts of the world. Crop pollination shortages are becoming increasingly common. We found that behavioral interactions between wild and honey bees increase the pollination efficiency of honey bees on hybrid sunflower up to 5-fold, effectively doubling honey bee pollination services on the average field. These indirect contributions caused by interspecific interactions between wild and honey bees were more than five times more important than the contributions wild bees make to sunflower pollination directly. Both proximity to natural habitat and crop planting practices were significantly correlated with pollination services provided directly and indirectly by wild bees. Our results suggest that conserving wild habitat at the landscape scale and altering selected farm management techniques could increase hybrid sunflower production. These findings also demonstrate the economic importance of interspecific interactions for ecosystem services and suggest that protecting wild bee populations can help buffer the human food supply from honey bee shortages.

Astrophysical uncertainties on the local dark matter distribution and direct detection experiments

NASA Astrophysics Data System (ADS)

Green, Anne M.

2017-08-01

The differential event rate in weakly interacting massive particle (WIMP) direct detection experiments depends on the local dark matter density and velocity distribution. Accurate modelling of the local dark matter distribution is therefore required to obtain reliable constraints on the WIMP particle physics properties. Data analyses typically use a simple standard halo model which might not be a good approximation to the real Milky Way (MW) halo. We review observational determinations of the local dark matter density, circular speed and escape speed and also studies of the local dark matter distribution in simulated MW-like galaxies. We discuss the effects of the uncertainties in these quantities on the energy spectrum and its time and direction dependence. Finally, we conclude with an overview of various methods for handling these astrophysical uncertainties.

Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay

PubMed Central

2011-01-01

Background Protein interactions control the regulatory networks underlying developmental processes. The understanding of developmental complexity will, therefore, require the characterization of protein interactions within their proper environment. The bimolecular fluorescence complementation (BiFC) technology offers this possibility as it enables the direct visualization of protein interactions in living cells. However, its potential has rarely been applied in embryos of animal model organisms and was only performed under transient protein expression levels. Results Using a Hox protein partnership as a test case, we investigated the suitability of BiFC for the study of protein interactions in the living Drosophila embryo. Importantly, all BiFC parameters were established with constructs that were stably expressed under the control of endogenous promoters. Under these physiological conditions, we showed that BiFC is specific and sensitive enough to analyse dynamic protein interactions. We next used BiFC in a candidate interaction screen, which led to the identification of several Hox protein partners. Conclusion Our results establish the general suitability of BiFC for revealing and studying protein interactions in their physiological context during the rapid course of Drosophila embryonic development. PMID:21276241

Directional charge separation in isolated organic semiconductor crystalline nanowires

DOE PAGES

Labastide, J. A.; Thompson, H. B.; Marques, S. R.; ...

2016-02-25

One of the fundamental design paradigms in organic photovoltaic device engineering is based on the idea that charge separation is an extrinsically driven process requiring an interface for exciton fission. This idea has driven an enormous materials science engineering effort focused on construction of domain sizes commensurate with a nominal exciton diffusion length of order 10 nm. Here, we show that polarized optical excitation of isolated pristine crystalline nanowires of a small molecule n-type organic semiconductor, 7,8,15,16-tetraazaterrylene, generates a significant population of charge-separated polaron pairs along the π-stacking direction. Charge separation was signalled by pronounced power-law photoluminescence decay polarized alongmore » the same axis. In the transverse direction, we observed exponential decay associated with excitons localized on individual monomers. We propose that this effect derives from an intrinsic directional charge-transfer interaction that can ultimately be programmed by molecular packing geometry.« less

Direct Imaging of Protein Organization in an Intact Bacterial Organelle Using High-Resolution Atomic Force Microscopy

PubMed Central

2016-01-01

The function of bioenergetic membranes is strongly influenced by the spatial arrangement of their constituent membrane proteins. Atomic force microscopy (AFM) can be used to probe protein organization at high resolution, allowing individual proteins to be identified. However, previous AFM studies of biological membranes have typically required that curved membranes are ruptured and flattened during sample preparation, with the possibility of disruption of the native protein arrangement or loss of proteins. Imaging native, curved membranes requires minimal tip–sample interaction in both lateral and vertical directions. Here, long-range tip–sample interactions are reduced by optimizing the imaging buffer. Tapping mode AFM with high-resonance-frequency small and soft cantilevers, in combination with a high-speed AFM, reduces the forces due to feedback error and enables application of an average imaging force of tens of piconewtons. Using this approach, we have imaged the membrane organization of intact vesicular bacterial photosynthetic “organelles”, chromatophores. Despite the highly curved nature of the chromatophore membrane and lack of direct support, the resolution was sufficient to identify the photosystem complexes and quantify their arrangement in the native state. Successive imaging showed the proteins remain surprisingly static, with minimal rotation or translation over several-minute time scales. High-order assemblies of RC-LH1-PufX complexes are observed, and intact ATPases are successfully imaged. The methods developed here are likely to be applicable to a broad range of protein-rich vesicles or curved membrane systems, which are an almost ubiquitous feature of native organelles. PMID:28114766

Long-term economic benefits attributed to IVF-conceived children: a lifetime tax calculation.

PubMed

Connolly, Mark P; Pollard, Michael S; Hoorens, Stijn; Kaplan, Brian R; Oskowitz, Selwyn P; Silber, Sherman J

2008-09-01

To evaluate whether lifetime future net tax revenues from an in vitro fertilization (IVF)-conceived child are substantial enough to warrant public subsidy relative to the mean IVF treatment costs required to obtain 1 live birth. Mathematical generational accounting model. The model estimates direct financial interactions between the IVF-conceived child and the government during the child's projected lifetime. In the model, we accrue IVF costs required to conceive the child to the government, and then we estimate future net tax revenue to the federal and state governments from this individual, offset by direct financial transfers from the government (eg, child allowances, education, Medicare, and Social Security). We discount lifetime costs and gross tax payments at Treasury Department rates to establish the present value of investing in IVF. We applied US Congressional Budget Office projected changes in tax rates over the course of the model. An IVF-conceived child, average in every respect (eg, future earnings, healthcare consumption, and life expectancy), represents a net positive return to the government. Based on an average employed individual born in 2005, the projected net lifetime tax contribution is US $606,200. Taking into consideration IVF costs and all direct financial interactions, the net present value is US $155,870. Lifetime net taxes paid from a child relative to the child's initial IVF investment represent a 700% net return to the government in discounted US dollars from fully employed individuals. This suggests that removing barriers to IVF would have positive tax benefits for the government, notwithstanding its beneficial effect on overall economic growth.

Stc1: A Critical Link between RNAi and Chromatin Modification Required for Heterochromatin Integrity

PubMed Central

Bayne, Elizabeth H.; White, Sharon A.; Kagansky, Alexander; Bijos, Dominika A.; Sanchez-Pulido, Luis; Hoe, Kwang-Lae; Kim, Dong-Uk; Park, Han-Oh; Ponting, Chris P.; Rappsilber, Juri; Allshire, Robin C.

2010-01-01

Summary In fission yeast, RNAi directs heterochromatin formation at centromeres, telomeres, and the mating type locus. Noncoding RNAs transcribed from repeat elements generate siRNAs that are incorporated into the Argonaute-containing RITS complex and direct it to nascent homologous transcripts. This leads to recruitment of the CLRC complex, including the histone methyltransferase Clr4, promoting H3K9 methylation and heterochromatin formation. A key question is what mediates the recruitment of Clr4/CLRC to transcript-bound RITS. We have identified a LIM domain protein, Stc1, that is required for centromeric heterochromatin integrity. Our analyses show that Stc1 is specifically required to establish H3K9 methylation via RNAi, and interacts both with the RNAi effector Ago1, and with the chromatin-modifying CLRC complex. Moreover, tethering Stc1 to a euchromatic locus is sufficient to induce silencing and heterochromatin formation independently of RNAi. We conclude that Stc1 associates with RITS on centromeric transcripts and recruits CLRC, thereby coupling RNAi to chromatin modification. PMID:20211136

Local Interactions of Hydrometeors by Diffusion in Mixed-Phase Clouds

NASA Astrophysics Data System (ADS)

Baumgartner, Manuel; Spichtinger, Peter

2017-04-01

Mixed-phase clouds, containing both ice particles and liquid droplets, are important for the Earth-Atmosphere system. They modulate the radiation budget by a combination of albedo effect and greenhouse effect. In contrast to liquid water clouds, the radiative impact of clouds containing ice particles is still uncertain. Scattering and absorption highly depends in microphysical properties of ice crystals, e.g. size and shape. In addition, most precipitation on Earth forms via the ice phase. Thus, better understanding of ice processes as well as their representation in models is required. A key process for determining shape and size of ice crystals is diffusional growth. Diffusion processes in mixed-phase clouds are highly uncertain; in addition they are usually highly simplified in cloud models, especially in bulk microphysics parameterizations. The direct interaction between cloud droplets and ice particles, due to spatial inhomogeneities, is ignored; the particles can only interact via their environmental conditions. Local effects as supply of supersaturation due to clusters of droplets around ice particles are usually not represented, although they form the physical basis of the Wegener-Bergeron-Findeisen process. We present direct numerical simulations of the interaction of single ice particles and droplets, especially their local competition for the available water vapor. In addition, we show an approach to parameterize local interactions by diffusion. The suggested parameterization uses local steady-state solutions of the diffusion equations for water vapor for an ice particle as well as a droplet. The individual solutions are coupled together to obtain the desired interaction. We show some results of the scheme as implemented in a parcel model.

Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein–protein interactions directly from DNA

PubMed Central

Layton, Curtis J; Hellinga, Homme W

2011-01-01

Assays that integrate detection of binding with cell-free protein expression directly from DNA can dramatically increase the pace at which protein–protein interactions (PPIs) can be analyzed by mutagenesis. In this study, we present a method that combines in vitro protein production with an enzyme-linked immunosorbent assay (ELISA) to measure PPIs. This method uses readily available commodity instrumentation and generic antibody–affinity tag interactions. It is straightforward and rapid to execute, enabling many interactions to be assessed in parallel. In traditional ELISAs, reporter complexes are assembled stepwise with one layer at a time. In the method presented here, all the members of the reporter complex are present and assembled together. The signal strength is dependent on all the intercomponent interaction affinities and concentrations. Although this assay is straightforward to execute, establishing proper conditions and analysis of the results require a thorough understanding of the processes that determine the signal strength. The formation of the fully assembled reporter sandwich can be modeled as a competition between Langmuir adsorption isotherms for the immobilized components and binding equilibria of the solution components. We have shown that modeling this process provides semiquantitative understanding of the effects of affinity and concentration and can guide strategies for the development of experimental protocols. We tested the method experimentally using the interaction between a synthetic ankyrin repeat protein (Off7) and maltose-binding protein. Measurements obtained for a collection of alanine mutations in the interface between these two proteins demonstrate that a range of affinities can be analyzed. PMID:21674663

Do intraspecific or interspecific interactions determine responses to predators feeding on a shared size-structured prey community?

PubMed

ten Brink, Hanna; Mazumdar, Abul Kalam Azad; Huddart, Joseph; Persson, Lennart; Cameron, Tom C

2015-03-01

Coexistence of predators that share the same prey is common. This is still the case in size-structured predator communities where predators consume prey species of different sizes (interspecific prey responses) or consume different size classes of the same species of prey (intraspecific prey responses). A mechanism has recently been proposed to explain coexistence between predators that differ in size but share the same prey species, emergent facilitation, which is dependent on strong intraspecific responses from one or more prey species. Under emergent facilitation, predators can depend on each other for invasion, persistence or success in a size-structured prey community. Experimental evidence for intraspecific size-structured responses in prey populations remains rare, and further questions remain about direct interactions between predators that could prevent or limit any positive effects between predators [e.g. intraguild predation (IGP)]. Here, we provide a community-wide experiment on emergent facilitation including natural predators. We investigate both the direct interactions between two predators that differ in body size (fish vs. invertebrate predator), and the indirect interaction between them via their shared prey community (zooplankton). Our evidence supports the most likely expectation of interactions between differently sized predators that IGP rates are high, and interspecific interactions in the shared prey community dominate the response to predation (i.e. predator-mediated competition). The question of whether emergent facilitation occurs frequently in nature requires more empirical and theoretical attention, specifically to address the likelihood that its pre-conditions may co-occur with high rates of IGP. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Dynamic Policy-Driven Quality of Service in Service-Oriented Information Management Systems

DTIC Science & Technology

2011-01-01

both DiffServ and IntServ net- work QoS mechanisms. Wang et al [48] provide middleware APIs to shield applications from directly interacting with...complex network QoS mechanism APIs . Middleware frameworks transparently converted the specified application QoS requirements into low- er-level network...QoS mechanism APIs and provided network QoS assurances. Deployment-time resource allocation. Other prior work has focused on deploying ap- plications

Design Guidelines and Criteria for User/Operator Transactions with Battlefield Automated Systems. Volume 2. Technical Discussion

DTIC Science & Technology

1981-02-01

Continue on tevetee «Id* If necemtery mid Identify br black number) Battlefield automated systems Human- computer interaction. Design criteria System...Report (this report) In-Depth Analyses of Individual Systems A. Tactical Fire Direction System (TACFIRE) (RP 81-26) B. Tactical Computer Terminal...select the design features and operating procedures of the human- computer Interface which best match the require- ments and capabilities of anticipated

Interaction with a kinesin-2 tail propels choline acetyltransferase flow towards synapse

PubMed Central

Sadananda, Aparna; Hamid, Runa; Doodhi, Harinath; Ghosal, Debnath; Girotra, Mukul; Jana, Swadhin Chandra; Ray, Krishanu

2012-01-01

Bulk flow constitutes a substantial part of the slow transport of soluble proteins in axons. Though the underlying mechanism is unclear, evidences indicate that intermittent, kinesin based movement of large protein-aggregates aids this process. Choline acetyl-transferase (ChAT), a soluble enzyme catalyzing acetylcholine synthesis, propagates towards synapse at an intermediate, slow rate. The presynaptic enrichment of ChAT requires heterotrimeric kinesin-2, comprising KLP64D, KLP68D and DmKAP, in Drosophila. Here, we show that the bulk flow of a recombinant Green Fluorescent Protein-tagged ChAT (GFP::ChAT), in Drosophila axons, lacks particulate features. It occurs for a brief period during the larval stages. In addition, both the endogenous ChAT and GFP::ChAT directly bind to the KLP64D tail, which is essential for the GFP::ChAT entry and anterograde flow in axon. These evidences suggest that a direct interaction with motor proteins could regulate the bulk flow of soluble proteins, and thus establish their asymmetric distribution. PMID:22486887

[Propranolol beta-blocker decrease in the concentration of high-affinity binding sites for calcium ions by sarcolemma membranes of the rat heart].

PubMed

Seleznev, Iu M; Martynov, A V; Smirnov, V N

1982-05-01

In vivo administration of propranolol considerably inhibits the isoproterenol-stimulated increase in 45Ca accumulation by the myocardium and completely eliminates the potentiation of isoproterenol effect by hydrocortisone. A significant lowering of the concentration of high affinity binding sites for calcium in the sarcolemmal membranes can be produced by propranolol in vitro. Under these conditions, the glucocorticoids do not change the sarcolemmal Ca2+-binding parameters or modulate the propranolol effect. Therefore, for the manifestation of glucocorticoid action to be brought about, the integrity of the cells is apparently required, while propranolol seems to change calcium binding by direct interaction with the sarcolemmal membranes. It is suggested that in vivo propranolol inhibition of catecholamine effect on calcium ion accumulation by the myocardium depends on the interaction with the beta-receptors and direct modulation of the concentration of high affinity binding sites for calcium ions on the surface of the sarcolemma.

Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

PubMed Central

Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

2015-01-01

Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. DOI: http://dx.doi.org/10.7554/eLife.06181.001 PMID:25902402

Understanding mechanism of in vitro maturation, fertilization and culture of sheep embryoes through in silico analysis.

PubMed

Sreenivas, Dulam; Kaladhar, Dowluru Svgk; Samy, A Palni; Kumar, R Sangeeth

2012-01-01

Protein interations are presently required to understand the mechanisms of in vitro maturation, fertilization and culture of sheep embryoes through in silico analysis. The present work has been conducted on TCM-199 supplemented with epidermal growth factor (EGF), fetal bovine serum (FBS) or wheat peptones The maturation rate of oocyte was significantly higher in the FBS supplemented group when compared with BSA and wheat peptone supplemented groups. The in silico protein interaction studies has shown that the proteins EGFR (epidermal growth factor receptor), CCK (cholecystokinin)- a peptide hormone, Alb - a serum albumin, ESR- estrogen receptor 1, TGFA- transforming growth factor, STAT- signal transducer and FN1- fibronectin 1 has direct interaction and produces cell growth in in vitro culture. Alb is directly activates EGF and promotes MAPK3 that mediates diverse biological functions such as cell growth, adhesion and proliferation. Alb may also involve in stress response signalling and may be in cell cycle control.

Coordination of planar cell polarity pathways through Spiny-legs

PubMed Central

Ambegaonkar, Abhijit A; Irvine, Kenneth D

2015-01-01

Morphogenesis and physiology of tissues and organs requires planar cell polarity (PCP) systems that orient and coordinate cells and their behaviors, but the relationship between PCP systems has been controversial. We have characterized how the Frizzled and Dachsous-Fat PCP systems are connected through the Spiny-legs isoform of the Prickle-Spiny-legs locus. Two different components of the Dachsous-Fat system, Dachsous and Dachs, can each independently interact with Spiny-legs and direct its localization in vivo. Through characterization of the contributions of Prickle, Spiny-legs, Dachsous, Fat, and Dachs to PCP in the Drosophila wing, eye, and abdomen, we define where Dachs-Spiny-legs and Dachsous-Spiny-legs interactions contribute to PCP, and provide a new understanding of the orientation of polarity and the basis of PCP phenotypes. Our results support the direct linkage of PCP systems through Sple in specific locales, while emphasizing that cells can be subject to and must ultimately resolve distinct, competing PCP signals. DOI: http://dx.doi.org/10.7554/eLife.09946.001 PMID:26505959

Skype Me! Astronomers, Students, and Cutting-Edge Research

NASA Astrophysics Data System (ADS)

Hickox, Ryan C.; Gauthier, Adrienne J.

2014-06-01

A primary goal of many university science courses is to promote understanding of the process of contemporary scientific inquiry. One powerful way to achieve this is for students to explore current research and then interact directly with the leading scientist, the feasibility of which has recently increased dramatically due to free online video communication tools. We report on a program implemented at Dartmouth College in which students connect with a guest astronomer through Skype (video chat). The Skype session is wrapped in a larger activity where students explore current research articles, interact with the astronomer, and then reflect on the experience. The in-class Skype discussions require a small time commitment from scientists (20-30 minutes, with little or no need for preparation) while providing students direct access to researchers at the cutting edge of modern astronomy. We outline the procedures used to implement these discussions, and present qualitative assessments of student's understanding of the process of research, as well as feedback from the guest astronomers.

Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

DOE PAGES

Sunden, Fanny; Peck, Ariana; Salzman, Julia; ...

2015-04-22

Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modesmore » of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.« less

Targeting the FANCJ–BRCA1 interaction promotes a switch from recombination to polη-dependent bypass

PubMed Central

Xie, J; Litman, R; Wang, S; Peng, M; Guillemette, S; Rooney, T; Cantor, SB

2010-01-01

BRCA1 and the DNA helicase FANCJ (also known as BACH1 or BRIP1) have common functions in breast cancer suppression and DNA repair. However, the functional significance of the direct interaction between BRCA1 and FANCJ remains unclear. Here, we have discovered that BRCA1 binding to FANCJ regulates DNA damage repair choice. Thus, when FANCJ binding to BRCA1 is ablated, the molecular mechanism chosen for the repair of damaged DNA is dramatically altered. Specifically, a FANCJ protein that cannot be phosphorylated at serine 990 or bind BRCA1 inhibits DNA repair via homologous recombination and promotes polη-dependent bypass. Furthermore, the polη-dependent bypass promoted by FANCJ requires the direct binding to the mismatch repair (MMR) protein, MLH1. Together, our findings implicate that in human cells BRCA1 binding to FANCJ is critical to regulate DNA repair choice and promote genomic stability. Moreover, unregulated FANCJ function could be associated with cancer and/or chemoresistance. PMID:20173781

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

Kim, Sung-Hak; Park, Jinah; Choi, Moon-Chang

DNA methyltransferases (DNMT) 3B is a de novo DNMT that represses transcription independent of DNMT activity. In order to gain a better insight into DNMT3B-mediated transcriptional repression, we performed a yeast two-hybrid analysis using DNMT3B as a bait. Of the various binding candidates, ZHX1, a member of zinc-finger and homeobox protein, was found to interact with DNMT3B in vivo and in vitro. N-terminal PWWP domain of DNMT3B was required for its interaction with homeobox motifs of ZHX1. ZHX1 contains nuclear localization signal at C-terminal homeobox motif, and both ZHX1 and DNMT3B were co-localized in nucleus. Furthermore, we found that ZHX1more » enhanced the transcriptional repression mediated by DNMT3B when DNMT3B is directly targeted to DNA. These results showed for First the direct linkage between DNMT and zinc-fingers homeoboxes protein, leading to enhanced gene silencing by DNMT3B.« less

Suppress to Forget: The Effect of a Mindfulness-Based Strategy during an Emotional Item-Directed Forgetting Paradigm.

PubMed

Gamboa, Olga L; Garcia-Campayo, Javier; Müller, Teresa; von Wegner, Frederic

2017-01-01

Forgetting is a common phenomenon in everyday life. Although it often has negative connotations, forgetting is an important adaptive mechanism to avoid loading the memory storage with irrelevant information. A very important aspect of forgetting is its interaction with emotion. Affective events are often granted special and priority treatment over neutral ones with regards to memory storage. As a consequence, emotional information is more resistant to extinction than neutral information. It has been suggested that intentional forgetting serves as a mechanism to cope with unwanted or disruptive emotional memories and the main goal of this study was to assess forgetting of emotional auditory material using the item-method directed forgetting (DF) paradigm using a forgetting strategy based on mindfulness as a means to enhance DF. Contrary to our prediction, the mindfulness-based strategy not only did not improve DF but reduced it for neutral material. These results suggest that an interaction between processes such as response inhibition and attention is required for intentional forgetting to succeed.

Microscopic diffusion and hydrodynamic interactions of hemoglobin in red blood cells.

PubMed

Doster, Wolfgang; Longeville, Stéphane

2007-08-15

The cytoplasm of red blood cells is congested with the oxygen storage protein hemoglobin occupying a quarter of the cell volume. The high protein concentration leads to a reduced mobility; the self-diffusion coefficient of hemoglobin in blood cells is six times lower than in dilute solution. This effect is generally assigned to excluded volume effects in crowded media. However, the collective or gradient diffusion coefficient of hemoglobin is only weakly dependent on concentration, suggesting the compensation of osmotic and friction forces. This would exclude hydrodynamic interactions, which are of dynamic origin and do not contribute to the osmotic pressure. Hydrodynamic coupling between protein molecules is dominant at short time- and length scales before direct interactions are fully established. Employing neutron spin-echo-spectroscopy, we study hemoglobin diffusion on a nanosecond timescale and protein displacements on the scale of a few nanometers. A time- and wave-vector dependent diffusion coefficient is found, suggesting the crossover of self- and collective diffusion. Moreover, a wave-vector dependent friction function is derived, which is a characteristic feature of hydrodynamic interactions. The wave-vector and concentration dependence of the long-time self-diffusion coefficient of hemoglobin agree qualitatively with theoretical results on hydrodynamics in hard spheres suspensions. Quantitative agreement requires us to adjust the volume fraction by including part of the hydration shell: Proteins exhibit a larger surface/volume ratio compared to standard colloids of much larger size. It is concluded that hydrodynamic and not direct interactions dominate long-range molecular transport at high concentration.

Contact processes with competitive dynamics in bipartite lattices: effects of distinct interactions

NASA Astrophysics Data System (ADS)

Pianegonda, Salete; Fiore, Carlos E.

2014-05-01

The two-dimensional contact process (CP) with a competitive dynamics proposed by Martins et al (2011 Phys. Rev. E 84 011125) leads to the appearance of an unusual active-asymmetric phase, in which the system sublattices are unequally populated. It differs from the usual CP only by the fact that particles also interact with their next-nearest neighbor sites via a distinct strength creation rate, and for the inclusion of an inhibition effect, proportional to the local density. Aimed at investigating the robustness of such an asymmetric phase, in this paper we study the influence of distinct interactions for two bidimensional CPs. In the first model, the interaction between first neighbors requires a minimal neighborhood of adjacent particles for creating new offspring, whereas second neighbors interact as usual (e.g. at least one neighboring particle is required). The second model takes the opposite situation, in which the restrictive dynamics is in the interaction between next-nearest neighbor sites. Both models are investigated under mean field theory (MFT) and Monte Carlo simulations. In similarity with results by Martins et al, the inclusion of distinct sublattice interactions maintains the occurrence of an asymmetric active phase and re-entrant transition lines. In contrast, remarkable differences are presented, such as discontinuous phase transitions (even between the active phases), the appearance of tricritical points and the stabilization of active phases under larger values of control parameters. Finally, we have shown that the critical behaviors are not altered due to the change of interactions, in which the absorbing transitions belong to the directed percolation (DP) universality class, whereas second-order active phase transitions belong to the Ising universality class.

A loop-gap resonator for chirality-sensitive nuclear magneto-electric resonance (NMER)

NASA Astrophysics Data System (ADS)

Garbacz, Piotr; Fischer, Peer; Krämer, Steffen

2016-09-01

Direct detection of molecular chirality is practically impossible by methods of standard nuclear magnetic resonance (NMR) that is based on interactions involving magnetic-dipole and magnetic-field operators. However, theoretical studies provide a possible direct probe of chirality by exploiting an enantiomer selective additional coupling involving magnetic-dipole, magnetic-field, and electric field operators. This offers a way for direct experimental detection of chirality by nuclear magneto-electric resonance (NMER). This method uses both resonant magnetic and electric radiofrequency (RF) fields. The weakness of the chiral interaction though requires a large electric RF field and a small transverse RF magnetic field over the sample volume, which is a non-trivial constraint. In this study, we present a detailed study of the NMER concept and a possible experimental realization based on a loop-gap resonator. For this original device, the basic principle and numerical studies as well as fabrication and measurements of the frequency dependence of the scattering parameter are reported. By simulating the NMER spin dynamics for our device and taking the 19F NMER signal of enantiomer-pure 1,1,1-trifluoropropan-2-ol, we predict a chirality induced NMER signal that accounts for 1%-5% of the standard achiral NMR signal.

Sequence-encoded colloidal origami and microbot assemblies from patchy magnetic cubes

PubMed Central

Han, Koohee; Shields, C. Wyatt; Diwakar, Nidhi M.; Bharti, Bhuvnesh; López, Gabriel P.; Velev, Orlin D.

2017-01-01

Colloidal-scale assemblies that reconfigure on demand may serve as the next generation of soft “microbots,” artificial muscles, and other biomimetic devices. This requires the precise arrangement of particles into structures that are preprogrammed to reversibly change shape when actuated by external fields. The design and making of colloidal-scale assemblies with encoded directional particle-particle interactions remain a major challenge. We show how assemblies of metallodielectric patchy microcubes can be engineered to store energy through magnetic polarization and release it on demand by microscale reconfiguration. The dynamic pattern of folding and reconfiguration of the chain-like assemblies can be encoded in the sequence of the cube orientation. The residual polarization of the metallic facets on the microcubes leads to local interactions between the neighboring particles, which is directed by the conformational restrictions of their shape after harvesting energy from external magnetic fields. These structures can also be directionally moved, steered, and maneuvered by global forces from external magnetic fields. We illustrate these capabilities by examples of assemblies of specific sequences that can be actuated, reoriented, and spatially maneuvered to perform microscale operations such as capturing and transporting live cells, acting as prototypes of microbots, micromixers, and other active microstructures. PMID:28798960

Software-type Wave-Particle Interaction Analyzer on board the Arase satellite

NASA Astrophysics Data System (ADS)

Katoh, Yuto; Kojima, Hirotsugu; Hikishima, Mitsuru; Takashima, Takeshi; Asamura, Kazushi; Miyoshi, Yoshizumi; Kasahara, Yoshiya; Kasahara, Satoshi; Mitani, Takefumi; Higashio, Nana; Matsuoka, Ayako; Ozaki, Mitsunori; Yagitani, Satoshi; Yokota, Shoichiro; Matsuda, Shoya; Kitahara, Masahiro; Shinohara, Iku

2018-01-01

We describe the principles of the Wave-Particle Interaction Analyzer (WPIA) and the implementation of the Software-type WPIA (S-WPIA) on the Arase satellite. The WPIA is a new type of instrument for the direct and quantitative measurement of wave-particle interactions. The S-WPIA is installed on the Arase satellite as a software function running on the mission data processor. The S-WPIA on board the Arase satellite uses an electromagnetic field waveform that is measured by the waveform capture receiver of the plasma wave experiment (PWE), and the velocity vectors of electrons detected by the medium-energy particle experiment-electron analyzer (MEP-e), the high-energy electron experiment (HEP), and the extremely high-energy electron experiment (XEP). The prime objective of the S-WPIA is to measure the energy exchange between whistler-mode chorus emissions and energetic electrons in the inner magnetosphere. It is essential for the S-WPIA to synchronize instruments to a relative time accuracy better than the time period of the plasma wave oscillations. Since the typical frequency of chorus emissions in the inner magnetosphere is a few kHz, a relative time accuracy of better than 10 μs is required in order to measure the relative phase angle between the wave and velocity vectors. In the Arase satellite, a dedicated system has been developed to realize the time resolution required for inter-instrument communication. Here, both the time index distributed over all instruments through the satellite system and an S-WPIA clock signal are used, that are distributed from the PWE to the MEP-e, HEP, and XEP through a direct line, for the synchronization of instruments within a relative time accuracy of a few μs. We also estimate the number of particles required to obtain statistically significant results with the S-WPIA and the expected accumulation time by referring to the specifications of the MEP-e and assuming a count rate for each detector.

Grasping objects by their handles: a necessary interaction between cognition and action

NASA Technical Reports Server (NTRS)

Creem, S. H.; Proffitt, D. R.; Kaiser, M. K. (Principal Investigator)

2001-01-01

Research has illustrated dissociations between "cognitive" and "action" systems, suggesting that different representations may underlie phenomenal experience and visuomotor behavior. However, these systems also interact. The present studies show a necessary interaction when semantic processing of an object is required for an appropriate action. Experiment 1 demonstrated that a semantic task interfered with grasping objects appropriately by their handles, but a visuospatial task did not. Experiment 2 assessed performance on a visuomotor task that had no semantic component and showed a reversal of the effects of the concurrent tasks. In Experiment 3, variations on concurrent word tasks suggested that retrieval of semantic information was necessary for appropriate grasping. In all, without semantic processing, the visuomotor system can direct the effective grasp of an object, but not in a manner that is appropriate for its use.

Protein-Phospholipid Interactions in Nonclassical Protein Secretion: Problem and Methods of Study

PubMed Central

Prudovsky, Igor; Kumar, Thallapuranam Krishnaswamy Suresh; Sterling, Sarah; Neivandt, David

2013-01-01

Extracellular proteins devoid of signal peptides use nonclassical secretion mechanisms for their export. These mechanisms are independent of the endoplasmic reticulum and Golgi. Some nonclassically released proteins, particularly fibroblast growth factors (FGF) 1 and 2, are exported as a result of their direct translocation through the cell membrane. This process requires specific interactions of released proteins with membrane phospholipids. In this review written by a cell biologist, a structural biologist and two membrane engineers, we discuss the following subjects: (i) Phenomenon of nonclassical protein release and its biological significance; (ii) Composition of the FGF1 multiprotein release complex (MRC); (iii) The relationship between FGF1 export and acidic phospholipid externalization; (iv) Interactions of FGF1 MRC components with acidic phospholipids; (v) Methods to study the transmembrane translocation of proteins; (vi) Membrane models to study nonclassical protein release. PMID:23396106

Action Recognition and Movement Direction Discrimination Tasks Are Associated with Different Adaptation Patterns

PubMed Central

de la Rosa, Stephan; Ekramnia, Mina; Bülthoff, Heinrich H.

2016-01-01

The ability to discriminate between different actions is essential for action recognition and social interactions. Surprisingly previous research has often probed action recognition mechanisms with tasks that did not require participants to discriminate between actions, e.g., left-right direction discrimination tasks. It is not known to what degree visual processes in direction discrimination tasks are also involved in the discrimination of actions, e.g., when telling apart a handshake from a high-five. Here, we examined whether action discrimination is influenced by movement direction and whether direction discrimination depends on the type of action. We used an action adaptation paradigm to target action and direction discrimination specific visual processes. In separate conditions participants visually adapted to forward and backward moving handshake and high-five actions. Participants subsequently categorized either the action or the movement direction of an ambiguous action. The results showed that direction discrimination adaptation effects were modulated by the type of action but action discrimination adaptation effects were unaffected by movement direction. These results suggest that action discrimination and direction categorization rely on partly different visual information. We propose that action discrimination tasks should be considered for the exploration of visual action recognition mechanisms. PMID:26941633

Detailed requirements document for common software of shuttle program information management system

NASA Technical Reports Server (NTRS)

Everette, J. M.; Bradfield, L. D.; Horton, C. L.

1975-01-01

Common software was investigated as a method for minimizing development and maintenance cost of the shuttle program information management system (SPIMS) applications while reducing the time-frame of their development. Those requirements satisfying these criteria are presented along with the stand-alone modules which may be used directly by applications. The SPIMS applications operating on the CYBER 74 computer, are specialized information management systems which use System 2000 as a data base manager. Common software provides the features to support user interactions on a CRT terminal using form input and command response capabilities. These features are available as subroutines to the applications.

Effective communication with primary care providers.

PubMed

Smith, Karen

2014-08-01

Effective communication requires direct interaction between the hospitalist and the primary care provider using a standardized method of information exchange with the opportunity to ask questions and assign accountability for follow-up roles. The discharge summary is part of the process but does not provide the important aspects of handoff, such as closed loop communication and role assignments. Hospital discharge is a significant safety risk for patients, with more than half of discharged patients experiencing at least one error. Hospitalist and primary care providers need to collaborate to develop a standardized system to communicate about shared patients that meets handoff requirements. Copyright © 2014 Elsevier Inc. All rights reserved.

Visual-vestibular integration as a function of adaptation to space flight and return to Earth

NASA Technical Reports Server (NTRS)

Reschke, Millard R.; Bloomberg, Jacob J.; Harm, Deborah L.; Huebner, William P.; Krnavek, Jody M.; Paloski, William H.; Berthoz, Alan

1999-01-01

Research on perception and control of self-orientation and self-motion addresses interactions between action and perception . Self-orientation and self-motion, and the perception of that orientation and motion are required for and modified by goal-directed action. Detailed Supplementary Objective (DSO) 604 Operational Investigation-3 (OI-3) was designed to investigate the integrated coordination of head and eye movements within a structured environment where perception could modify responses and where response could be compensatory for perception. A full understanding of this coordination required definition of spatial orientation models for the microgravity environment encountered during spaceflight.

Recruitment of Mcm10 to Sites of Replication Initiation Requires Direct Binding to the Minichromosome Maintenance (MCM) Complex.

PubMed

Douglas, Max E; Diffley, John F X

2016-03-11

Mcm10 is required for the initiation of eukaryotic DNA replication and contributes in some unknown way to the activation of the Cdc45-MCM-GINS (CMG) helicase. How Mcm10 is localized to sites of replication initiation is unclear, as current models indicate that direct binding to minichromosome maintenance (MCM) plays a role, but the details and functional importance of this interaction have not been determined. Here, we show that purified Mcm10 can bind both DNA-bound double hexamers and soluble single hexamers of MCM. The binding of Mcm10 to MCM requires the Mcm10 C terminus. Moreover, the binding site for Mcm10 on MCM includes the Mcm2 and Mcm6 subunits and overlaps that for the loading factor Cdt1. Whether Mcm10 recruitment to replication origins depends on CMG helicase assembly has been unclear. We show that Mcm10 recruitment occurs via two modes: low affinity recruitment in the absence of CMG assembly ("G1-like") and high affinity recruitment when CMG assembly takes place ("S-phase-like"). Mcm10 that cannot bind directly to MCM is defective in both modes of recruitment and is unable to support DNA replication. These findings indicate that Mcm10 is localized to replication initiation sites by directly binding MCM through the Mcm10 C terminus. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Halide peroxidase in tissues that interact with bacteria in the host squid Euprymna scolopes.

PubMed

Small, A L; McFall-Ngai, M J

1999-03-15

An enzyme with similarities to myeloperoxidase, the antimicrobial halide peroxidase in mammalian neutrophils, occurs abundantly in the light organ tissue of Euprymna scolopes, a squid that maintains a beneficial association with the luminous bacterium Vibrio fischeri. Using three independent assays typically applied to the analysis of halide peroxidase enzymes, we directly compared the activity of the squid enzyme with that of human myeloperoxidase. One of these methods, the diethanolamine assay, confirmed that the squid peroxidase requires halide ions for its activity. The identification of a halide peroxidase in a cooperative bacterial association suggested that this type of enzyme can function not only to control pathogens, but also to modulate the interactions of host animals with their beneficial partners. To determine whether the squid peroxidase functions under both circumstances, we examined its distribution in a variety of host tissues, including those that typically interact with bacteria and those that do not. Tissues interacting with bacteria included those that have specific cooperative associations with bacteria (i.e., the light organ and accessory nidamental gland) and those that have transient nonspecific interactions with bacteria (i.e., the gills, which clear the cephalopod circulatory system of invading microorganisms). These bacteria-associated tissues were compared with the eye, digestive gland, white body, and ink-producing tissues, which do not typically interact directly with bacteria. Peroxidase enzyme assays, immunocytochemical localization, and DNA-RNA hybridizations showed that the halide-dependent peroxidase is consistently expressed in high concentration in tissues that interact bacteria. Elevated levels of the peroxidase were also found in the ink-producing tissues, which are known to have enzymatic pathways associated with antimicrobial activity. Taken together, these data suggest that the host uses a common biochemical response to the variety of types of associations that it forms with microorganisms.

The molecular mechanism for interaction of ceruloplasmin and myeloperoxidase

NASA Astrophysics Data System (ADS)

Bakhautdin, Bakytzhan; Bakhautdin, Esen Göksöy

2016-04-01

Ceruloplasmin (Cp) is a copper-containing ferroxidase with potent antioxidant activity. Cp is expressed by hepatocytes and activated macrophages and has been known as physiologic inhibitor of myeloperoxidase (MPO). Enzymatic activity of MPO produces anti-microbial agents and strong prooxidants such as hypochlorous acid and has a potential to damage host tissue at the sites of inflammation and infection. Thus Cp-MPO interaction and inhibition of MPO has previously been suggested as an important control mechanism of excessive MPO activity. Our aim in this study was to identify minimal Cp domain or peptide that interacts with MPO. We first confirmed Cp-MPO interaction by ELISA and surface plasmon resonance (SPR). SPR analysis of the interaction yielded 30 nM affinity between Cp and MPO. We then designed and synthesized 87 overlapping peptides spanning the entire amino acid sequence of Cp. Each of the peptides was tested whether it binds to MPO by direct binding ELISA. Two of the 87 peptides, P18 and P76 strongly interacted with MPO. Amino acid sequence analysis of identified peptides revealed high sequence and structural homology between them. Further structural analysis of Cp's crystal structure by PyMOL software unfolded that both peptides represent surface-exposed sites of Cp and face nearly the same direction. To confirm our finding we raised anti-P18 antisera in rabbit and demonstrated that this antisera disrupts Cp-MPO binding and rescues MPO activity. Collectively, our results confirm Cp-MPO interaction and identify two nearly identical sites on Cp that specifically bind MPO. We propose that inhibition of MPO by Cp requires two nearly identical sites on Cp to bind homodimeric MPO simultaneously and at an angle of at least 120 degrees, which, in turn, exerts tension on MPO and results in conformational change.

Project Review: Teleoperation and Time Delays

NASA Technical Reports Server (NTRS)

Adelstein, Bernard D.; Ellis, Stephen; Yeom, Kiwon; Kaiser, Mary K.

2013-01-01

We plan to study the invariance in the shift in control strategy from continuous control to move-and-wait as a function of latency and control difficulty. To do so we have developed a theoretically understood way of introducing measurable levels of control difficulty using misalignment between display and control axes . We now use this understanding to study the interaction of control difficulty and system latency. We have conducted an experiment to calibrate our imposition of control difficulty using more representative control rotations. We use these levels of difficulty to directly study the interaction of control difficulty with latency. Results suggest a way to generalize latency requirements across control difficulties that should aid establishment of standards for managing latency in teleoperation.

Engaging patients through your website.

PubMed

Snyder, Kimberlee; Ornes, Lynne L; Paulson, Pat

2014-01-01

Legislation requires the healthcare industry to directly engage patients through technology. This paper proposes a model that can be used to review hospital websites for features that engage patients in their healthcare. The model describes four levels of patient engagement in website design. The sample consisted of 130 hospital websites from hospitals listed on 2010 and 2011 Most Wired Hospitals. Hospital websites were analyzed for features that encouraged patient interaction with their healthcare according to the levels in the model. Of the four levels identified in the model, websites ranged from "informing" to "collaborative" in website design. There was great variation of features offered on hospital websites with few being engaging and interactive. © 2012 National Association for Healthcare Quality.

Workshop on Spaceflight Alterations in Host-Microorganism Interactions

NASA Technical Reports Server (NTRS)

Ott, C. Mark

2010-01-01

On June 11, 2009, a workshop that included internal and external experts was convened to determine the risk of changes in microorganisms that could alter host-microorganism interactions during a mission. The evidence is based in part on multiple flight experiments which indicate altered virulence in Salmonella typhimurium when cultured in flight. The workshop participants were tasked to determine if adequate information was available to initiate changes in NASA's current approach to infectious disease risk assessment and medical operations. The consensus of the participants is that the current evidence was not adequate to provide direction for operational changes; however, the evidence is compelling and clearly indicates that changes to microorganisms were occurring during spaceflight and further research is required.

Pathogen reduction requirements for direct potable reuse in Antarctica: evaluating human health risks in small communities.

PubMed

Barker, S Fiona; Packer, Michael; Scales, Peter J; Gray, Stephen; Snape, Ian; Hamilton, Andrew J

2013-09-01

Small, remote communities often have limited access to energy and water. Direct potable reuse of treated wastewater has recently gained attention as a potential solution for water-stressed regions, but requires further evaluation specific to small communities. The required pathogen reduction needed for safe implementation of direct potable reuse of treated sewage is an important consideration but these are typically quantified for larger communities and cities. A quantitative microbial risk assessment (QMRA) was conducted, using norovirus, giardia and Campylobacter as reference pathogens, to determine the level of treatment required to meet the tolerable annual disease burden of 10(-6) DALYs per person per year, using Davis Station in Antarctica as an example of a small remote community. Two scenarios were compared: published municipal sewage pathogen loads and estimated pathogen loads during a gastroenteritis outbreak. For the municipal sewage scenario, estimated required log10 reductions were 6.9, 8.0 and 7.4 for norovirus, giardia and Campylobacter respectively, while for the outbreak scenario the values were 12.1, 10.4 and 12.3 (95th percentiles). Pathogen concentrations are higher under outbreak conditions as a function of the relatively greater degree of contact between community members in a small population, compared with interactions in a large city, resulting in a higher proportion of the population being at risk of infection and illness. While the estimates of outbreak conditions may overestimate sewage concentration to some degree, the results suggest that additional treatment barriers would be required to achieve regulatory compliance for safe drinking water in small communities. Copyright © 2013 Elsevier B.V. All rights reserved.

Distinct roles of autophagy-dependent and -independent functions of FIP200 revealed by generation and analysis of a mutant knock-in mouse model

PubMed Central

Chen, Song; Wang, Chenran; Yeo, Syn; Liang, Chun-Chi; Okamoto, Takako; Sun, Shaogang; Wen, Jian; Guan, Jun-Lin

2016-01-01

Autophagy is an evolutionarily conserved cellular process controlled through a set of essential autophagy genes (Atgs). However, there is increasing evidence that most, if not all, Atgs also possess functions independent of their requirement in canonical autophagy, making it difficult to distinguish the contributions of autophagy-dependent or -independent functions of a particular Atg to various biological processes. To distinguish these functions for FIP200 (FAK family-interacting protein of 200 kDa), an Atg in autophagy induction, we examined FIP200 interaction with its autophagy partner, Atg13. We found that residues 582–585 (LQFL) in FIP200 are required for interaction with Atg13, and mutation of these residues to AAAA (designated the FIP200-4A mutant) abolished its canonical autophagy function in vitro. Furthermore, we created a FIP200-4A mutant knock-in mouse model and found that specifically blocking FIP200 interaction with Atg13 abolishes autophagy in vivo, providing direct support for the essential role of the ULK1/Atg13/FIP200/Atg101 complex in the process beyond previous studies relying on the complete knockout of individual components. Analysis of the new mouse model showed that nonautophagic functions of FIP200 are sufficient to fully support embryogenesis by maintaining a protective role in TNFα-induced apoptosis. However, FIP200-mediated canonical autophagy is required to support neonatal survival and tumor cell growth. These studies provide the first genetic evidence linking an Atg's autophagy and nonautophagic functions to different biological processes in vivo. PMID:27013233

Highly specific salt bridges govern bacteriophage P22 icosahedral capsid assembly: identification of the site in coat protein responsible for interaction with scaffolding protein.

PubMed

Cortines, Juliana R; Motwani, Tina; Vyas, Aashay A; Teschke, Carolyn M

2014-05-01

Icosahedral virus assembly requires a series of concerted and highly specific protein-protein interactions to produce a proper capsid. In bacteriophage P22, only coat protein (gp5) and scaffolding protein (gp8) are needed to assemble a procapsid-like particle, both in vivo and in vitro. In scaffolding protein's coat binding domain, residue R293 is required for procapsid assembly, while residue K296 is important but not essential. Here, we investigate the interaction of scaffolding protein with acidic residues in the N-arm of coat protein, since this interaction has been shown to be electrostatic. Through site-directed mutagenesis of genes 5 and 8, we show that changing coat protein N-arm residue 14 from aspartic acid to alanine causes a lethal phenotype. Coat protein residue D14 is shown by cross-linking to interact with scaffolding protein residue R293 and, thus, is intimately involved in proper procapsid assembly. To a lesser extent, coat protein N-arm residue E18 is also implicated in the interaction with scaffolding protein and is involved in capsid size determination, since a cysteine mutation at this site generated petite capsids. The final acidic residue in the N-arm that was tested, E15, is shown to only weakly interact with scaffolding protein's coat binding domain. This work supports growing evidence that surface charge density may be the driving force of virus capsid protein interactions. Bacteriophage P22 infects Salmonella enterica serovar Typhimurium and is a model for icosahedral viral capsid assembly. In this system, coat protein interacts with an internal scaffolding protein, triggering the assembly of an intermediate called a procapsid. Previously, we determined that there is a single amino acid in scaffolding protein required for P22 procapsid assembly, although others modulate affinity. Here, we identify partners in coat protein. We show experimentally that relatively weak interactions between coat and scaffolding proteins are capable of driving correctly shaped and sized procapsids and that the lack of these proper protein-protein interfaces leads to aberrant structures. The present work represents an important contribution supporting the hypothesis that virus capsid assembly is governed by seemingly simple interactions. The highly specific nature of the subunit interfaces suggests that these could be good targets for antivirals.

Wake Geometry Effects on Rotor Blade-Vortex Interaction Noise Directivity

NASA Technical Reports Server (NTRS)

Martin, R. M.; Marcolini, Michael A.; Splettstoesser, W. R.; Schultz, K.-J.

1990-01-01

Acoustic measurements from a model rotor wind tunnel test are presented which show that the directionality of rotor blade vortex interaction (BVI) noise is strongly dependent on the rotor advance ratio and disk attitude. A rotor free wake analysis is used to show that the general locus of interactions on the rotor disk is also strongly dependent on advance ratio and disk attitude. A comparison of the changing directionality of the BVI noise with changes in the interaction locations shows that the strongest noise radiation occurs in the direction of motion normal to the blade span at the time of interaction, for both advancing and retreating side BVI. For advancing side interactions, the BVI radiation angle down from the tip-path plane appears relatively insensitive to rotor operating condition and is typically between 40 and 55 deg below the disk. However, the azimuthal radiation direction shows a clear trend with descent speed, moving towards the right of the flight path with increasing descent speed. The movement of the strongest radiation direction is attributed to the movement of the interaction locations on the rotor disk with increasing descent speed.

Validation of coupled atmosphere-fire behavior models

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

Bossert, J.E.; Reisner, J.M.; Linn, R.R.

1998-12-31

Recent advances in numerical modeling and computer power have made it feasible to simulate the dynamical interaction and feedback between the heat and turbulence induced by wildfires and the local atmospheric wind and temperature fields. At Los Alamos National Laboratory, the authors have developed a modeling system that includes this interaction by coupling a high resolution atmospheric dynamics model, HIGRAD, with a fire behavior model, BEHAVE, to predict the spread of wildfires. The HIGRAD/BEHAVE model is run at very high resolution to properly resolve the fire/atmosphere interaction. At present, these coupled wildfire model simulations are computationally intensive. The additional complexitymore » of these models require sophisticated methods for assuring their reliability in real world applications. With this in mind, a substantial part of the research effort is directed at model validation. Several instrumented prescribed fires have been conducted with multi-agency support and participation from chaparral, marsh, and scrub environments in coastal areas of Florida and inland California. In this paper, the authors first describe the data required to initialize the components of the wildfire modeling system. Then they present results from one of the Florida fires, and discuss a strategy for further testing and improvement of coupled weather/wildfire models.« less

Ventral Fronto-Temporal Pathway Supporting Cognitive Control of Episodic Memory Retrieval

PubMed Central

Barredo, Jennifer; Öztekin, Ilke; Badre, David

2015-01-01

Achieving our goals often requires guiding access to relevant information from memory. Such goal-directed retrieval requires interactions between systems supporting cognitive control, including ventrolateral prefrontal cortex (VLPFC), and those supporting declarative memory, such as the medial temporal lobes (MTL). However, the pathways by which VLPFC interacts with MTL during retrieval are underspecified. Prior neuroanatomical evidence suggests that a polysynaptic ventral fronto-temporal pathway may support VLPFC–MTL interactions. To test this hypothesis, human participants were scanned using fMRI during performance of a source-monitoring task. The strength of source information was varied via repetition during encoding. Single encoding events should produce a weaker memory trace, thus recovering source information about these items should demand greater cognitive control. Results demonstrated that cortical targets along the ventral path—anterior VLPFC, temporal pole, anterior parahippocampus, and hippocampus—exhibited increases in univariate BOLD response correlated with increases in controlled retrieval demand, independent of factors related to response selection. Further, a functional connectivity analysis indicated that these regions functionally couple and are distinguishable from a dorsal pathway related to response selection demands. These data support a ventral retrieval pathway linking PFC and MTL. PMID:24177990

High frequency flow-structural interaction in dense subsonic fluids

NASA Technical Reports Server (NTRS)

Liu, Baw-Lin; Ofarrell, J. M.

1995-01-01

Prediction of the detailed dynamic behavior in rocket propellant feed systems and engines and other such high-energy fluid systems requires precise analysis to assure structural performance. Designs sometimes require placement of bluff bodies in a flow passage. Additionally, there are flexibilities in ducts, liners, and piping systems. A design handbook and interactive data base have been developed for assessing flow/structural interactions to be used as a tool in design and development, to evaluate applicable geometries before problems develop, or to eliminate or minimize problems with existing hardware. This is a compilation of analytical/empirical data and techniques to evaluate detailed dynamic characteristics of both the fluid and structures. These techniques have direct applicability to rocket engine internal flow passages, hot gas drive systems, and vehicle propellant feed systems. Organization of the handbook is by basic geometries for estimating Strouhal numbers, added mass effects, mode shapes for various end constraints, critical onset flow conditions, and possible structural response amplitudes. Emphasis is on dense fluids and high structural loading potential for fatigue at low subsonic flow speeds where high-frequency excitations are possible. Avoidance and corrective measure illustrations are presented together with analytical curve fits for predictions compiled from a comprehensive data base.

Novel substituted 1,4-anthracenediones with antitumor activity directly induce permeability transition in isolated mitochondria.

PubMed

Perchellet, Elisabeth M; Wang, Yang; Lou, Kaiyan; Zhao, Huiping; Battina, Srinivas K; Hua, Duy H; Perchellet, Jean-Pierre H

2007-11-01

Synthetic analogs of 1,4-anthraquinone (AQ code number), which block nucleoside transport, decrease DNA, RNA and protein syntheses, trigger cytochrome c release without caspase activation, induce apoptotic DNA fragmentation and inhibit the proliferation of wild-type and multidrug resistant tumor cells in the nM range in vitro, rapidly cause the collapse of mitochondrial transmembrane potential in cell and cell-free systems. Because mitochondrial permeability transition (MPT) requires more than depolarization to occur, antitumor AQs were tested for their ability to directly trigger specific markers of MPT in isolated mitochondria. In contrast to a spectrum of conventional anticancer drugs that are inactive, various AQs interact with isolated mitochondria in a concentration- and time-dependent manner to rapidly cause large amplitude swelling and Ca2+ release in relation with their effectiveness against L1210, HL-60 and LL/2 tumor cells in vitro. Indeed, the lead antitumor AQ8, AQ9 and AQ17 are also the most effective inducers of MPT in isolated mitochondria, whereas all AQ derivatives devoid of anti-proliferative activity also fail to trigger mitochondrial swelling and Ca2+ release. Moreover, the ability of 4 microM AQ17 to maximally induce mitochondrial swelling and Ca2+ release within 15 min is similar to that of classic MPT-inducing agents, such as 5 microg/ml alamethicin, 200 microM atractyloside, 5 microM phenylarsine oxide, 100 microM arsenic trioxide and a 100 microM Ca2+ overload. Interestingly, AQ17 requires a priming concentration of 20 microM Ca2+ to trigger mitochondrial swelling and Ca2+ release and these 0.1 microM ruthenium red-sensitive MPT events are abolished by 1 microM cyclosporin A, 2 mM ADP and 20 microM bongkrekic acid, which block components of the permeability transition pore (PTP), and also inhibited by 50-100 microM of various ubiquinones, which interact with the quinone binding site of the PTP and raise the Ca2+ load required for PTP opening. Hence, antitumor AQs that target isolated mitochondria and trigger MPT might directly interact with components of the PTP to induce conformational changes that increase its Ca2+ sensitivity and transition from the closed to the open state.

Structural and functional characterization of a new recombinant histidine-tagged acyl coenzyme A binding protein (ACBP) from mouse

PubMed Central

Petrescu, Anca D.; Huang, Huan; Hostetler, Heather A.; Schroeder, Friedhelm; Kier, Ann B.

2008-01-01

Acyl-coenzyme A binding protein (ACBP) has been proposed to transport fatty acyl-CoAs intracellularly, facilitating their metabolism. In this study, a new mouse recombinant ACBP was produced by insertion of a histidine (his) tag at the C-terminus to allow efficient purification by Ni-affinity chromatography. The his-tag was inserted at the C-terminus since ACBP is a small molecular size (10 kDa) protein whose structure and activity are sensitive to amino acid substitutions in the N-terminus. The his tag had no or little effect on ACBP structure or ligand binding affinity and specificity. His-ACBP bound the naturally-occurring fluorescent cis-parinaroyl-CoA with very high affinity (Kd=2.15 nM), but exhibited no affinity for non-esterified cis-parinaric acid. To determine if the presence of the C-terminal his tag altered ACBP interactions with other proteins, direct binding to hepatocyte nuclear factor 4α (HNF-4α), a nuclear receptor regulating transcription of genes involved in lipid metabolism, was examined. His-ACBP and HNF-4α were labeled with Cy5 and Cy3, respectively, and direct interaction was determined by a novel fluorescence resonance energy transfer (FRET) binding assay. FRET analysis showed that his-ACBP directly interacted with HNF-4α (intermolecular distance of 73 Å) at high affinity (Kd=64-111 nM) similar to native ACBP. The his-tag also had no effect on ACBPs ability to interact with and stimulate microsomal enzymes utilizing or forming fatty acyl CoA. Thus, C-terminal his-tagged-ACBP maintained very similar structural and functional features of the untagged native protein and can be used in further in vitro experiments that require pure recombinant ACBP. PMID:18178100

Direct interaction of CaVβ with actin up-regulates L-type calcium currents in HL-1 cardiomyocytes.

PubMed

Stölting, Gabriel; de Oliveira, Regina Campos; Guzman, Raul E; Miranda-Laferte, Erick; Conrad, Rachel; Jordan, Nadine; Schmidt, Silke; Hendriks, Johnny; Gensch, Thomas; Hidalgo, Patricia

2015-02-20

Expression of the β-subunit (CaVβ) is required for normal function of cardiac L-type calcium channels, and its up-regulation is associated with heart failure. CaVβ binds to the α1 pore-forming subunit of L-type channels and augments calcium current density by facilitating channel opening and increasing the number of channels in the plasma membrane, by a poorly understood mechanism. Actin, a key component of the intracellular trafficking machinery, interacts with Src homology 3 domains in different proteins. Although CaVβ encompasses a highly conserved Src homology 3 domain, association with actin has not yet been explored. Here, using co-sedimentation assays and FRET experiments, we uncover a direct interaction between CaVβ and actin filaments. Consistently, single-molecule localization analysis reveals streaklike structures composed by CaVβ2 that distribute over several micrometers along actin filaments in HL-1 cardiomyocytes. Overexpression of CaVβ2-N3 in HL-1 cells induces an increase in L-type current without altering voltage-dependent activation, thus reflecting an increased number of channels in the plasma membrane. CaVβ mediated L-type up-regulation, and CaVβ-actin association is prevented by disruption of the actin cytoskeleton with cytochalasin D. Our study reveals for the first time an interacting partner of CaVβ that is directly involved in vesicular trafficking. We propose a model in which CaVβ promotes anterograde trafficking of the L-type channels by anchoring them to actin filaments in their itinerary to the plasma membrane. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Hyper-Rayleigh scattering in centrosymmetric systems

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

Williams, Mathew D.; Ford, Jack S.; Andrews, David L., E-mail: david.andrews@physics.org

Hyper-Rayleigh scattering (HRS) is an incoherent mechanism for optical second harmonic generation. The frequency-doubled light that emerges from this mechanism is not emitted in a laser-like manner, in the forward direction; it is scattered in all directions. The underlying theory for this effect involves terms that are quadratic in the incident field and involves an even-order optical susceptibility (for a molecule, its associated hyperpolarizability). In consequence, HRS is often regarded as formally forbidden in centrosymmetric media. However, for the fundamental three-photon interaction, theory based on the standard electric dipole approximation, representable as E1{sup 3}, does not account for all experimentalmore » observations. The relevant results emerge upon extending the theory to include E1{sup 2}M1 and E1{sup 2}E2 contributions, incorporating one magnetic dipolar or electric quadrupolar interaction, respectively, to a consistent level of multipolar expansion. Both additional interactions require the deployment of higher orders in the multipole expansion, with the E1{sup 2}E2 interaction analogous in rank and parity to a four-wave susceptibility. To elicit the correct form of response from fluid or disordered media invites a tensor representation which does not oversimplify the molecular components, yet which can produce results to facilitate the interpretation of experimental observations. The detailed derivation in this work leads to results which are summarized for the following: perpendicular detection of polarization components both parallel and perpendicular to the pump radiation, leading to distinct polarization ratio results, as well as a reversal ratio for forward scattered circular polarizations. The results provide a route to handling data with direct physical interpretation, to enable the more sophisticated design of molecules with sought nonlinear optical properties.« less

Hyper-Rayleigh scattering in centrosymmetric systems

NASA Astrophysics Data System (ADS)

Williams, Mathew D.; Ford, Jack S.; Andrews, David L.

2015-09-01

Hyper-Rayleigh scattering (HRS) is an incoherent mechanism for optical second harmonic generation. The frequency-doubled light that emerges from this mechanism is not emitted in a laser-like manner, in the forward direction; it is scattered in all directions. The underlying theory for this effect involves terms that are quadratic in the incident field and involves an even-order optical susceptibility (for a molecule, its associated hyperpolarizability). In consequence, HRS is often regarded as formally forbidden in centrosymmetric media. However, for the fundamental three-photon interaction, theory based on the standard electric dipole approximation, representable as E13, does not account for all experimental observations. The relevant results emerge upon extending the theory to include E12M1 and E12E2 contributions, incorporating one magnetic dipolar or electric quadrupolar interaction, respectively, to a consistent level of multipolar expansion. Both additional interactions require the deployment of higher orders in the multipole expansion, with the E12E2 interaction analogous in rank and parity to a four-wave susceptibility. To elicit the correct form of response from fluid or disordered media invites a tensor representation which does not oversimplify the molecular components, yet which can produce results to facilitate the interpretation of experimental observations. The detailed derivation in this work leads to results which are summarized for the following: perpendicular detection of polarization components both parallel and perpendicular to the pump radiation, leading to distinct polarization ratio results, as well as a reversal ratio for forward scattered circular polarizations. The results provide a route to handling data with direct physical interpretation, to enable the more sophisticated design of molecules with sought nonlinear optical properties.

Direct Measurement of the Surface Energy of Graphene.

PubMed

van Engers, Christian D; Cousens, Nico E A; Babenko, Vitaliy; Britton, Jude; Zappone, Bruno; Grobert, Nicole; Perkin, Susan

2017-06-14

Graphene produced by chemical vapor deposition (CVD) is a promising candidate for implementing graphene in a range of technologies. In most device configurations, one side of the graphene is supported by a solid substrate, wheras the other side is in contact with a medium of interest, such as a liquid or other two-dimensional material within a van der Waals stack. In such devices, graphene interacts on both faces via noncovalent interactions and therefore surface energies are key parameters for device fabrication and operation. In this work, we directly measured adhesive forces and surface energies of CVD-grown graphene in dry nitrogen, water, and sodium cholate using a modified surface force balance. For this, we fabricated large (∼1 cm 2 ) and clean graphene-coated surfaces with smooth topography at both macro- and nanoscales. By bringing two such surfaces into contact and measuring the force required to separate them, we measured the surface energy of single-layer graphene in dry nitrogen to be 115 ± 4 mJ/m 2 , which was similar to that of few-layer graphene (119 ± 3 mJ/m 2 ). In water and sodium cholate, we measured interfacial energies of 83 ± 7 and 29 ± 6 mJ/m 2 , respectively. Our work provides the first direct measurement of graphene surface energy and is expected to have an impact both on the development of graphene-based devices and contribute to the fundamental understanding of surface interactions.

Interactions between mitoNEET and NAF-1 in cells

PubMed Central

Tamir, Sagi; Luo, Yuting; Bai, Fang; Adenwalla, Ammar; Darash-Yahana, Merav; Sohn, Yang-Sung; Jennings, Patricia A.; Azad, Rajeev K.; Onuchic, Jose' N.; Morcos, Faruck; Nechushtai, Rachel

2017-01-01

The NEET proteins mitoNEET (mNT) and nutrient-deprivation autophagy factor-1 (NAF-1) are required for cancer cell proliferation and resistance to oxidative stress. NAF-1 and mNT are also implicated in a number of other human pathologies including diabetes, neurodegeneration and cardiovascular disease, as well as in development, differentiation and aging. Previous studies suggested that mNT and NAF-1 could function in the same pathway in mammalian cells, preventing the over-accumulation of iron and reactive oxygen species (ROS) in mitochondria. Nevertheless, it is unknown whether these two proteins directly interact in cells, and how they mediate their function. Here we demonstrate, using yeast two-hybrid, in vivo bimolecular fluorescence complementation (BiFC), direct coupling analysis (DCA), RNA-sequencing, ROS and iron imaging, and single and double shRNA lines with suppressed mNT, NAF-1 and mNT/NAF-1 expression, that mNT and NAF-1 directly interact in mammalian cells and could function in the same cellular pathway. We further show using an in vitro cluster transfer assay that mNT can transfer its clusters to NAF-1. Our study highlights the possibility that mNT and NAF-1 function as part of an iron-sulfur (2Fe-2S) cluster relay to maintain the levels of iron and Fe-S clusters under control in the mitochondria of mammalian cells, thereby preventing the activation of apoptosis and/or autophagy and supporting cellular proliferation. PMID:28426722

Direct benefits and indirect costs of warm temperatures for high-elevation populations of a solitary bee.

PubMed

Forrest, Jessica R K; Chisholm, Sarah P M

2017-02-01

Warm temperatures are required for insect flight. Consequently, warming could benefit many high-latitude and high-altitude insects by increasing opportunities for foraging or oviposition. However, warming can also alter species interactions, including interactions with natural enemies, making the net effect of rising temperatures on population growth rate difficult to predict. We investigated the temperature-dependence of nesting activity and lifetime reproductive output over 3 yr in subalpine populations of a pollen-specialist bee, Osmia iridis. Rates of nest provisioning increased with ambient temperatures and with availability of floral resources, as expected. However, warmer conditions did not increase lifetime reproductive output. Lifetime offspring production was best explained by rates of brood parasitism (by the wasp Sapyga), which increased with temperature. Direct observations of bee and parasite activity suggest that although activity of both species is favored by warmer temperatures, bees can be active at lower ambient temperatures, while wasps are active only at higher temperatures. Thus, direct benefits to the bees of warmer temperatures were nullified by indirect costs associated with increased parasite activity. To date, most studies of climate-change effects on pollinators have focused on changing interactions between pollinators and their floral host-plants (i.e., bottom-up processes). Our results suggest that natural enemies (i.e., top-down forces) can play a key role in pollinator population regulation and should not be overlooked in forecasts of pollinator responses to climate change. © 2016 by the Ecological Society of America.

Phosphorylated STAT5 directly facilitates parvovirus B19 DNA replication in human erythroid progenitors through interaction with the MCM complex.

PubMed

Ganaie, Safder S; Zou, Wei; Xu, Peng; Deng, Xuefeng; Kleiboeker, Steve; Qiu, Jianming

2017-05-01

Productive infection of human parvovirus B19 (B19V) exhibits high tropism for burst forming unit erythroid (BFU-E) and colony forming unit erythroid (CFU-E) progenitor cells in human bone marrow and fetal liver. This exclusive restriction of the virus replication to human erythroid progenitor cells is partly due to the intracellular factors that are essential for viral DNA replication, including erythropoietin signaling. Efficient B19V replication also requires hypoxic conditions, which upregulate the signal transducer and activator of transcription 5 (STAT5) pathway, and phosphorylated STAT5 is essential for virus replication. In this study, our results revealed direct involvement of STAT5 in B19V DNA replication. Consensus STAT5-binding elements were identified adjacent to the NS1-binding element within the minimal origins of viral DNA replication in the B19V genome. Phosphorylated STAT5 specifically interacted with viral DNA replication origins both in vivo and in vitro, and was actively recruited within the viral DNA replication centers. Notably, STAT5 interacted with minichromosome maintenance (MCM) complex, suggesting that STAT5 directly facilitates viral DNA replication by recruiting the helicase complex of the cellular DNA replication machinery to viral DNA replication centers. The FDA-approved drug pimozide dephosphorylates STAT5, and it inhibited B19V replication in ex vivo expanded human erythroid progenitors. Our results demonstrated that pimozide could be a promising antiviral drug for treatment of B19V-related diseases.

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

Cellular Scale Anisotropic Topography Guides Schwann Cell Motility

PubMed Central

Mitchel, Jennifer A.; Hoffman-Kim, Diane

2011-01-01

Directed migration of Schwann cells (SC) is critical for development and repair of the peripheral nervous system. Understanding aspects of motility specific to SC, along with SC response to engineered biomaterials, may inform strategies to enhance nerve regeneration. Rat SC were cultured on laminin-coated microgrooved poly(dimethyl siloxane) platforms that were flat or presented repeating cellular scale anisotropic topographical cues, 30 or 60 µm in width, and observed with timelapse microscopy. SC motion was directed parallel to the long axis of the topography on both the groove floor and the plateau, with accompanying differences in velocity and directional persistence in comparison to SC motion on flat substrates. In addition, feature dimension affected SC morphology, alignment, and directional persistence. Plateaus and groove floors presented distinct cues which promoted differential motility and variable interaction with the topographical features. SC on the plateau surfaces tended to have persistent interactions with the edge topography, while SC on the groove floors tended to have infrequent contact with the corners and walls. Our observations suggest the capacity of SC to be guided without continuous contact with a topographical cue. SC exhibited a range of distinct motile morphologies, characterized by their symmetry and number of extensions. Across all conditions, SC with a single extension traveled significantly faster than cells with more or no extensions. We conclude that SC motility is complex, where persistent motion requires cellular asymmetry, and that anisotropic topography with cellular scale features can direct SC motility. PMID:21949703

Effect of direct eye contact in women with PTSD related to interpersonal trauma: Psychophysiological interaction analysis of connectivity of an innate alarm system.

PubMed

Steuwe, Carolin; Daniels, Judith K; Frewen, Paul A; Densmore, Maria; Theberge, Jean; Lanius, Ruth A

2015-05-30

In healthy individuals, direct eye contact is thought to modulate a cortical route eliciting social cognitive processes via activation of a fast subcortical pathway. This study aimed to examine functional brain connectivity during direct eye contact in women with posttraumatic stress disorder (PTSD) related to childhood abuse as compared with healthy controls. We conducted psychophysiological interaction (PPI) analyses in Statistical Parametric Mapping-8 (SPM8) using the superior colliculus (SC) and locus coeruleus (LC) as seed regions while 16 healthy subjects and 16 patients with a primary diagnosis of PTSD related to childhood maltreatment viewed a functional magnetic resonance imaging (fMRI) paradigm involving direct (D) versus averted (A) gaze (happy, sad, neutral). The PTSD group showed a significantly enhanced connectivity between the SC and the anterior cingulate, and between the LC and the thalamus, caudate, putamen, insula, cingulate gyrus, and amygdala, as compared with healthy individuals. Symptom severity scores on the Clinician-Administered PTSD Scale (CAPS) showed significant positive correlations with superior colliculus connectivity with the perigenual and posterior cingulate, insula, and sublenticular extended amygdala. Functional connectivity data suggest increased recruitment of brain regions involved in emotion processing during direct gaze in PTSD in association with the fast subcortical pathway. The interpretation of eye contact as a signal of threat may require more emotion regulatory capacities in patients with PTSD. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

The carboxyl-terminus directs TAF(I)48 to the nucleus and nucleolus and associates with multiple nuclear import receptors.

PubMed

Dynes, Joseph L; Xu, Shuping; Bothner, Sarah; Lahti, Jill M; Hori, Roderick T

2004-03-01

The protein complex Selectivity Factor 1, composed of TBP, TAF(I)48, TAF(I)63 and TAF(I)110, is required for rRNA transcription by RNA polymerase I in the nucleolus. The steps involved in targeting Selectivity Factor 1 will be dependent on the transport pathways that are used and the localization signals that direct this trafficking. In order to investigate these issues, we characterized human TAF(I)48, a subunit of Selectivity Factor 1. By domain analysis of TAF(I)48, the carboxyl-terminal 51 residues were found to be required for the localization of TAF(I)48, as well as sufficient to direct Green Fluorescent Protein to the nucleus and nucleolus. The carboxyl-terminus of TAF(I)48 also has the ability to associate with multiple members of the beta-karyopherin family of nuclear import receptors, including importin beta (karyopherin beta1), transportin (karyopherin beta2) and RanBP5 (karyopherin beta3), in a Ran-dependent manner. This property of interacting with multiple beta-karyopherins has been previously reported for the nuclear localization signals of some ribosomal proteins that are likewise directed to the nucleolus. This study identifies the first nuclear import sequence identified within the TBP-Associated Factor subunits of Selectivity Factor 1.

Bimolecular fluorescence complementation: visualization of molecular interactions in living cells.

PubMed

Kerppola, Tom K

2008-01-01

A variety of experimental methods have been developed for the analysis of protein interactions. The majority of these methods either require disruption of the cells to detect molecular interactions or rely on indirect detection of the protein interaction. The bimolecular fluorescence complementation (BiFC) assay provides a direct approach for the visualization of molecular interactions in living cells and organisms. The BiFC approach is based on the facilitated association between two fragments of a fluorescent protein when the fragments are brought together by an interaction between proteins fused to the fragments. The BiFC approach has been used for visualization of interactions among a variety of structurally diverse interaction partners in many different cell types. It enables detection of transient complexes as well as complexes formed by a subpopulation of the interaction partners. It is essential to include negative controls in each experiment in which the interface between the interaction partners has been mutated or deleted. The BiFC assay has been adapted for simultaneous visualization of multiple protein complexes in the same cell and the competition for shared interaction partners. A ubiquitin-mediated fluorescence complementation assay has also been developed for visualization of the covalent modification of proteins by ubiquitin family peptides. These fluorescence complementation assays have a great potential to illuminate a variety of biological interactions in the future.

Inelastic Boosted Dark Matter at direct detection experiments

NASA Astrophysics Data System (ADS)

Giudice, Gian F.; Kim, Doojin; Park, Jong-Chul; Shin, Seodong

2018-05-01

We explore a novel class of multi-particle dark sectors, called Inelastic Boosted Dark Matter (iBDM). These models are constructed by combining properties of particles that scatter off matter by making transitions to heavier states (Inelastic Dark Matter) with properties of particles that are produced with a large Lorentz boost in annihilation processes in the galactic halo (Boosted Dark Matter). This combination leads to new signals that can be observed at ordinary direct detection experiments, but require unconventional searches for energetic recoil electrons in coincidence with displaced multi-track events. Related experimental strategies can also be used to probe MeV-range boosted dark matter via their interactions with electrons inside the target material.

Signature of hydrophobic hydration in a single polymer

PubMed Central

Li, Isaac T. S.; Walker, Gilbert C.

2011-01-01

Hydrophobicity underpins self-assembly in many natural and synthetic molecular and nanoscale systems. A signature of hydrophobicity is its temperature dependence. The first experimental evaluation of the temperature and size dependence of hydration free energy in a single hydrophobic polymer is reported, which tests key assumptions in models of hydrophobic interactions in protein folding. Herein, the hydration free energy required to extend three hydrophobic polymers with differently sized aromatic side chains was directly measured by single molecule force spectroscopy. The results are threefold. First, the hydration free energy per monomer is found to be strongly dependent on temperature and does not follow interfacial thermodynamics. Second, the temperature dependence profiles are distinct among the three hydrophobic polymers as a result of a hydrophobic size effect at the subnanometer scale. Third, the hydration free energy of a monomer on a macromolecule is different from a free monomer; corrections for the reduced hydration free energy due to hydrophobic interaction from neighboring units are required. PMID:21911397

Dorsolateral prefrontal lesions do not impair tests of scene learning and decision-making that require frontal–temporal interaction

PubMed Central

Baxter, Mark G; Gaffan, David; Kyriazis, Diana A; Mitchell, Anna S

2008-01-01

Theories of dorsolateral prefrontal cortex (DLPFC) involvement in cognitive function variously emphasize its involvement in rule implementation, cognitive control, or working and/or spatial memory. These theories predict broad effects of DLPFC lesions on tests of visual learning and memory. We evaluated the effects of DLPFC lesions (including both banks of the principal sulcus) in rhesus monkeys on tests of scene learning and strategy implementation that are severely impaired following crossed unilateral lesions of frontal cortex and inferotemporal cortex. Dorsolateral lesions had no effect on learning of new scene problems postoperatively, or on the implementation of preoperatively acquired strategies. They were also without effect on the ability to adjust choice behaviour in response to a change in reinforcer value, a capacity that requires interaction between the amygdala and frontal lobe. These intact abilities following DLPFC damage support specialization of function within the prefrontal cortex, and suggest that many aspects of memory and strategic and goal-directed behaviour can survive ablation of this structure. PMID:18702721

Interacting with a security system: The Argus user interface

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

Behrin, E.; Davis, G.E.

1993-12-31

In the mid-1980s the Lawrence Livermore National Laboratory (LLNL) developed the Argus Security System. Key requirements were to eliminate the telephone as a verification device for opening and closing alarm stations and to allow need-to-know access through local enrollment at alarm stations. Resulting from these requirements was an LLNL-designed user interface called the Remote Access Panel (RAP). The Argus RAP interacts with Argus field processors to allow secure station mode changes and local station enrollment, provides user direction and response, and assists station maintenance personnel. It consists of a tamper-detecting housing containing a badge reader, a keypad with sight screen,more » special-purpose push buttons and a liquid-crystal display. This paper discusses Argus system concepts, RAP design, functional characteristics and its physical configurations. The paper also describes the RAP`s use in access-control booths, it`s integration with biometrics and its operation for multi-person-rule stations and compartmented facilities.« less

Centromeric binding and activity of Protein Phosphatase 4

PubMed Central

Lipinszki, Zoltan; Lefevre, Stephane; Savoian, Matthew S.; Singleton, Martin R.; Glover, David M.; Przewloka, Marcin R.

2015-01-01

The cell division cycle requires tight coupling between protein phosphorylation and dephosphorylation. However, understanding the cell cycle roles of multimeric protein phosphatases has been limited by the lack of knowledge of how their diverse regulatory subunits target highly conserved catalytic subunits to their sites of action. Phosphoprotein phosphatase 4 (PP4) has been recently shown to participate in the regulation of cell cycle progression. We now find that the EVH1 domain of the regulatory subunit 3 of Drosophila PP4, Falafel (Flfl), directly interacts with the centromeric protein C (CENP-C). Unlike other EVH1 domains that interact with proline-rich ligands, the crystal structure of the Flfl amino-terminal EVH1 domain bound to a CENP-C peptide reveals a new target-recognition mode for the phosphatase subunit. We also show that binding of Flfl to CENP-C is required to bring PP4 activity to centromeres to maintain CENP-C and attached core kinetochore proteins at chromosomes during mitosis. PMID:25562660

Indian hedgehog signaling from endothelial cells is required for sclera and retinal pigment epithelium development in the mouse eye.

PubMed

Dakubo, Gabriel D; Mazerolle, Chantal; Furimsky, Marosh; Yu, Chuan; St-Jacques, Benoit; McMahon, Andrew P; Wallace, Valerie A

2008-08-01

The development of extraocular orbital structures, in particular the choroid and sclera, is regulated by a complex series of interactions between neuroectoderm, neural crest and mesoderm derivatives, although in many instances the signals that mediate these interactions are not known. In this study we have investigated the function of Indian hedgehog (Ihh) in the developing mammalian eye. We show that Ihh is expressed in a population of non-pigmented cells located in the developing choroid adjacent to the RPE. The analysis of Hh mutant mice demonstrates that the RPE and developing scleral mesenchyme are direct targets of Ihh signaling and that Ihh is required for the normal pigmentation pattern of the RPE and the condensation of mesenchymal cells to form the sclera. Our findings also indicate that Ihh signals indirectly to promote proliferation and photoreceptor specification in the neural retina. This study identifies Ihh as a novel choroid-derived signal that regulates RPE, sclera and neural retina development.

Anthrax toxin receptor 1 is the cellular receptor for Seneca Valley virus

PubMed Central

Miles, Linde A.; Burga, Laura N.; Gardner, Eric E.; Bostina, Mihnea; Poirier, John T.; Rudin, Charles M.

2017-01-01

Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. It has shown promise as a cancer therapeutic in preclinical studies and early-phase clinical trials. Here, we have identified anthrax toxin receptor 1 (ANTXR1) as the receptor for SVV using genome-wide loss-of-function screens. ANTXR1 is necessary for permissivity in vitro and in vivo. However, robust SVV replication requires an additional innate immune defect. We found that SVV interacts directly and specifically with ANTXR1, that this interaction is required for SVV binding to permissive cells, and that ANTXR1 expression is necessary and sufficient for infection in cell lines with decreased expression of antiviral IFN genes at baseline. Finally, we identified the region of the SVV capsid that is responsible for receptor recognition using cryoelectron microscopy of the SVV-ANTXR1-Fc complex. These studies identify ANTXR1, a class of receptor that is shared by a mammalian virus and a bacterial toxin, as the cellular receptor for SVV. PMID:28650343

Construction of the optical part of a time-of-flight detector prototype for the AFP detector

DOE PAGES

Nozka, L.; Adamczyk, L.; Avoni, G.; ...

2016-11-22

We present the construction of the optical part of the ToF (time-of-flight) subdetector prototype for the AFP (ATLAS Forward Proton) detector. The ToF detector in conjunction with a 3D silicon pixel tracker will tag and measure protons originating in central exclusive interactions p + p → p + X + p, where the two outgoing protons are scattered in the very forward directions. The ToF is required to reduce so-called pileup backgrounds that arise from multiple proton interactions in the same bunch crossing at high luminosity. The background can fake the signal of interest, and the extra rejection from themore » ToF allows the proton tagger to operate at the high luminosity required for measurement of the processes. The prototype detector uses fused silica bars emitting Cherenkov radiation as a relativistic particle passes through it. Finally, the emitted Cherenkov photons are detected by a micro-channel plate multi-anode Photomultiplier Tube (MCP-PMT) and processed by fast electronics.« less

Construction of the optical part of a time-of-flight detector prototype for the AFP detector

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

Nozka, L.; Adamczyk, L.; Avoni, G.

We present the construction of the optical part of the ToF (time-of-flight) subdetector prototype for the AFP (ATLAS Forward Proton) detector. The ToF detector in conjunction with a 3D silicon pixel tracker will tag and measure protons originating in central exclusive interactions p + p → p + X + p, where the two outgoing protons are scattered in the very forward directions. The ToF is required to reduce so-called pileup backgrounds that arise from multiple proton interactions in the same bunch crossing at high luminosity. The background can fake the signal of interest, and the extra rejection from themore » ToF allows the proton tagger to operate at the high luminosity required for measurement of the processes. The prototype detector uses fused silica bars emitting Cherenkov radiation as a relativistic particle passes through it. Finally, the emitted Cherenkov photons are detected by a micro-channel plate multi-anode Photomultiplier Tube (MCP-PMT) and processed by fast electronics.« less

Development of an e-learning portal for pediatric endocrinology: educational considerations.

PubMed

Grijpink-van den Biggelaar, K; Drop, S L S; Schuwirth, L

2010-01-01

Global accessibility and dissemination of developments in pediatric endocrinology prompted to examine how to develop an educational interactive e-SPE web portal. A systematic approach was used to identify the relevant aspects of accessibility and dissemination. An orientation at the big idea was made, executed by an analysis of the needs of student and teacher pediatric endocrinologists, a definition of the learning objectives, a research in educational literature and an exploration of ICT design specifications. The intensive collaboration between medical, educational and information technology disciplines resulted in a portal design. The portal meets requirements of adult learning, stresses interaction between partners in learning and offers direct feedback during the learning process. The portal supports the development of not only knowledge but also competences both at junior and advanced levels. When the e-SPE portal is completed, the options for summative assessment will be examined as a medium for international certification in conjunction with local and national requirements (http://espe.elearning.nl). Copyright 2010 S. Karger AG, Basel.

Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis.

PubMed

Park, Yumi; Pacitto, Angela; Bayliss, Tracy; Cleghorn, Laura A T; Wang, Zhe; Hartman, Travis; Arora, Kriti; Ioerger, Thomas R; Sacchettini, Jim; Rizzi, Menico; Donini, Stefano; Blundell, Tom L; Ascher, David B; Rhee, Kyu; Breda, Ardala; Zhou, Nian; Dartois, Veronique; Jonnala, Surendranadha Reddy; Via, Laura E; Mizrahi, Valerie; Epemolu, Ola; Stojanovski, Laste; Simeons, Fred; Osuna-Cabello, Maria; Ellis, Lucy; MacKenzie, Claire J; Smith, Alasdair R C; Davis, Susan H; Murugesan, Dinakaran; Buchanan, Kirsteen I; Turner, Penelope A; Huggett, Margaret; Zuccotto, Fabio; Rebollo-Lopez, Maria Jose; Lafuente-Monasterio, Maria Jose; Sanz, Olalla; Diaz, Gracia Santos; Lelièvre, Joël; Ballell, Lluis; Selenski, Carolyn; Axtman, Matthew; Ghidelli-Disse, Sonja; Pflaumer, Hannah; Bösche, Markus; Drewes, Gerard; Freiberg, Gail M; Kurnick, Matthew D; Srikumaran, Myron; Kempf, Dale J; Green, Simon R; Ray, Peter C; Read, Kevin; Wyatt, Paul; Barry, Clifton E; Boshoff, Helena I

2017-01-13

A potent, noncytotoxic indazole sulfonamide was identified by high-throughput screening of >100,000 synthetic compounds for activity against Mycobacterium tuberculosis (Mtb). This noncytotoxic compound did not directly inhibit cell wall biogenesis but triggered a slow lysis of Mtb cells as measured by release of intracellular green fluorescent protein (GFP). Isolation of resistant mutants followed by whole-genome sequencing showed an unusual gene amplification of a 40 gene region spanning from Rv3371 to Rv3411c and in one case a potential promoter mutation upstream of guaB2 (Rv3411c) encoding inosine monophosphate dehydrogenase (IMPDH). Subsequent biochemical validation confirmed direct inhibition of IMPDH by an uncompetitive mode of inhibition, and growth inhibition could be rescued by supplementation with guanine, a bypass mechanism for the IMPDH pathway. Beads containing immobilized indazole sulfonamides specifically interacted with IMPDH in cell lysates. X-ray crystallography of the IMPDH-IMP-inhibitor complex revealed that the primary interactions of these compounds with IMPDH were direct pi-pi interactions with the IMP substrate. Advanced lead compounds in this series with acceptable pharmacokinetic properties failed to show efficacy in acute or chronic murine models of tuberculosis (TB). Time-kill experiments in vitro suggest that sustained exposure to drug concentrations above the minimum inhibitory concentration (MIC) for 24 h were required for a cidal effect, levels that have been difficult to achieve in vivo. Direct measurement of guanine levels in resected lung tissue from tuberculosis-infected animals and patients revealed 0.5-2 mM concentrations in caseum and normal lung tissue. The high lesional levels of guanine and the slow lytic, growth-rate-dependent effect of IMPDH inhibition pose challenges to developing drugs against this target for use in treating TB.

Essential but not vulnerable: indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis

PubMed Central

Park, Yumi; Pacitto, Angela; Bayliss, Tracy; Cleghorn, Laura A. T.; Wang, Zhe; Hartman, Travis; Arora, Kriti; Ioerger, Thomas R.; Sacchettini, Jim; Rizzi, Menico; Donini, Stefano; Blundell, Tom L.; Ascher, David B.; Rhee, Kyu; Breda, Ardala; Zhou, Nian; Dartois, Veronique; Jonnala, Surendranadha Reddy; Via, Laura E.; Mizrahi, Valerie; Epemolu, Ola; Stojanovski, Laste; Simeons, Fred; Osuna-Cabello, Maria; Ellis, Lucy; MacKenzie, Claire J.; Smith, Alasdair R. C.; Davis, Susan H.; Murugesan, Dinakaran; Buchanan, Kirsteen I.; Turner, Penelope A.; Huggett, Margaret; Zuccotto, Fabio; Rebollo-Lopez, Maria Jose; Lafuente-Monasterio, Maria Jose; Sanz, Olalla; Santos Diaz, Gracia; Lelièvre, Joël; Ballell, Lluis; Selenski, Carolyn; Axtman, Matthew; Ghidelli-Disse, Sonja; Pflaumer, Hannah; Bösche, Markus; Drewes, Gerard; Freiberg, Gail M.; Kurnick, Matthew D.; Srikumaran, Myron; Kempf, Dale J.; Green, Simon R.; Ray, Peter C.; Read, Kevin; Wyatt, Paul; Barry, Clifton E; Boshoff, Helena I.

2018-01-01

A potent, non-cytotoxic indazole sulfonamide was identified by high-throughput screening of >100,000 synthetic compounds for activity against Mycobacterium tuberculosis (Mtb). This non-cytotoxic compound did not directly inhibit cell wall biogenesis but triggered a slow lysis of Mtb cells as measured by release of intracellular green fluorescent protein (GFP). Isolation of resistant mutants followed by whole-genome sequencing showed an unusual gene amplification of a 40 gene region spanning Rv3371 to Rv3411c and in one case a potential promoter mutation upstream of guaB2 (Rv3411c) encoding inosine monophosphate dehydrogenase (IMPDH). Subsequent biochemical validation confirmed direct inhibition of IMPDH by an uncompetitive mode of inhibition and growth inhibition could be rescued by supplementation with guanine, a bypass mechanism for the IMPDH pathway. Beads containing immobilized indazole sulfonamides specifically interacted with IMPDH in cell lysates. X-ray crystallography of the IMPDH-IMP-inhibitor complex revealed that the primary interactions of these compounds with IMPDH were direct pi-pi interactions with the IMP substrate. Advanced lead compounds in this series with acceptable pharmacokinetic properties failed to show efficacy in acute or chronic murine models of tuberculosis (TB). Time-kill experiments in vitro suggest that sustained exposure to drug concentrations above MIC for 24 hours were required for a cidal effect, levels that have been difficult to achieve in vivo. Direct measurement of guanine levels in resected lung tissue from tuberculosis infected animals and patients revealed 0.5–2 mM concentrations in caseum and normal lung tissue. The high lesional levels of guanine and the slow lytic, growth-rate dependent, effect of IMPDH inhibition pose challenges to developing drugs against this target for use in treating TB. PMID:27704782

Core Histones and HIRIP3, a Novel Histone-Binding Protein, Directly Interact with WD Repeat Protein HIRA

PubMed Central

Lorain, Stéphanie; Quivy, Jean-Pierre; Monier-Gavelle, Frédérique; Scamps, Christine; Lécluse, Yann; Almouzni, Geneviève; Lipinski, Marc

1998-01-01

The human HIRA gene has been named after Hir1p and Hir2p, two corepressors which together appear to act on chromatin structure to control gene transcription in Saccharomyces cerevisiae. HIRA homologs are expressed in a regulated fashion during mouse and chicken embryogenesis, and the human gene is a major candidate for the DiGeorge syndrome and related developmental disorders caused by a reduction to single dose of a fragment of chromosome 22q. Western blot analysis and double-immunofluorescence experiments using a specific antiserum revealed a primary nuclear localization of HIRA. Similar to Hir1p, HIRA contains seven amino-terminal WD repeats and probably functions as part of a multiprotein complex. HIRA and core histone H2B were found to physically interact in a yeast double-hybrid protein interaction trap, in GST pull-down assays, and in coimmunoprecipitation experiments performed from cellular extracts. In vitro, HIRA also interacted with core histone H4. H2B- and H4-binding domains were overlapping but distinguishable in the carboxy-terminal region of HIRA, and the region for HIRA interaction was mapped to the amino-terminal tail of H2B and the second α helix of H4. HIRIP3 (HIRA-interacting protein 3) is a novel gene product that was identified from its HIRA-binding properties in the yeast protein interaction trap. In vitro, HIRIP3 directly interacted with HIRA but also with core histones H2B and H3, suggesting that a HIRA-HIRIP3-containing complex could function in some aspects of chromatin and histone metabolism. Insufficient production of HIRA, which we report elsewhere interacts with homeodomain-containing DNA-binding factors during mammalian embryogenesis, could perturb the stoichiometric assembly of multimolecular complexes required for normal embryonic development. PMID:9710638

Genetic interactions underlying otic placode induction and formation.

PubMed

Solomon, Keely S; Kwak, Su-Jin; Fritz, Andreas

2004-07-01

The formation of the otic placode is a complex process requiring multiple inductive signals. In zebrafish, fgf3 and fgf8, dlx3b and dlx4b, and foxi1 have been identified as the earliest-acting genes in this process. fgf3 and fgf8 are required as inductive signals, whereas dlx3b, dlx4b, and foxi1 appear to act directly within otic primordia. We have investigated potential interactions among these genes. Depletion of either dlx3b and dlx4b or foxi1 leads to a delay of pax2a expression in the otic primordia and reduction of the otic vesicle. Depletion of both foxi1 and dlx3b results in a complete ablation of otic placode formation. A strong synergistic interaction is also observed among foxi1, fgf3, and fgf8, and a weaker interaction among dlx3b, fgf3, and fgf8. Misexpression of foxi1 can induce expression of pax8, an early marker for the otic primordia, in embryos treated with an inhibitor of fibroblast growth factor (FGF) signaling. Conversely, morpholino knockdown of foxi1 blocks ectopic pax8 expression and otic vesicle formation induced by misexpression of fgf3 and/or fgf8. The observed genetic interactions suggest a model in which foxi1 and dlx3b/dlx4b act in independent pathways together with distinct phases of FGF signaling to promote otic placode induction and development. Copyright 2004 Wiley-Liss, Inc.

Chlamydia trachomatis inclusion membrane protein CT850 interacts with the dynein light chain DYNLT1 (Tctex1).

PubMed

Mital, Jeffrey; Lutter, Erika I; Barger, Alexandra C; Dooley, Cheryl A; Hackstadt, Ted

2015-06-26

Chlamydia trachomatis actively subverts the minus-end directed microtubule motor, dynein, to traffic along microtubule tracks to the Microtubule Organizing Center (MTOC) where it remains within a membrane bound replicative vacuole for the duration of its intracellular development. Unlike most substrates of the dynein motor, disruption of the dynactin cargo-linking complex by over-expression of the p50 dynamitin subunit does not inhibit C. trachomatis transport. A requirement for chlamydial protein synthesis to initiate this process suggests that a chlamydial product supersedes a requirement for p50 dynamitin. A yeast 2-hybrid system was used to screen the chlamydia inclusion membrane protein CT850 against a HeLa cell cDNA library and identified an interaction with the dynein light chain DYNLT1 (Tctex1). This interaction was at least partially dependent upon an (R/K-R/K-X-X-R/K) motif that is characteristic of DYNLT1 binding domains. CT850 expressed ectopically in HeLa cells localized at the MTOC and this localization is similarly dependent upon the predicted DYNLT1 binding domain. Furthermore, DYNLT1 is enriched at focal concentrations of CT850 on the chlamydial inclusion membrane that are known to interact with dynein and microtubules. Depletion of DYNLT1 disrupts the characteristic association of the inclusion membrane with centrosomes. Collectively, the results suggest that CT850 interacts with DYNLT1 to promote appropriate positioning of the inclusion at the MTOC. Published by Elsevier Inc.

Determinants in the Ig Variable Domain of Human HAVCR1 (TIM-1) Are Required To Enhance Hepatitis C Virus Entry.

PubMed

Kachko, Alla; Costafreda, Maria Isabel; Zubkova, Iryna; Jacques, Jerome; Takeda, Kazuyo; Wells, Frances; Kaplan, Gerardo; Major, Marian E

2018-03-15

Hepatitis C virus (HCV) is the leading cause of chronic hepatitis in humans. Several host molecules participate in HCV cell entry, but this process remains unclear. The complete unraveling of the HCV entry process is important to further understand viral pathogenesis and develop therapeutics. Human hepatitis A virus (HAV) cellular receptor 1 (HAVCR1), CD365, also known as TIM-1, functions as a phospholipid receptor involved in cell entry of several enveloped viruses. Here, we studied the role of HAVCR1 in HCV infection. HAVCR1 antibody inhibited entry in a dose-dependent manner. HAVCR1 soluble constructs neutralized HCV, which did not require the HAVCR1 mucinlike region and was abrogated by a mutation of N to A at position 94 (N94A) in the Ig variable (IgV) domain phospholipid-binding pocket, indicating a direct interaction of the HAVCR1 IgV domain with HCV virions. However, knockout of HAVCR1 in Huh7 cells reduced but did not prevent HCV growth. Interestingly, the mouse HAVCR1 ortholog, also a phospholipid receptor, did not enhance infection and a soluble form failed to neutralize HCV, although replacement of the mouse IgV domain with the human HAVCR1 IgV domain restored the enhancement of HCV infection. Mutations in the cytoplasmic tail revealed that direct HAVCR1 signaling is not required to enhance HCV infection. Our data show that the phospholipid-binding function and other determinant(s) in the IgV domain of human HAVCR1 enhance HCV infection. Although the exact mechanism is not known, it is possible that HAVCR1 facilitates entry by stabilizing or enhancing attachment, leading to direct interactions with specific receptors, such as CD81. IMPORTANCE Hepatitis C virus (HCV) enters cells through a multifaceted process. We identified the human hepatitis A virus cellular receptor 1 (HAVCR1), CD365, also known as TIM-1, as a facilitator of HCV entry. Antibody blocking and silencing or knockout of HAVCR1 in hepatoma cells reduced HCV entry. Our findings that the interaction of HAVCR1 with HCV early during infection enhances entry but is not required for infection support the hypothesis that HAVCR1 facilitates entry by stabilizing or enhancing virus binding to the cell surface membrane and allowing the correct virus-receptor positioning for interaction with the main HCV receptors. Furthermore, our data show that in addition to the phospholipid-binding function of HAVCR1, the enhancement of HCV infection involves other determinants in the IgV domain of HAVCR1. These findings expand the repertoire of molecules that HCV uses for cell entry, adding to the already complex mechanism of HCV infection and pathogenesis. This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

Replication protein A: directing traffic at the intersection of replication and repair.

PubMed

Oakley, Greg G; Patrick, Steve M

2010-06-01

Since the initial discovery of replication protein A (RPA) as a DNA replication factor, much progress has been made on elucidating critical roles for RPA in other DNA metabolic pathways. RPA has been shown to be required for DNA replication, DNA repair, DNA recombination, and the DNA damage response pathway with roles in checkpoint activation. This review summarizes the current understanding of RPA structure, phosphorylation and protein-protein interactions in mediating these DNA metabolic processes.

Development of integrated programs for Aerospace-vehicle Design (IPAD): Product program management systems

NASA Technical Reports Server (NTRS)

Isenberg, J. M.; Southall, J. W.

1979-01-01

The Integrated Programs for Aerospace Vehicle Design (IPAD) is a computing system to support company-wide design information processing. This document presents a brief description of the management system used to direct and control a product-oriented program. This document, together with the reference design process (CR 2981) and the manufacture interactions with the design process (CR 2982), comprises the reference information that forms the basis for specifying IPAD system requirements.

Group Contribution Methods for Phase Equilibrium Calculations.

PubMed

Gmehling, Jürgen; Constantinescu, Dana; Schmid, Bastian

2015-01-01

The development and design of chemical processes are carried out by solving the balance equations of a mathematical model for sections of or the whole chemical plant with the help of process simulators. For process simulation, besides kinetic data for the chemical reaction, various pure component and mixture properties are required. Because of the great importance of separation processes for a chemical plant in particular, a reliable knowledge of the phase equilibrium behavior is required. The phase equilibrium behavior can be calculated with the help of modern equations of state or g(E)-models using only binary parameters. But unfortunately, only a very small part of the experimental data for fitting the required binary model parameters is available, so very often these models cannot be applied directly. To solve this problem, powerful predictive thermodynamic models have been developed. Group contribution methods allow the prediction of the required phase equilibrium data using only a limited number of group interaction parameters. A prerequisite for fitting the required group interaction parameters is a comprehensive database. That is why for the development of powerful group contribution methods almost all published pure component properties, phase equilibrium data, excess properties, etc., were stored in computerized form in the Dortmund Data Bank. In this review, the present status, weaknesses, advantages and disadvantages, possible applications, and typical results of the different group contribution methods for the calculation of phase equilibria are presented.

Directionality of coupling of physiological subsystems: age-related changes of cardiorespiratory interaction during different sleep stages in babies.

PubMed

Mrowka, Ralf; Cimponeriu, Laura; Patzak, Andreas; Rosenblum, Michael G

2003-12-01

Activity of many physiological subsystems has a well-expressed rhythmic character. Often, a dependency between physiological rhythms is established due to interaction between the corresponding subsystems. Traditional methods of data analysis allow one to quantify the strength of interaction but not the causal interrelation that is indispensable for understanding the mechanisms of interaction. Here we present a recently developed method for quantification of coupling direction and apply it to an important problem. Namely, we study the mutual influence of respiratory and cardiovascular rhythms in healthy newborns within the first 6 mo of life in quiet and active sleep. We find an age-related change of the coupling direction: the interaction is nearly symmetric during the first days and becomes practically unidirectional (from respiration to heart rhythm) at the age of 6 mo. Next, we show that the direction of interaction is mainly determined by respiratory frequency. If the latter is less than approximately 0.6 Hz, the interaction occurs dominantly from respiration to heart. With higher respiratory frequencies that only occur at very young ages, the dominating direction is less pronounced or even abolished. The observed dependencies are not related to sleep stage, suggesting that the coupling direction is determined by system-inherent dynamical processes, rather than by functional modulations. The directional analysis may be applied to other interacting narrow band oscillatory systems, e.g., in the central nervous system. Thus it is an important step forward in revealing and understanding causal mechanisms of interactions.

Type I γ Phosphatidylinositol Phosphate 5-Kinase i5 Controls the Ubiquitination and Degradation of the Tumor Suppressor Mitogen-inducible Gene 6.

PubMed

Sun, Ming; Cai, Jinyang; Anderson, Richard A; Sun, Yue

2016-10-07

Mitogen-inducible gene 6 (Mig6) is a tumor suppressor, and the disruption of Mig6 expression is associated with cancer development. Mig6 directly interacts with epidermal growth factor receptor (EGFR) to suppress the activation and downstream signaling of EGFR. Therefore, loss of Mig6 enhances EGFR-mediated signaling and promotes EGFR-dependent carcinogenesis. The molecular mechanism modulating Mig6 expression in cancer remains unclear. Here we demonstrate that type I γ phosphatidylinositol phosphate 5-kinase i5 (PIPKIγi5), an enzyme producing phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P 2 ), stabilizes Mig6 expression. Knockdown of PIPKIγi5 leads to the loss of Mig6 expression, which dramatically enhances and prolongs EGFR-mediated cell signaling. Loss of PIPKIγi5 significantly promotes Mig6 protein degradation via proteasomes, but it does not affect the Mig6 mRNA level. PIPKIγi5 directly interacts with the E3 ubiquitin ligase neuronal precursor cell-expressed developmentally down-regulated 4-1 (NEDD4-1). The C-terminal domain of PIPKIγi5 and the WW1 and WW2 domains of NEDD4-1 are required for their interaction. The C2 domain of NEDD4-1 is required for its interaction with PtdIns(4,5)P 2 By binding with NEDD4-1 and producing PtdIns(4,5)P 2 , PIPKIγi5 perturbs NEDD4-1-mediated Mig6 ubiquitination and the subsequent proteasomal degradation. Thus, loss of NEDD4-1 can rescue Mig6 expression in PIPKIγi5 knockdown cells. In this way, PIPKIγi5, NEDD4-1, and Mig6 form a novel molecular nexus that controls EGFR activation and downstream signaling. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

mDia1 and WAVE2 proteins interact directly with IRSp53 in filopodia and are involved in filopodium formation.

PubMed

Goh, Wah Ing; Lim, Kim Buay; Sudhaharan, Thankiah; Sem, Kai Ping; Bu, Wenyu; Chou, Ai Mei; Ahmed, Sohail

2012-02-10

Filopodia are dynamic actin-rich cell surface protrusions involved in cell migration, axon guidance, and wound healing. The RhoGTPase Cdc42 generates filopodia via IRSp53, a multidomain protein that links the processes of plasma membrane deformation and actin dynamics required for their formation in mammalian cells. The Src homology 3 domain of IRSp53 binds to the actin regulators Mena, Eps8, WAVE1, WAVE2, mDia1, and mDia2. We show that mDia1 and WAVE2 synergize with IRSp53 to form filopodia. IRSp53 also interacts directly with these two proteins within filopodia, as observed in acceptor photobleaching FRET studies. Measurement of filopodium formation by time-lapse imaging of live cells also revealed that depleting neuronal cells of either mDia1 or WAVE2 protein decreases the ability of IRSp53 to induce filopodia. In contrast, IRSp53 does not appear to partner WAVE1 or mDia2 to give rise to these structures. In addition, although all three isoforms of mDia are capable of inducing filopodia, IRSp53 requires only mDia1 to do so. These findings suggest that mDia1 and WAVE2 are important Src homology 3 domain partners of IRSp53 in forming filopodia.

mDia1 and WAVE2 Proteins Interact Directly with IRSp53 in Filopodia and Are Involved in Filopodium Formation

PubMed Central

Goh, Wah Ing; Lim, Kim Buay; Sudhaharan, Thankiah; Sem, Kai Ping; Bu, Wenyu; Chou, Ai Mei; Ahmed, Sohail

2012-01-01

Filopodia are dynamic actin-rich cell surface protrusions involved in cell migration, axon guidance, and wound healing. The RhoGTPase Cdc42 generates filopodia via IRSp53, a multidomain protein that links the processes of plasma membrane deformation and actin dynamics required for their formation in mammalian cells. The Src homology 3 domain of IRSp53 binds to the actin regulators Mena, Eps8, WAVE1, WAVE2, mDia1, and mDia2. We show that mDia1 and WAVE2 synergize with IRSp53 to form filopodia. IRSp53 also interacts directly with these two proteins within filopodia, as observed in acceptor photobleaching FRET studies. Measurement of filopodium formation by time-lapse imaging of live cells also revealed that depleting neuronal cells of either mDia1 or WAVE2 protein decreases the ability of IRSp53 to induce filopodia. In contrast, IRSp53 does not appear to partner WAVE1 or mDia2 to give rise to these structures. In addition, although all three isoforms of mDia are capable of inducing filopodia, IRSp53 requires only mDia1 to do so. These findings suggest that mDia1 and WAVE2 are important Src homology 3 domain partners of IRSp53 in forming filopodia. PMID:22179776

Modulators of 14-3-3 Protein–Protein Interactions

PubMed Central

2017-01-01

Direct interactions between proteins are essential for the regulation of their functions in biological pathways. Targeting the complex network of protein–protein interactions (PPIs) has now been widely recognized as an attractive means to therapeutically intervene in disease states. Even though this is a challenging endeavor and PPIs have long been regarded as “undruggable” targets, the last two decades have seen an increasing number of successful examples of PPI modulators, resulting in growing interest in this field. PPI modulation requires novel approaches and the integrated efforts of multiple disciplines to be a fruitful strategy. This perspective focuses on the hub-protein 14-3-3, which has several hundred identified protein interaction partners, and is therefore involved in a wide range of cellular processes and diseases. Here, we aim to provide an integrated overview of the approaches explored for the modulation of 14-3-3 PPIs and review the examples resulting from these efforts in both inhibiting and stabilizing specific 14-3-3 protein complexes by small molecules, peptide mimetics, and natural products. PMID:28968506

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

Software packages offering interactive modeling techniques are now available for use on microcomputer hardware systems. These packages are reasonably priced for both company and independent explorationists; they do not require users to have high levels of computer literacy; they are capable of rapidly completing complex ranges of sophisticated geologic and geophysical modeling tasks; and they can produce presentation-quality output for comparison with real-world data. For example, interactive packages are available for mapping, log analysis, seismic modeling, reservoir studies, and financial projects as well as for applying a variety of statistical and geostatistical techniques to analysis of exploration data. More importantly,more » these packages enable explorationists to directly apply their geologic expertise when developing and fine-tuning models for identifying new prospects and for extending producing fields. As a result of these features, microcomputers and interactive modeling software are becoming common tools in many exploration offices. Gravity and magnetics software programs illustrate some of the capabilities of such exploration tools.« less

CD9 tetraspanin generates fusion competent sites on the egg membrane for mammalian fertilization

PubMed Central

Jégou, Antoine; Ziyyat, Ahmed; Barraud-Lange, Virginie; Perez, Eric; Wolf, Jean Philippe; Pincet, Frédéric; Gourier, Christine

2011-01-01

CD9 tetraspanin is the only egg membrane protein known to be essential for fertilization. To investigate its role, we have measured, on a unique acrosome reacted sperm brought in contact with an egg, the adhesion probability and strength with a sensitivity of a single molecule attachment. Probing the binding events at different locations of wild-type egg we described different modes of interaction. Here, we show that more gamete adhesion events occur on Cd9 null eggs but that the strongest interaction mode disappears. We propose that sperm–egg fusion is a direct consequence of CD9 controlled sperm–egg adhesion properties. CD9 generates adhesion sites responsible for the strongest of the observed gamete interaction. These strong adhesion sites impose, during the whole interaction lifetime, a tight proximity of the gamete membranes, which is a requirement for fusion to take place. The CD9-induced adhesion sites would be the actual location where fusion occurs. PMID:21690351

Mass spectrometric identification of proteins that interact through specific domains of the poly(A) binding protein

PubMed Central

Zhang, Chongxu; Nielsen, Maria E. O.; Chiang, Yueh-Chin; Kierkegaard, Morten; Wang, Xin; Lee, Darren J.; Andersen, Jens S.; Yao, Gang

2013-01-01

Poly(A) binding protein (PAB1) is involved in a number of RNA metabolic functions in eukaryotic cells and correspondingly is suggested to associate with a number of proteins. We have used mass spectrometric analysis to identify 55 non-ribosomal proteins that specifically interact with PAB1 from Saccharomyces cerevisiae. Because many of these factors may associate only indirectly with PAB1 by being components of the PAB1-mRNP structure, we additionally conducted mass spectrometric analyses on seven metabolically defined PAB1 deletion derivatives to delimit the interactions between these proteins and PAB1. These latter analyses identified 13 proteins whose associations with PAB1 were reduced by deleting one or another of PAB1’s defined domains. Included in this list of 13 proteins were the translation initiation factors eIF4G1 and eIF4G2, translation termination factor eRF3, and PBP2, all of whose previously known direct interactions with specific PAB1 domains were either confirmed, delimited, or extended. The remaining nine proteins that interacted through a specific PAB1 domain were CBF5, SLF1, UPF1, CBC1, SSD1, NOP77, yGR250c, NAB6, and GBP2. In further study, UPF1, involved in nonsense-mediated decay, was confirmed to interact with PAB1 through the RRM1 domain. We additionally established that while the RRM1 domain of PAB1 was required for UPF1-induced acceleration of deadenylation during nonsense-mediated decay, it was not required for the more critical step of acceleration of mRNA decapping. These results begin to identify the proteins most likely to interact with PAB1 and the domains of PAB1 through which these contacts are made. PMID:22836166

Mass spectrometric identification of proteins that interact through specific domains of the poly(A) binding protein.

PubMed

Richardson, Roy; Denis, Clyde L; Zhang, Chongxu; Nielsen, Maria E O; Chiang, Yueh-Chin; Kierkegaard, Morten; Wang, Xin; Lee, Darren J; Andersen, Jens S; Yao, Gang

2012-09-01

Poly(A) binding protein (PAB1) is involved in a number of RNA metabolic functions in eukaryotic cells and correspondingly is suggested to associate with a number of proteins. We have used mass spectrometric analysis to identify 55 non-ribosomal proteins that specifically interact with PAB1 from Saccharomyces cerevisiae. Because many of these factors may associate only indirectly with PAB1 by being components of the PAB1-mRNP structure, we additionally conducted mass spectrometric analyses on seven metabolically defined PAB1 deletion derivatives to delimit the interactions between these proteins and PAB1. These latter analyses identified 13 proteins whose associations with PAB1 were reduced by deleting one or another of PAB1's defined domains. Included in this list of 13 proteins were the translation initiation factors eIF4G1 and eIF4G2, translation termination factor eRF3, and PBP2, all of whose previously known direct interactions with specific PAB1 domains were either confirmed, delimited, or extended. The remaining nine proteins that interacted through a specific PAB1 domain were CBF5, SLF1, UPF1, CBC1, SSD1, NOP77, yGR250c, NAB6, and GBP2. In further study, UPF1, involved in nonsense-mediated decay, was confirmed to interact with PAB1 through the RRM1 domain. We additionally established that while the RRM1 domain of PAB1 was required for UPF1-induced acceleration of deadenylation during nonsense-mediated decay, it was not required for the more critical step of acceleration of mRNA decapping. These results begin to identify the proteins most likely to interact with PAB1 and the domains of PAB1 through which these contacts are made.

Electrostatic interaction map reveals a new binding position for tropomyosin on F-actin.

PubMed

Rynkiewicz, Michael J; Schott, Veronika; Orzechowski, Marek; Lehman, William; Fischer, Stefan

2015-12-01

Azimuthal movement of tropomyosin around the F-actin thin filament is responsible for muscle activation and relaxation. Recently a model of αα-tropomyosin, derived from molecular-mechanics and electron microscopy of different contractile states, showed that tropomyosin is rather stiff and pre-bent to present one specific face to F-actin during azimuthal transitions. However, a new model based on cryo-EM of troponin- and myosin-free filaments proposes that the interacting-face of tropomyosin can differ significantly from that in the original model. Because resolution was insufficient to assign tropomyosin side-chains, the interacting-face could not be unambiguously determined. Here, we use structural analysis and energy landscapes to further examine the proposed models. The observed bend in seven crystal structures of tropomyosin is much closer in direction and extent to the original model than to the new model. Additionally, we computed the interaction map for repositioning tropomyosin over the F-actin surface, but now extended over a much larger surface than previously (using the original interacting-face). This map shows two energy minima-one corresponding to the "blocked-state" as in the original model, and the other related by a simple 24 Å translation of tropomyosin parallel to the F-actin axis. The tropomyosin-actin complex defined by the second minimum fits perfectly into the recent cryo-EM density, without requiring any change in the interacting-face. Together, these data suggest that movement of tropomyosin between regulatory states does not require interacting-face rotation. Further, they imply that thin filament assembly may involve an interplay between initially seeded tropomyosin molecules growing from distinct binding-site regions on actin.

mDia2 and CXCL12/CXCR4 chemokine signaling intersect to drive tumor cell amoeboid morphological transitions.

PubMed

Wyse, Meghan M; Goicoechea, Silvia; Garcia-Mata, Rafael; Nestor-Kalinoski, Andrea L; Eisenmann, Kathryn M

2017-03-04

Morphological plasticity in response to environmental cues in migrating cancer cells requires F-actin cytoskeletal rearrangements. Conserved formin family proteins play critical roles in cell shape, tumor cell motility, invasion and metastasis, in part, through assembly of non-branched actin filaments. Diaphanous-related formin-2 (mDia2/Diaph3/Drf3/Dia) regulates mesenchymal-to-amoeboid morphological conversions and non-apoptotic blebbing in tumor cells by interacting with its inhibitor diaphanous-interacting protein (DIP), and disrupting cortical F-actin assembly and bundling. F-actin disruption is initiated by a CXCL12-dependent mechanism. Downstream CXCL12 signaling partners inducing mDia2-dependent amoeboid conversions remain enigmatic. We found in MDA-MB-231 tumor cells CXCL12 induces DIP and mDia2 interaction in blebs, and engages its receptor CXCR4 to induce RhoA-dependent blebbing. mDia2 and CXCR4 associate in blebs upon CXCL12 stimulation. Both CXCR4 and RhoA are required for CXCL12-induced blebbing. Neither CXCR7 nor other Rho GTPases that activate mDia2 are required for CXCL12-induced blebbing. The Rho Guanine Nucleotide Exchange Factor (GEF) Net1 is required for CXCL12-driven RhoA activation and subsequent blebbing. These results reveal CXCL12 signaling, through CXCR4, directs a Net1/RhoA/mDia-dependent signaling hub to drive cytoskeleton rearrangements to regulate morphological plasticity in tumor cells. These signaling hubs may be conserved during normal and cancer cells responding to chemotactic cues. Copyright © 2017 Elsevier Inc. All rights reserved.

The bar-halo interaction - I. From fundamental dynamics to revised N-body requirements

NASA Astrophysics Data System (ADS)

Weinberg, Martin D.; Katz, Neal

2007-02-01

A galaxy remains near equilibrium for most of its history. Only through resonances can non-axisymmetric features, such as spiral arms and bars, exert torques over large scales and change the overall structure of the galaxy. In this paper, we describe the resonant interaction mechanism in detail, derive explicit criteria for the particle number required to simulate these dynamical processes accurately using N-body simulations, and illustrate them with numerical experiments. To do this, we perform a direct numerical solution of perturbation theory, in short, by solving for each orbit in an ensemble and make detailed comparisons with N-body simulations. The criteria include: sufficient particle coverage in phase space near the resonance and enough particles to minimize gravitational potential fluctuations that will change the dynamics of the resonant encounter. These criteria are general in concept and can be applied to any dynamical interaction. We use the bar-halo interaction as our primary example owing to its technical simplicity and astronomical ubiquity. Some of our more surprising findings are as follows. First, the inner Lindblad like resonance, responsible for coupling the bar to the central halo cusp, requires more than equal-mass particles within the virial radius or inside the bar radius for a Milky Way like bar in a Navarro, Frenk & White profile. Secondly, orbits that linger near the resonance receive more angular momentum than orbits that move through the resonance quickly. Small-scale fluctuations present in state-of-the-art particle-particle simulations can knock orbits out of resonance, preventing them from lingering and, thereby, decrease the torque per orbit. This can be offset by the larger number of orbits affected by the resonance due to the diffusion. However, noise from orbiting substructure remains at least an order of magnitude too small to be of consequence. Applied to N-body simulations, the required particle numbers are sufficiently high for scenarios of interest that apparent convergence in particle number is misleading: the convergence with N may still be in the noise-dominated regime. State-of-the-art simulations are not adequate to follow all aspects of secular evolution driven by the bar-halo interaction. It is not possible to derive particle number requirements that apply to all situations, for example, more subtle interactions may be even more difficult to simulate. Therefore, we present a procedure to test the requirements for individual N-body codes to the actual problem of interest.

Herpes simplex virus glycoprotein D relocates nectin-1 from intercellular contacts

PubMed Central

Bhargava, Arjun K.; Rothlauf, Paul W.; Krummenacher, Claude

2016-01-01

Herpes simplex virus (HSV) uses the cell adhesion molecule nectin-1 as a receptor to enter neurons and epithelial cells. The viral glycoprotein D (gD) is used as a non-canonical ligand for nectin-1. The gD binding site on nectin-1 overlaps with a functional adhesive site involved in nectin-nectin homophilic trans-interaction. Consequently, when nectin-1 is engaged with a cellular ligand at cell junctions, the gD binding site is occupied. Here we report that HSV gD is able to disrupt intercellular homophilic trans-interaction of nectin-1 and induce a rapid redistribution of nectin-1 from cell junctions. This movement does not require the receptor’s interaction with the actin-binding adaptor afadin. Interaction of nectin-1 with afadin is also dispensable for virion surfing along nectin-1-rich filopodia. Cells seeded on gD-coated surfaces also fail to accumulate nectin-1 at cell contact. These data indicate that HSV gD affects nectin-1 locally through direct interaction and more globally through signaling. PMID:27723487

Studying plant–pollinator interactions in a changing climate: A review of approaches1

PubMed Central

Byers, Diane L.

2017-01-01

Plant–pollinator interactions are potentially at risk due to climate change. Because of the spatial and temporal variation associated with the effects of climate change and the responses of both actors, research to assess this interaction requires creative approaches. This review focuses on assessments of plants’ and pollinators’ altered phenology in response to environmental changes, as phenology is one of the key responses. I reviewed research methods with the goal of presenting the wide diversity of available techniques for addressing changes in these interactions. Approaches ranged from use of historical specimens to multisite experimental community studies; while differing in depth of historical information and community interactions, all contribute to assessment of phenology changes. Particularly insightful were those studies that directly assessed the environmental changes across spatial and temporal scales and the responses of plants and pollinators at these scales. Longer-term studies across environmental gradients, potentially with reciprocal transplants, enable an assessment of climate impacts at both scales. While changes in phenology are well studied, the impacts of phenology changes are not. Future research should include approaches to address this gap. PMID:28690933

Marine crude-oil biodegradation: a central role for interspecies interactions

PubMed Central

2012-01-01

The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such “microbial modules” interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons. PMID:22591596

Herpes simplex virus glycoprotein D relocates nectin-1 from intercellular contacts.

PubMed

Bhargava, Arjun K; Rothlauf, Paul W; Krummenacher, Claude

2016-12-01

Herpes simplex virus (HSV) uses the cell adhesion molecule nectin-1 as a receptor to enter neurons and epithelial cells. The viral glycoprotein D (gD) is used as a non-canonical ligand for nectin-1. The gD binding site on nectin-1 overlaps with a functional adhesive site involved in nectin-nectin homophilic trans-interaction. Consequently, when nectin-1 is engaged with a cellular ligand at cell junctions, the gD binding site is occupied. Here we report that HSV gD is able to disrupt intercellular homophilic trans-interaction of nectin-1 and induce a rapid redistribution of nectin-1 from cell junctions. This movement does not require the receptor's interaction with the actin-binding adaptor afadin. Interaction of nectin-1 with afadin is also dispensable for virion surfing along nectin-1-rich filopodia. Cells seeded on gD-coated surfaces also fail to accumulate nectin-1 at cell contact. These data indicate that HSV gD affects nectin-1 locally through direct interaction and more globally through signaling. Copyright © 2016 Elsevier Inc. All rights reserved.

The interacting effects of temperature and food chain length on trophic abundance and ecosystem function.

PubMed

Beveridge, Oliver S; Humphries, Stuart; Petchey, Owen L

2010-05-01

1. While much is known about the independent effects of trophic structure and temperature on density and ecosystem processes, less is known about the interaction(s) between the two. 2. We manipulated the temperature of laboratory-based bacteria-protist communities that contained communities with one, two, or three trophic levels, and recorded species' densities and bacterial decomposition. 3. Temperature, food chain length and their interaction produced significant responses in microbial density and bacterial decomposition. Prey and resource density expressed different patterns of temperature dependency during different phases of population dynamics. The addition of a predator altered the temperature-density relationship of prey, from a unimodal trend to a negative one. Bacterial decomposition was greatest in the presence of consumers at higher temperatures. 4. These results are qualitatively consistent with a recent model of direct and indirect temperature effects on resource-consumer population dynamics. Results highlight and reinforce the importance of indirect effects of temperature mediated through trophic interactions. Understanding and predicting the consequences of environmental change will require that indirect effects, trophic structure, and individual species' tolerances be incorporated into theory and models.

Phenomenology of BWR fuel assembly degradation

NASA Astrophysics Data System (ADS)

Kurata, Masaki; Barrachin, Marc; Haste, Tim; Steinbrueck, Martin

2018-03-01

Severe accidents occurred at the Fukushima-Daiichi Nuclear Power Station (FDNPS) which required an immediate re-examination of fuel degradation phenomenology. The present paper reviews the updated knowledge on the phenomenology of the fuel degradation, focusing mainly on the BWR fuel assembly degradation at the macroscopic scale and that of the individual interactions at the meso-scale. Oxidation of boron carbide (B4C) control rods potentially generates far larger amounts of heat and hydrogen under BWR accident conditions. All integral tests with B4C control rods or control blades have shown early failure, liquefaction, relocation and oxidation of B4C starting at temperatures around 1250 °C, well below the significant interaction temperatures of UO2-Zry. These interactions or reactions potentially influence the progress of fuel degradation in the early phase. The steam-starved conditions, which are being discussed as a likely scenario at the FDNPS accident, highly influence the individual interactions and potentially lead the fuel degradation in non-prototypical directions. The detailed phenomenology of individual interactions and their influence on the transient and on the late phase of the severe accidents are also discussed.

Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations

PubMed Central

Kitchen, James L.; Allaby, Robin G.

2013-01-01

Selection and adaptation of individuals to their underlying environments are highly dynamical processes, encompassing interactions between the individual and its seasonally changing environment, synergistic or antagonistic interactions between individuals and interactions amongst the regulatory genes within the individual. Plants are useful organisms to study within systems modeling because their sedentary nature simplifies interactions between individuals and the environment, and many important plant processes such as germination or flowering are dependent on annual cycles which can be disrupted by climate behavior. Sedentism makes plants relevant candidates for spatially explicit modeling that is tied in with dynamical environments. We propose that in order to fully understand the complexities behind plant adaptation, a system that couples aspects from systems biology with population and landscape genetics is required. A suitable system could be represented by spatially explicit individual-based models where the virtual individuals are located within time-variable heterogeneous environments and contain mutable regulatory gene networks. These networks could directly interact with the environment, and should provide a useful approach to studying plant adaptation. PMID:27137364

Lidar characterizations of atmospheric aerosols and clouds

NASA Astrophysics Data System (ADS)

Ferrare, R. A.; Hostetler, C. A.; Hair, J. W.; Burton, S. P.

2017-12-01

Knowledge of the vertical profile, composition, concentration, and size distribution of aerosols is required to quantify the impacts of aerosols on human health, global and regional climate, clouds and precipitation. In particular, radiative forcing due to anthropogenic aerosols is the most uncertain part of anthropogenic radiative forcing, with aerosol-cloud interactions (ACI) as the largest source of uncertainty in current estimates of global radiative forcing. Improving aerosol transport model predictions of the vertical profile of aerosol optical and microphysical characteristics is crucial for improving assessments of aerosol radiative forcing. Understanding how aerosols and clouds interact is essential for investigating the aerosol indirect effect and ACI. Through its ability to provide vertical profiles of aerosol and cloud distributions as well as important information regarding the optical and physical properties of aerosols and clouds, lidar is a crucial tool for addressing these science questions. This presentation describes how surface, airborne, and satellite lidar measurements have been used to address these questions, and in particular how High Spectral Resolution Lidar (HSRL) measurements provide profiles of aerosol properties (backscatter, extinction, depolarization, concentration, size) important for characterizing radiative forcing. By providing a direct measurement of aerosol extinction, HSRL provides more accurate aerosol measurement profiles and more accurate constraints for models than standard retrievals from elastic backscatter lidar, which loses accuracy and precision at lower altitudes due to attenuation from overlying layers. Information regarding particle size and abundance from advanced lidar retrievals provides better proxies for cloud-condensation-nuclei (CCN), which are required for assessing aerosol-cloud interactions. When combined with data from other sensors, advanced lidar measurements can provide information on aerosol and cloud properties for addressing both direct and indirect radiative forcing.

Molecular and functional characterization of clathrin- and AP-2-binding determinants within a disordered domain of auxilin.

PubMed

Scheele, Urte; Alves, Jurgen; Frank, Ronald; Duwel, Michael; Kalthoff, Christoph; Ungewickell, Ernst

2003-07-11

Uncoating of clathrin-coated vesicles requires the J-domain protein auxilin for targeting hsc70 to the clathrin coats and for stimulating the hsc70 ATPase activity. This results in the release of hsc70-complexed clathrin triskelia and concomitant dissociation of the coat. To understand the complex role of auxilin in uncoating and clathrin assembly in more detail, we analyzed the molecular organization of its clathrin-binding domain (amino acids 547-813). CD spectroscopy of auxilin fragments revealed that the clathrin-binding domain is almost completely disordered in solution. By systematic mapping using synthetic peptides and by site-directed mutagenesis, we identified short peptide sequences involved in clathrin heavy chain and AP-2 binding and evaluated their significance for the function of auxilin. Some of the binding determinants, including those containing sequences 674DPF and 636WDW, showed dual specificity for both clathrin and AP-2. In contrast, the two DLL motifs within the clathrin-binding domain were exclusively involved in clathrin binding. Surprisingly, they interacted not only with the N-terminal domain of the heavy chain, but also with the distal domain. Moreover, both DLL peptides proved to be essential for clathrin assembly and uncoating. In addition, we found that the motif 726NWQ is required for efficient clathrin assembly activity. Auxilin shares a number of protein-protein interaction motifs with other endocytic proteins, including AP180. We demonstrate that AP180 and auxilin compete for binding to the alpha-ear domain of AP-2. Like AP180, auxilin also directly interacts with the ear domain of beta-adaptin. On the basis of our data, we propose a refined model for the uncoating mechanism of clathrin-coated vesicles.

Formation and release of arrestin domain-containing protein 1-mediated microvesicles (ARMMs) at plasma membrane by recruitment of TSG101 protein.

PubMed

Nabhan, Joseph F; Hu, Ruoxi; Oh, Raymond S; Cohen, Stanley N; Lu, Quan

2012-03-13

Mammalian cells are capable of delivering multiple types of membrane capsules extracellularly. The limiting membrane of late endosomes can fuse with the plasma membrane, leading to the extracellular release of multivesicular bodies (MVBs), initially contained within the endosomes, as exosomes. Budding viruses exploit the TSG101 protein and endosomal sorting complex required for transport (ESCRT) machinery used for MVB formation to mediate the egress of viral particles from host cells. Here we report the discovery of a virus-independent cellular process that generates microvesicles that are distinct from exosomes and which, like budding viruses, are produced by direct plasma membrane budding. Such budding is driven by a specific interaction of TSG101 with a tetrapeptide PSAP motif of an accessory protein, arrestin domain-containing protein 1 (ARRDC1), which we show is localized to the plasma membrane through its arrestin domain. This interaction results in relocation of TSG101 from endosomes to the plasma membrane and mediates the release of microvesicles that contain TSG101, ARRDC1, and other cellular proteins. Unlike exosomes, which are derived from MVBs, ARRDC1-mediated microvesicles (ARMMs) lack known late endosomal markers. ARMMs formation requires VPS4 ATPase and is enhanced by the E3 ligase WWP2, which interacts with and ubiquitinates ARRDC1. ARRDC1 protein discharged into ARMMs was observed in co-cultured cells, suggesting a role for ARMMs in intercellular communication. Our findings reveal an intrinsic cellular mechanism that results in direct budding of microvesicles from the plasma membrane, providing a formal paradigm for the evolutionary recruitment of ESCRT proteins in the release of budding viruses.

Murine Polyomavirus Cell Surface Receptors Activate Distinct Signaling Pathways Required for Infection.

PubMed

O'Hara, Samantha D; Garcea, Robert L

2016-11-01

Virus binding to the cell surface triggers an array of host responses, including activation of specific signaling pathways that facilitate steps in virus entry. Using mouse polyomavirus (MuPyV), we identified host signaling pathways activated upon virus binding to mouse embryonic fibroblasts (MEFs). Pathways activated by MuPyV included the phosphatidylinositol 3-kinase (PI3K), FAK/SRC, and mitogen-activated protein kinase (MAPK) pathways. Gangliosides and α4-integrin are required receptors for MuPyV infection. MuPyV binding to both gangliosides and the α4-integrin receptors was required for activation of the PI3K pathway; however, either receptor interaction alone was sufficient for activation of the MAPK pathway. Using small-molecule inhibitors, we confirmed that the PI3K and FAK/SRC pathways were required for MuPyV infection, while the MAPK pathway was dispensable. Mechanistically, the PI3K pathway was required for MuPyV endocytosis, while the FAK/SRC pathway enabled trafficking of MuPyV along microtubules. Thus, MuPyV interactions with specific cell surface receptors facilitate activation of signaling pathways required for virus entry and trafficking. Understanding how different viruses manipulate cell signaling pathways through interactions with host receptors could lead to the identification of new therapeutic targets for viral infection. Virus binding to cell surface receptors initiates outside-in signaling that leads to virus endocytosis and subsequent virus trafficking. How different viruses manipulate cell signaling through interactions with host receptors remains unclear, and elucidation of the specific receptors and signaling pathways required for virus infection may lead to new therapeutic targets. In this study, we determined that gangliosides and α4-integrin mediate mouse polyomavirus (MuPyV) activation of host signaling pathways. Of these pathways, the PI3K and FAK/SRC pathways were required for MuPyV infection. Both the PI3K and FAK/SRC pathways have been implicated in human diseases, such as heart disease and cancer, and inhibitors directed against these pathways are currently being investigated as therapies. It is possible that these pathways play a role in human PyV infections and could be targeted to inhibit PyV infection in immunosuppressed patients. Copyright © 2016 O’Hara and Garcea.

Counter-propagating wave interaction for contrast-enhanced ultrasound imaging

NASA Astrophysics Data System (ADS)

Renaud, G.; Bosch, J. G.; ten Kate, G. L.; Shamdasani, V.; Entrekin, R.; de Jong, N.; van der Steen, A. F. W.

2012-11-01

Most techniques for contrast-enhanced ultrasound imaging require linear propagation to detect nonlinear scattering of contrast agent microbubbles. Waveform distortion due to nonlinear propagation impairs their ability to distinguish microbubbles from tissue. As a result, tissue can be misclassified as microbubbles, and contrast agent concentration can be overestimated; therefore, these artifacts can significantly impair the quality of medical diagnoses. Contrary to biological tissue, lipid-coated gas microbubbles used as a contrast agent allow the interaction of two acoustic waves propagating in opposite directions (counter-propagation). Based on that principle, we describe a strategy to detect microbubbles that is free from nonlinear propagation artifacts. In vitro images were acquired with an ultrasound scanner in a phantom of tissue-mimicking material with a cavity containing a contrast agent. Unlike the default mode of the scanner using amplitude modulation to detect microbubbles, the pulse sequence exploiting counter-propagating wave interaction creates no pseudoenhancement behind the cavity in the contrast image.

Protein prenylation: a new mode of host-pathogen interaction.

PubMed

Amaya, Moushimi; Baranova, Ancha; van Hoek, Monique L

2011-12-09

Post translational modifications are required for proteins to be fully functional. The three step process, prenylation, leads to farnesylation or geranylgeranylation, which increase the hydrophobicity of the prenylated protein for efficient anchoring into plasma membranes and/or organellar membranes. Prenylated proteins function in a number of signaling and regulatory pathways that are responsible for basic cell operations. Well characterized prenylated proteins include Ras, Rac and Rho. Recently, pathogenic prokaryotic proteins, such as SifA and AnkB, have been shown to be prenylated by eukaryotic host cell machinery, but their functions remain elusive. The identification of other bacterial proteins undergoing this type of host-directed post-translational modification shows promise in elucidating host-pathogen interactions to develop new therapeutics. This review incorporates new advances in the study of protein prenylation into a broader aspect of biology with a focus on host-pathogen interaction. Copyright © 2011 Elsevier Inc. All rights reserved.

Linking dietary patterns with gut microbial composition and function

PubMed Central

Sheflin, Amy M.; Carbonero, Franck; Weir, Tiffany L.

2017-01-01

ABSTRACT Emerging insights have implicated the gut microbiota as an important factor in the maintenance of human health. Although nutrition research has focused on how direct interactions between dietary components and host systems influence human health, it is becoming increasingly important to consider nutrient effects on the gut microbiome for a more complete picture. Understanding nutrient-host-microbiome interactions promises to reveal novel mechanisms of disease etiology and progression, offers new disease prevention strategies and therapeutic possibilities, and may mandate alternative criteria to evaluate the safety of food ingredients. Here we review the current literature on diet effects on the microbiome and the generation of microbial metabolites of dietary constituents that may influence human health. We conclude with a discussion of the relevance of these studies to nutrition and public health and summarize further research needs required to realize the potential of exploiting diet-microbiota interactions for improved health. PMID:27960648

Phosphorylation regulates the Star-PAP-PIPKIα interaction and directs specificity toward mRNA targets.

PubMed

Mohan, Nimmy; Sudheesh, A P; Francis, Nimmy; Anderson, Richard; Laishram, Rakesh S

2015-08-18

Star-PAP is a nuclear non-canonical poly(A) polymerase (PAP) that shows specificity toward mRNA targets. Star-PAP activity is stimulated by lipid messenger phosphatidyl inositol 4,5 bisphoshate (PI4,5P2) and is regulated by the associated Type I phosphatidylinositol-4-phosphate 5-kinase that synthesizes PI4,5P2 as well as protein kinases. These associated kinases act as coactivators of Star-PAP that regulates its activity and specificity toward mRNAs, yet the mechanism of control of these interactions are not defined. We identified a phosphorylated residue (serine 6, S6) on Star-PAP in the zinc finger region, the domain required for PIPKIα interaction. We show that S6 is phosphorylated by CKIα within the nucleus which is required for Star-PAP nuclear retention and interaction with PIPKIα. Unlike the CKIα mediated phosphorylation at the catalytic domain, Star-PAP S6 phosphorylation is insensitive to oxidative stress suggesting a signal mediated regulation of CKIα activity. S6 phosphorylation together with coactivator PIPKIα controlled select subset of Star-PAP target messages by regulating Star-PAP-mRNA association. Our results establish a novel role for phosphorylation in determining Star-PAP target mRNA specificity and regulation of 3'-end processing. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Human PIRH2 Enhances Androgen Receptor Signaling through Inhibition of Histone Deacetylase 1 and Is Overexpressed in Prostate Cancer

PubMed Central

Logan, Ian R.; Gaughan, Luke; McCracken, Stuart R. C.; Sapountzi, Vasileia; Leung, Hing Y.; Robson, Craig N.

2006-01-01

The androgen receptor (AR) is a hormone-dependent transcription factor critically involved in human prostate carcinogenesis. Optimal transcriptional control of androgen-responsive genes by AR may require complex interaction among multiple coregulatory proteins. We have previously shown that the AR coregulator TIP60 can interact with human PIRH2 (hPIRH2). In this study, we uncover important new functional role(s) for hPIRH2 in AR signaling: (i) hPIRH2 interacts with AR and enhances AR-mediated transcription with a dynamic pattern of recruitment to androgen response elements in the prostate-specific antigen (PSA) gene; (ii) hPIRH2 interacts with the AR corepressor HDAC1, leading to reduced HDAC1 protein levels and inhibition of transcriptional repression; (iii) hPIRH2 is required for optimal PSA expression; and (iv) hPIRH2 is involved in prostate cancer cell proliferation. In addition, overexpression of hPIRH2 protein was detected in 73 of 82 (89%) resected prostate cancers, with a strong correlation between increased hPIRH2 expression and aggressive disease, as signified by high Gleason sum scores and the presence of metastatic disease (P = <0.0001 and 0.0004, respectively). Collectively, our data establish hPIRH2 as a key modulator of AR function, opening a new direction for targeted therapy in aggressive human prostate cancer. PMID:16914734

Human PIRH2 enhances androgen receptor signaling through inhibition of histone deacetylase 1 and is overexpressed in prostate cancer.

PubMed

Logan, Ian R; Gaughan, Luke; McCracken, Stuart R C; Sapountzi, Vasileia; Leung, Hing Y; Robson, Craig N

2006-09-01

The androgen receptor (AR) is a hormone-dependent transcription factor critically involved in human prostate carcinogenesis. Optimal transcriptional control of androgen-responsive genes by AR may require complex interaction among multiple coregulatory proteins. We have previously shown that the AR coregulator TIP60 can interact with human PIRH2 (hPIRH2). In this study, we uncover important new functional role(s) for hPIRH2 in AR signaling: (i) hPIRH2 interacts with AR and enhances AR-mediated transcription with a dynamic pattern of recruitment to androgen response elements in the prostate-specific antigen (PSA) gene; (ii) hPIRH2 interacts with the AR corepressor HDAC1, leading to reduced HDAC1 protein levels and inhibition of transcriptional repression; (iii) hPIRH2 is required for optimal PSA expression; and (iv) hPIRH2 is involved in prostate cancer cell proliferation. In addition, overexpression of hPIRH2 protein was detected in 73 of 82 (89%) resected prostate cancers, with a strong correlation between increased hPIRH2 expression and aggressive disease, as signified by high Gleason sum scores and the presence of metastatic disease (P = <0.0001 and 0.0004, respectively). Collectively, our data establish hPIRH2 as a key modulator of AR function, opening a new direction for targeted therapy in aggressive human prostate cancer.

Cultural differences in self-recognition: the early development of autonomous and related selves?

PubMed

Ross, Josephine; Yilmaz, Mandy; Dale, Rachel; Cassidy, Rose; Yildirim, Iraz; Suzanne Zeedyk, M

2017-05-01

Fifteen- to 18-month-old infants from three nationalities were observed interacting with their mothers and during two self-recognition tasks. Scottish interactions were characterized by distal contact, Zambian interactions by proximal contact, and Turkish interactions by a mixture of contact strategies. These culturally distinct experiences may scaffold different perspectives on self. In support, Scottish infants performed best in a task requiring recognition of the self in an individualistic context (mirror self-recognition), whereas Zambian infants performed best in a task requiring recognition of the self in a less individualistic context (body-as-obstacle task). Turkish infants performed similarly to Zambian infants on the body-as-obstacle task, but outperformed Zambians on the mirror self-recognition task. Verbal contact (a distal strategy) was positively related to mirror self-recognition and negatively related to passing the body-as-obstacle task. Directive action and speech (proximal strategies) were negatively related to mirror self-recognition. Self-awareness performance was best predicted by cultural context; autonomous settings predicted success in mirror self-recognition, and related settings predicted success in the body-as-obstacle task. These novel data substantiate the idea that cultural factors may play a role in the early expression of self-awareness. More broadly, the results highlight the importance of moving beyond the mark test, and designing culturally sensitive tests of self-awareness. © 2016 John Wiley & Sons Ltd.

ALIX and ESCRT-III Coordinately Control Cytokinetic Abscission during Germline Stem Cell Division In Vivo

PubMed Central

Eikenes, Åsmund H.; Malerød, Lene; Christensen, Anette Lie; Steen, Chloé B.; Mathieu, Juliette; Nezis, Ioannis P.; Liestøl, Knut; Huynh, Jean-René; Stenmark, Harald; Haglund, Kaisa

2015-01-01

Abscission is the final step of cytokinesis that involves the cleavage of the intercellular bridge connecting the two daughter cells. Recent studies have given novel insight into the spatiotemporal regulation and molecular mechanisms controlling abscission in cultured yeast and human cells. The mechanisms of abscission in living metazoan tissues are however not well understood. Here we show that ALIX and the ESCRT-III component Shrub are required for completion of abscission during Drosophila female germline stem cell (fGSC) division. Loss of ALIX or Shrub function in fGSCs leads to delayed abscission and the consequent formation of stem cysts in which chains of daughter cells remain interconnected to the fGSC via midbody rings and fusome. We demonstrate that ALIX and Shrub interact and that they co-localize at midbody rings and midbodies during cytokinetic abscission in fGSCs. Mechanistically, we show that the direct interaction between ALIX and Shrub is required to ensure cytokinesis completion with normal kinetics in fGSCs. We conclude that ALIX and ESCRT-III coordinately control abscission in Drosophila fGSCs and that their complex formation is required for accurate abscission timing in GSCs in vivo. PMID:25635693

Biochemical and biophysical investigations of the interaction between human glucokinase and pro-apoptotic BAD.

PubMed

Rexford, Alix; Zorio, Diego A R; Miller, Brian G

2017-01-01

The glycolytic enzyme glucokinase (GCK) and the pro-apoptotic protein BAD reportedly reside within a five-membered complex that localizes to the mitochondria of mammalian hepatocytes and pancreatic β-cells. Photochemical crosslinking studies using a synthetic analog of BAD's BH3 domain and in vitro transcription/translation experiments support a direct interaction between BAD and GCK. To investigate the biochemical and biophysical consequences of the BAD:GCK interaction, we developed a method for the production of recombinant human BAD. Consistent with published reports, recombinant BAD displays high affinity for Bcl-xL (KD = 7 nM), and phosphorylation of BAD at S118, within the BH3 domain, abolishes this interaction. Unexpectedly, we do not detect association of recombinant, full-length BAD with recombinant human pancreatic GCK over a range of protein concentrations using various biochemical methods including size-exclusion chromatography, chemical cross-linking, analytical ultracentrifugation, and isothermal titration calorimetry. Furthermore, fluorescence polarization assays and isothermal titration calorimetry detect no direct interaction between GCK and BAD BH3 peptides. Kinetic characterization of GCK in the presence of high concentrations of recombinant BAD show modest (<15%) increases in GCK activity, observable only at glucose concentrations well below the K0.5 value. GCK activity is unaffected by BAD BH3 peptides. These results raise questions as to the mechanism of action of stapled peptide analogs modeled after the BAD BH3 domain, which reportedly enhance the Vmax value of GCK and stimulate insulin release in BAD-deficient islets. Based on our results, we postulate that the BAD:GCK interaction, and any resultant regulatory effect(s) upon GCK activity, requires the participation of additional members of the mitochondrial complex.

Fibroblasts Influence Survival and Therapeutic Response in a 3D Co-Culture Model

PubMed Central

Majety, Meher; Pradel, Leon P.; Gies, Manuela; Ries, Carola H.

2015-01-01

In recent years, evidence has indicated that the tumor microenvironment (TME) plays a significant role in tumor progression. Fibroblasts represent an abundant cell population in the TME and produce several growth factors and cytokines. Fibroblasts generate a suitable niche for tumor cell survival and metastasis under the influence of interactions between fibroblasts and tumor cells. Investigating these interactions requires suitable experimental systems to understand the cross-talk involved. Most in vitro experimental systems use 2D cell culture and trans-well assays to study these interactions even though these paradigms poorly represent the tumor, in which direct cell-cell contacts in 3D spaces naturally occur. Investigating these interactions in vivo is of limited value due to problems regarding the challenges caused by the species-specificity of many molecules. Thus, it is essential to use in vitro models in which human fibroblasts are co-cultured with tumor cells to understand their interactions. Here, we developed a 3D co-culture model that enables direct cell-cell contacts between pancreatic, breast and or lung tumor cells and human fibroblasts/ or tumor-associated fibroblasts (TAFs). We found that co-culturing with fibroblasts/TAFs increases the proliferation in of several types of cancer cells. We also observed that co-culture induces differential expression of soluble factors in a cancer type-specific manner. Treatment with blocking antibodies against selected factors or their receptors resulted in the inhibition of cancer cell proliferation in the co-cultures. Using our co-culture model, we further revealed that TAFs can influence the response to therapeutic agents in vitro. We suggest that this model can be reliably used as a tool to investigate the interactions between a tumor and the TME. PMID:26053043

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology.

PubMed

DeBlasio, Stacy L; Chavez, Juan D; Alexander, Mariko M; Ramsey, John; Eng, Jimmy K; Mahoney, Jaclyn; Gray, Stewart M; Bruce, James E; Cilia, Michelle

2016-02-15

Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection-hallmarks of host-pathogen interactions-were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction reporter (PIR) technology to illustrate how viruses exploit host proteins during plant infection. PIR technology enabled our team to precisely describe the sites of functional virus-virus, virus-host, and host-host protein interactions using a mass spectrometry analysis that takes just a few hours. Applications of PIR technology in host-pathogen interactions will enable researchers studying recalcitrant pathogens, such as animal pathogens where host proteins are incorporated directly into the infectious agents, to investigate how proteins interact during infection and transmission as well as develop new tools for interdiction and therapy. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Acquired versus innate prey capturing skills in super-precocial live-bearing fish.

PubMed

Lankheet, Martin J; Stoffers, Twan; van Leeuwen, Johan L; Pollux, Bart J A

2016-07-13

Live-bearing fish start hunting for mobile prey within hours after birth, an example of extreme precociality. Because prenatal, in utero, development of this behaviour is constrained by the lack of free-swimming sensory-motor interactions, immediate success after birth depends on innate, evolutionarily acquired patterns. Optimal performance however requires flexible adjustment to an unpredictable environment. To distinguish innate from postnatally developing patterns we analysed over 2000 prey capture events for 28 metallic livebearers (Girardinus metallicus; Poeciliidae), during their first 3 days after birth. We show that the use of synchronous pectoral fin beats for final acceleration and ingestion is fixed and presumably innate. It allows for direct, symmetrical control of swimming speed and direction, while avoiding head yaw. Eye movements and body curvatures, however, change considerably in the first few days, showing that eye-tail coordination requires postnatal development. The results show how successful prey captures for newborn, live-bearing fish are based on a combination of fixed motor programmes and rapid, postnatal development. © 2016 The Author(s).

Planar cell polarity controls directional Notch signaling in the Drosophila leg

PubMed Central

Capilla, Amalia; Johnson, Ruth; Daniels, Maki; Benavente, María; Bray, Sarah J.; Galindo, Máximo Ibo

2012-01-01

The generation of functional structures during development requires tight spatial regulation of signaling pathways. Thus, in Drosophila legs, in which Notch pathway activity is required to specify joints, only cells distal to ligand-producing cells are capable of responding. Here, we show that the asymmetric distribution of planar cell polarity (PCP) proteins correlates with this spatial restriction of Notch activation. Frizzled and Dishevelled are enriched at distal sides of each cell and hence localize at the interface with ligand-expressing cells in the non-responding cells. Elimination of PCP gene function in cells proximal to ligand-expressing cells is sufficient to alleviate the repression, resulting in ectopic Notch activity and ectopic joint formation. Mutations that compromise a direct interaction between Dishevelled and Notch reduce the efficacy of repression. Likewise, increased Rab5 levels or dominant-negative Deltex can suppress the ectopic joints. Together, these results suggest that PCP coordinates the spatial activity of the Notch pathway by regulating endocytic trafficking of the receptor. PMID:22736244

Mena binds α5 integrin directly and modulates α5β1 function.

PubMed

Gupton, Stephanie L; Riquelme, Daisy; Hughes-Alford, Shannon K; Tadros, Jenny; Rudina, Shireen S; Hynes, Richard O; Lauffenburger, Douglas; Gertler, Frank B

2012-08-20

Mena is an Ena/VASP family actin regulator with roles in cell migration, chemotaxis, cell-cell adhesion, tumor cell invasion, and metastasis. Although enriched in focal adhesions, Mena has no established function within these structures. We find that Mena forms an adhesion-regulated complex with α5β1 integrin, a fibronectin receptor involved in cell adhesion, motility, fibronectin fibrillogenesis, signaling, and growth factor receptor trafficking. Mena bound directly to the carboxy-terminal portion of the α5 cytoplasmic tail via a 91-residue region containing 13 five-residue "LERER" repeats. In fibroblasts, the Mena-α5 complex was required for "outside-in" α5β1 functions, including normal phosphorylation of FAK and paxillin and formation of fibrillar adhesions. It also supported fibrillogenesis and cell spreading and controlled cell migration speed. Thus, fibroblasts require Mena for multiple α5β1-dependent processes involving bidirectional interactions between the extracellular matrix and cytoplasmic focal adhesion proteins.

Mena binds α5 integrin directly and modulates α5β1 function

PubMed Central

Riquelme, Daisy; Hughes-Alford, Shannon K.; Tadros, Jenny; Rudina, Shireen S.; O.Hynes, Richard; Lauffenburger, Douglas

2012-01-01

Mena is an Ena/VASP family actin regulator with roles in cell migration, chemotaxis, cell–cell adhesion, tumor cell invasion, and metastasis. Although enriched in focal adhesions, Mena has no established function within these structures. We find that Mena forms an adhesion-regulated complex with α5β1 integrin, a fibronectin receptor involved in cell adhesion, motility, fibronectin fibrillogenesis, signaling, and growth factor receptor trafficking. Mena bound directly to the carboxy-terminal portion of the α5 cytoplasmic tail via a 91-residue region containing 13 five-residue “LERER” repeats. In fibroblasts, the Mena–α5 complex was required for “outside-in” α5β1 functions, including normal phosphorylation of FAK and paxillin and formation of fibrillar adhesions. It also supported fibrillogenesis and cell spreading and controlled cell migration speed. Thus, fibroblasts require Mena for multiple α5β1-dependent processes involving bidirectional interactions between the extracellular matrix and cytoplasmic focal adhesion proteins. PMID:22908313

40-Gb/s directly-modulated photonic crystal lasers under optical injection-locking

NASA Astrophysics Data System (ADS)

Chen, Chin-Hui; Takeda, Koji; Shinya, Akihiko; Nozaki, Kengo; Sato, Tomonari; Kawaguchi, Yoshihiro; Notomi, Masaya; Matsuo, Shinji

2011-08-01

CMOS integrated circuits (IC) usually requires high data bandwidth for off-chip input/output (I/O) data transport with sufficiently low power consumption in order to overcome pin-count limitation. In order to meet future requirements of photonic network interconnect, we propose an optical output device based on an optical injection-locked photonic crystal (PhC) laser to realize low-power and high-speed off-chip interconnects. This device enables ultralow-power operation and is suitable for highly integrated photonic circuits because of its strong light-matter interaction in the PhC nanocavity and ultra-compact size. High-speed operation is achieved by using the optical injection-locking (OIL) technique, which has been shown as an effective means to enhance modulation bandwidth beyond the relaxation resonance frequency limit. In this paper, we report experimental results of the OIL-PhC laser under various injection conditions and also demonstrate 40-Gb/s large-signal direct modulation with an ultralow energy consumption of 6.6 fJ/bit.

Common Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) Epitopes Mediate Multiple Routes for Internalization and Function

PubMed Central

DeVay, Rachel M.; Yamamoto, Lynn; Shelton, David L.; Liang, Hong

2015-01-01

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a soluble protein that directs membrane-bound receptors to lysosomes for degradation. In the most studied example of this, PCSK9 binding leads to the degradation of low density lipoprotein receptor (LDLR), significantly affecting circulating LDL-C levels. The mechanism mediating this degradation, however, is not completely understood. We show here that LDLR facilitates PCSK9 interactions with amyloid precursor like protein 2 (APLP2) at neutral pH leading to PCSK9 internalization, although direct binding between PCSK9 and LDLR is not required. Moreover, binding to APLP2 or LDLR is independently sufficient for PCSK9 endocytosis in hepatocytes, while LDL can compete with APLP2 for PCSK9 binding to indirectly mediate PCSK9 endocytosis. Finally, we show that APLP2 and LDLR are also required for the degradation of another PCSK9 target, APOER2, necessitating a general role for LDLR and APLP2 in PCSK9 function. Together, these findings provide evidence that PCSK9 has at least two endocytic epitopes that are utilized by a variety of internalization mechanisms and clarifies how PCSK9 may direct proteins to lysosomes. PMID:25905719

A new root-based direction-finding algorithm

NASA Astrophysics Data System (ADS)

Wasylkiwskyj, Wasyl; Kopriva, Ivica; DoroslovačKi, Miloš; Zaghloul, Amir I.

2007-04-01

Polynomial rooting direction-finding (DF) algorithms are a computationally efficient alternative to search-based DF algorithms and are particularly suitable for uniform linear arrays of physically identical elements provided that mutual interaction among the array elements can be either neglected or compensated for. A popular algorithm in such situations is Root Multiple Signal Classification (Root MUSIC (RM)), wherein the estimation of the directions of arrivals (DOA) requires the computation of the roots of a (2N - 2) -order polynomial, where N represents number of array elements. The DOA are estimated from the L pairs of roots closest to the unit circle, where L represents number of sources. In this paper we derive a modified root polynomial (MRP) algorithm requiring the calculation of only L roots in order to estimate the L DOA. We evaluate the performance of the MRP algorithm numerically and show that it is as accurate as the RM algorithm but with a significantly simpler algebraic structure. In order to demonstrate that the theoretically predicted performance can be achieved in an experimental setting, a decoupled array is emulated in hardware using phase shifters. The results are in excellent agreement with theory.

Nonlinear Directed Interactions Between HRV and EEG Activity in Children With TLE.

PubMed

Schiecke, Karin; Pester, Britta; Piper, Diana; Benninger, Franz; Feucht, Martha; Leistritz, Lutz; Witte, Herbert

2016-12-01

Epileptic seizure activity influences the autonomic nervous system (ANS) in different ways. Heart rate variability (HRV) is used as indicator for alterations of the ANS. It was shown that linear, nondirected interactions between HRV and EEG activity before, during, and after epileptic seizure occur. Accordingly, investigations of directed nonlinear interactions are logical steps to provide, e.g., deeper insight into the development of seizure onsets. Convergent cross mapping (CCM) investigates nonlinear, directed interactions between time series by using nonlinear state space reconstruction. CCM is applied to simulated and clinically relevant data, i.e., interactions between HRV and specific EEG components of children with temporal lobe epilepsy (TLE). In addition, time-variant multivariate Autoregressive model (AR)-based estimation of partial directed coherence (PDC) was performed for the same data. Influence of estimation parameters and time-varying behavior of CCM estimation could be demonstrated by means of simulated data. AR-based estimation of PDC failed for the investigation of our clinical data. Time-varying interval-based application of CCM on these data revealed directed interactions between HRV and delta-related EEG activity. Interactions between HRV and alpha-related EEG activity were visible but less pronounced. EEG components mainly drive HRV. The interaction pattern and directionality clearly changed with onset of seizure. Statistical relevant interactions were quantified by bootstrapping and surrogate data approach. In contrast to AR-based estimation of PDC CCM was able to reveal time-courses and frequency-selective views of nonlinear interactions for the further understanding of complex interactions between the epileptic network and the ANS in children with TLE.

Nanostructure-directed chemical sensing: The IHSAB principle and the dynamics of acid/base-interface interaction

PubMed Central

Laminack, William

2013-01-01

Summary Nanostructure-decorated n-type semiconductor interfaces are studied in order to develop chemical sensing with nanostructured materials. We couple the tenets of acid/base chemistry with the majority charge carriers of an extrinsic semiconductor. Nanostructured islands are deposited in a process that does not require self-assembly in order to direct a dominant electron-transduction process that forms the basis for reversible chemical sensing in the absence of chemical-bond formation. Gaseous analyte interactions on a metal-oxide-decorated n-type porous silicon interface show a dynamic electron transduction to and from the interface depending upon the relative strength of the gas and metal oxides. The dynamic interaction of NO with TiO2, SnO2, NiO, CuxO, and AuxO (x >> 1), in order of decreasing acidity, demonstrates this effect. Interactions with the metal-oxide-decorated interface can be modified by the in situ nitridation of the oxide nanoparticles, enhancing the basicity of the decorated interface. This process changes the interaction of the interface with the analyte. The observed change to the more basic oxinitrides does not represent a simple increase in surface basicity but appears to involve a change in molecular electronic structure, which is well explained by using the recently developed IHSAB model. The optical pumping of a TiO2 and TiO2− xNx decorated interface demonstrates a significant enhancement in the ability to sense NH3 and NO2. Comparisons to traditional metal-oxide sensors are also discussed. PMID:23400337

Do Gestural Interfaces Promote Thinking? Embodied Interaction: Congruent Gestures and Direct Touch Promote Performance in Math

ERIC Educational Resources Information Center

Segal, Ayelet

2011-01-01

Can action support cognition? Can direct touch support performance? Embodied interaction involving digital devices is based on the theory of grounded cognition. Embodied interaction with gestural interfaces involves more of our senses than traditional (mouse-based) interfaces, and in particular includes direct touch and physical movement, which…

Three axis vector atomic magnetometer utilizing polarimetric technique

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

Pradhan, Swarupananda, E-mail: spradhan@barc.gov.in, E-mail: pradhans75@gmail.com

2016-09-15

The three axis vector magnetic field measurement based on the interaction of a single elliptically polarized light beam with an atomic system is described. The magnetic field direction dependent atomic responses are extracted by the polarimetric detection in combination with laser frequency modulation and magnetic field modulation techniques. The magnetometer geometry offers additional critical requirements like compact size and large dynamic range for space application. Further, the three axis magnetic field is measured using only the reflected signal (one polarization component) from the polarimeter and thus can be easily expanded to make spatial array of detectors and/or high sensitivity fieldmore » gradient measurement as required for biomedical application.« less

Working Group Report: Dark Matter Complementarity (Dark Matter in the Coming Decade: Complementary Paths to Discovery and Beyond)

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

Arrenberg, Sebastian; et al.,

2013-10-31

In this Report we discuss the four complementary searches for the identity of dark matter: direct detection experiments that look for dark matter interacting in the lab, indirect detection experiments that connect lab signals to dark matter in our own and other galaxies, collider experiments that elucidate the particle properties of dark matter, and astrophysical probes sensitive to non-gravitational interactions of dark matter. The complementarity among the different dark matter searches is discussed qualitatively and illustrated quantitatively in several theoretical scenarios. Our primary conclusion is that the diversity of possible dark matter candidates requires a balanced program based on allmore » four of those approaches.« less

Convective dynamics - Panel report

NASA Technical Reports Server (NTRS)

Carbone, Richard; Foote, G. Brant; Moncrieff, Mitch; Gal-Chen, Tzvi; Cotton, William; Heymsfield, Gerald

1990-01-01

Aspects of highly organized forms of deep convection at midlatitudes are reviewed. Past emphasis in field work and cloud modeling has been directed toward severe weather as evidenced by research on tornadoes, hail, and strong surface winds. A number of specific issues concerning future thrusts, tactics, and techniques in convective dynamics are presented. These subjects include; convective modes and parameterization, global structure and scale interaction, convective energetics, transport studies, anvils and scale interaction, and scale selection. Also discussed are analysis workshops, four-dimensional data assimilation, matching models with observations, network Doppler analyses, mesoscale variability, and high-resolution/high-performance Doppler. It is also noted, that, classical surface measurements and soundings, flight-level research aircraft data, passive satellite data, and traditional photogrammetric studies are examples of datasets that require assimilation and integration.

Development of an integrated BEM approach for hot fluid structure interaction

NASA Technical Reports Server (NTRS)

Dargush, Gary F.; Banerjee, Prasanta K.; Honkala, Keith A.

1988-01-01

In the present work, the boundary element method (BEM) is chosen as the basic analysis tool, principally because the definition of temperature, flux, displacement and traction are very precise on a boundary-based discretization scheme. One fundamental difficulty is, of course, that a BEM formulation requires a considerable amount of analytical work, which is not needed in the other numerical methods. Progress made toward the development of a boundary element formulation for the study of hot fluid-structure interaction in Earth-to-Orbit engine hot section components is reported. The primary thrust of the program to date has been directed quite naturally toward the examination of fluid flow, since boundary element methods for fluids are at a much less developed state.

Plant stem cell niches.

PubMed

Stahl, Yvonne; Simon, Rüdiger

2005-01-01

Stem cells are required to support the indeterminate growth style of plants. Meristems are a plants stem cell niches that foster stem cell survival and the production of descendants destined for differentiation. In shoot meristems, stem cell fate is decided at the populational level. The size of the stem cell domain at the meristem tip depends on signals that are exchanged with cells of the organizing centre underneath. In root meristems, individual stem cells are controlled by direct interaction with cells of the quiescent centre that lie in the immediate neighbourhood. Analysis of the interactions and signaling processes in the stem cell niches has delivered some insights into the molecules that are involved and revealed that the two major niches for plant stem cells are more similar than anticipated.

Human microcephaly protein RTTN interacts with STIL and is required to build full-length centrioles.

PubMed

Chen, Hsin-Yi; Wu, Chien-Ting; Tang, Chieh-Ju C; Lin, Yi-Nan; Wang, Won-Jing; Tang, Tang K

2017-08-15

Mutations in many centriolar protein-encoding genes cause primary microcephaly. Using super-resolution and electron microscopy, we find that the human microcephaly protein, RTTN, is recruited to the proximal end of the procentriole at early S phase, and is located at the inner luminal walls of centrioles. Further studies demonstrate that RTTN directly interacts with STIL and acts downstream of STIL-mediated centriole assembly. CRISPR/Cas9-mediated RTTN gene knockout in p53-deficient cells induce amplification of primitive procentriole bodies that lack the distal-half centriolar proteins, POC5 and POC1B. Additional analyses show that RTTN serves as an upstream effector of CEP295, which mediates the loading of POC1B and POC5 to the distal-half centrioles. Interestingly, the naturally occurring microcephaly-associated mutant, RTTN (A578P), shows a low affinity for STIL binding and blocks centriole assembly. These findings reveal that RTTN contributes to building full-length centrioles and illuminate the molecular mechanism through which the RTTN (A578P) mutation causes primary microcephaly.Mutations in many centriolar protein-encoding genes cause primary microcephaly. Here the authors show that human microcephaly protein RTTN directly interacts with STIL and acts downstream of STIL-mediated centriole assembly, contributing to building full-length centrioles.

Photoreactive “Nanorulers” Detect a Novel Conformation of Full length HDAC3-SMRT Complex in Solution

PubMed Central

Abdelkarim, Hazem; Brunsteiner, Michael; Neelarapu, Raghupathi; Bai, He; Madriaga, Antonett; van Breemen, Richard B.; Blond, Sylvie Y.; Gaponenko, Vadim; Petukhov, Pavel A.

2013-01-01

Histone deacetylase 3 (HDAC3) is a promising epigenetic drug target for multiple therapeutic applications. Direct interaction between the Deacetylase Activating Domain of the silencing mediator for retinoid or thyroid hormone receptors (SMRT-DAD) is required for activation of enzymatic activity of HDAC3. The structure of this complex and the nature of interactions with HDAC inhibitors in solution are unknown. Using novel photoreactive HDAC probes – “nanorulers”, we determined the distance between the catalytic site of the full-length HDAC3 and SMRT-DAD in solution at physiologically relevant conditions and found it to be substantially different from that predicted by the X-ray model with a Δ379-428aa truncated HDAC3. Further experiments indicated that in solution this distance might change in response to chemical stimuli, while the enzymatic activity remained unaffected. These observations were further validated by Saturation Transfer Difference (STD) NMR experiments. We propose that the observed changes in the distance are an important part of the histone code that remains to be explored. Mapping direct interactions and distances between macromolecules with such “nanorulers” as a function of cellular events facilitates better understanding of basic biology and ways for its manipulation in cell and tissue specific manner. PMID:24010878

Human T-cell leukemia virus type 1 Tax interacts with Chk1 and attenuates DNA-damage induced G2 arrest mediated by Chk1.

PubMed

Park, Hyeon Ung; Jeong, Jae-Hoon; Chung, Jay H; Brady, John N

2004-06-24

Checkpoint kinase 1 (Chk1) mediates diverse cellular responses to genotoxic stress, regulating the network of genome-surveillance pathways that coordinate cell cycle progression with DNA repair. Chk1 is essential for mammalian development and viability, and has been shown to be important for both S and G(2) checkpoints. We now present evidence that the HTLV-1 Tax protein interacts directly with Chk1 and impairs its kinase activities in vitro and in vivo. The direct and physical interaction of Chk1 and Tax was observed in HTLV-1-infected T cells (C81, HuT 102 and MT-2) and transfected fibroblasts (293 T) by coimmunoprecipitation and by in vitro GST pull-down assays. Interestingly, Tax inhibited the kinase activity of Chk1 protein in in vitro and in vivo kinase assays. Consistent with these results, Tax inhibited the phosphorylation-dependent degradation of Cdc25A and G(2) arrest in response to gamma-irradiation (IR) in a dose-dependent manner in vivo. The G(2) arrest did not require Chk2 or p53. These studies provide the first example of a viral transforming protein targeting Chk1 and provide important insights into checkpoint pathway regulation.

The Control of Auxin Transport in Parasitic and Symbiotic Root–Microbe Interactions

PubMed Central

Ng, Jason Liang Pin; Perrine-Walker, Francine; Wasson, Anton P.; Mathesius, Ulrike

2015-01-01

Most field-grown plants are surrounded by microbes, especially from the soil. Some of these, including bacteria, fungi and nematodes, specifically manipulate the growth and development of their plant hosts, primarily for the formation of structures housing the microbes in roots. These developmental processes require the correct localization of the phytohormone auxin, which is involved in the control of cell division, cell enlargement, organ development and defense, and is thus a likely target for microbes that infect and invade plants. Some microbes have the ability to directly synthesize auxin. Others produce specific signals that indirectly alter the accumulation of auxin in the plant by altering auxin transport. This review highlights root–microbe interactions in which auxin transport is known to be targeted by symbionts and parasites to manipulate the development of their host root system. We include case studies for parasitic root–nematode interactions, mycorrhizal symbioses as well as nitrogen fixing symbioses in actinorhizal and legume hosts. The mechanisms to achieve auxin transport control that have been studied in model organisms include the induction of plant flavonoids that indirectly alter auxin transport and the direct targeting of auxin transporters by nematode effectors. In most cases, detailed mechanisms of auxin transport control remain unknown. PMID:27135343

Physical and Functional Interaction between the Eukaryotic Orthologs of Prokaryotic Translation Initiation Factors IF1 and IF2

PubMed Central

Choi, Sang Ki; Olsen, DeAnne S.; Roll-Mecak, Antonina; Martung, Agnes; Remo, Keith L.; Burley, Stephen K.; Hinnebusch, Alan G.; Dever, Thomas E.

2000-01-01

To initiate protein synthesis, a ribosome with bound initiator methionyl-tRNA must be assembled at the start codon of an mRNA. This process requires the coordinated activities of three translation initiation factors (IF) in prokaryotes and at least 12 translation initiation factors in eukaryotes (eIF). The factors eIF1A and eIF5B from eukaryotes show extensive amino acid sequence similarity to the factors IF1 and IF2 from prokaryotes. By a combination of two-hybrid, coimmunoprecipitation, and in vitro binding assays eIF1A and eIF5B were found to interact directly, and the eIF1A binding site was mapped to the C-terminal region of eIF5B. This portion of eIF5B was found to be critical for growth in vivo and for translation in vitro. Overexpression of eIF1A exacerbated the slow-growth phenotype of yeast strains expressing C-terminally truncated eIF5B. These findings indicate that the physical interaction between the evolutionarily conserved factors eIF1A and eIF5B plays an important role in translation initiation, perhaps to direct or stabilize the binding of methionyl-tRNA to the ribosomal P site. PMID:10982835

Interface-Resolving Simulation of Collision Efficiency of Cloud Droplets

NASA Astrophysics Data System (ADS)

Wang, Lian-Ping; Peng, Cheng; Rosa, Bodgan; Onishi, Ryo

2017-11-01

Small-scale air turbulence could enhance the geometric collision rate of cloud droplets while large-scale air turbulence could augment the diffusional growth of cloud droplets. Air turbulence could also enhance the collision efficiency of cloud droplets. Accurate simulation of collision efficiency, however, requires capture of the multi-scale droplet-turbulence and droplet-droplet interactions, which has only been partially achieved in the recent past using the hybrid direct numerical simulation (HDNS) approach. % where Stokes disturbance flow is assumed. The HDNS approach has two major drawbacks: (1) the short-range droplet-droplet interaction is not treated rigorously; (2) the finite-Reynolds number correction to the collision efficiency is not included. In this talk, using two independent numerical methods, we will develop an interface-resolved simulation approach in which the disturbance flows are directly resolved numerically, combined with a rigorous lubrication correction model for near-field droplet-droplet interaction. This multi-scale approach is first used to study the effect of finite flow Reynolds numbers on the droplet collision efficiency in still air. Our simulation results show a significant finite-Re effect on collision efficiency when the droplets are of similar sizes. Preliminary results on integrating this approach in a turbulent flow laden with droplets will also be presented. This work is partially supported by the National Science Foundation.

Sibling cooperation in earwig families provides insights into the early evolution of social life.

PubMed

Falk, Joachim; Wong, Janine W Y; Kölliker, Mathias; Meunier, Joël

2014-04-01

The evolutionary transition from solitary to social life is driven by direct and indirect fitness benefits of social interactions. Understanding the conditions promoting the early evolution of social life therefore requires identification of these benefits in nonderived social systems, such as animal families where offspring are mobile and able to disperse and will survive independently. Family life is well known to provide benefits to offspring through parental care, but research on sibling interactions generally focused on fitness costs to offspring due to competitive behaviors. Here we show experimentally that sibling interactions also reflect cooperative behaviors in the form of food sharing in nonderived families of the European earwig, Forficula auricularia. Food ingested by individual offspring was transferred to their siblings through mouth-to-anus contacts and active allo-coprophagy. These transfers occurred in both the presence and the absence of the tending mothers, even though the direct contact with the mothers limited sibling food sharing. Neither food deprivation or relatedness influenced the total amount of transferred food, but relatedness affected frass release and the behavioral mechanisms mediating food sharing. Related offspring obtained food predominately through allo-coprophagy, whereas unrelated offspring obtained food through mouth-to-anus contacts. Overall, this study emphasizes that sibling cooperation may be a key process promoting the early evolution of social life.

SH2 domains: modulators of nonreceptor tyrosine kinase activity.

PubMed

Filippakopoulos, Panagis; Müller, Susanne; Knapp, Stefan

2009-12-01

The Src homology 2 (SH2) domain is a sequence-specific phosphotyrosine-binding module present in many signaling molecules. In cytoplasmic tyrosine kinases, the SH2 domain is located N-terminally to the catalytic kinase domain (SH1) where it mediates cellular localization, substrate recruitment, and regulation of kinase activity. Initially, structural studies established a role of the SH2 domain stabilizing the inactive state of Src family members. However, biochemical characterization showed that the presence of the SH2 domain is frequently required for catalytic activity, suggesting a crucial function stabilizing the active state of many nonreceptor tyrosine kinases. Recently, the structure of the SH2-kinase domain of Fes revealed that the SH2 domain stabilizes the active kinase conformation by direct interactions with the regulatory helix alphaC. Stabilizing interactions between the SH2 and the kinase domains have also been observed in the structures of active Csk and Abl. Interestingly, mutations in the SH2 domain found in human disease can be explained by SH2 domain destabilization or incorrect positioning of the SH2. Here we summarize our understanding of mechanisms that lead to tyrosine kinase activation by direct interactions mediated by the SH2 domain and discuss how mutations in the SH2 domain trigger kinase inactivation.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology

PubMed Central

DeBlasio, Stacy L.; Chavez, Juan D.; Alexander, Mariko M.; Ramsey, John; Eng, Jimmy K.; Mahoney, Jaclyn; Gray, Stewart M.; Bruce, James E.

2015-01-01

ABSTRACT Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection—hallmarks of host-pathogen interactions—were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. IMPORTANCE The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction reporter (PIR) technology to illustrate how viruses exploit host proteins during plant infection. PIR technology enabled our team to precisely describe the sites of functional virus-virus, virus-host, and host-host protein interactions using a mass spectrometry analysis that takes just a few hours. Applications of PIR technology in host-pathogen interactions will enable researchers studying recalcitrant pathogens, such as animal pathogens where host proteins are incorporated directly into the infectious agents, to investigate how proteins interact during infection and transmission as well as develop new tools for interdiction and therapy. PMID:26656710

Direct counterfactual transmission of a quantum state

NASA Astrophysics Data System (ADS)

Li, Zheng-Hong; Al-Amri, M.; Zubairy, M. Suhail

2015-11-01

We show that an unknown quantum state can be transferred with neither quantum nor classical particle traveling in the transmission channel. Our protocol does not require prearranged entangled photon pairs and Bell measurements. By utilizing quantum Zeno effect and counterfactuality, we can entangle and disentangle a photon and an atom by nonlocal interaction. It is shown that quantum information is completely transferred from an atom to photon due to controllable disentanglement processes. There is no need to cross-check the result via classical channels.