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Sample records for non-canonical dimension

  1. Refining inflation using non-canonical scalars

    SciTech Connect

    Unnikrishnan, Sanil; Sahni, Varun; Toporensky, Aleksey E-mail: varun@iucaa.ernet.in

    2012-08-01

    This paper revisits the Inflationary scenario within the framework of scalar field models possessing a non-canonical kinetic term. We obtain closed form solutions for all essential quantities associated with chaotic inflation including slow roll parameters, scalar and tensor power spectra, spectral indices, the tensor-to-scalar ratio, etc. We also examine the Hamilton-Jacobi equation and demonstrate the existence of an inflationary attractor. Our results highlight the fact that non-canonical scalars can significantly improve the viability of inflationary models. They accomplish this by decreasing the tensor-to-scalar ratio while simultaneously increasing the value of the scalar spectral index, thereby redeeming models which are incompatible with the cosmic microwave background (CMB) in their canonical version. For instance, the non-canonical version of the chaotic inflationary potential, V(φ) ∼ λφ{sup 4}, is found to agree with observations for values of λ as large as unity! The exponential potential can also provide a reasonable fit to CMB observations. A central result of this paper is that steep potentials (such as V∝φ{sup −n}) usually associated with dark energy, can drive inflation in the non-canonical setting. Interestingly, non-canonical scalars violate the consistency relation r = −8n{sub T}, which emerges as a smoking gun test for this class of models.

  2. Lessons from non-canonical splicing

    PubMed Central

    Ule, Jernej

    2016-01-01

    Recent improvements in experimental and computational techniques used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons, and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimises their potential to disrupt gene expression. While non-canonical splicing can lead to aberrant transcripts that cause many diseases, we also explain how it can be exploited for new therapeutic strategies. PMID:27240813

  3. Canonical and non-canonical Notch ligands

    PubMed Central

    D’SOUZA, BRENDAN; MELOTY-KAPELLA, LAURENCE; WEINMASTER, GERRY

    2015-01-01

    Notch signaling induced by canonical Notch ligands is critical for normal embryonic development and tissue homeostasis through the regulation of a variety of cell fate decisions and cellular processes. Activation of Notch signaling is normally tightly controlled by direct interactions with ligand-expressing cells and dysregulated Notch signaling is associated with developmental abnormalities and cancer. While canonical Notch ligands are responsible for the majority of Notch signaling, a diverse group of structurally unrelated non-canonical ligands has also been identified that activate Notch and likely contribute to the pleiotropic effects of Notch signaling. Soluble forms of both canonical and non-canonical ligands have been isolated, some of which block Notch signaling and could serve as natural inhibitors of this pathway. Ligand activity can also be indirectly regulated by other signaling pathways at the level of ligand expression, serving to spatio-temporally compartmentalize Notch signaling activity and integrate Notch signaling into a molecular network that orchestrates developmental events. Here, we review the molecular mechanisms underlying the dual role of Notch ligands as activators and inhibitors of Notch signaling. Additionally, evidence that Notch ligands function independent of Notch are presented. We also discuss how ligand post-translational modification, endocytosis, proteolysis and spatio-temporal expression regulate their signaling activity. PMID:20816393

  4. Non-canonical modulators of nuclear receptors.

    PubMed

    Tice, Colin M; Zheng, Ya-Jun

    2016-09-01

    Like G protein-coupled receptors (GPCRs) and protein kinases, nuclear receptors (NRs) are a rich source of pharmaceutical targets. Over 80 NR-targeting drugs have been approved for 18 NRs. The focus of drug discovery in NRs has hitherto been on identifying ligands that bind to the canonical ligand binding pockets of the C-terminal ligand binding domains (LBDs). Due to the development of drug resistance and selectivity concerns, there has been considerable interest in exploring other, non-canonical ligand binding sites. Unfortunately, the potencies of compounds binding at other sites have generally not been sufficient for clinical development. However, the situation has changed dramatically over the last 3years, as compounds with sufficient potency have been reported for several NR targets. Here we review recent developments in this area from a medicinal chemistry point of view in the hope of stimulating further interest in this area of research.

  5. Non-canonical actions of mismatch repair

    PubMed Central

    Crouse, Gray F.

    2015-01-01

    At the heart of the mismatch repair (MMR) system are proteins that recognize mismatches in DNA. Such mismatches can be mispairs involving normal or damaged bases or insertion/deletion loops due to strand misalignment. When such mispairs are generated during replication or recombination, MMR will direct removal of an incorrectly paired base or block recombination between nonidentical sequences. However, when mispairs are recognized outside the context of replication, proper strand discrimination between old and new DNA is lost, and MMR can act randomly and mutagenically on mispaired DNA. Such non-canonical actions of MMR are important in somatic hypermutation and class switch recombination, expansion of triplet repeats, and potentially in mutations arising in nondividing cells. MMR involvement in damage recognition and signaling is complex, with the end result likely dependent on the amount of DNA damage in a cell. PMID:26698648

  6. Relations between canonical and non-canonical inflation

    SciTech Connect

    Gwyn, Rhiannon; Rummel, Markus; Westphal, Alexander E-mail: markus.rummel@physics.ox.ac.uk

    2013-12-01

    We look for potential observational degeneracies between canonical and non-canonical models of inflation of a single field φ. Non-canonical inflationary models are characterized by higher than linear powers of the standard kinetic term X in the effective Lagrangian p(X,φ) and arise for instance in the context of the Dirac-Born-Infeld (DBI) action in string theory. An on-shell transformation is introduced that transforms non-canonical inflationary theories to theories with a canonical kinetic term. The 2-point function observables of the original non-canonical theory and its canonical transform are found to match in the case of DBI inflation.

  7. Non-canonical inflation coupled to matter

    SciTech Connect

    Céspedes, Sebastián; Davis, Anne-Christine E-mail: a.c.davis@damtp.cam.ac.uk

    2015-11-01

    We compute corrections to the inflationary potential due to conformally coupled non-relativistic matter. We find that under certain conditions of the matter coupling, inflation may be interrupted abruptly. We display this in the superconformal Starobinsky model, where matter is conformally coupled to the Einstein frame metric. These corrections may easily stop inflation provided that there is an initial density of non-relativistic matter. Since these additional heavy degrees of freedom generically occur in higher dimension theories, for example as Kaluza-Klein modes, this effect can arise in multiple scenarios.

  8. Non-canonical WNT signalling in the lung

    PubMed Central

    Li, Changgong; Bellusci, Saverio; Borok, Zea; Minoo, Parviz

    2015-01-01

    The role of WNT signalling in metazoan organogenesis has been a topic of widespread interest. In the lung, while the role of canonical WNT signalling has been examined in some detail by multiple studies, the non-canonical WNT signalling has received limited attention. Reliable evidence shows that this important signalling mechanism constitutes a major regulatory pathway in lung development. In addition, accumulating evidence has also shown that the non-canonical WNT pathway is critical for maintaining lung homeostasis and that aberrant activation of this pathway may underlie several debilitating lung diseases. Functional analyses have further revealed that the non-canonical WNT pathway regulates multiple cellular activities in the lung that are dependent on the specific cellular context. In most cell types, non-canonical WNT signalling regulates canonical WNT activity, which is also critical for many aspects of lung biology. This review will summarize what is currently known about the role of non-canonical WNT signalling in lung development, homeostasis and pathogenesis of disease. PMID:26261051

  9. Non-canonical WNT signalling in the lung.

    PubMed

    Li, Changgong; Bellusci, Saverio; Borok, Zea; Minoo, Parviz

    2015-11-01

    The role of WNT signalling in metazoan organogenesis has been a topic of widespread interest. In the lung, while the role of canonical WNT signalling has been examined in some detail by multiple studies, the non-canonical WNT signalling has received limited attention. Reliable evidence shows that this important signalling mechanism constitutes a major regulatory pathway in lung development. In addition, accumulating evidence has also shown that the non-canonical WNT pathway is critical for maintaining lung homeostasis and that aberrant activation of this pathway may underlie several debilitating lung diseases. Functional analyses have further revealed that the non-canonical WNT pathway regulates multiple cellular activities in the lung that are dependent on the specific cellular context. In most cell types, non-canonical WNT signalling regulates canonical WNT activity, which is also critical for many aspects of lung biology. This review will summarize what is currently known about the role of non-canonical WNT signalling in lung development, homeostasis and pathogenesis of disease.

  10. Accretion of the Moon from non-canonical discs.

    PubMed

    Salmon, J; Canup, R M

    2014-09-13

    Impacts that leave the Earth-Moon system with a large excess in angular momentum have recently been advocated as a means of generating a protolunar disc with a composition that is nearly identical to that of the Earth's mantle. We here investigate the accretion of the Moon from discs generated by such 'non-canonical' impacts, which are typically more compact than discs produced by canonical impacts and have a higher fraction of their mass initially located inside the Roche limit. Our model predicts a similar overall accretional history for both canonical and non-canonical discs, with the Moon forming in three consecutive steps over hundreds of years. However, we find that, to yield a lunar-mass Moon, the more compact non-canonical discs must initially be more massive than implied by prior estimates, and only a few of the discs produced by impact simulations to date appear to meet this condition. Non-canonical impacts require that capture of the Moon into the evection resonance with the Sun reduced the Earth-Moon angular momentum by a factor of 2 or more. We find that the Moon's semi-major axis at the end of its accretion is approximately 7R⊕, which is comparable to the location of the evection resonance for a post-impact Earth with a 2.5 h rotation period in the absence of a disc. Thus, the dynamics of the Moon's assembly may directly affect its ability to be captured into the resonance.

  11. Non-canonical generalizations of slow-roll inflation models

    NASA Astrophysics Data System (ADS)

    Tzirakis, Konstantinos; Kinney, William H.

    2009-01-01

    We consider non-canonical generalizations of two classes of single-field inflation models. First, we study the non-canonical version of ''ultra-slow roll'' inflation, which is a class of inflation models for which quantum modes do not freeze at horizon crossing, but instead evolve rapidly on superhorizon scales. Second, we consider the non-canonical generalization of the simplest ''chaotic'' inflation scenario, with a potential dominated by a quadratic (mass) term for the inflaton. We find a class of related non-canonical solutions with polynomial potentials, but with varying speed of sound. These solutions are characterized by a constant field velocity, and we dub such models isokinetic inflation. As in the canonical limit, isokinetic inflation has a slightly red-tilted power spectrum, consistent with current data. Unlike the canonical case, however, these models can have an arbitrarily small tensor/scalar ratio. Of particular interest is that isokinetic inflation is marked by a correlation between the tensor/scalar ratio and the amplitude of non-Gaussianity such that parameter regimes with small tensor/scalar ratio have large associated non-Gaussianity, which is a distinct observational signature.

  12. Non-canonical Stat3 signaling in cancer.

    PubMed

    Srivastava, Jaya; DiGiovanni, John

    2016-12-01

    Stat3 is a member of the signal transducers and activators of transcription family and is a known regulator of essential biologic processes including angiogenesis, apoptosis, cell cycle progression, and cell migration. Canonical Stat3-mediated signaling involves tyrosine phosphorylation on specific residues that leads to homodimerization and translocation to the nucleus. For many years it was presumed that most, if not all, of the functions of Stat3, both normal and aberrant, were due to the canonical cytokine and growth factor signaling mechanisms. Recent studies suggest that Stat3 functions through alternate non-canonical pathways to bring about some of these biological functions both in normal cells as well as during cancer development and progression. A number of studies have now shown that Stat3 has a function in mitochondria and that unphosphorylated Stat3 (uStat3) can also function as a transcription factor broadening the potential mechanisms involved in Stat3 action. In this review article, we discuss these two main non-canonical functions of Stat3 and their potential roles in oncogenesis. Given the many facets of Stat3 signaling, additional comprehensive investigations are required to fully understand the role of non-canonical Stat3 signaling in cancer and whether these pathways can be targeted for cancer prevention and treatment. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  13. Non-Canonical Cell Death Induced by p53

    PubMed Central

    Ranjan, Atul; Iwakuma, Tomoo

    2016-01-01

    Programmed cell death is a vital biological process for multicellular organisms to maintain cellular homeostasis, which is regulated in a complex manner. Over the past several years, apart from apoptosis, which is the principal mechanism of caspase-dependent cell death, research on non-apoptotic forms of programmed cell death has gained momentum. p53 is a well characterized tumor suppressor that controls cell proliferation and apoptosis and has also been linked to non-apoptotic, non-canonical cell death mechanisms. p53 impacts these non-canonical forms of cell death through transcriptional regulation of its downstream targets, as well as direct interactions with key players involved in these mechanisms, in a cell type- or tissue context-dependent manner. In this review article, we summarize and discuss the involvement of p53 in several non-canonical modes of cell death, including caspase-independent apoptosis (CIA), ferroptosis, necroptosis, autophagic cell death, mitotic catastrophe, paraptosis, and pyroptosis, as well as its role in efferocytosis which is the process of clearing dead or dying cells. PMID:27941671

  14. Non-Canonical Cell Death Induced by p53.

    PubMed

    Ranjan, Atul; Iwakuma, Tomoo

    2016-12-09

    Programmed cell death is a vital biological process for multicellular organisms to maintain cellular homeostasis, which is regulated in a complex manner. Over the past several years, apart from apoptosis, which is the principal mechanism of caspase-dependent cell death, research on non-apoptotic forms of programmed cell death has gained momentum. p53 is a well characterized tumor suppressor that controls cell proliferation and apoptosis and has also been linked to non-apoptotic, non-canonical cell death mechanisms. p53 impacts these non-canonical forms of cell death through transcriptional regulation of its downstream targets, as well as direct interactions with key players involved in these mechanisms, in a cell type- or tissue context-dependent manner. In this review article, we summarize and discuss the involvement of p53 in several non-canonical modes of cell death, including caspase-independent apoptosis (CIA), ferroptosis, necroptosis, autophagic cell death, mitotic catastrophe, paraptosis, and pyroptosis, as well as its role in efferocytosis which is the process of clearing dead or dying cells.

  15. Intermediate inflation from a non-canonical scalar field

    NASA Astrophysics Data System (ADS)

    Rezazadeh, K.; Karami, K.; Karimi, P.

    2015-09-01

    We study the intermediate inflation in a non-canonical scalar field framework with a power-like Lagrangian. We show that in contrast with the standard canonical intermediate inflation, our non-canonical model is compatible with the observational results of Planck 2015. Also, we estimate the equilateral non-Gaussianity parameter which is in well agreement with the prediction of Planck 2015. Then, we obtain an approximation for the energy scale at the initial time of inflation and show that it can be of order of the Planck energy scale, i.e. MP ~ 1018GeV. We will see that after a short period of time, inflation enters in the slow-roll regime that its energy scale is of order MP/100 ~ 1016GeV and the horizon exit takes place in this energy scale. We also examine an idea in our non-canonical model to overcome the central drawback of intermediate inflation which is the fact that inflation never ends. We solve this problem without disturbing significantly the nature of the intermediate inflation until the time of horizon exit.

  16. Intermediate inflation from a non-canonical scalar field

    SciTech Connect

    Rezazadeh, K.; Karami, K.; Karimi, P. E-mail: KKarami@uok.ac.ir

    2015-09-01

    We study the intermediate inflation in a non-canonical scalar field framework with a power-like Lagrangian. We show that in contrast with the standard canonical intermediate inflation, our non-canonical model is compatible with the observational results of Planck 2015. Also, we estimate the equilateral non-Gaussianity parameter which is in well agreement with the prediction of Planck 2015. Then, we obtain an approximation for the energy scale at the initial time of inflation and show that it can be of order of the Planck energy scale, i.e. M{sub P} ∼ 10{sup 18}GeV. We will see that after a short period of time, inflation enters in the slow-roll regime that its energy scale is of order M{sub P}/100 ∼ 10{sup 16}GeV and the horizon exit takes place in this energy scale. We also examine an idea in our non-canonical model to overcome the central drawback of intermediate inflation which is the fact that inflation never ends. We solve this problem without disturbing significantly the nature of the intermediate inflation until the time of horizon exit.

  17. The degeneracy problem in non-canonical inflation

    SciTech Connect

    Easson, Damien A.; Powell, Brian A. E-mail: brian.powell007@gmail.com

    2013-03-01

    While attempting to connect inflationary theories to observational physics, a potential difficulty is the degeneracy problem: a single set of observables maps to a range of different inflaton potentials. Two important classes of models affected by the degeneracy problem are canonical and non-canonical models, the latter marked by the presence of a non-standard kinetic term that generates observables beyond the scalar and tensor two-point functions on CMB scales. The degeneracy problem is manifest when these distinguishing observables go undetected. We quantify the size of the resulting degeneracy in this case by studying the most well-motivated non-canonical theory having Dirac-Born-Infeld Lagrangian. Beyond the scalar and tensor two-point functions on CMB scales, we then consider the possible detection of equilateral non-Gaussianity at Planck-precision and a measurement of primordial gravitational waves from prospective space-based laser interferometers. The former detection breaks the degeneracy with canonical inflation but results in poor reconstruction prospects, while the latter measurement enables a determination of n{sub T} which, while not breaking the degeneracy, can be shown to greatly improve the non-canonical reconstruction.

  18. Accretion of the Moon from non-canonical discs

    PubMed Central

    Salmon, J.; Canup, R. M

    2014-01-01

    Impacts that leave the Earth–Moon system with a large excess in angular momentum have recently been advocated as a means of generating a protolunar disc with a composition that is nearly identical to that of the Earth's mantle. We here investigate the accretion of the Moon from discs generated by such ‘non-canonical’ impacts, which are typically more compact than discs produced by canonical impacts and have a higher fraction of their mass initially located inside the Roche limit. Our model predicts a similar overall accretional history for both canonical and non-canonical discs, with the Moon forming in three consecutive steps over hundreds of years. However, we find that, to yield a lunar-mass Moon, the more compact non-canonical discs must initially be more massive than implied by prior estimates, and only a few of the discs produced by impact simulations to date appear to meet this condition. Non-canonical impacts require that capture of the Moon into the evection resonance with the Sun reduced the Earth–Moon angular momentum by a factor of 2 or more. We find that the Moon's semi-major axis at the end of its accretion is approximately 7R⊕, which is comparable to the location of the evection resonance for a post-impact Earth with a 2.5 h rotation period in the absence of a disc. Thus, the dynamics of the Moon's assembly may directly affect its ability to be captured into the resonance. PMID:25114307

  19. Mechanisms of Non-canonical Activation of Ataxia Telangiectasia Mutated.

    PubMed

    Khoronenkova, S V

    2016-12-01

    ATM is a master regulator of the cellular response to DNA damage. The classical mechanism of ATM activation involves its monomerization in response to DNA double-strand breaks, resulting in ATM-dependent phosphorylation of more than a thousand substrates required for cell cycle progression, DNA repair, and apoptosis. Here, new experimental evidence for non-canonical mechanisms of ATM activation in response to stimuli distinct from DNA double-strand breaks is discussed. It includes cytoskeletal changes, chromatin modifications, RNA-DNA hybrids, and DNA single-strand breaks. Noncanonical ATM activation may be important for the pathology of the multisystemic disease Ataxia Telangiectasia.

  20. Non-Canonical Replication Initiation: You're Fired!

    PubMed

    Ravoitytė, Bazilė; Wellinger, Ralf Erik

    2017-01-27

    The division of prokaryotic and eukaryotic cells produces two cells that inherit a perfect copy of the genetic material originally derived from the mother cell. The initiation of canonical DNA replication must be coordinated to the cell cycle to ensure the accuracy of genome duplication. Controlled replication initiation depends on a complex interplay of cis-acting DNA sequences, the so-called origins of replication (ori), with trans-acting factors involved in the onset of DNA synthesis. The interplay of cis-acting elements and trans-acting factors ensures that cells initiate replication at sequence-specific sites only once, and in a timely order, to avoid chromosomal endoreplication. However, chromosome breakage and excessive RNA:DNA hybrid formation can cause breakinduced (BIR) or transcription-initiated replication (TIR), respectively. These non-canonical replication events are expected to affect eukaryotic genome function and maintenance, and could be important for genome evolution and disease development. In this review, we describe the difference between canonical and non-canonical DNA replication, and focus on mechanistic differences and common features between BIR and TIR. Finally, we discuss open issues on the factors and molecular mechanisms involved in TIR.

  1. Non-Canonical Replication Initiation: You’re Fired!

    PubMed Central

    Ravoitytė, Bazilė; Wellinger, Ralf Erik

    2017-01-01

    The division of prokaryotic and eukaryotic cells produces two cells that inherit a perfect copy of the genetic material originally derived from the mother cell. The initiation of canonical DNA replication must be coordinated to the cell cycle to ensure the accuracy of genome duplication. Controlled replication initiation depends on a complex interplay of cis-acting DNA sequences, the so-called origins of replication (ori), with trans-acting factors involved in the onset of DNA synthesis. The interplay of cis-acting elements and trans-acting factors ensures that cells initiate replication at sequence-specific sites only once, and in a timely order, to avoid chromosomal endoreplication. However, chromosome breakage and excessive RNA:DNA hybrid formation can cause break-induced (BIR) or transcription-initiated replication (TIR), respectively. These non-canonical replication events are expected to affect eukaryotic genome function and maintenance, and could be important for genome evolution and disease development. In this review, we describe the difference between canonical and non-canonical DNA replication, and focus on mechanistic differences and common features between BIR and TIR. Finally, we discuss open issues on the factors and molecular mechanisms involved in TIR. PMID:28134821

  2. Novel perspectives on non-canonical inflammasome activation

    PubMed Central

    Diamond, Catherine Emma; Khameneh, Hanif Javanmard; Brough, David; Mortellaro, Alessandra

    2015-01-01

    Inflammasomes are cytosolic multi-protein complexes that regulate the secretion of the proinflammatory cytokines, IL-1β and IL-18, and induce pyroptosis, an inflammatory form of cell death. The NLRP3 inflammasome is the most well-characterized member of this family and functions by sensing intracellular pathogen- and damage-associated molecular patterns and activating caspase-1, which processes the biologically inactive IL-1β and IL-18 precursors into active cytokines. Recent studies have identified an alternative mechanism of inflammasome activation, termed the non-canonical inflammasome, which is triggered by cytosolic sensing of lipopolysaccharide (LPS) derived from bacteria that have escaped phagolysosomes. This pathway is independent of Toll-like receptor 4 (TLR4), the well-known extracellular receptor for LPS, but instead depends on the inflammatory protease, caspase-11. Although our understanding of caspase-11 activation is still in its infancy, it appears to be an essential mediator of septic shock and attenuates intestinal inflammation. In this review, we bring together the latest data on the roles of caspase-11 and the mechanisms underlying caspase-11-mediated activation of the non-canonical inflammasome, and consider the implications of this pathway on TLR4-independent immune responses to LPS. PMID:27471719

  3. Non-canonical Translation in Plant RNA Viruses.

    PubMed

    Miras, Manuel; Miller, W Allen; Truniger, Verónica; Aranda, Miguel A

    2017-01-01

    Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5' cap structure and/or the 3' poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. We also describe other translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. Finally, future research perspectives on the unusual translational strategies of +ssRNA viruses are discussed, including parallelisms between viral and host mRNAs mechanisms of translation, particularly for host mRNAs which are translated under stress conditions.

  4. The non-canonical functions of the heme oxygenases.

    PubMed

    Vanella, Luca; Barbagallo, Ignazio; Tibullo, Daniele; Forte, Stefano; Zappalà, Agata; Li Volti, Giovanni

    2016-10-18

    Heme oxygenase (HO) isoforms catalyze the conversion of heme to carbon monoxide (CO) and biliverdin with a concurrent release of iron, which can drive the synthesis of ferritin for iron sequestration. Most of the studies so far were directed at evaluating the protective effect of these enzymes because of their ability to generate antioxidant and antiapoptotic molecules such as CO and bilirubin. Recent evidences are suggesting that HO may possess other important physiological functions, which are not related to its enzymatic activity and for which we would like to introduce for the first time the term "non canonical functions". Recent evidence suggest that both HO isoforms may form protein-protein interactions (i.e. cytochrome P450, adiponectin, CD91) thus serving as chaperone-like protein. In addition, truncated HO-1 isoform was localized in the nuclear compartment under certain experimental conditions (i.e. excitotoxicity, hypoxia) regulating the activity of important nuclear transcription factors (i.e. Nrf2) and DNA repair. In the present review, we discuss three potential signaling mechanisms that we refer to as the non-canonical functions of the HO isoforms: protein-protein interaction, intracellular compartmentalization, and extracellular secretion. The aim of the present review is to describe each of this mechanism and all the aspects warranting additional studies in order to unravel all the functions of the HO system.

  5. Non-canonical Translation in Plant RNA Viruses

    PubMed Central

    Miras, Manuel; Miller, W. Allen; Truniger, Verónica; Aranda, Miguel A.

    2017-01-01

    Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5′ cap structure and/or the 3′ poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. We also describe other translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. Finally, future research perspectives on the unusual translational strategies of +ssRNA viruses are discussed, including parallelisms between viral and host mRNAs mechanisms of translation, particularly for host mRNAs which are translated under stress conditions. PMID:28428795

  6. Unsaturated fatty acids induce non-canonical autophagy

    PubMed Central

    Niso-Santano, Mireia; Malik, Shoaib Ahmad; Pietrocola, Federico; Bravo-San Pedro, José Manuel; Mariño, Guillermo; Cianfanelli, Valentina; Ben-Younès, Amena; Troncoso, Rodrigo; Markaki, Maria; Sica, Valentina; Izzo, Valentina; Chaba, Kariman; Bauvy, Chantal; Dupont, Nicolas; Kepp, Oliver; Rockenfeller, Patrick; Wolinski, Heimo; Madeo, Frank; Lavandero, Sergio; Codogno, Patrice; Harper, Francis; Pierron, Gérard; Tavernarakis, Nektarios; Cecconi, Francesco; Maiuri, Maria Chiara; Galluzzi, Lorenzo; Kroemer, Guido

    2015-01-01

    To obtain mechanistic insights into the cross talk between lipolysis and autophagy, two key metabolic responses to starvation, we screened the autophagy-inducing potential of a panel of fatty acids in human cancer cells. Both saturated and unsaturated fatty acids such as palmitate and oleate, respectively, triggered autophagy, but the underlying molecular mechanisms differed. Oleate, but not palmitate, stimulated an autophagic response that required an intact Golgi apparatus. Conversely, autophagy triggered by palmitate, but not oleate, required AMPK, PKR and JNK1 and involved the activation of the BECN1/PIK3C3 lipid kinase complex. Accordingly, the downregulation of BECN1 and PIK3C3 abolished palmitate-induced, but not oleate-induced, autophagy in human cancer cells. Moreover, Becn1+/− mice as well as yeast cells and nematodes lacking the ortholog of human BECN1 mounted an autophagic response to oleate, but not palmitate. Thus, unsaturated fatty acids induce a non-canonical, phylogenetically conserved, autophagic response that in mammalian cells relies on the Golgi apparatus. PMID:25586377

  7. A comprehensive survey of non-canonical splice sites in the human transcriptome

    PubMed Central

    Parada, Guillermo E.; Munita, Roberto; Cerda, Cledi A.; Gysling, Katia

    2014-01-01

    We uncovered the diversity of non-canonical splice sites at the human transcriptome using deep transcriptome profiling. We mapped a total of 3.7 billion human RNA-seq reads and developed a set of stringent filters to avoid false non-canonical splice site detections. We identified 184 splice sites with non-canonical dinucleotides and U2/U12-like consensus sequences. We selected 10 of the herein identified U2/U12-like non-canonical splice site events and successfully validated 9 of them via reverse transcriptase-polymerase chain reaction and Sanger sequencing. Analyses of the 184 U2/U12-like non-canonical splice sites indicate that 51% of them are not annotated in GENCODE. In addition, 28% of them are conserved in mouse and 76% are involved in alternative splicing events, some of them with tissue-specific alternative splicing patterns. Interestingly, our analysis identified some U2/U12-like non-canonical splice sites that are converted into canonical splice sites by RNA A-to-I editing. Moreover, the U2/U12-like non-canonical splice sites have a differential distribution of splicing regulatory sequences, which may contribute to their recognition and regulation. Our analysis provides a high-confidence group of U2/U12-like non-canonical splice sites, which exhibit distinctive features among the total human splice sites. PMID:25123659

  8. Complete Hamiltonian analysis of cosmological perturbations at all orders II: non-canonical scalar field

    NASA Astrophysics Data System (ADS)

    Nandi, Debottam; Shankaranarayanan, S.

    2016-10-01

    In this work, we present a consistent Hamiltonian analysis of cosmological perturbations for generalized non-canonical scalar fields. In order to do so, we introduce a new phase-space variable that is uniquely defined for different non-canonical scalar fields. We also show that this is the simplest and efficient way of expressing the Hamiltonian. We extend the Hamiltonian approach of [1] to non-canonical scalar field and obtain an unique expression of speed of sound in terms of phase-space variable. In order to invert generalized phase-space Hamilton's equations to Euler-Lagrange equations of motion, we prescribe a general inversion formulae and show that our approach for non-canonical scalar field is consistent. We also obtain the third and fourth order interaction Hamiltonian for generalized non-canonical scalar fields and briefly discuss the extension of our method to generalized Galilean scalar fields.

  9. Non-Canonical Interleukin 23 Receptor Complex Assembly

    PubMed Central

    Schröder, Jutta; Moll, Jens M.; Baran, Paul; Grötzinger, Joachim; Scheller, Jürgen; Floss, Doreen M.

    2015-01-01

    IL-23, composed of the cytokine subunit p19 and the soluble α receptor subunit p40, binds to a receptor complex consisting of the IL-23 receptor (IL-23R) and the IL-12 receptor β1 (IL-12Rβ1). Complex formation was hypothesized to follow the “site I-II-III” architectural paradigm, with site I of p19 being required for binding to p40, whereas sites II and III of p19 mediate binding to IL-12Rβ1 and IL-23R, respectively. Here we show that the binding mode of p19 to p40 and of p19 to IL-23R follow the canonical site I and III paradigm but that interaction of IL-23 to IL-12Rβ1 is independent of site II in p19. Instead, binding of IL-23 to the cytokine binding module of IL-12Rβ1 is mediated by domains 1 and 2 of p40 via corresponding site II amino acids of IL-12Rβ1. Moreover, domains 2 and 3 of p40 were sufficient for complex formation with p19 and to induce binding of p19 to IL-23R. The Fc-tagged fusion protein of p40_D2D3/p19 did, however, not act as a competitive IL-23 antagonist but, at higher concentrations, induced proliferation via IL-23R but independent of IL-12Rβ1. On the basis of our experimental validation, we propose a non-canonical topology of the IL-23·IL-23R·IL-12Rβ1 complex. Furthermore, our data help to explain why p40 is an antagonist of IL-23 and IL-12 signaling and show that site II of p19 is dispensable for IL-23 signaling. PMID:25371211

  10. Accretion of the Moon from non-canonical impacts

    NASA Astrophysics Data System (ADS)

    Salmon, Julien; Canup, R. M.

    2013-10-01

    The generally accepted scenario for the formation of the Moon involves the impact of a Mars-size object into the proto-Earth, resulting in the formation of a disk from which the Moon accretes (Cameron and Ward 1976). In a first paper (Salmon & Canup 2012), we showed that the disks resulting from these “canonical” impacts can lead to the accretion of a 1 lunar mass object on a timescale of order 10^2 yr. Recent works have focused on alternative impact configurations: bigger impactors (Canup 2012) or higher speed impacts into a fast spinning Earth (Cuk & Stewart 2012). These impacts leave the Earth-Moon system with an angular momentum about twice that in the current system. This quantity can be made consistent with its current value if the newly formed Moon is captured for a prolonged period in the evection resonance with the Sun (Cuk & Stewart 2012). The protolunar disks that are formed from these “non-canonical” impacts are generally more massive and more compact, containing a much greater fraction of their total disk mass in the Roche-interior portion of the disk, compared to canonical impacts. We have investigated the dynamics of the accretion of the Moon from such disks. While the overall accretion process is similar to that found from disks typical of canonical impacts, the more massive, compact disks typically produce a final moon with a much larger initial eccentricity, i.e. > 0.1 vs. 10^-3 to 10^-2 in canonical disks. Such high initial eccentricities may substantially reduce the probability of capture of the Moon into the evection resonance (e.g., Touma & Wisdom 1998), which is required to lower the angular momentum of the system in the non-canonical impacts. We will discuss which disk configurations can lead to the successful formation of the Moon, and how the Moon’s initial orbital properties vary for different impact scenarios.

  11. The Plasmodium falciparum exportome contains non-canonical PEXEL/HT proteins.

    PubMed

    Schulze, Jana; Kwiatkowski, Marcel; Borner, Janus; Schlüter, Hartmut; Bruchhaus, Iris; Burmester, Thorsten; Spielmann, Tobias; Pick, Christian

    2015-07-01

    The pathogenicity of Plasmodium falciparum is partly due to parasite-induced host cell modifications. These modifications are facilitated by exported P. falciparum proteins, collectively referred to as the exportome. Export of several hundred proteins is mediated by the PEXEL/HT, a protease cleavage site. The PEXEL/HT is usually comprised of five amino acids, of which R at position 1, L at position 3 and E, D or Q at position 5 are conserved and important for export. Non-canonical PEXEL/HTs with K or H at position 1 and/or I at position 3 are presently considered non-functional. Here, we show that non-canonical PEXEL/HT proteins are overrepresented in P. falciparum and other Plasmodium species. Furthermore, we show that non-canonical PEXEL/HTs can be cleaved and can promote export in both a REX3 and a GBP reporter, but not in a KAHRP reporter, indicating that non-canonical PEXEL/HTs are functional in concert with a supportive sequence environment. We then selected P. falciparum proteins with a non-canonical PEXEL/HT and show that some of these proteins are exported and that their export depends on non-canonical PEXEL/HTs. We conclude that PEXEL/HT plasticity is higher than appreciated and that non-canonical PEXEL/HT proteins cannot categorically be excluded from Plasmodium exportome predictions.

  12. Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations.

    PubMed

    Seligmann, Hervé

    2016-01-01

    Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (a) deleting mono-, dinucleotides after trinucleotides (delRNAs), (b) exchanging nucleotides according to 23 bijective transformations. Nine symmetric and fourteen asymmetric nucleotide exchanges (X ↔ Y, e.g. A ↔ C; and X → Y → Z → X, e.g. A → C → G → A) produce swinger RNAs. Here unbiased reanalyses of these proteomic data detect preferentially non-canonical tryptic peptides despite assuming random cleavage. Unbiased analyses couldn't reconstruct experimental tryptic digestion if most detected non-canonical peptides were false positives. Detected non-tryptic non-canonical peptides map preferentially on corresponding, previously described non-canonical transcripts, as for tryptic non-canonical peptides. Hence unbiased analyses independently confirm previous trypsin-biased analyses that showed translations of del- and swinger RNA and expanded codons. Accounting for natural proteolysis completes trypsin-biased mitopeptidome analyses, independently confirms non-canonical transcriptions and translations.

  13. Splitting K-symplectic methods for non-canonical separable Hamiltonian problems

    NASA Astrophysics Data System (ADS)

    Zhu, Beibei; Zhang, Ruili; Tang, Yifa; Tu, Xiongbiao; Zhao, Yue

    2016-10-01

    Non-canonical Hamiltonian systems have K-symplectic structures which are preserved by K-symplectic numerical integrators. There is no universal method to construct K-symplectic integrators for arbitrary non-canonical Hamiltonian systems. However, in many cases of interest, by using splitting, we can construct explicit K-symplectic methods for separable non-canonical systems. In this paper, we identify situations where splitting K-symplectic methods can be constructed. Comparative numerical experiments in three non-canonical Hamiltonian problems show that symmetric/non-symmetric splitting K-symplectic methods applied to the non-canonical systems are more efficient than the same-order Gauss' methods/non-symmetric symplectic methods applied to the corresponding canonicalized systems; for the non-canonical Lotka-Volterra model, the splitting algorithms behave better in efficiency and energy conservation than the K-symplectic method we construct via generating function technique. In our numerical experiments, the favorable energy conservation property of the splitting K-symplectic methods is apparent.

  14. Complex phylogenetic distribution of a non-canonical genetic code in green algae

    PubMed Central

    2010-01-01

    Background A non-canonical nuclear genetic code, in which TAG and TAA have been reassigned from stop codons to glutamine, has evolved independently in several eukaryotic lineages, including the ulvophycean green algal orders Dasycladales and Cladophorales. To study the phylogenetic distribution of the standard and non-canonical genetic codes, we generated sequence data of a representative set of ulvophycean green algae and used a robust green algal phylogeny to evaluate different evolutionary scenarios that may account for the origin of the non-canonical code. Results This study demonstrates that the Dasycladales and Cladophorales share this alternative genetic code with the related order Trentepohliales and the genus Blastophysa, but not with the Bryopsidales, which is sister to the Dasycladales. This complex phylogenetic distribution whereby all but one representative of a single natural lineage possesses an identical deviant genetic code is unique. Conclusions We compare different evolutionary scenarios for the complex phylogenetic distribution of this non-canonical genetic code. A single transition to the non-canonical code followed by a reversal to the canonical code in the Bryopsidales is highly improbable due to the profound genetic changes that coincide with codon reassignment. Multiple independent gains of the non-canonical code, as hypothesized for ciliates, are also unlikely because the same deviant code has evolved in all lineages. Instead we favor a stepwise acquisition model, congruent with the ambiguous intermediate model, whereby the non-canonical code observed in these green algal orders has a single origin. We suggest that the final steps from an ambiguous intermediate situation to a non-canonical code have been completed in the Trentepohliales, Dasycladales, Cladophorales and Blastophysa but not in the Bryopsidales. We hypothesize that in the latter lineage an initial stage characterized by translational ambiguity was not followed by final

  15. Natural chymotrypsin-like-cleaved human mitochondrial peptides confirm tetra-, pentacodon, non-canonical RNA translations.

    PubMed

    Seligmann, Hervé

    2016-09-01

    Mass spectra of human mitochondrial peptides match non-canonical transcripts systematically (a) deleting mono/dinucleotides after trinucleotides (delRNA), (b) exchanging nucleotides (swinger RNA), translated according to tri, (c) tetra- and pentacodons (codons expanded by a 4th (and 5th) silent nucleotide(s)). Swinger transcriptions are 23 bijective transformations, nine symmetric (X<->Y, e.g. A<->C) and fourteen asymmetric exchanges (X->Y->Z->X, e.g. A->C->G->A). Here, proteomic analyses assuming cleavage after W,Y, F (chymotrypsin-like, for trypsinized samples) detect fewer chymotrypsinized than trypsinized peptides. Detected non-canonical peptides map preferentially on detected non-canonical RNAs for chymotrypsinized peptides, as previously found for trypsinized peptides. This suggests residual natural chymotrypsin-like digestion detectable within experimentally trypsinized peptide data. Some trypsinized peptides are detected twice, by analyses assuming trypsin, and those assuming chymotrypsin cleavages. They have higher spectra counts than peptides detected only once, meaning that abundant peptides are more frequently detected, but detection certainties resemble those for peptides detected only once. Analyses assuming 'incorrect' digestions are inadequate negative controls for digestion enzymes naturally active in biological samples. Chymotrypsin-analyses confirm non-canonical transcriptions/translations independently of results obtained assuming trypsinization, increase non-canonical peptidome coverage, indicating mitogenome-encoding of yet undetected proteins.

  16. Generalized second law of thermodynamics for non-canonical scalar field model with corrected-entropy

    NASA Astrophysics Data System (ADS)

    Das, Sudipta; Debnath, Ujjal; Mamon, Abdulla Al

    2015-10-01

    In this work, we have considered a non-canonical scalar field dark energy model in the framework of flat FRW background. It has also been assumed that the dark matter sector interacts with the non-canonical dark energy sector through some interaction term. Using the solutions for this interacting non-canonical scalar field dark energy model, we have investigated the validity of generalized second law (GSL) of thermodynamics in various scenarios using first law and area law of thermodynamics. For this purpose, we have assumed two types of horizons viz apparent horizon and event horizon for the universe and using first law of thermodynamics, we have examined the validity of GSL on both apparent and event horizons. Next, we have considered two types of entropy-corrections on apparent and event horizons. Using the modified area law, we have examined the validity of GSL of thermodynamics on apparent and event horizons under some restrictions of model parameters.

  17. Non-Canonical Hh Signaling in Cancer-Current Understanding and Future Directions.

    PubMed

    Gu, Dongsheng; Xie, Jingwu

    2015-08-27

    As a major regulatory pathway for embryonic development and tissue patterning, hedgehog signaling is not active in most adult tissues, but is reactivated in a number of human cancer types. A major milestone in hedgehog signaling in cancer is the Food and Drug Administration (FDA) approval of a smoothened inhibitor Vismodegib for treatment of basal cell carcinomas. Vismodegib can block ligand-mediated hedgehog signaling, but numerous additional clinical trials have failed to show significant improvements in cancer patients. Amounting evidence indicate that ligand-independent hedgehog signaling plays an essential role in cancer. Ligand-independent hedgehog signaling, also named non-canonical hedgehog signaling, generally is not sensitive to smoothened inhibitors. What we know about non-canonical hedgehog signaling in cancer, and how should we prevent its activation? In this review, we will summarize recent development of non-canonical hedgehog signaling in cancer, and will discuss potential ways to prevent this type of hedgehog signaling.

  18. Teaching old NCATs new tricks: using non-canonical amino acid tagging to study neuronal plasticity.

    PubMed

    Hinz, F I; Dieterich, D C; Schuman, E M

    2013-10-01

    The non-canonical amino acid labeling techniques BONCAT (bioorthogonal non-canonical amino acid tagging) and FUNCAT (fluorescent non-canonical amino acid tagging) enable the specific identification and visualization of newly synthesized proteins. Recently, these techniques have been applied to neuronal systems to elucidate protein synthesis dynamics during plasticity, identify stimulation-induced proteomes and subproteomes and to investigate local protein synthesis in specific subcellular compartments. The next generation of tools and applications, reviewed here, includes the development of new tags, the quantitative identification of newly synthesized proteins, the application of NCAT to whole animals, and the ability to genetically restrict NCAT labeling. These techniques will enable not only improved detection but also allow new scientific questions to be tackled.

  19. Non-canonical NFκB activation promotes chemokine expression in podocytes

    PubMed Central

    Valiño-Rivas, Lara; Gonzalez-Lafuente, Laura; Sanz, Ana B.; Ruiz-Ortega, Marta; Ortiz, Alberto; Sanchez-Niño, Maria D.

    2016-01-01

    TNF-like weak inducer of apoptosis (TWEAK) receptor Fn14 is expressed by podocytes and Fn14 deficiency protects from experimental proteinuric kidney disease. However, the downstream effectors of TWEAK/Fn14 in podocytes are poorly characterized. We have explored TWEAK activation of non-canonical NFκB signaling in cultured podocytes. In cultured podocytes, TWEAK increased the expression of the chemokines CCL21, CCL19 and RANTES in a time-dependent manner. The inhibitor of canonical NFκB activation parthenolide inhibited the CCL19 and the early RANTES responses, but not the CCL21 or late RANTES responses. In this regard, TWEAK induced non-canonical NFκB activation in podocytes, characterized by NFκB2/p100 processing to NFκB2/p52 and nuclear migration of RelB/p52. Silencing by a specific siRNA of NIK, the upstream kinase of the non-canonical NFκB pathway, prevented CCL21 upregulation but did not modulate CCL19 or RANTES expression in response to TWEAK, thus establishing CCL21 as a non-canonical NFκB target in podocytes. Increased kidney Fn14 and CCL21 expression was also observed in rat proteinuric kidney disease induced by puromycin, and was localized to podocytes. In conclusion, TWEAK activates the non-canonical NFκB pathway in podocytes, leading to upregulation of CCL21 expression. The non-canonical NFκB pathway should be explored as a potential therapeutic target in proteinuric kidney disease. PMID:27353019

  20. Power spectra beyond the slow roll approximation in theories with non-canonical kinetic terms

    SciTech Connect

    De Bruck, Carsten van; Robinson, Mathew E-mail: app11mrr@sheffield.ac.uk

    2014-08-01

    We derive analytical expressions for the power spectra at the end of inflation in theories with two inflaton fields and non-canonical kinetic terms. We find that going beyond the slow-roll approximation is necessary and that the nature of the non-canonical terms have an important impact on the final power spectra at the end of inflation. We study five models numerically and find excellent agreement with our analytical results. Our results emphasise the fact that going beyond the slow-roll approximation is important in times of high-precision data coming from cosmological observations.

  1. Multiple site-selective insertions of non-canonical amino acids into sequence-repetitive polypeptides

    PubMed Central

    Wu, I-Lin; Patterson, Melissa A.; Carpenter Desai, Holly E.; Mehl, Ryan A.; Giorgi, Gianluca

    2013-01-01

    A simple and efficient method is described for introduction of non-canonical amino acids at multiple, structurally defined sites within recombinant polypeptide sequences. E. coli MRA30, a bacterial host strain with attenuated activity for release factor 1 (RF1), is assessed for its ability to support the incorporation of a diverse range of non-canonical amino acids in response to multiple encoded amber (TAG) codons within genetic templates derived from superfolder GFP and an elastin-mimetic protein polymer. Suppression efficiency and isolated protein yield were observed to depend on the identity of the orthogonal aminoacyl-tRNA synthetase/tRNACUA pair and the non-canonical amino acid substrate. This approach afforded elastin-mimetic protein polymers containing non-canonical amino acid derivatives at up to twenty-two positions within the repeat sequence with high levels of substitution. The identity and position of the variant residues was confirmed by mass spectrometric analysis of the full-length polypeptides and proteolytic cleavage fragments resulting from thermolysin digestion. The accumulated data suggest that this multi-site suppression approach permits the preparation of protein-based materials in which novel chemical functionality can be introduced at precisely defined positions within the polypeptide sequence. PMID:23625817

  2. Resurrecting the exponential and inverse power-law potentials in non-canonical inflation

    NASA Astrophysics Data System (ADS)

    Teimoori, Zeinab; Karami, Kayoomars

    2017-08-01

    We study inflation within the framework of non-canonical scalar field. In this scenario, we obtain the inflationary observables such as the scalar spectral index, the tensor-to-scalar ratio, the running of the scalar spectral index as well as the equilateral non-Gaussianity parameter. Then, we apply these results for the exponential and inverse power-law potentials. Our investigation shows that although the predictions of these potentials in the standard canonical inflation are completely ruled out by the Planck 2015 observations, their results in non-canonical scenario can lie inside the allowed regions of the Planck 2015 data. We also find that in non-canonical inflation, the predictions of the aforementioned potentials for the running of the scalar spectral index and the equilateral non-Gaussianity parameter are in well agreement with the Planck 2015 results. Furthermore, we show that in the context of non-canonical inflation, the graceful exit problem of the exponential and inverse power-law potentials is resolved.

  3. Non-canonical NF-κB signaling in rheumatoid arthritis: Dr Jekyll and Mr Hyde?

    PubMed

    Noort, Ae R; Tak, Paul P; Tas, Sander W

    2015-01-28

    The nuclear factor-κB (NF-κB) family of transcription factors is essential for the expression of pro-inflammatory cytokines, but can also induce regulatory pathways. NF-κB can be activated via two distinct pathways: the classical or canonical pathway, and the alternative or non-canonical pathway. It is well established that the canonical NF-κB pathway is essential both in acute inflammatory responses and in chronic inflammatory diseases, including rheumatoid arthritis (RA). Although less extensively studied, the non-canonical NF-κB pathway is not only central in lymphoid organ development and adaptive immune responses, but is also thought to play an important role in the pathogenesis of RA. Importantly, this pathway appears to have cell type-specific functions and, since many different cell types are involved in the pathogenesis of RA, it is difficult to predict the net overall contribution of the non-canonical NF-κB pathway to synovial inflammation. In this review, we describe the current understanding of non-canonical NF-κB signaling in various important cell types in the context of RA and consider the relevance to the pathogenesis of the disease. In addition, we discuss current drugs targeting this pathway, as well as future therapeutic prospects.

  4. Signature and Pathophysiology of Non-canonical Pores in Voltage-Dependent Cation Channels.

    PubMed

    Held, Katharina; Voets, Thomas; Vriens, Joris

    2016-01-01

    Opening and closing of voltage-gated cation channels allows the regulated flow of cations such as Na(+), K(+), and Ca(2+) across cell membranes, which steers essential physiological processes including shaping of action potentials and triggering Ca(2+)-dependent processes. Classical textbooks describe the voltage-gated cation channels as membrane proteins with a single, central aqueous pore. In recent years, however, evidence has accumulated for the existence of additional ion permeation pathways in this group of cation channels, distinct from the central pore, which here we collectively name non-canonical pores. Whereas the first non-canonical pores were unveiled only after making specific point mutations in the voltage-sensor region of voltage-gated Na(+) and K(+) channels, recent evidence indicates that they may also be functional in non-mutated channels. Moreover, several channelopathies have been linked to mutations that cause the appearance of a non-canonical ion permeation pathway as a new pathological mechanism. This review provides an integrated overview of the biophysical properties of non-canonical pores described in voltage-dependent cation channels (KV, NaV, Cav, Hv1, and TRPM3) and of the (patho)physiological impact of opening of such pores.

  5. Macrophages Mediate a Switch between Canonical and Non-Canonical Wnt Pathways in Canine Mammary Tumors

    PubMed Central

    Król, Magdalena; Mucha, Joanna; Majchrzak, Kinga; Homa, Agata; Bulkowska, Małgorzata; Majewska, Alicja; Gajewska, Małgorzata; Pietrzak, Marta; Perszko, Mikołaj; Romanowska, Karolina; Pawłowski, Karol; Manuali, Elisabetta; Hellmen, Eva; Motyl, Tomasz

    2014-01-01

    Objective According to the current hypothesis, tumor-associated macrophages (TAMs) are “corrupted” by cancer cells and subsequently facilitate, rather than inhibit, tumor metastasis. Because the molecular mechanisms of cancer cell–TAM interactions are complicated and controversial we aimed to better define this phenomenon. Methods and Results Using microRNA microarrays, Real-time qPCR and Western blot we showed that co-culture of canine mammary tumor cells with TAMs or treatment with macrophage-conditioned medium inhibited the canonical Wnt pathway and activated the non-canonical Wnt pathway in tumor cells. We also showed that co-culture of TAMs with tumor cells increased expression of canonical Wnt inhibitors in TAMs. Subsequently, we demonstrated macrophage-induced invasive growth patterns and epithelial–mesenchymal transition of tumor cells. Validation of these results in canine mammary carcinoma tissues (n = 50) and xenograft tumors indicated the activation of non-canonical and canonical Wnt pathways in metastatic tumors and non-metastatic malignancies, respectively. Activation of non-canonical Wnt pathway correlated with number of TAMs. Conclusions We demonstrated that TAMs mediate a “switch” between canonical and non-canonical Wnt signaling pathways in canine mammary tumors, leading to increased tumor invasion and metastasis. Interestingly, similar changes in neoplastic cells were observed in the presence of macrophage-conditioned medium or live macrophages. These observations indicate that rather than being “corrupted” by cancer cells, TAMs constitutively secrete canonical Wnt inhibitors that decrease tumor proliferation and development, but as a side effect, they induce the non-canonical Wnt pathway, which leads to tumor metastasis. These data challenge the conventional understanding of TAM–cancer cell interactions. PMID:24404146

  6. Non-canonical WNT/PCP signalling in cancer: Fzd6 takes centre stage.

    PubMed

    Corda, G; Sala, A

    2017-07-24

    Frizzled receptors are the mediators of the wnt canonical and non-canonical pathways, which play fundamental roles in cell differentiation and organism development. A large body of work indicates that dysregulation of wnt signalling is a feature of oncogenic transformation, but most of the studies published so far focus on the assessment of the consequences of aberrations of the canonical pathway in human cancer. In this review, we discuss the emerging role of the wnt non-canonical pathway regulated by frizzled receptor 6 (Fzd6) in the pathogenesis of different types of human malignancies. The function played by Fzd6 in the physiology of normal and cancer cells has been highlighted in the view that an increased knowledge of the signalling pathways upstream and downstream of this receptor could ultimately result in the identification of new targets for cancer therapy.

  7. Non-canonical WNT/PCP signalling in cancer: Fzd6 takes centre stage

    PubMed Central

    Corda, G; Sala, A

    2017-01-01

    Frizzled receptors are the mediators of the wnt canonical and non-canonical pathways, which play fundamental roles in cell differentiation and organism development. A large body of work indicates that dysregulation of wnt signalling is a feature of oncogenic transformation, but most of the studies published so far focus on the assessment of the consequences of aberrations of the canonical pathway in human cancer. In this review, we discuss the emerging role of the wnt non-canonical pathway regulated by frizzled receptor 6 (Fzd6) in the pathogenesis of different types of human malignancies. The function played by Fzd6 in the physiology of normal and cancer cells has been highlighted in the view that an increased knowledge of the signalling pathways upstream and downstream of this receptor could ultimately result in the identification of new targets for cancer therapy. PMID:28737757

  8. Non-Canonical EZH2 Transcriptionally Activates RelB in Triple Negative Breast Cancer

    PubMed Central

    Lawrence, Cortney L.; Baldwin, Albert S.

    2016-01-01

    Enhancer of zeste homology 2 (EZH2) is the methyltransferase component of the polycomb repressive complex (PRC2) which represses gene transcription via histone H3 trimethylation at lysine 23 (H3K27me3). EZH2 activity has been linked with oncogenesis where it is thought to block expression of certain tumor suppressors. Relative to a role in cancer, EZH2 functions to promote self-renewal and has been shown to be important for the tumor-initiating cell (TIC) phenotype in breast cancer. Recently a non-canonical role for EZH2 has been identified where it promotes transcriptional activation of certain genes. Here we show that EZH2, through a methyltransferase-independent mechanism, promotes the transcriptional activation of the non-canonical NF-κB subunit RelB to drive self-renewal and the TIC phenotype of triple-negative breast cancer cells. PMID:27764181

  9. Non-Canonical Roles of Dengue Virus Non-Structural Proteins

    PubMed Central

    Zeidler, Julianna D.; Fernandes-Siqueira, Lorena O.; Barbosa, Glauce M.; Da Poian, Andrea T.

    2017-01-01

    The Flaviviridae family comprises a number of human pathogens, which, although sharing structural and functional features, cause diseases with very different outcomes. This can be explained by the plurality of functions exerted by the few proteins coded by viral genomes, with some of these functions shared among members of a same family, but others being unique for each virus species. These non-canonical functions probably have evolved independently and may serve as the base to the development of specific therapies for each of those diseases. Here it is discussed what is currently known about the non-canonical roles of dengue virus (DENV) non-structural proteins (NSPs), which may account for some of the effects specifically observed in DENV infection, but not in other members of the Flaviviridae family. This review explores how DENV NSPs contributes to the physiopathology of dengue, evasion from host immunity, metabolic changes, and redistribution of cellular components during infection. PMID:28335410

  10. Non-canonical functions of the tuberous sclerosis complex-Rheb signalling axis.

    PubMed

    Neuman, Nicole A; Henske, Elizabeth Petri

    2011-04-01

    The protein products of the tuberous sclerosis complex (TSC) genes, TSC1 and TSC2, form a complex, which inhibits the small G-protein, Ras homolog enriched in brain (Rheb). The vast majority of research regarding these proteins has focused on mammalian Target of Rapamycin (mTOR), a target of Rheb. Here, we propose that there are clinically relevant functions and targets of TSC1, TSC2 and Rheb, which are independent of mTOR. We present evidence that such non-canonical functions of the TSC-Rheb signalling network exist, propose a standard of evidence for these non-canonical functions, and discuss their potential clinical and therapeutic implications for patients with TSC and lymphangioleiomyomatosis (LAM).

  11. Non-Canonical Roles of Dengue Virus Non-Structural Proteins.

    PubMed

    Zeidler, Julianna D; Fernandes-Siqueira, Lorena O; Barbosa, Glauce M; Da Poian, Andrea T

    2017-03-13

    The Flaviviridae family comprises a number of human pathogens, which, although sharing structural and functional features, cause diseases with very different outcomes. This can be explained by the plurality of functions exerted by the few proteins coded by viral genomes, with some of these functions shared among members of a same family, but others being unique for each virus species. These non-canonical functions probably have evolved independently and may serve as the base to the development of specific therapies for each of those diseases. Here it is discussed what is currently known about the non-canonical roles of dengue virus (DENV) non-structural proteins (NSPs), which may account for some of the effects specifically observed in DENV infection, but not in other members of the Flaviviridae family. This review explores how DENV NSPs contributes to the physiopathology of dengue, evasion from host immunity, metabolic changes, and redistribution of cellular components during infection.

  12. Regulation of angiogenesis by a non-canonical Wnt-Flt1 pathway in myeloid cells.

    PubMed

    Stefater, James A; Lewkowich, Ian; Rao, Sujata; Mariggi, Giovanni; Carpenter, April C; Burr, Adam R; Fan, Jieqing; Ajima, Rieko; Molkentin, Jeffery D; Williams, Bart O; Wills-Karp, Marsha; Pollard, Jeffrey W; Yamaguchi, Terry; Ferrara, Napoleone; Gerhardt, Holger; Lang, Richard A

    2011-05-29

    Myeloid cells are a feature of most tissues. Here we show that during development, retinal myeloid cells (RMCs) produce Wnt ligands to regulate blood vessel branching. In the mouse retina, where angiogenesis occurs postnatally, somatic deletion in RMCs of the Wnt ligand transporter Wntless results in increased angiogenesis in the deeper layers. We also show that mutation of Wnt5a and Wnt11 results in increased angiogenesis and that these ligands elicit RMC responses via a non-canonical Wnt pathway. Using cultured myeloid-like cells and RMC somatic deletion of Flt1, we show that an effector of Wnt-dependent suppression of angiogenesis by RMCs is Flt1, a naturally occurring inhibitor of vascular endothelial growth factor (VEGF). These findings indicate that resident myeloid cells can use a non-canonical, Wnt-Flt1 pathway to suppress angiogenic branching.

  13. Differential expression of canonical and non-canonical Wnt ligands in ameloblastoma.

    PubMed

    Siar, Chong Huat; Nagatsuka, Hitoshi; Han, Phuu Pwint; Buery, Rosario Rivera; Tsujigiwa, Hidetsugu; Nakano, Keisuke; Ng, Kok Han; Kawakami, Toshiyuki

    2012-04-01

    Canonical and non-canonical Wnt signaling pathways modulate diverse cellular processes during embryogenesis and post-natally. Their deregulations have been implicated in cancer development and progression. Wnt signaling is essential for odontogenesis. The ameloblastoma is an odontogenic epithelial neoplasm of enamel organ origin. Altered expressions of Wnts-1, -2, -5a, and -10a are detected in this tumor. The activity of other Wnt members remains unclarified. Canonical (Wnts-1, -2, -3, -8a, -8b, -10a, and -10b), non-canonical (Wnts-4, -5a, -5b, -6, 7a, -7b, and -11), and indeterminate groups (Wnts-2b and -9b) were examined immunohistochemically in 72 cases of ameloblastoma (19 unicystic [UA], 35 solid/multicystic [SMA], eight desmoplastic [DA], and 10 recurrent [RA]). Canonical Wnt proteins (except Wnt-10b) were heterogeneously expressed in ameloblastoma. Their distribution patterns were distinctive with some overlap. Protein localization was mainly membranous and/or cytoplasmic. Overexpression of Wnt-1 in most subsets (UA = 19/19; SMA = 35/35; DA = 5/8; RA = 7/10) (P < 0.05), Wnt-3 in granular cell variant (n = 3/3), and Wnt-8b in DA (n = 8/8) was key observations. Wnts-8a and -10a demonstrated enhanced expression in tumoral buddings and acanthomatous areas. Non-canonical and indeterminate Wnts were absent except for limited Wnt-7b immunoreactivity in UA (n = 1/19) and SMA (n = 1/35). Stromal components expressed variable Wnt positivity. Differential expression of Wnt ligands in different ameloblastoma subtypes suggests that the canonical and non-canonical Wnt pathways are selectively activated or repressed depending on the tumor cell differentiation status. Canonical Wnt pathway is most likely the main transduction pathway while Wnt-1 might be the key signaling molecule involved in ameloblastoma tumorigenesis. © 2011 John Wiley & Sons A/S.

  14. Impacts of non-canonical El Niño patterns on Atlantic hurricane activity

    NASA Astrophysics Data System (ADS)

    Larson, Sarah; Lee, Sang-Ki; Wang, Chunzai; Chung, Eui-Seok; Enfield, David

    2012-07-01

    The impact of non-canonical El Niño patterns, typically characterized by warmer than normal sea surface temperatures (SSTs) in the central tropical Pacific, on Atlantic tropical cyclone (TC) is explored by using composites of key Atlantic TC indices and tropospheric vertical wind shear over the Atlantic main development region (MDR). The highlight of our major findings is that, while the canonical El Niño pattern has a strong suppressing influence on Atlantic TC activity, non-canonical El Niño patterns considered in this study, namely central Pacific warming, El Niño Modoki, positive phase Trans-Niño, and positive phase Pacific meridional mode, all have insubstantial impact on Atlantic TC activity. This result becomes more conclusive when the impact of MDR SST is removed from the Atlantic TC indices and MDR wind shear by using the method of linear regression. Further analysis suggests that the tropical Pacific SST anomalies associated with the non-canonical El Niño patterns are not strong enough to cause a substantial warming of the tropical troposphere in the Atlantic region, which is the key factor that increases the wind shear and atmospheric static stability over the MDR. During the recent decades, the non-canonical El Niños have been more frequent while the canonical El Niño has been less frequent. If such a trend continues in the future, it is expected that the suppressing effect of El Niño on Atlantic TC activity will diminish and thus the MDR SST will play a more important role in controlling Atlantic TC activity in the coming decades.

  15. Impacts of non-canonical El Niño patterns on Atlantic hurricane activity

    NASA Astrophysics Data System (ADS)

    Larson, S.; Lee, S.; Wang, C.; Chung, E.; Enfield, D. B.

    2012-12-01

    The impact of non-canonical El Niño patterns, typically characterized by warmer than normal sea surface tempera- tures (SSTs) in the central tropical Pacific, on Atlantic tropical cyclone (TC) is explored by using composites of key Atlantic TC indices and tropospheric vertical wind shear over the Atlantic main development region (MDR). The highlight of our major findings is that, while the canonical El Niño pattern has a strong suppressing influence on Atlantic TC activity, non-canonical El Niño patterns con- sidered in this study, namely central Pacific warming, El Niño Modoki, positive phase Trans-Niño, and positive phase Pacific meridional mode, all have insubstantial impact on Atlantic TC activity. This result becomes more conclu- sive when the impact of MDR SST is removed from the Atlantic TC indices and MDR wind shear by using the method of linear regression. Further analysis suggests that the tropical Pacific SST anomalies associated with the non- canonical El Niño patterns are not strong enough to cause a substantial warming of the tropical troposphere in the Atlantic region, which is the key factor that increases the wind shear and atmospheric static stability over the MDR. During the recent decades, the non-canonical El Niños have been more frequent while the canonical El Niño has been less frequent. If such a trend continues in the future, it is expected that the suppressing effect of El Niño on Atlantic TC activity will diminish and thus the MDR SST will play a more important role in controlling Atlantic TC activity in the coming decades.

  16. Ciliary IFT80 balances canonical versus non-canonical hedgehog signalling for osteoblast differentiation.

    PubMed

    Yuan, Xue; Cao, Jay; He, Xiaoning; Serra, Rosa; Qu, Jun; Cao, Xu; Yang, Shuying

    2016-03-21

    Intraflagellar transport proteins (IFT) are required for hedgehog (Hh) signalling transduction that is essential for bone development, however, how IFT proteins regulate Hh signalling in osteoblasts (OBs) remains unclear. Here we show that deletion of ciliary IFT80 in OB precursor cells (OPC) in mice results in growth retardation and markedly decreased bone mass with impaired OB differentiation. Loss of IFT80 blocks canonical Hh-Gli signalling via disrupting Smo ciliary localization, but elevates non-canonical Hh-Gαi-RhoA-stress fibre signalling by increasing Smo and Gαi binding. Inhibition of RhoA and ROCK activity partially restores osteogenic differentiation of IFT80-deficient OPCs by inhibiting non-canonical Hh-RhoA-Cofilin/MLC2 signalling. Cytochalasin D, an actin destabilizer, dramatically restores OB differentiation of IFT80-deficient OPCs by disrupting actin stress fibres and promoting cilia formation and Hh-Gli signalling. These findings reveal that IFT80 is required for OB differentiation by balancing between canonical Hh-Gli and non-canonical Hh-Gαi-RhoA pathways and highlight IFT80 as a therapeutic target for craniofacial and skeletal abnormalities.

  17. Ciliary IFT80 balances canonical versus non-canonical hedgehog signalling for osteoblast differentiation

    PubMed Central

    Yuan, Xue; Cao, Jay; He, Xiaoning; Serra, Rosa; Qu, Jun; Cao, Xu; Yang, Shuying

    2016-01-01

    Intraflagellar transport proteins (IFT) are required for hedgehog (Hh) signalling transduction that is essential for bone development, however, how IFT proteins regulate Hh signalling in osteoblasts (OBs) remains unclear. Here we show that deletion of ciliary IFT80 in OB precursor cells (OPC) in mice results in growth retardation and markedly decreased bone mass with impaired OB differentiation. Loss of IFT80 blocks canonical Hh–Gli signalling via disrupting Smo ciliary localization, but elevates non-canonical Hh–Gαi–RhoA–stress fibre signalling by increasing Smo and Gαi binding. Inhibition of RhoA and ROCK activity partially restores osteogenic differentiation of IFT80-deficient OPCs by inhibiting non-canonical Hh–RhoA–Cofilin/MLC2 signalling. Cytochalasin D, an actin destabilizer, dramatically restores OB differentiation of IFT80-deficient OPCs by disrupting actin stress fibres and promoting cilia formation and Hh–Gli signalling. These findings reveal that IFT80 is required for OB differentiation by balancing between canonical Hh–Gli and non-canonical Hh–Gαi–RhoA pathways and highlight IFT80 as a therapeutic target for craniofacial and skeletal abnormalities. PMID:26996322

  18. Zebrafish Naked 1 and Naked 2 antagonize both canonical and non-canonical Wnt signaling

    PubMed Central

    Van Raay, Terence J.; Coffey, Robert J.; Solnica-Krezel, Lilianna

    2007-01-01

    Wnt signaling controls a wide range of developmental processes and its aberrant regulation can lead to disease. To better understand the regulation of this pathway, we identified zebrafish homologues of Naked Cuticle (Nkd), Nkd1 and Nkd2, which have previously been shown to inhibit canonical Wnt/β-catenin signaling. Zebrafish nkd1 expression increases substantially after the mid-blastula transition in a pattern mirroring that of activated canonical Wnt/β-catenin signaling, being expressed in both the ventrolateral blastoderm margin and also in the axial mesendoderm. In contrast, zebrafish nkd2 is maternally and ubiquitously expressed. Overexpression of Nkd1 or Nkd2a suppressed canonical Wnt/β-catenin signaling at multiple stages of early zebrafish development and also exacerbated the cyclopia and axial mesendoderm convergence and extension (C&E) defect in the non-canonical Wnt/PCP mutant silberblick (slb/wnt11). Thus, Nkds are sufficient to antagonize both canonical and non-canonical Wnt signaling. Reducing Nkd function using antisense morpholino oligonucleotides resulted in increased expression of canonical Wnt/β-catenin target genes. Finally, reducing Nkd1 function in slb mutants suppressed the axial mesendoderm C&E defect. These data indicate that zebrafish Nkd1 and Nkd2 function to limit both canonical and non-canonical Wnt signaling. PMID:17689523

  19. Generalization between canonical and non-canonical views in object recognition

    PubMed Central

    Ghose, Tandra; Liu, Zili

    2013-01-01

    Viewpoint generalization in object recognition is the process that allows recognition of a given 3D object from many different viewpoints despite variations in its 2D projections. We used the canonical view effects as a foundation to empirically test the validity of a major theory in object recognition, the view-approximation model (Poggio & Edelman, 1990). This model predicts that generalization should be better when an object is first seen from a non-canonical view and then a canonical view than when seen in the reversed order. We also manipulated object similarity to study the degree to which this view generalization was constrained by shape details and task instructions (object vs. image recognition). Old-new recognition performance for basic and subordinate level objects was measured in separate blocks. We found that for object recognition, view generalization between canonical and non-canonical views was comparable for basic level objects. For subordinate level objects, recognition performance was more accurate from non-canonical to canonical views than the other way around. When the task was changed from object recognition to image recognition, the pattern of the results reversed. Interestingly, participants responded “old” to “new” images of “old” objects with a substantially higher rate than to “new” objects, despite instructions to the contrary, thereby indicating involuntary view generalization. Our empirical findings are incompatible with the prediction of the view-approximation theory, and argue against the hypothesis that views are stored independently. PMID:23283692

  20. A Non-Canonical Function of Zebrafish Telomerase Reverse Transcriptase Is Required for Developmental Hematopoiesis

    PubMed Central

    Koshimizu, Eriko; Hanai, Jun-ichi; Raftopoulou, Christina; Murphey, Ryan D.; Bayliss, Peter E.; Imai, Yoichi; Burns, Caroline Erter; Masutomi, Kenkichi; Gagos, Sarantis; Zon, Leonard I.; Roberts, Thomas M.; Kishi, Shuji

    2008-01-01

    Although it is clear that telomerase expression is crucial for the maintenance of telomere homeostasis, there is increasing evidence that the TERT protein can have physiological roles that are independent of this central function. To further examine the role of telomerase during vertebrate development, the zebrafish telomerase reverse transcriptase (zTERT) was functionally characterized. Upon zTERT knockdown, zebrafish embryos show reduced telomerase activity and are viable, but develop pancytopenia resulting from aberrant hematopoiesis. The blood cell counts in TERT-depleted zebrafish embryos are markedly decreased and hematopoietic cell differentiation is impaired, whereas other somatic lineages remain morphologically unaffected. Although both primitive and definitive hematopoiesis is disrupted by zTERT knockdown, the telomere lengths are not significantly altered throughout early development. Induced p53 deficiency, as well as overexpression of the anti-apoptotic proteins Bcl-2 and E1B-19K, significantly relieves the decreased blood cells numbers caused by zTERT knockdown, but not the impaired blood cell differentiation. Surprisingly, only the reverse transcriptase motifs of zTERT are crucial, but the telomerase RNA-binding domain of zTERT is not required, for rescuing complete hematopoiesis. This is therefore the first demonstration of a non-canonical catalytic activity of TERT, which is different from “authentic” telomerase activity, is required for during vertebrate hematopoiesis. On the other hand, zTERT deficiency induced a defect in hematopoiesis through a potent and specific effect on the gene expression of key regulators in the absence of telomere dysfunction. These results suggest that TERT non-canonically functions in hematopoietic cell differentiation and survival in vertebrates, independently of its role in telomere homeostasis. The data also provide insights into a non-canonical pathway by which TERT functions to modulate specification of

  1. Drosophila melanogaster Hedgehog cooperates with Frazzled to guide axons through a non-canonical signalling pathway.

    PubMed

    Ricolo, Delia; Butí, Elisenda; Araújo, Sofia J

    2015-08-01

    We report that the morphogen Hedgehog (Hh) is an axonal chemoattractant in the midline of Drosophila melanogaster embryos. Hh is present in the ventral nerve cord during axonal guidance and overexpression of hh in the midline causes ectopic midline crossing of FasII-positive axonal tracts. In addition, we show that Hh influences axonal guidance via a non-canonical signalling pathway dependent on Ptc. Our results reveal that the Hh pathway cooperates with the Netrin/Frazzled pathway to guide axons through the midline in invertebrates.

  2. Sodium tungstate activates glycogen synthesis through a non-canonical mechanism involving G-proteins.

    PubMed

    Zafra, Delia; Nocito, Laura; Domínguez, Jorge; Guinovart, Joan J

    2013-01-31

    Tungstate treatment ameliorates experimental diabetes by increasing liver glycogen deposition through an as yet unidentified mechanism. The signalling mechanism of tungstate was studied in CHOIR cells and primary cultured hepatocytes. This compound exerted its pro-glycogenic effects through a new G-protein-dependent and Tyr-Kinase Receptor-independent mechanism. Chemical or genetic disruption of G-protein signalling prevented the activation of the Ras/ERK cascade and the downstream induction of glycogen synthesis caused by tungstate. Thus, these findings unveil a novel non-canonical signalling pathway that leads to the activation of glycogen synthesis and that could be exploited as an approach to treat diabetes.

  3. Dynamical Characteristics of a Non-canonical Scalar-Torsion Model of Dark Energy

    NASA Astrophysics Data System (ADS)

    Banijamali, A.; Ghasemi, E.

    2016-08-01

    In this paper, we analyze the phase-space of a model of dark energy in which a non-canonical scalar field (tachyon) non-minimally coupled to torsion scalar in the framework of teleparallelism. Scalar field potential and non-minimal coupling function are chosen as V( ϕ) = V 0 ϕ n and f( ϕ) = ϕ N , respectively. We obtain a critical point that behaves like a stable or saddle point depending on the values of N and n. Additionally we find an unstable critical line. We have shown such a behavior of critical points using numerical computations and phase-space trajectories explicitly.

  4. Production of non-canonical sentences in agrammatic aphasia: limits in representation or rule application?

    PubMed

    Burchert, Frank; Meissner, Nadine; De Bleser, Ria

    2008-02-01

    The study reported here compares two linguistically informed hypotheses on agrammatic sentence production, the TPH [Friedmann, N., & Grodzinsky, Y. (1997). Tense and agreement in agrammatic production: Pruning the syntactic tree. Brain and Language, 56, 397-425.] and the DOP [Bastiaanse, R., & van Zonneveld, R. (2005). Sentence production with verbs of alternating transitivity in agrammatic Broca's aphasia. Journal of Neurolinguistics, 18, 59-66]. To explain impaired production of non-canonical sentences in agrammatism, the TPH basically relies on deleted or pruned clause structure positions in the left periphery, whereas the DOP appeals to limitations in the application of movement rules. Certain non-canonical sentences such as object-questions and object-relative clauses require the availability of nodes in the left periphery as well as movement to these nodes. In languages with relatively fixed word order such as English, the relevant test cases generally involve a coincidence of left periphery and movement, such that the predictions of the TPH and the DOP are identical although for different reasons. In languages with relatively free word order such as German, on the other hand, it is possible to devise specific tests of the different predictions due to the availability of scrambling. Scrambled object sentences, for example, do not involve the left periphery but do require application of movement in a domain below the left periphery. A study was conducted with German agrammatic subjects which elicited canonical sentences without object movement and non-canonical scrambled sentences with object movement. The results show that agrammatic speakers have a particular problem with the production of scrambled sentences. Further evidence reported in the study from spontaneous speech, elicitation of object relatives, questions and passives and with different agrammatic subjects confirms that non-canonical sentences are generally harder to produce for agrammatics. These

  5. Non-canonical functions of cell cycle cyclins and cyclin-dependent kinases

    PubMed Central

    Hydbring, Per; Malumbres, Marcos; Sicinski, Piotr

    2016-01-01

    The role of cyclins and their catalytic partners, the cyclin-dependent kinases (CDKs), as core components of the machinery that drives cell cycle progression is well established. Increasing evidence indicates that mammalian cyclins and CDKs also carry out important roles in other cellular processes such as transcription, DNA damage repair, the control of cell death, differentiation, the immune response and metabolism. Some of these non-canonical functions are performed by cyclins or by CDKs, independent of their respective cell cycle partners, suggesting a substantial divergence in the function of these proteins during evolution. PMID:27033256

  6. Canonical and non-canonical VEGF pathways: New developments in biology and signal transduction

    PubMed Central

    Domigan, Courtney K.; Ziyad, Safiyyah; Iruela-Arispe, M. Luisa

    2014-01-01

    The last five years have witnessed a significant expansion in our understanding of VEGF signaling. In particular, the process of canonical activation of VEGFR tyrosine kinases by homodimeric VEGF molecules have now been broadened by the realization that heterodimeric ligands and receptors are also active participants in the signaling process. While heterodimer receptors were described two decades ago, their impact, along with the effect of additional cell surface partners and novel autocrine VEGF signaling pathways, are only now starting to be clarified. Furthermore, ligand-independent signaling (non-canonical) has been identified which occurs through galectin and gremlin binding, and upon rise of intracellular levels of reactive oxygen species. Activation of the VEGF receptors in the absence of ligand holds immediate implications for therapeutic approaches that exclusively target VEGF. The present review provides a concise summary of the recent developments in both canonical and non-canonical VEGF signaling and places these findings in perspective to their potential clinical and biological ramifications. PMID:25278287

  7. Non-canonical Glucocorticoid Receptor Transactivation of gilz by Alcohol Suppresses Cell Inflammatory Response

    PubMed Central

    Ng, Hang Pong; Jennings, Scott; Wang, Jack; Molina, Patricia E.; Nelson, Steve; Wang, Guoshun

    2017-01-01

    Acute alcohol exposure suppresses cell inflammatory response. The underlying mechanism has not been fully defined. Here we report that alcohol was able to activate glucocorticoid receptor (GR) signaling in the absence of glucocorticoids (GCs) and upregulated glucocorticoid-induced leucine zipper (gilz), a prominent GC-responsive gene. Such a non-canonical activation of GR was not blocked by mifepristone, a potent GC competitor. The proximal promoter of gilz, encompassing five GC-responsive elements (GREs), was incorporated and tested in a luciferase reporter system. Deletion and/or mutation of the GREs abrogated the promoter responsiveness to alcohol. Thus, the GR–GRE interaction transduced the alcohol action on gilz. Alcohol induced GR nuclear translocation, which was enhanced by the alcohol dehydrogenase inhibitor fomepizole, suggesting that it was alcohol, not its metabolites, that engendered the effect. Gel mobility shift assay showed that unliganded GR was able to bind GREs and such interaction withstood clinically relevant levels of alcohol. GR knockout via CRISPR/Cas9 gene targeting or GILZ depletion via small RNA interference diminished alcohol suppression of cell inflammatory response to LPS. Thus, a previously unrecognized, non-canonical GR activation of gilz is involved in alcohol modulation of cell immune response. PMID:28638383

  8. Hedgehog associated to microparticles inhibits adipocyte differentiation via a non-canonical pathway

    PubMed Central

    Fleury, Audrey; Hoch, Lucile; Martinez, M. Carmen; Faure, Hélène; Taddei, Maurizio; Petricci, Elena; Manetti, Fabrizio; Girard, Nicolas; Mann, André; Jacques, Caroline; Larghero, Jérôme; Ruat, Martial; Andriantsitohaina, Ramaroson; Le Lay, Soazig

    2016-01-01

    Hedgehog (Hh) is a critical regulator of adipogenesis. Extracellular vesicles are natural Hh carriers, as illustrated by activated/apoptotic lymphocytes specifically shedding microparticles (MP) bearing the morphogen (MPHh+). We show that MPHh+ inhibit adipocyte differentiation and orientate mesenchymal stem cells towards a pro-osteogenic program. Despite a Smoothened (Smo)-dependency, MPHh+ anti-adipogenic effects do not activate a canonical Hh signalling pathway in contrast to those elicited either by the Smo agonist SAG or recombinant Sonic Hedgehog. The Smo agonist GSA-10 recapitulates many of the hallmarks of MPHh+ anti-adipogenic effects. The adipogenesis blockade induced by MPHh+ and GSA-10 was abolished by the Smo antagonist LDE225. We further elucidate a Smo/Lkb1/Ampk axis as the non-canonical Hh pathway used by MPHh+ and GSA-10 to inhibit adipocyte differentiation. Our results highlight for the first time the ability of Hh-enriched MP to signal via a non-canonical pathway opening new perspectives to modulate fat development. PMID:27010359

  9. Ptk7 and Mcc, Unfancied Components in Non-Canonical Wnt Signaling and Cancer

    PubMed Central

    Dunn, Norris Ray; Tolwinski, Nicholas S.

    2016-01-01

    Human development uses a remarkably small number of signal transduction pathways to organize vastly complicated tissues. These pathways are commonly associated with disease in adults if activated inappropriately. One such signaling pathway, Wnt, solves the too few pathways conundrum by having many alternate pathways within the Wnt network. The main or “canonical” Wnt pathway has been studied in great detail, and among its numerous downstream components, several have been identified as drug targets that have led to cancer treatments currently in clinical trials. In contrast, the non-canonical Wnt pathways are less well characterized, and few if any possible drug targets exist to tackle cancers caused by dysregulation of these Wnt offshoots. In this review, we focus on two molecules—Protein Tyrosine Kinase 7 (Ptk7) and Mutated in Colorectal Cancer (Mcc)—that do not fit perfectly into the non-canonical pathways described to date and whose roles in cancer are ill defined. We will summarize work from our laboratories as well as many others revealing unexpected links between these two proteins and Wnt signaling both in cancer progression and during vertebrate and invertebrate embryonic development. We propose that future studies focused on delineating the signaling machinery downstream of Ptk7 and Mcc will provide new, hitherto unanticipated drug targets to combat cancer metastasis. PMID:27438854

  10. Translocation of Non-Canonical Polypeptides into Cells Using Protective Antigen

    PubMed Central

    Rabideau, Amy E.; Liao, Xiaoli; Akçay, Gizem; Pentelute, Bradley L.

    2015-01-01

    A variety of pathogenic bacteria infect host eukaryotic cells using protein toxins, which enter the cytosol and exert their cytotoxic effects. Anthrax lethal toxin, for example, utilizes the membrane-spanning translocase, protective antigen (PA) pore, to deliver the protein toxin lethal factor (LF) from the endosome into the cytosol of cells. Previous work has investigated the delivery of natural peptides and enzymatic domains appended to the C-terminus of the PA-binding domain of lethal factor (LFN) into the cytosol via PA pore. Here, we move beyond natural amino acids and systematically investigate the translocation of polypeptide cargo containing non-canonical amino acids and functionalities through PA pore. Our results indicate translocation is not perturbed with alterations to the peptide backbone or side-chain. Moreover, despite their structural complexity, we found that the small molecule drugs, doxorubicin and monomethyl auristatin F (MMAF) translocated efficiently through PA pore. However, we found cyclic peptides and the small molecule drug docetaxel abrogated translocation due to their large size and structural rigidity. For cargos that reached the cytosol, we demonstrated that each remained intact after translocation. These studies show PA is capable of translocating non-canonical cargo provided it is in a conformational state conducive for passage through the narrow pore. PMID:26178180

  11. Incorporation of non-canonical amino acids into the developing murine proteome

    PubMed Central

    Calve, Sarah; Witten, Andrew J.; Ocken, Alexander R.; Kinzer-Ursem, Tamara L.

    2016-01-01

    Analysis of the developing proteome has been complicated by a lack of tools that can be easily employed to label and identify newly synthesized proteins within complex biological mixtures. Here, we demonstrate that the methionine analogs azidohomoalanine and homopropargylglycine can be globally incorporated into the proteome of mice through facile intraperitoneal injections. These analogs contain bio-orthogonal chemical handles to which fluorescent tags can be conjugated to identify newly synthesized proteins. We show these non-canonical amino acids are incorporated into various tissues in juvenile mice and in a concentration dependent manner. Furthermore, administration of these methionine analogs to pregnant dams during a critical stage of murine development, E10.5–12.5 when many tissues are assembling, does not overtly disrupt development as assessed by proteomic analysis and normal parturition and growth of pups. This successful demonstration that non-canonical amino acids can be directly administered in vivo will enable future studies that seek to characterize the murine proteome during growth, disease and repair. PMID:27572480

  12. Non-canonical Wnt signalling modulates the endothelial shear stress flow sensor in vascular remodelling

    PubMed Central

    Franco, Claudio A; Jones, Martin L; Bernabeu, Miguel O; Vion, Anne-Clemence; Barbacena, Pedro; Fan, Jieqing; Mathivet, Thomas; Fonseca, Catarina G; Ragab, Anan; Yamaguchi, Terry P; Coveney, Peter V; Lang, Richard A; Gerhardt, Holger

    2016-01-01

    Endothelial cells respond to molecular and physical forces in development and vascular homeostasis. Deregulation of endothelial responses to flow-induced shear is believed to contribute to many aspects of cardiovascular diseases including atherosclerosis. However, how molecular signals and shear-mediated physical forces integrate to regulate vascular patterning is poorly understood. Here we show that endothelial non-canonical Wnt signalling regulates endothelial sensitivity to shear forces. Loss of Wnt5a/Wnt11 renders endothelial cells more sensitive to shear, resulting in axial polarization and migration against flow at lower shear levels. Integration of flow modelling and polarity analysis in entire vascular networks demonstrates that polarization against flow is achieved differentially in artery, vein, capillaries and the primitive sprouting front. Collectively our data suggest that non-canonical Wnt signalling stabilizes forming vascular networks by reducing endothelial shear sensitivity, thus keeping vessels open under low flow conditions that prevail in the primitive plexus. DOI: http://dx.doi.org/10.7554/eLife.07727.001 PMID:26845523

  13. Remarks on the "Non-canonicity Puzzle": Lagrangian Symmetries of the Einstein-Hilbert Action

    NASA Astrophysics Data System (ADS)

    Kiriushcheva, N.; Komorowski, P. G.; Kuzmin, S. V.

    2012-07-01

    Given the non-canonical relationship between variables used in the Hamiltonian formulations of the Einstein-Hilbert action (due to Pirani, Schild, Skinner (PSS) and Dirac) and the Arnowitt-Deser-Misner (ADM) action, and the consequent difference in the gauge transformations generated by the first-class constraints of these two formulations, the assumption that the Lagrangians from which they were derived are equivalent leads to an apparent contradiction that has been called "the non-canonicity puzzle". In this work we shall investigate the group properties of two symmetries derived for the Einstein-Hilbert action: diffeomorphism, which follows from the PSS and Dirac formulations, and the one that arises from the ADM formulation. We demonstrate that unlike the diffeomorphism transformations, the ADM transformations (as well as others, which can be constructed for the Einstein-Hilbert Lagrangian using Noether's identities) do not form a group. This makes diffeomorphism transformations unique (the term "canonical" symmetry might be suggested). If the two Lagrangians are to be called equivalent, canonical symmetry must be preserved. The interplay between general covariance and the canonicity of the variables used is discussed.

  14. Unambiguous generalization effects after treatment of non-canonical sentence production in German agrammatism.

    PubMed

    Stadie, Nicole; Schröder, Astrid; Postler, Jenny; Lorenz, Antje; Swoboda-Moll, Maria; Burchert, Frank; De Bleser, Ria

    2008-03-01

    Agrammatism is-among others, characterized by a deficit in producing grammatical structures. Of specific difficulty is the utilization of complex, non-canonical sentence structures (e.g. object-questions, passives, object-clefts). Several studies have documented positive effects when applying a specific treatment protocol in terms of increasingly correct production of target complex sentence structures with some variance in generalization patterns noted across individuals. The objective of this intervention study was to evaluate an intervention program focussing on the production of non-canonical sentences. Hypotheses about the occurrence of treatment effects were formulated on the basis of syntactic complexity, referring to the amount of syntactic phrase structures necessary to generate specific German sentence structures. A multiple single case study with seven agrammatic participants was applied, each participant receiving training in the production of object-relative-clauses and who-questions. The investigation was designed to unambiguously evaluate for each individual, structure specific and generalized learning effects with respect to the production of object-relative-clauses, who-questions and passive sentences. Results showed significant improvements for all sentences types. This outcome is considered within methodological issues of treatment studies. Theoretical and clinical implications are discussed.

  15. Rational design of a non-canonical "sticky-ended" collagen triple helix.

    PubMed

    Jalan, Abhishek A; Jochim, Katherine A; Hartgerink, Jeffrey D

    2014-05-28

    In a canonical collagen triple helix, three peptides self-assemble into a supercoiled motif with a one-amino-acid offset between the peptide chains. Design of triple helices that contain more than one residue offset is lucrative, as it leaves the non-covalent interactions unsatisfied at the termini and renders the termini "sticky" to further self-assemble into collagen-like nanofibers. Here we use lysine-glutamate axial salt-bridges to design a heterotrimeric collagen triple helix, ABC-1, containing a non-canonical offset of four residues between the peptide chains. The four-residue offset is necessary to prevent aggregation, which would prevent characterization of the non-canonical chain arrangement at the molecular level by NMR spectroscopy. A second heterotrimer, ABC-2, also stabilized by axial salt-bridges, is designed containing a canonical one-amino-acid offset to facilitate comparison of structure and stability by CD and NMR. ABC-1 and ABC-2 demonstrate our ability to modulate chain offset in a collagen triple helix. This lays the groundwork to design longer, and therefore stickier, offsets allowing access to a new class of collagen-related nanostructures.

  16. Hedgehog Signaling Non-Canonical Activated by Pro-Inflammatory Cytokines in Pancreatic Ductal Adenocarcinoma

    PubMed Central

    Wang, Yuqiong; Jin, Gang; Li, Quanjiang; Wang, Zhiping; Hu, Weimin; Li, Ping; Li, Shude; Wu, Hongyu; Kong, Xiangyu; Gao, Jun; Li, Zhaoshen

    2016-01-01

    Hedgehog(HH) pathway is found to be activated through a manner of canonical, or the non-canonical HH pathways. Distinct hyperplasia stroma around tumor cells is supposed to express pro-inflammatory cytokines abundantly, such as tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β), etc. in pancreatic ductal adenocarcinoma (PDAC) tissues. In this study we observed the effects of TNF-α and IL-1β on HH pathway activation in PDAC cells, and explored their activation manners. Our results showed that pro-inflammatory cytokines, TNF-α and IL-1β, could up-regulate the expression of GLI1 gene, increase its nuclear protein expression and promote malignant cell behaviors including migration, invasion, epithelial-mesenchymal transition (EMT) and drug resistance as well. Moreover, GLI1 promoter-reporter assay in combination with blocking either NF-κB or Smoothened (SMO) suggested that TNF-α and IL-1β could transcriptionally up-regulate expression of GLI1 completely via NF-κB, whereas ablation of SMO could not completely attenuate the regulation effects of TNF-α and IL-1β on GLI1 expression. Collectively, our results indicated that TNF-α and IL-1β in hyperplasia stroma can promote the PDAC cell development by activating HH pathway, through both the canonical and non-canonical HH activation ways. PMID:27877222

  17. A non-canonical function of telomerase RNA in the regulation of developmental myelopoiesis in zebrafish

    NASA Astrophysics Data System (ADS)

    Alcaraz-Pérez, Francisca; García-Castillo, Jesús; García-Moreno, Diana; López-Muñoz, Azucena; Anchelin, Monique; Angosto, Diego; Zon, Leonard I.; Mulero, Victoriano; Cayuela, María L.

    2014-02-01

    Dyskeratosis congenita (DC) is an inherited disorder with mutations affecting telomerase or telomeric proteins. DC patients usually die of bone marrow failure. Here we show that genetic depletion of the telomerase RNA component (TR) in the zebrafish results in impaired myelopoiesis, despite normal development of haematopoietic stem cells (HSCs). The neutropenia caused by TR depletion is independent of telomere length and telomerase activity. Genetic analysis shows that TR modulates the myeloid-erythroid fate decision by controlling the levels of the master myeloid and erythroid transcription factors spi1 and gata1, respectively. The alteration in spi1 and gata1 levels occurs through stimulation of gcsf and mcsf. Our model of TR deficiency in the zebrafish illuminates the non-canonical roles of TR, and could establish therapeutic targets for DC.

  18. Expanding the genetic code of Salmonella with non-canonical amino acids

    PubMed Central

    Gan, Qinglei; Lehman, Brent P.; Bobik, Thomas A.; Fan, Chenguang

    2016-01-01

    The diversity of non-canonical amino acids (ncAAs) endows proteins with new features for a variety of biological studies and biotechnological applications. The genetic code expansion strategy, which co-translationally incorporates ncAAs into specific sites of target proteins, has been applied in many organisms. However, there have been only few studies on pathogens using genetic code expansion. Here, we introduce this technique into the human pathogen Salmonella by incorporating p-azido-phenylalanine, benzoyl-phenylalanine, acetyl-lysine, and phosphoserine into selected Salmonella proteins including a microcompartment shell protein (PduA), a type III secretion effector protein (SteA), and a metabolic enzyme (malate dehydrogenase), and demonstrate practical applications of genetic code expansion in protein labeling, photocrosslinking, and post-translational modification studies in Salmonella. This work will provide powerful tools for a wide range of studies on Salmonella. PMID:28008993

  19. Non-canonical protein-DNA interactions identified by ChIP are not artifacts

    PubMed Central

    2013-01-01

    Background ChIP-chip and ChIP-seq are widely used methods to map protein-DNA interactions on a genomic scale in vivo. Waldminghaus and Skarstad recently reported, in this journal, a modified method for ChIP-chip. Based on a comparison of our previously-published ChIP-chip data for Escherichia coli σ32 with their own data, Waldminghaus and Skarstad concluded that many of the σ32 targets identified in our earlier work are false positives. In particular, we identified many non-canonical σ32 targets that are located inside genes or are associated with genes that show no detectable regulation by σ32. Waldminghaus and Skarstad propose that such non-canonical sites are artifacts, identified due to flaws in the standard ChIP methodology. Waldminghaus and Skarstad suggest specific changes to the standard ChIP procedure that reportedly eliminate the claimed artifacts. Results We reanalyzed our published ChIP-chip datasets for σ32 and the datasets generated by Waldminghaus and Skarstad to assess data quality and reproducibility. We also performed targeted ChIP/qPCR for σ32 and an unrelated transcription factor, AraC, using the standard ChIP method and the modified ChIP method proposed by Waldminghaus and Skarstad. Furthermore, we determined the association of core RNA polymerase with disputed σ32 promoters, with and without overexpression of σ32. We show that (i) our published σ32 ChIP-chip datasets have a consistently higher dynamic range than those of Waldminghaus and Skarstad, (ii) our published σ32 ChIP-chip datasets are highly reproducible, whereas those of Waldminghaus and Skarstad are not, (iii) non-canonical σ32 target regions are enriched in a σ32 ChIP in a heat shock-dependent manner, regardless of the ChIP method used, (iv) association of core RNA polymerase with some disputed σ32 target genes is induced by overexpression of σ32, (v) σ32 targets disputed by Waldminghaus and Skarstad are predominantly those that are most weakly bound, and (vi) the

  20. Non-canonical protein-DNA interactions identified by ChIP are not artifacts.

    PubMed

    Bonocora, Richard P; Fitzgerald, Devon M; Stringer, Anne M; Wade, Joseph T

    2013-04-15

    ChIP-chip and ChIP-seq are widely used methods to map protein-DNA interactions on a genomic scale in vivo. Waldminghaus and Skarstad recently reported, in this journal, a modified method for ChIP-chip. Based on a comparison of our previously-published ChIP-chip data for Escherichia coli σ32 with their own data, Waldminghaus and Skarstad concluded that many of the σ32 targets identified in our earlier work are false positives. In particular, we identified many non-canonical σ32 targets that are located inside genes or are associated with genes that show no detectable regulation by σ32. Waldminghaus and Skarstad propose that such non-canonical sites are artifacts, identified due to flaws in the standard ChIP methodology. Waldminghaus and Skarstad suggest specific changes to the standard ChIP procedure that reportedly eliminate the claimed artifacts. We reanalyzed our published ChIP-chip datasets for σ32 and the datasets generated by Waldminghaus and Skarstad to assess data quality and reproducibility. We also performed targeted ChIP/qPCR for σ32 and an unrelated transcription factor, AraC, using the standard ChIP method and the modified ChIP method proposed by Waldminghaus and Skarstad. Furthermore, we determined the association of core RNA polymerase with disputed σ32 promoters, with and without overexpression of σ32. We show that (i) our published σ32 ChIP-chip datasets have a consistently higher dynamic range than those of Waldminghaus and Skarstad, (ii) our published σ32 ChIP-chip datasets are highly reproducible, whereas those of Waldminghaus and Skarstad are not, (iii) non-canonical σ32 target regions are enriched in a σ32 ChIP in a heat shock-dependent manner, regardless of the ChIP method used, (iv) association of core RNA polymerase with some disputed σ32 target genes is induced by overexpression of σ32, (v) σ32 targets disputed by Waldminghaus and Skarstad are predominantly those that are most weakly bound, and (vi) the modifications to the

  1. Canonical and non-canonical Hedgehog signalling and the control of metabolism

    PubMed Central

    Teperino, Raffaele; Aberger, Fritz; Esterbauer, Harald; Riobo, Natalia; Pospisilik, John Andrew

    2014-01-01

    Obesity and diabetes represent key healthcare challenges of our day, affecting upwards of one billion people worldwide. These individuals are at higher risk for cancer, stroke, blindness, heart and cardiovascular disease, and to date, have no effective long-term treatment options available. Recent and accumulating evidence has implicated the developmental morphogen Hedgehog and its downstream signalling in metabolic control. Generally thought to be quiescent in adults, Hedgehog is associated with several human cancers, and as such, has already emerged as a therapeutic target in oncology. Here, we attempt to give a comprehensive overview of the key signalling events associated with both canonical and non-canonical Hedgehog signalling, and highlight the increasingly complex regulatory modalities that appear to link Hedgehog and control metabolism. We highlight these key findings and discuss their impact for therapeutic development, cancer and metabolic disease. PMID:24862854

  2. Insider trading: Extracellular matrix proteins and their non-canonical intracellular roles.

    PubMed

    Hellewell, Andrew L; Adams, Josephine C

    2016-01-01

    In metazoans, the extracellular matrix (ECM) provides a dynamic, heterogeneous microenvironment that has important supportive and instructive roles. Although the primary site of action of ECM proteins is extracellular, evidence is emerging for non-canonical intracellular roles. Examples include osteopontin, thrombospondins, IGF-binding protein 3 and biglycan, and relate to roles in transcription, cell-stress responses, autophagy and cancer. These findings pose conceptual problems on how proteins signalled for secretion can be routed to the cytosol or nucleus, or can function in environments with diverse redox, pH and ionic conditions. We review evidence for intracellular locations and functions of ECM proteins, and current knowledge of the mechanisms by which they may enter intracellular compartments. We evaluate the experimental methods that are appropriate to obtain rigorous evidence for intracellular localisation and function. Better insight into this under-researched topic is needed to decipher the complete spectrum of physiological and pathological roles of ECM proteins.

  3. Promiscuous Mutations Activate the Non-Canonical NF-kB Pathway in Multiple Myeloma

    PubMed Central

    Keats, Jonathan J.; Fonseca, Rafael; Chesi, Marta; Schop, Roelandt; Baker, Angela; Chng, Wee-Joo; Van Wier, Scott; Tiedemann, Rodger; Shi, Chang-Xin; Sebag, Michael; Braggio, Esteban; Henry, Travis; Zhu, Yuan-Xiao; Fogle, Homer; Price-Troska, Tammy; Ahmann, Gregory; Mancini, Catherine; Brents, Leslie A.; Kumar, Shaji; Greipp, Philip; Dispenzieri, Angela; Bryant, Barb; Mulligan, George; Bruhn, Laurakay; Barrett, Michael; Valdez, Riccardo; Trent, Jeff; Stewart, A. Keith; Carpten, John; Bergsagel, P. Leif

    2007-01-01

    Summary Activation of NF-kB has been noted in many tumor types, however only rarely has this been linked to an underlying genetic mutation. An integrated analysis of high-density oligonucleotide array CGH and gene expression profiling data from 155 multiple myeloma samples identified a promiscuous array of abnormalities contributing to the dysregulation of NF-kB in approximately 20% of patients. We report mutations in ten genes causing the inactivation of TRAF2, TRAF3, CYLD, cIAP1/cIAP2, and activation of NFKB1, NFKB2, CD40, LTBR, TACI, and NIK that result primarily in constitutive activation of the non-canonical NF-kB pathway, with the single most common abnormality being inactivation of TRAF3. These results highlight the critical importance of the NF-kB pathway in the pathogenesis of multiple myeloma. PMID:17692805

  4. A non-canonical landscape of the microRNA system

    PubMed Central

    Cipolla, Gabriel A.

    2014-01-01

    Microribonucleic acids, best known as microRNAs or miRNAs, are small, non-coding RNAs with important regulatory roles in eukaryotic cells. Here, I present a broad review on highly relevant but generally non-depicted features of miRNAs, among which stand out the non-conventional miRNA seed sites, the unusual messenger RNA (mRNA) target regions, the non-canonical miRNA-guided mechanisms of gene expression regulation, and the recently identified new class of miRNA ligands. Furthermore, I address the miRNA uncommon genomic location, transcription, and subcellular localization. Altogether, these unusual features and roles place the miRNA system as a very diverse, complex, and intriguing biological mechanism. PMID:25295056

  5. The non-canonical BMP and Wnt/β-catenin signaling pathways orchestrate early tooth development.

    PubMed

    Yuan, Guohua; Yang, Guobin; Zheng, Yuqian; Zhu, Xiaojing; Chen, Zhi; Zhang, Zunyi; Chen, YiPing

    2015-01-01

    BMP and Wnt signaling pathways play a crucial role in organogenesis, including tooth development. Despite extensive studies, the exact functions, as well as if and how these two pathways act coordinately in regulating early tooth development, remain elusive. In this study, we dissected regulatory functions of BMP and Wnt pathways in early tooth development using a transgenic noggin (Nog) overexpression model (K14Cre;pNog). It exhibits early arrested tooth development, accompanied by reduced cell proliferation and loss of odontogenic fate marker Pitx2 expression in the dental epithelium. We demonstrated that overexpression of Nog disrupted BMP non-canonical activity, which led to a dramatic reduction of cell proliferation rate but did not affect Pitx2 expression. We further identified a novel function of Nog by inhibiting Wnt/β-catenin signaling, causing loss of Pitx2 expression. Co-immunoprecipitation and TOPflash assays revealed direct binding of Nog to Wnts to functionally prevent Wnt/β-catenin signaling. In situ PLA and immunohistochemistry on Nog mutants confirmed in vivo interaction between endogenous Nog and Wnts and modulation of Wnt signaling by Nog in tooth germs. Genetic rescue experiments presented evidence that both BMP and Wnt signaling pathways contribute to cell proliferation regulation in the dental epithelium, with Wnt signaling also controlling the odontogenic fate. Reactivation of both BMP and Wnt signaling pathways, but not of only one of them, rescued tooth developmental defects in K14Cre;pNog mice, in which Wnt signaling can be substituted by transgenic activation of Pitx2. Our results reveal the orchestration of non-canonical BMP and Wnt/β-catenin signaling pathways in the regulation of early tooth development.

  6. Linkage-specific conformational ensembles of non-canonical polyubiquitin chains

    PubMed Central

    Castañeda, Carlos A.; Chaturvedi, Apurva; Camara, Christina M.; Curtis, Joseph E.; Krueger, Susan; Fushman, David

    2015-01-01

    Polyubiquitination is a critical protein post-translational modification involved in a variety of processes in eukaryotic cells. The molecular basis for selective recognition of the polyubiquitin signals by cellular receptors is determined by the conformations polyubiquitin chains adopt; this has been demonstrated for K48- and K63-linked chains. Recent studies of the so-called non-canonical chains (linked via K6, K11, K27, K29, or K33) suggest they play important regulatory roles in growth, development, and immune system pathways, but biophysical studies are needed to elucidate the physical/structural basis of their interactions with receptors. A first step towards this goal is characterization of the conformations these chains adopt in solution. We assembled diubiquitins (Ub2) comprised of every lysine linkage. Using solution NMR measurements, small-angle neutron scattering (SANS), and in silico ensemble generation, we determined population-weighted conformational ensembles that shed light on the structure and dynamics of the non-canonical polyubiquitin chains. We found that polyubiquitin is conformationally heterogeneous, and each chain type exhibits unique conformational ensembles. For example, K6-Ub2 and K11-Ub2 (at physiological salt concentration) are in dynamic equilibrium between at least two conformers, where one exhibits a unique Ub/Ub interface, distinct from that observed in K48-Ub2 but similar to crystal structures of these chains. Conformers for K29-Ub2 and K33-Ub2 resemble recent crystal structures in the ligand-bound state. Remarkably, a number of diubiquitins adopt conformers similar to K48-Ub2 or K63-Ub2, suggesting potential overlap of biological function among different lysine linkages. These studies highlight the potential power of determining function from elucidation of conformational states. PMID:26422168

  7. Carbon-14 decay as a source of non-canonical bases in DNA.

    PubMed

    Sassi, Michel; Carter, Damien J; Uberuaga, Blas P; Stanek, Chris R; Marks, Nigel A

    2014-01-01

    Significant experimental effort has been applied to study radioactive beta-decay in biological systems. Atomic-scale knowledge of this transmutation process is lacking due to the absence of computer simulations. Carbon-14 is an important beta-emitter, being ubiquitous in the environment and an intrinsic part of the genetic code. Over a lifetime, around 50 billion (14)C decays occur within human DNA. We apply ab initio molecular dynamics to quantify (14)C-induced bond rupture in a variety of organic molecules, including DNA base pairs. We show that double bonds and ring structures confer radiation resistance. These features, present in the canonical bases of the DNA, enhance their resistance to (14)C-induced bond-breaking. In contrast, the sugar group of the DNA and RNA backbone is vulnerable to single-strand breaking. We also show that Carbon-14 decay provides a mechanism for creating mutagenic wobble-type mispairs. The observation that DNA has a resistance to natural radioactivity has not previously been recognized. We show that (14)C decay can be a source for generating non-canonical bases. Our findings raise questions such as how the genetic apparatus deals with the appearance of an extra nitrogen in the canonical bases. It is not obvious whether or not the DNA repair mechanism detects this modification nor how DNA replication is affected by a non-canonical nucleobase. Accordingly, (14)C may prove to be a source of genetic alteration that is impossible to avoid due to the universal presence of radiocarbon in the environment. © 2013.

  8. Red-Shifted Aequorin Variants Incorporating Non-Canonical Amino Acids: Applications in In Vivo Imaging

    PubMed Central

    Grinstead, Kristen M.; Rowe, Laura; Ensor, Charles M.; Joel, Smita; Daftarian, Pirouz; Dikici, Emre; Zingg, Jean-Marc; Daunert, Sylvia

    2016-01-01

    The increased importance of in vivo diagnostics has posed new demands for imaging technologies. In that regard, there is a need for imaging molecules capable of expanding the applications of current state-of-the-art imaging in vivo diagnostics. To that end, there is a desire for new reporter molecules capable of providing strong signals, are non-toxic, and can be tailored to diagnose or monitor the progression of a number of diseases. Aequorin is a non-toxic photoprotein that can be used as a sensitive marker for bioluminescence in vivo imaging. The sensitivity of aequorin is due to the fact that bioluminescence is a rare phenomenon in nature and, therefore, it does not suffer from autofluorescence, which contributes to background emission. Emission of bioluminescence in the blue-region of the spectrum by aequorin only occurs when calcium, and its luciferin coelenterazine, are bound to the protein and trigger a biochemical reaction that results in light generation. It is this reaction that endows aequorin with unique characteristics, making it ideally suited for a number of applications in bioanalysis and imaging. Herein we report the site-specific incorporation of non-canonical or non-natural amino acids and several coelenterazine analogues, resulting in a catalog of 72 cysteine-free, aequorin variants which expand the potential applications of these photoproteins by providing several red-shifted mutants better suited to use in vivo. In vivo studies in mouse models using the transparent tissue of the eye confirmed the activity of the aequorin variants incorporating L-4-iodophehylalanine and L-4-methoxyphenylalanine after injection into the eye and topical addition of coelenterazine. The signal also remained localized within the eye. This is the first time that aequorin variants incorporating non-canonical amino acids have shown to be active in vivo and useful as reporters in bioluminescence imaging. PMID:27367859

  9. Red-Shifted Aequorin Variants Incorporating Non-Canonical Amino Acids: Applications in In Vivo Imaging.

    PubMed

    Grinstead, Kristen M; Rowe, Laura; Ensor, Charles M; Joel, Smita; Daftarian, Pirouz; Dikici, Emre; Zingg, Jean-Marc; Daunert, Sylvia

    2016-01-01

    The increased importance of in vivo diagnostics has posed new demands for imaging technologies. In that regard, there is a need for imaging molecules capable of expanding the applications of current state-of-the-art imaging in vivo diagnostics. To that end, there is a desire for new reporter molecules capable of providing strong signals, are non-toxic, and can be tailored to diagnose or monitor the progression of a number of diseases. Aequorin is a non-toxic photoprotein that can be used as a sensitive marker for bioluminescence in vivo imaging. The sensitivity of aequorin is due to the fact that bioluminescence is a rare phenomenon in nature and, therefore, it does not suffer from autofluorescence, which contributes to background emission. Emission of bioluminescence in the blue-region of the spectrum by aequorin only occurs when calcium, and its luciferin coelenterazine, are bound to the protein and trigger a biochemical reaction that results in light generation. It is this reaction that endows aequorin with unique characteristics, making it ideally suited for a number of applications in bioanalysis and imaging. Herein we report the site-specific incorporation of non-canonical or non-natural amino acids and several coelenterazine analogues, resulting in a catalog of 72 cysteine-free, aequorin variants which expand the potential applications of these photoproteins by providing several red-shifted mutants better suited to use in vivo. In vivo studies in mouse models using the transparent tissue of the eye confirmed the activity of the aequorin variants incorporating L-4-iodophehylalanine and L-4-methoxyphenylalanine after injection into the eye and topical addition of coelenterazine. The signal also remained localized within the eye. This is the first time that aequorin variants incorporating non-canonical amino acids have shown to be active in vivo and useful as reporters in bioluminescence imaging.

  10. The non-canonical BMP and Wnt/β-catenin signaling pathways orchestrate early tooth development

    PubMed Central

    Yuan, Guohua; Yang, Guobin; Zheng, Yuqian; Zhu, Xiaojing; Chen, Zhi; Zhang, Zunyi; Chen, YiPing

    2015-01-01

    BMP and Wnt signaling pathways play a crucial role in organogenesis, including tooth development. Despite extensive studies, the exact functions, as well as if and how these two pathways act coordinately in regulating early tooth development, remain elusive. In this study, we dissected regulatory functions of BMP and Wnt pathways in early tooth development using a transgenic noggin (Nog) overexpression model (K14Cre;pNog). It exhibits early arrested tooth development, accompanied by reduced cell proliferation and loss of odontogenic fate marker Pitx2 expression in the dental epithelium. We demonstrated that overexpression of Nog disrupted BMP non-canonical activity, which led to a dramatic reduction of cell proliferation rate but did not affect Pitx2 expression. We further identified a novel function of Nog by inhibiting Wnt/β-catenin signaling, causing loss of Pitx2 expression. Co-immunoprecipitation and TOPflash assays revealed direct binding of Nog to Wnts to functionally prevent Wnt/β-catenin signaling. In situ PLA and immunohistochemistry on Nog mutants confirmed in vivo interaction between endogenous Nog and Wnts and modulation of Wnt signaling by Nog in tooth germs. Genetic rescue experiments presented evidence that both BMP and Wnt signaling pathways contribute to cell proliferation regulation in the dental epithelium, with Wnt signaling also controlling the odontogenic fate. Reactivation of both BMP and Wnt signaling pathways, but not of only one of them, rescued tooth developmental defects in K14Cre;pNog mice, in which Wnt signaling can be substituted by transgenic activation of Pitx2. Our results reveal the orchestration of non-canonical BMP and Wnt/β-catenin signaling pathways in the regulation of early tooth development. PMID:25428587

  11. XEDAR activates the non-canonical NF-κB pathway

    SciTech Connect

    Verhelst, Kelly; Gardam, Sandra; Borghi, Alice; Kreike, Marja; Carpentier, Isabelle; Beyaert, Rudi

    2015-09-18

    Members of the tumor necrosis factor receptor (TNFR) superfamily are involved in a number of physiological and pathological responses by activating a wide variety of intracellular signaling pathways. The X-linked ectodermal dysplasia receptor (XEDAR; also known as EDA2R or TNFRSF27) is a member of the TNFR superfamily that is highly expressed in ectodermal derivatives during embryonic development and binds to ectodysplasin-A2 (EDA-A2), a member of the TNF family that is encoded by the anhidrotic ectodermal dysplasia (EDA) gene. Although XEDAR was first described in the year 2000, its function and molecular mechanism of action is still largely unclear. XEDAR has been reported to activate canonical nuclear factor κB (NF-κB) signaling and mitogen-activated protein (MAP) kinases. Here we report that XEDAR is also able to trigger the non-canonical NF-κB pathway, characterized by the processing of p100 (NF-κB2) into p52, followed by nuclear translocation of p52 and RelB. We provide evidence that XEDAR-induced p100 processing relies on the binding of XEDAR to TRAF3 and TRAF6, and requires the kinase activity of NIK and IKKα. We also show that XEDAR stimulation results in NIK accumulation and that p100 processing is negatively regulated by TRAF3, cIAP1 and A20. - Highlights: • XEDAR activates the non-canonical NF-κB pathway. • XEDAR-induced processing of p100 depends on XEDAR interaction with TRAF3 and TRAF6. • XEDAR-induced processing of p100 depends on NIK and IKKα activity. • Overexpression of XEDAR leads to NIK accumulation. • XEDAR-induced processing of p100 is negatively regulated by TRAF3 cIAP1 and A20.

  12. The non-canonical Wnt receptor Ryk regulates hematopoietic stem cell repopulation in part by controlling proliferation and apoptosis

    PubMed Central

    Famili, Farbod; Perez, Laura Garcia; Naber, Brigitta AE; Noordermeer, Jasprina N; Fradkin, Lee G; Staal, Frank JT

    2016-01-01

    The development of blood and immune cells requires strict control by various signaling pathways in order to regulate self-renewal, differentiation and apoptosis in stem and progenitor cells. Recent evidence indicates critical roles for the canonical and non-canonical Wnt pathways in hematopoiesis. The non-canonical Wnt pathway is important for establishment of cell polarity and cell migration and regulates apoptosis in the thymus. We here investigate the role of the non-canonical Wnt receptor Ryk in hematopoiesis and lymphoid development. We show that there are dynamic changes in Ryk expression during development and in different hematopoietic tissues. Functionally, Ryk regulates NK cell development in a temporal fashion. Moreover, Ryk-deficient mice show diminished, but not absent self-renewal of hematopoietic stem cells (HSC), via effects on mildly increased proliferation and apoptosis. Thus, Ryk deficiency in HSCs from fetal liver reduces their quiescence, leading to proliferation-induced apoptosis and decreased self-renewal. PMID:27882948

  13. Wnt5a-mediated non-canonical Wnt signalling regulates human endothelial cell proliferation and migration

    SciTech Connect

    Cheng Chingwen Yeh Juching; Fan Taiping; Smith, Stephen K.; Charnock-Jones, D. Stephen

    2008-01-11

    Cell to cell interaction is one of the key processes effecting angiogenesis and endothelial cell function. Wnt signalling is mediated through cell-cell interaction and is involved in many developmental processes and cellular functions. In this study, we investigated the possible function of Wnt5a and the non-canonical Wnt pathway in human endothelial cells. We found that Wnt5a-mediated non-canonical Wnt signalling regulated endothelial cell proliferation. Blocking this pathway using antibody, siRNA or a down-stream inhibitor led to suppression of endothelial cell proliferation, migration, and monolayer wound closure. We also found that the mRNA level of Wnt5a is up-regulated when endothelial cells are treated with a cocktail of inflammatory cytokines. Our findings suggest non-canonical Wnt signalling plays a role in regulating endothelial cell growth and possibly in angiogenesis.

  14. Complex Breakpoints and Template Switching Associated with Non-canonical Termination of Homologous Recombination in Mammalian Cells

    PubMed Central

    Hartlerode, Andrea J.; Rajendran, Anbazhagan; Manis, John P.

    2016-01-01

    A proportion of homologous recombination (HR) events in mammalian cells resolve by “long tract” gene conversion, reflecting copying of several kilobases from the donor sister chromatid prior to termination. Cells lacking the major hereditary breast/ovarian cancer predisposition genes, BRCA1 or BRCA2, or certain other HR-defective cells, reveal a bias in favor of long tract gene conversion, suggesting that this aberrant HR outcome might be connected with genomic instability. If termination of gene conversion occurs in regions lacking homology with the second end of the break, the normal mechanism of HR termination by annealing (i.e., homologous pairing) is not available and termination must occur by as yet poorly defined non-canonical mechanisms. Here we use a previously described HR reporter to analyze mechanisms of non-canonical termination of long tract gene conversion in mammalian cells. We find that non-canonical HR termination can occur in the absence of the classical non-homologous end joining gene XRCC4. We observe obligatory use of microhomology (MH)-mediated end joining and/or nucleotide addition during rejoining with the second end of the break. Notably, non-canonical HR termination is associated with complex breakpoints. We identify roles for homology-mediated template switching and, potentially, MH-mediated template switching/microhomology-mediated break-induced replication, in the formation of complex breakpoints at sites of non-canonical HR termination. This work identifies non-canonical HR termination as a potential contributor to genomic instability and to the formation of complex breakpoints in cancer. PMID:27832076

  15. Markedness and Salience in Language Contact and Second-Language Acquisition: Evidence from a Non-Canonical Contact Language.

    ERIC Educational Resources Information Center

    Deumert, Ana

    2003-01-01

    Argues that the study of contact varieties of a language are relevant to understanding of second language acquisition and use, because non-canonical contact languages are often situated on a continuum between pidginization and the more general processes of untutored second language acquisition. Data on participle regularization in Namibian Black…

  16. Markedness and Salience in Language Contact and Second-Language Acquisition: Evidence from a Non-Canonical Contact Language.

    ERIC Educational Resources Information Center

    Deumert, Ana

    2003-01-01

    Argues that the study of contact varieties of a language are relevant to understanding of second language acquisition and use, because non-canonical contact languages are often situated on a continuum between pidginization and the more general processes of untutored second language acquisition. Data on participle regularization in Namibian Black…

  17. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site

    NASA Astrophysics Data System (ADS)

    Liu, Chuang; Perilla, Juan R.; Ning, Jiying; Lu, Manman; Hou, Guangjin; Ramalho, Ruben; Himes, Benjamin A.; Zhao, Gongpu; Bedwell, Gregory J.; Byeon, In-Ja; Ahn, Jinwoo; Gronenborn, Angela M.; Prevelige, Peter E.; Rousso, Itay; Aiken, Christopher; Polenova, Tatyana; Schulten, Klaus; Zhang, Peijun

    2016-03-01

    The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection.

  18. A non-canonical peptide synthetase adenylates 3-methyl-2-oxovaleric acid for auriculamide biosynthesis

    PubMed Central

    Braga, Daniel; Hoffmeister, Dirk

    2016-01-01

    Auriculamide is the first natural product known from the predatory bacterium Herpetosiphon aurantiacus. It is composed of three unusual building blocks, including the non-proteinogenic amino acid 3-chloro-L-tyrosine, the α-hydroxy acid L-isoleucic acid, and a methylmalonyl-CoA-derived ethane unit. A candidate genetic locus for auriculamide biosynthesis was identified and encodes four enzymes. Among them, the non-canonical 199 kDa four-domain nonribosomal peptide synthetase, AulA, is extraordinary in that it features two consecutive adenylation domains. Here, we describe the functional characterization of the recombinantly produced AulA. The observed activation of 3-methyl-2-oxovaleric acid by the enzyme supports the hypothesis that it participates in the biosynthesis of auriculamide. An artificially truncated version of AulA that lacks the first adenylation domain activated this substrate like the full-length enzyme which shows that the first adenylation domain is dispensable. Additionally, we provide evidence that the enzyme tolerates structural variation of the substrate. α-Carbon substituents significantly affected the substrate turnover. While all tested aliphatic α-keto acids were accepted by the enzyme and minor differences in chain size and branches did not interfere with the enzymatic activity, molecules with methylene α-carbons led to low turnover. Such enzymatic plasticity is an important attribute to help in the perpetual search for novel molecules and to access a greater structural diversity by mutasynthesis. PMID:28144348

  19. 20-hydroxyecdysone mediates non-canonical regulation of mosquito vitellogenins through alternative splicing

    PubMed Central

    Provost-Javier, K. N.; Rasgon, J. L.

    2015-01-01

    Vitellogenesis is one of the most well-studied physiological processes in mosquitoes. Expression of mosquito vitellogenin genes is classically described as being restricted to female adult reproduction. We report premature vitellogenin transcript expression in three vector mosquitoes: Culex tarsalis, Aedes aegypti and Anopheles gambiae. Vitellogenins expressed during non-reproductive stages are alternatively spliced to retain their first intron and encode premature termination codons. We show that intron retention results in transcript degradation by translation-dependent nonsense-mediated mRNA decay. This is probably an example of regulated unproductive splicing and translation (RUST), a mechanism known to regulate gene expression in numerous organisms but which has never been described in mosquitoes. We demonstrate that the hormone 20-hydroxyecdysone (20E) is responsible for regulating post-transcriptional splicing of vitellogenin. After exposure of previtellogenic fat bodies to 20E, vitellogenin expression switches from a non-productive intron-retaining transcript to a spliced protein-coding transcript. This effect is independent of factors classically known to influence transcription, such as juvenile hormone-mediated competence and amino acid signalling through the target of rapamycin pathway. Non-canonical regulation of vitellogenesis through RUST is a novel role for the multifunctional hormone 20E, and may have important implications for general patterns of gene regulation in mosquitoes. PMID:24720618

  20. Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification

    NASA Astrophysics Data System (ADS)

    Kugel, Susann; Baunach, Martin; Baer, Philipp; Ishida-Ito, Mie; Sundaram, Srividhya; Xu, Zhongli; Groll, Michael; Hertweck, Christian

    2017-06-01

    Terpenoid natural products comprise a wide range of molecular architectures that typically result from C-C bond formations catalysed by classical type I/II terpene cyclases. However, the molecular diversity of biologically active terpenoids is substantially increased by fully unrelated, non-canonical terpenoid cyclases. Their evolutionary origin has remained enigmatic. Here we report the in vitro reconstitution of an unusual flavin-dependent bacterial indoloterpenoid cyclase, XiaF, together with a designated flavoenzyme-reductase (XiaP) that mediates a key step in xiamycin biosynthesis. The crystal structure of XiaF with bound FADH2 (at 2.4 Å resolution) and phylogenetic analyses reveal that XiaF is, surprisingly, most closely related to xenobiotic-degrading enzymes. Biotransformation assays show that XiaF is a designated indole hydroxylase that can be used for the production of indigo and indirubin. We unveil a cryptic hydroxylation step that sets the basis for terpenoid cyclization and suggest that the cyclase has evolved from xenobiotics detoxification enzymes.

  1. Non-Canonical and Sexually Dimorphic X Dosage Compensation States in the Mouse and Human Germline.

    PubMed

    Sangrithi, Mahesh N; Royo, Helene; Mahadevaiah, Shantha K; Ojarikre, Obah; Bhaw, Leena; Sesay, Abdul; Peters, Antoine H F M; Stadler, Michael; Turner, James M A

    2017-02-06

    Somatic X dosage compensation requires two mechanisms: X inactivation balances X gene output between males (XY) and females (XX), while X upregulation, hypothesized by Ohno and documented in vivo, balances X gene with autosomal gene output. Whether X dosage compensation occurs in germ cells is unclear. We show that mouse and human germ cells exhibit non-canonical X dosage states that differ from the soma and between the sexes. Prior to genome-wide reprogramming, X upregulation is present, consistent with Ohno's hypothesis. Subsequently, however, it is erased. In females, erasure follows loss of X inactivation, causing X dosage excess. Conversely, in males, erasure leads to permanent X dosage decompensation. Sex chromosomally abnormal models exhibit a "sex-reversed" X dosage state: XX males, like XX females, develop X dosage excess, while XO females, like XY males, develop X dosage decompensation. Thus, germline X dosage compensation states are determined by X chromosome number, not phenotypic sex. These unexpected differences in X dosage compensation states between germline and soma offer unique perspectives on sex chromosome infertility. Copyright © 2017 The Francis Crick Institute. Published by Elsevier Inc. All rights reserved.

  2. Canonical and non-canonical effects of the NLRP3 inflammasome in kidney inflammation and fibrosis.

    PubMed

    Lorenz, Georg; Darisipudi, Murthy N; Anders, Hans-Joachim

    2014-01-01

    NLRP-3 inflammasome is one of several intracellular danger recognition platforms that integrates infectious or non-infectious types of danger into the expression of pro-inflammatory cytokines to set-up inflammation for danger control. NLRP3 activation induces three types of caspase-1-mediated responses: secretion of IL-1beta, secretion of IL-18 and a programmed form of cell death, referred to as pyroptosis. Similar to the well-documented impact of Toll-like receptor-driven danger signalling in kidney disease, evolving data now suggest a similar involvement of the NLRP3 inflammasome in renal inflammation. Here, we discuss the accumulating data on NLRP3 in the kidney: its IL-1beta and IL-18-dependent 'canonical' effects and the current evidence for its 'non-canonical' effects, e.g. in tumor growth factor (TGF)-beta signalling, epithelial-mesenchymal transition and fibrosis. Research in this area will certainly uncover yet unknown aspects of danger signalling in the kidney and how it drives renal inflammation and immunopathology.

  3. Database of non-canonical base pairs found in known RNA structures

    NASA Technical Reports Server (NTRS)

    Nagaswamy, U.; Voss, N.; Zhang, Z.; Fox, G. E.

    2000-01-01

    Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

  4. IL-21-mediated non-canonical pathway for IL-1β production in conventional dendritic cells

    PubMed Central

    Wan, Chi-Keung; Li, Peng; Spolski, Rosanne; Oh, Jangsuk; Andraski, Allison B.; Du, Ning; Yu, Zu-Xi; Dillon, Christopher P.; Green, Douglas R.; Leonard, Warren J.

    2015-01-01

    The canonical pathway for IL-1β production requires TLR-mediated NF-κB-dependent Il1b gene induction, followed by caspase-containing inflammasome-mediated processing of pro-IL-1β. Here we show that IL-21 unexpectedly induces IL-1β production in conventional dendritic cells (cDCs) via a STAT3-dependent but NF-κB-independent pathway. IL-21 does not induce Il1b expression in CD4+ T cells, with differential histone marks present in these cells versus cDCs. IL-21-induced IL-1β processing in cDCs does not require caspase-1 or caspase-8 but depends on IL-21-mediated death and activation of serine protease(s). Moreover, STAT3-dependent IL-1β expression in cDCs at least partially explains the IL-21-mediated pathologic response occurring during infection with pneumonia virus of mice. These results demonstrate lineage-restricted IL-21-induced IL-1β via a non-canonical pathway and provide evidence for its importance in vivo. PMID:26269257

  5. TRIM24 Links a Non-canonical Histone Signature to Breast Cancer

    SciTech Connect

    W Tsai; Z Wang; T Yiu; K Akdemir; W Xia; S Winter; C Tsai; X Shi; D Schwarzer; et al.

    2011-12-31

    Recognition of modified histone species by distinct structural domains within 'reader' proteins plays a critical role in the regulation of gene expression. Readers that simultaneously recognize histones with multiple marks allow transduction of complex chromatin modification patterns into specific biological outcomes. Here we report that chromatin regulator tripartite motif-containing 24 (TRIM24) functions in humans as a reader of dual histone marks by means of tandem plant homeodomain (PHD) and bromodomain (Bromo) regions. The three-dimensional structure of the PHD-Bromo region of TRIM24 revealed a single functional unit for combinatorial recognition of unmodified H3K4 (that is, histone H3 unmodified at lysine 4, H3K4me0) and acetylated H3K23 (histone H3 acetylated at lysine 23, H3K23ac) within the same histone tail. TRIM24 binds chromatin and oestrogen receptor to activate oestrogen-dependent genes associated with cellular proliferation and tumour development. Aberrant expression of TRIM24 negatively correlates with survival of breast cancer patients. The PHD-Bromo of TRIM24 provides a structural rationale for chromatin activation through a non-canonical histone signature, establishing a new route by which chromatin readers may influence cancer pathogenesis.

  6. FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases

    PubMed Central

    Kuchta, Krzysztof; Muszewska, Anna; Knizewski, Lukasz; Steczkiewicz, Kamil; Wyrwicz, Lucjan S.; Pawlowski, Krzysztof; Rychlewski, Leszek; Ginalski, Krzysztof

    2016-01-01

    FAM46 proteins, encoded in all known animal genomes, belong to the nucleotidyltransferase (NTase) fold superfamily. All four human FAM46 paralogs (FAM46A, FAM46B, FAM46C, FAM46D) are thought to be involved in several diseases, with FAM46C reported as a causal driver of multiple myeloma; however, their exact functions remain unknown. By using a combination of various bioinformatics analyses (e.g. domain architecture, cellular localization) and exhaustive literature and database searches (e.g. expression profiles, protein interactors), we classified FAM46 proteins as active non-canonical poly(A) polymerases, which modify cytosolic and/or nuclear RNA 3′ ends. These proteins may thus regulate gene expression and probably play a critical role during cell differentiation. A detailed analysis of sequence and structure diversity of known NTases possessing PAP/OAS1 SBD domain, combined with state-of-the-art comparative modelling, allowed us to identify potential active site residues responsible for catalysis and substrate binding. We also explored the role of single point mutations found in human cancers and propose that FAM46 genes may be involved in the development of other major malignancies including lung, colorectal, hepatocellular, head and neck, urothelial, endometrial and renal papillary carcinomas and melanoma. Identification of these novel enzymes taking part in RNA metabolism in eukaryotes may guide their further functional studies. PMID:27060136

  7. Swinger RNA self-hybridization and mitochondrial non-canonical swinger transcription, transcription systematically exchanging nucleotides.

    PubMed

    Seligmann, Hervé

    2016-06-21

    Stem-loop hairpins punctuate mitochondrial post-transcriptional processing. Regulation of mitochondrial swinger transcription, transcription producing RNAs matching the mitogenome only assuming systematic exchanges between nucleotides (23 bijective transformations along 9 symmetric exchanges X<>Y, e.g. A<>G, and 14 asymmetric exchanges X>Y>Z>X, e.g. A>G>C>A) remains unknown. Does swinger RNA self-hybridization regulate swinger, as regular, transcription? Groups of 8 swinger transformations share canonical self-hybridization properties within each group, group 0 includes identity (regular) transcription. The human mitogenome has more stem-loop hairpins than randomized sequences for all groups. Group 2 transformations reveal complementarity of the light strand replication origin (OL) loop and a neighboring tRNA gene, detecting the longtime presumed OL/tRNA homology. Non-canonical G=U pairings in hairpins increases with swinger RNA detection. These results confirm biological relevancy of swinger-transformed DNA/RNA, independently of, and in combination with, previously detected swinger DNA/RNA and swinger peptides. Swinger-transformed mitogenomes include unsuspected multilayered information.

  8. A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing

    PubMed Central

    Flamand, Mathieu N.; Gan, Hin Hark; Mayya, Vinay K.; Gunsalus, Kristin C.

    2017-01-01

    Abstract Although strong evidence supports the importance of their cooperative interactions, microRNA (miRNA)-binding sites are still largely investigated as functionally independent regulatory units. Here, a survey of alternative 3΄UTR isoforms implicates a non-canonical seedless site in cooperative miRNA-mediated silencing. While required for target mRNA deadenylation and silencing, this site is not sufficient on its own to physically recruit miRISC. Instead, it relies on facilitating interactions with a nearby canonical seed-pairing site to recruit the Argonaute complexes. We further show that cooperation between miRNA target sites is necessary for silencing in vivo in the C. elegans embryo, and for the recruitment of the Ccr4-Not effector complex. Using a structural model of cooperating miRISCs, we identified allosteric determinants of cooperative miRNA-mediated silencing that are required for both embryonic and larval miRNA functions. Our results delineate multiple cooperative mechanisms in miRNA-mediated silencing and further support the consideration of target site cooperation as a fundamental characteristic of miRNA function. PMID:28482037

  9. A non-canonical mechanism for Crm1-export cargo complex assembly.

    PubMed

    Fischer, Ute; Schäuble, Nico; Schütz, Sabina; Altvater, Martin; Chang, Yiming; Faza, Marius Boulos; Panse, Vikram Govind

    2015-04-21

    The transport receptor Crm1 mediates the export of diverse cargos containing leucine-rich nuclear export signals (NESs) through complex formation with RanGTP. To ensure efficient cargo release in the cytoplasm, NESs have evolved to display low affinity for Crm1. However, mechanisms that overcome low affinity to assemble Crm1-export complexes in the nucleus remain poorly understood. In this study, we reveal a new type of RanGTP-binding protein, Slx9, which facilitates Crm1 recruitment to the 40S pre-ribosome-associated NES-containing adaptor Rio2. In vitro, Slx9 binds Rio2 and RanGTP, forming a complex. This complex directly loads Crm1, unveiling a non-canonical stepwise mechanism to assemble a Crm1-export complex. A mutation in Slx9 that impairs Crm1-export complex assembly inhibits 40S pre-ribosome export. Thus, Slx9 functions as a scaffold to optimally present RanGTP and the NES to Crm1, therefore, triggering 40S pre-ribosome export. This mechanism could represent one solution to the paradox of weak binding events underlying rapid Crm1-mediated export.

  10. Cbx8 Acts Non-canonically with Wdr5 to Promote Mammary Tumorigenesis.

    PubMed

    Chung, Chi-Yeh; Sun, Zhen; Mullokandov, Gavriel; Bosch, Almudena; Qadeer, Zulekha A; Cihan, Esma; Rapp, Zachary; Parsons, Ramon; Aguirre-Ghiso, Julio A; Farias, Eduardo F; Brown, Brian D; Gaspar-Maia, Alexandre; Bernstein, Emily

    2016-07-12

    Chromatin-mediated processes influence the development and progression of breast cancer. Using murine mammary carcinoma-derived tumorspheres as a functional readout for an aggressive breast cancer phenotype, we performed a loss-of-function screen targeting 60 epigenetic regulators. We identified the Polycomb protein Cbx8 as a key regulator of mammary carcinoma both in vitro and in vivo. Accordingly, Cbx8 is overexpressed in human breast cancer and correlates with poor survival. Our genomic analyses revealed that Cbx8 positively regulates Notch signaling by maintaining H3K4me3 levels on Notch-network gene promoters. Ectopic expression of Notch1 partially rescues tumorsphere formation in Cbx8-depleted cells. We find that Cbx8 associates with non-PRC1 complexes containing the H3K4 methyltransferase complex component WDR5, which together regulate Notch gene expression. Thus, our study implicates a key non-canonical role for Cbx8 in promoting breast tumorigenesis.

  11. A non-canonical mechanism for Crm1-export cargo complex assembly

    PubMed Central

    Fischer, Ute; Schäuble, Nico; Schütz, Sabina; Altvater, Martin; Chang, Yiming; Boulos Faza, Marius; Panse, Vikram Govind

    2015-01-01

    The transport receptor Crm1 mediates the export of diverse cargos containing leucine-rich nuclear export signals (NESs) through complex formation with RanGTP. To ensure efficient cargo release in the cytoplasm, NESs have evolved to display low affinity for Crm1. However, mechanisms that overcome low affinity to assemble Crm1-export complexes in the nucleus remain poorly understood. In this study, we reveal a new type of RanGTP-binding protein, Slx9, which facilitates Crm1 recruitment to the 40S pre-ribosome-associated NES-containing adaptor Rio2. In vitro, Slx9 binds Rio2 and RanGTP, forming a complex. This complex directly loads Crm1, unveiling a non-canonical stepwise mechanism to assemble a Crm1-export complex. A mutation in Slx9 that impairs Crm1-export complex assembly inhibits 40S pre-ribosome export. Thus, Slx9 functions as a scaffold to optimally present RanGTP and the NES to Crm1, therefore, triggering 40S pre-ribosome export. This mechanism could represent one solution to the paradox of weak binding events underlying rapid Crm1-mediated export. DOI: http://dx.doi.org/10.7554/eLife.05745.001 PMID:25895666

  12. Non-Canonical Role of IKKα in the Regulation of STAT1 Phosphorylation in Antiviral Signaling

    PubMed Central

    Xing, Fei; Matsumiya, Tomoh; Shiba, Yuko; Hayakari, Ryo; Yoshida, Hidemi; Imaizumi, Tadaatsu

    2016-01-01

    Non-self RNA is recognized by retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs), inducing type I interferons (IFNs). Type I IFN promotes the expression of IFN-stimulated genes (ISGs), which requires the activation of signal transducer and activator of transcription-1 (STAT1). We previously reported that dsRNA induced STAT1 phosphorylation via a type I IFN-independent pathway in addition to the well-known type I IFN-dependent pathway. IκB kinase α (IKKα) is involved in antiviral signaling induced by dsRNA; however, its role is incompletely understood. Here, we explored the function of IKKα in RLR-mediated STAT1 phosphorylation. Silencing of IKKα markedly decreased the level of IFN-β and STAT1 phosphorylation inHeH response to dsRNA. However, the inhibition of IKKα did not alter the RLR signaling-mediated dimerization of interferon responsive factor 3 (IRF3) or the nuclear translocation of nuclear factor-κB (NFκB). These results suggest a non-canonical role of IKKα in RLR signaling. Furthermore, phosphorylation of STAT1 was suppressed by IKKα knockdown in cells treated with a specific neutralizing antibody for the type I IFN receptor (IFNAR) and in IFNAR-deficient cells. Collectively, the dual regulation of STAT1 by IKKα in antiviral signaling suggests a role for IKKα in the fine-tuning of antiviral signaling in response to non-self RNA. PMID:27992555

  13. Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification

    PubMed Central

    Kugel, Susann; Baunach, Martin; Baer, Philipp; Ishida-Ito, Mie; Sundaram, Srividhya; Xu, Zhongli; Groll, Michael; Hertweck, Christian

    2017-01-01

    Terpenoid natural products comprise a wide range of molecular architectures that typically result from C–C bond formations catalysed by classical type I/II terpene cyclases. However, the molecular diversity of biologically active terpenoids is substantially increased by fully unrelated, non-canonical terpenoid cyclases. Their evolutionary origin has remained enigmatic. Here we report the in vitro reconstitution of an unusual flavin-dependent bacterial indoloterpenoid cyclase, XiaF, together with a designated flavoenzyme-reductase (XiaP) that mediates a key step in xiamycin biosynthesis. The crystal structure of XiaF with bound FADH2 (at 2.4 Å resolution) and phylogenetic analyses reveal that XiaF is, surprisingly, most closely related to xenobiotic-degrading enzymes. Biotransformation assays show that XiaF is a designated indole hydroxylase that can be used for the production of indigo and indirubin. We unveil a cryptic hydroxylation step that sets the basis for terpenoid cyclization and suggest that the cyclase has evolved from xenobiotics detoxification enzymes. PMID:28643772

  14. 20-hydroxyecdysone mediates non-canonical regulation of mosquito vitellogenins through alternative splicing.

    PubMed

    Provost-Javier, K N; Rasgon, J L

    2014-08-01

    Vitellogenesis is one of the most well-studied physiological processes in mosquitoes. Expression of mosquito vitellogenin genes is classically described as being restricted to female adult reproduction. We report premature vitellogenin transcript expression in three vector mosquitoes: Culex tarsalis, Aedes aegypti and Anopheles gambiae. Vitellogenins expressed during non-reproductive stages are alternatively spliced to retain their first intron and encode premature termination codons. We show that intron retention results in transcript degradation by translation-dependent nonsense-mediated mRNA decay. This is probably an example of regulated unproductive splicing and translation (RUST), a mechanism known to regulate gene expression in numerous organisms but which has never been described in mosquitoes. We demonstrate that the hormone 20-hydroxyecdysone (20E) is responsible for regulating post-transcriptional splicing of vitellogenin. After exposure of previtellogenic fat bodies to 20E, vitellogenin expression switches from a non-productive intron-retaining transcript to a spliced protein-coding transcript. This effect is independent of factors classically known to influence transcription, such as juvenile hormone-mediated competence and amino acid signalling through the target of rapamycin pathway. Non-canonical regulation of vitellogenesis through RUST is a novel role for the multifunctional hormone 20E, and may have important implications for general patterns of gene regulation in mosquitoes.

  15. Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome.

    PubMed

    Bogenschutz, Naomi L; Rodriguez, Jairo; Tsukiyama, Toshio

    2014-01-01

    Eukaryotic DNA replication initiates from multiple sites on each chromosome called replication origins (origins). In the budding yeast Saccharomyces cerevisiae, origins are defined at discrete sites. Regular spacing and diverse firing characteristics of origins are thought to be required for efficient completion of replication, especially in the presence of replication stress. However, a S. cerevisiae chromosome III harboring multiple origin deletions has been reported to replicate relatively normally, and yet how an origin-deficient chromosome could accomplish successful replication remains unknown. To address this issue, we deleted seven well-characterized origins from chromosome VI, and found that these deletions do not cause gross growth defects even in the presence of replication inhibitors. We demonstrated that the origin deletions do cause a strong decrease in the binding of the origin recognition complex. Unexpectedly, replication profiling of this chromosome showed that DNA replication initiates from non-canonical loci around deleted origins in yeast. These results suggest that replication initiation can be unexpectedly flexible in this organism.

  16. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site

    PubMed Central

    Liu, Chuang; Perilla, Juan R.; Ning, Jiying; Lu, Manman; Hou, Guangjin; Ramalho, Ruben; Himes, Benjamin A.; Zhao, Gongpu; Bedwell, Gregory J.; Byeon, In-Ja; Ahn, Jinwoo; Gronenborn, Angela M.; Prevelige, Peter E.; Rousso, Itay; Aiken, Christopher; Polenova, Tatyana; Schulten, Klaus; Zhang, Peijun

    2016-01-01

    The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection. PMID:26940118

  17. A novel non-canonical Notch signaling regulates expression of synaptic vesicle proteins in excitatory neurons

    PubMed Central

    Hayashi, Yukari; Nishimune, Hiroshi; Hozumi, Katsuto; Saga, Yumiko; Harada, Akihiro; Yuzaki, Michisuke; Iwatsubo, Takeshi; Kopan, Raphael; Tomita, Taisuke

    2016-01-01

    Notch signaling plays crucial roles for cellular differentiation during development through γ-secretase-dependent intramembrane proteolysis followed by transcription of target genes. Although recent studies implicate that Notch regulates synaptic plasticity or cognitive performance, the molecular mechanism how Notch works in mature neurons remains uncertain. Here we demonstrate that a novel Notch signaling is involved in expression of synaptic proteins in postmitotic neurons. Levels of several synaptic vesicle proteins including synaptophysin 1 and VGLUT1 were increased when neurons were cocultured with Notch ligands-expressing NIH3T3 cells. Neuron-specific deletion of Notch genes decreased these proteins, suggesting that Notch signaling maintains the expression of synaptic vesicle proteins in a cell-autonomous manner. Unexpectedly, cGMP-dependent protein kinase (PKG) inhibitor, but not γ-secretase inhibitor, abolished the elevation of synaptic vesicle proteins, suggesting that generation of Notch intracellular domain is dispensable for this function. These data uncover a ligand-dependent, but γ-secretase-independent, non-canonical Notch signaling involved in presynaptic protein expression in postmitotic neurons. PMID:27040987

  18. Monitoring mRNA Translation in Neuronal Processes Using Fluorescent Non-Canonical Amino Acid Tagging.

    PubMed

    Kos, Aron; Wanke, Kai A; Gioio, Anthony; Martens, Gerard J; Kaplan, Barry B; Aschrafi, Armaz

    2016-05-01

    A steady accumulation of experimental data argues that protein synthesis in neurons is not merely restricted to the somatic compartment, but also occurs in several discrete cellular micro-domains. Local protein synthesis is critical for the establishment of synaptic plasticity in mature dendrites and in directing the growth cones of immature axons, and has been associated with cognitive impairment in mice and humans. Although in recent years a number of important mechanisms governing this process have been described, it remains technically challenging to precisely monitor local protein synthesis in individual neuronal cell parts independent from the soma. This report presents the utility of employing microfluidic chambers for the isolation and treatment of single neuronal cellular compartments. Furthermore, it is demonstrated that a protein synthesis assay, based on fluorescent non-canonical amino acid tagging (FUNCAT), can be combined with this cell culture system to label nascent proteins within a discrete structural and functional domain of the neuron. Together, these techniques could be employed for the detection of protein synthesis within developing and mature neurites, offering an effective approach to elucidate novel mechanisms controlling synaptic maintenance and plasticity. © 2016 The Histochemical Society.

  19. Thickness Mismatch of Coexisting Liquid Phases in Non-Canonical Lipid Bilayers

    PubMed Central

    Bleecker, Joan V.; Cox, Phillip A.; Foster, Rami N.; Litz, Jonathan P.; Blosser, Matthew C.; Castner, David G.; Keller, Sarah L.

    2016-01-01

    Lipid composition dictates membrane thickness, which in turn can influence membrane protein activity. Lipid composition also determines whether a membrane demixes into coexisting liquid-crystalline phases. Previous direct measurements of demixed lipid membranes have always found a liquid-ordered phase that is thicker than the liquid-disordered phase. Here we investigated non-canonical ternary lipid mixtures designed to produce bilayers with thicker disordered phases than ordered phases. The membranes were comprised of short, saturated (ordered) lipids; long, unsaturated (disordered) lipids; and cholesterol. We found that few of these systems yield coexisting liquid phases above 10 °C. For membranes that do demix into two liquid phases, we measured the thickness mismatch between the phases by atomic force microscopy and found that not one of the systems yields thicker disordered than ordered phases under standard experimental conditions. We found no monotonic relationship between demixing temperatures of these ternary systems and either estimated thickness mismatches between the liquid phases or the physical parameters of single-component membranes comprised of the individual lipids. These results highlight the robustness of a membrane’s liquid-ordered phase to be thicker than the liquid-disordered phase, regardless of the membrane’s lipid composition. PMID:26890258

  20. Assembly of proteasome subunits into non-canonical complexes in vivo.

    PubMed

    Hammack, Lindsay J; Kusmierczyk, Andrew R

    2017-01-01

    Proteasomes exist in all domains of life. In general, they are comprised of a compartmentalized protease whose activity is modulated by one or more regulatory complexes with which it interacts. The quaternary structure of this compartmentalized protease, called the 20S proteasome, is absolutely conserved and consists of four heptameric rings stacked coaxially. The rings are made of structurally related α and β subunits. In eukaryotes, assembly factors chaperone the α and β subunits during 20S biogenesis. Here we demonstrate that proteasome subunits can assemble into structures other than the canonical 20S proteasome in vivo. Specifically, the yeast α4 subunit forms high molecular weight complexes whose abundance increases when proteasome function is compromised. Results from a disulfide crosslinking approach are consistent with these complexes being ring-shaped. Though several eukaryotic α subunits can form rings when expressed recombinantly in bacteria, this is the first evidence that such non-canonical complexes exist in vivo. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Non-Canonical Amino Acids in the Interrogation of Cellular Protein Synthesis

    PubMed Central

    Ngo, John T.; Tirrell, David A.

    2011-01-01

    CONSPECTUS Proteins in living cells can be made receptive to bioorthogonal chemistries through metabolic labeling with appropriately designed, non-canonical amino acids (ncAAs). In the simplest approach to metabolic labeling, an amino acid analog replaces one of the natural amino acids specified by the protein’s gene (or genes) of interest. Through manipulation of experimental conditions, the extent of the replacement can be adjusted. This approach, often termed residue-specific incorporation, allows the ncAA to be incorporated in controlled proportions into positions normally occupied by the natural amino acid residue. For a protein to be labeled in this way with an ncAA, it must fulfill just two requirements: (i) the corresponding natural amino acid must be encoded within the sequence of the protein at the genetic level, and (ii) the protein must be expressed while the ncAA is in the cell. Because this approach permits labeling of proteins throughout the cell, it has enabled us to develop strategies to track cellular protein synthesis by tagging proteins with reactive ncAAs. In procedures similar to isotopic labeling, translationally active ncAAs are incorporated into proteins during a “pulse” in which newly synthesized proteins are tagged. The set of tagged proteins can be distinguished from those made before the pulse by bioorthogonally ligating the ncAA side chain to probes that permit detection, isolation, and visualization of the labeled proteins. Non-canonical amino acids with side chains containing azide, alkyne, or alkene groups have been especially useful in experiments of this kind. They have been incorporated into proteins in the form of methionine analogs that are substrates for the natural translational machinery. The selectivity of the method can be enhanced through the use of mutant aminoacyl transfer RNA synthetases (aaRSs) that permit incorporation of ncAAs not used by the endogenous biomachinery. Through expression of mutant aa

  2. Emerging Non-Canonical Functions and Regulation by p53: p53 and Stemness

    PubMed Central

    Olivos, David J.; Mayo, Lindsey D.

    2016-01-01

    Since its discovery nearly 40 years ago, p53 has ascended to the forefront of investigated genes and proteins across diverse research disciplines and is recognized most exclusively for its role in cancer as a tumor suppressor. Levine and Oren (2009) reviewed the evolution of p53 detailing the significant discoveries of each decade since its first report in 1979. In this review, we will highlight the emerging non-canonical functions and regulation of p53 in stem cells. We will focus on general themes shared among p53’s functions in non-malignant stem cells and cancer stem-like cells (CSCs) and the influence of p53 on the microenvironment and CSC niche. We will also examine p53 gain of function (GOF) roles in stemness. Mutant p53 (mutp53) GOFs that lead to survival, drug resistance and colonization are reviewed in the context of the acquisition of advantageous transformation processes, such as differentiation and dedifferentiation, epithelial-to-mesenchymal transition (EMT) and stem cell senescence and quiescence. Finally, we will conclude with therapeutic strategies that restore wild-type p53 (wtp53) function in cancer and CSCs, including RING finger E3 ligases and CSC maintenance. The mechanisms by which wtp53 and mutp53 influence stemness in non-malignant stem cells and CSCs or tumor-initiating cells (TICs) are poorly understood thus far. Further elucidation of p53’s effects on stemness could lead to novel therapeutic strategies in cancer research. PMID:27898034

  3. NLRP3 regulates a non-canonical platform for caspase-8 activation during epithelial cell apoptosis.

    PubMed

    Chung, H; Vilaysane, A; Lau, A; Stahl, M; Morampudi, V; Bondzi-Simpson, A; Platnich, J M; Bracey, N A; French, M-C; Beck, P L; Chun, J; Vallance, B A; Muruve, D A

    2016-08-01

    Nod-like receptor, pyrin containing 3 (NLRP3) is characterized primarily as a canonical caspase-1 activating inflammasome in macrophages. NLRP3 is also expressed in the epithelium of the kidney and gut; however, its function remains largely undefined. Primary mouse tubular epithelial cells (TEC) lacking Nlrp3 displayed reduced apoptosis downstream of the tumor necrosis factor (TNF) receptor and CD95. TECs were identified as type II apoptotic cells that activated caspase-8, tBid and mitochondrial apoptosis via caspase-9, responses that were reduced in Nlrp3-/- cells. The activation of caspase-8 during extrinsic apoptosis induced by TNFα/cycloheximide (TNFα/CHX) was dependent on adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC) and completely independent of caspase-1 or caspase-11. TECs and primary human proximal tubular epithelial cells (HPTC) did not activate a canonical inflammasome, caspase-1, or IL-1β secretion in response to TNFα/CHX or NLRP3-dependent triggers, such as ATP or nigericin. In cell fractionation studies and by confocal microscopy, NLRP3 colocalized with ASC and caspase-8 in speck-like complexes at the mitochondria during apoptosis. The formation of NLRP3/ASC/caspase-8 specks in response to TNFα/CHX was downstream of TNFR signaling and dependent on potassium efflux. Epithelial ASC specks were present in enteroids undergoing apoptosis and in the injured tubules of wild-type but not Nlrp3-/- or ASC-/- mice following ureteric unilateral obstruction in vivo. These data show that NLRP3 and ASC form a conserved non-canonical platform for caspase-8 activation, independent of the inflammasome that regulates apoptosis within epithelial cells.

  4. A novel non-canonical Wnt signature for prostate cancer aggressiveness.

    PubMed

    Sandsmark, Elise; Hansen, Ailin Falkmo; Selnæs, Kirsten M; Bertilsson, Helena; Bofin, Anna M; Wright, Alan J; Viset, Trond; Richardsen, Elin; Drabløs, Finn; Bathen, Tone F; Tessem, May-Britt; Rye, Morten B

    2017-02-07

    Activation of the Canonical Wnt pathway (CWP) has been linked to advanced and metastatic prostate cancer, whereas the Wnt5a-induced non-canonical Wnt pathway (NCWP) has been associated with both good and poor prognosis. A newly discovered NCWP, Wnt5/Fzd2, has been shown to induce epithelial-to-mesenchymal transition (EMT) in cancers, but has not been investigated in prostate cancer. The aim of this study was to investigate if the CWP and NCWP, in combination with EMT, are associated with metabolic alterations, aggressive disease and biochemical recurrence in prostate cancer. An initial analysis was performed using integrated transcriptomics, ex vivo and in vivo metabolomics, and histopathology of prostatectomy samples (n=129), combined with at least five-year follow-up. This analysis detected increased activation of NCWP through Wnt5a/ Fzd2 as the most common mode of Wnt activation in prostate cancer. This activation was associated with increased expression of EMT markers and higher Gleason score. The transcriptional association between NCWP and EMT was confirmed in five other publicly available patient cohorts (1519 samples in total). A novel gene expression signature of concordant activation of NCWP and EMT (NCWP-EMT) was developed, and this signature was significantly associated with metastasis and shown to be a significant predictor of biochemical recurrence. The NCWP-EMT signature was also associated with decreased concentrations of the metabolites citrate and spermine, which have previously been linked to aggressive prostate cancer. Our results demonstrate the importance of NCWP and EMT in prostate cancer aggressiveness, suggest a novel gene signature for improved risk stratification, and give new molecular insight.

  5. A non-canonical start codon in the Drosophila fragile X gene yields two functional isoforms

    PubMed Central

    Beerman, Rebecca W.; Jongens, Thomas A.

    2011-01-01

    Fragile X syndrome is caused by the loss of expression of the fragile X mental retardation protein (FMRP). As a RNA binding protein, FMRP functions in translational regulation, localization, and stability of its neuronal target transcripts. The Drosophila homologue, dFMR1, is well conserved in sequence and function with respect to human FMRP. Although dFMR1 is known to express two main isoforms, the mechanism behind production of the second, more slowly migrating isoform has remained elusive. Furthermore, it remains unknown whether the two isoforms may also contribute differentially to dFMR1 function. We have found that this second dFMR1 isoform is generated through an alternative translational start site in the dfmr1 5’UTR. This 5'UTR coding sequence is well conserved in the melanogaster group. Translation of the predominant, smaller form of dFMR1 (dFMR1-SN) begins at a canonical start codon (ATG), whereas translation of the minor, larger form (dFMR1-LN) begins upstream at a non-canonical start codon (CTG). To assess the contribution of the N-terminal extension toward dFMR1 activity, we generated transgenic flies that exclusively express either dFMR1-SN or dFMR1-LN. Expression analyses throughout development revealed that dFMR1-SN is required for normal dFMR1-LN expression levels in adult brains. In situ expression analyses showed that either dFMR1-SN or dFMR1-LN is individually sufficient for proper dFMR1 localization in the nervous system. Functional studies demonstrated that both dFMR1-SN and dFMR1-LN can function independently to rescue dfmr1 null defects in synaptogenesis and axon guidance. Thus, dfmr1 encodes two functional isoforms with respect to expression and activity throughout neuronal development. PMID:21333716

  6. Multireference M[oslash]ller Plesset perturbation theory with non-canonical and non-orthogonal orbitals

    NASA Astrophysics Data System (ADS)

    Finley, James P.; Hirao, Kimihiko

    2000-09-01

    Using non-orthogonal secondary orbitals and non-canonical (localized) inactive and active orbitals, a second-order multireference perturbation theory is formulated, based on a complete active space self-consistent field (CASSCF) wavefunction. The equations of interest are derived from the first-order Bloch equation by using an approach based on a bi-orthogonal basis and operators expressed in second-quantization.

  7. Structural Analyses of the Slm1-PH Domain Demonstrate Ligand Binding in the Non-Canonical Site

    PubMed Central

    Anand, Kanchan; Maeda, Kenji; Gavin, Anne-Claude

    2012-01-01

    Background Pleckstrin homology (PH) domains are common membrane-targeting modules and their best characterized ligands are a set of important signaling lipids that include phosphatidylinositol phosphates (PtdInsPs). PH domains recognize PtdInsPs through two distinct mechanisms that use different binding pockets on opposite sides of the β-strands 1 and 2: i) a canonical binding site delimited by the β1-β2 and β3-β4loops and ii) a non-canonical binding site bordered by the β1-β2 and β5-β6loops. The PH domain-containing protein Slm1 from budding yeast Saccharomyces cerevisiae is required for actin cytoskeleton polarization and cell growth. We recently reported that this PH domain binds PtdInsPs and phosphorylated sphingolipids in a cooperative manner. Principal Findings To study the structural basis for the Slm1-PH domain (Slm1-PH) specificity, we co-crystallized this domain with different soluble compounds that have structures analogous to anionic lipid head groups of reported Slm1 ligands: inositol 4-phosphate, which mimics phosphatidylinositol-4-phosphate (PtdIns(4)P), and phosphoserine as a surrogate for dihydrosphingosine 1-phosphate (DHS1-P). We found electron densities for the ligands within the so-called non-canonical binding site. An additional positively charged surface that contacts a phosphate group was identified next to the canonical binding site. Conclusions Our results suggest that Slm1-PH utilizes a non-canonical binding site to bind PtdInsPs, similar to that described for the PH domains of β-spectrin, Tiam1 and ArhGAP9. Additionally, Slm1-PH may have retained an active canonical site. We propose that the presence of both a canonical and a non-canonical binding pocket in Slm1-PH may account for the cooperative binding to PtdInsPs and DHS-1P. PMID:22574179

  8. Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells.

    PubMed

    Zhang, Yilan; Ge, Xianglian; Yang, Fayu; Zhang, Liping; Zheng, Jiayong; Tan, Xuefang; Jin, Zi-Bing; Qu, Jia; Gu, Feng

    2014-06-23

    CRISPR/Cas9-mediated DNA cleavage (CCMDC) is becoming increasingly used for efficient genome engineering. Proto-spacer adjacent motif (PAM) adjacent to target sequence is one of the key components in the design of CCMDC strategies. It has been reported that NAG sequences are the predominant non-canonical PAM for CCMDC at the human EMX locus, but it is not clear whether it is universal at other loci. In the present study, we attempted to use a GFP-reporter system to comprehensively and quantitatively test the efficiency of CCMDC with non-canonical PAMs in human cells. The initial results indicated that the effectiveness of NGA PAM for CCMDC is much higher than that of other 14 PAMs including NAG. Then we further designed another three pairs of NGG, NGA and NAG PAMs at different locations in the GFP gene and investigated the corresponding DNA cleavage efficiency. We observed that one group of NGA PAMs have a relatively higher DNA cleavage efficiency, while the other groups have lower efficiency, compared with the corresponding NAG PAMs. Our study clearly demonstrates that NAG may not be the universally predominant non-canonical PAM for CCMDC in human cells. These findings raise more concerns over off-target effects in CRISPR/Cas9-mediated genome engineering.

  9. Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems

    NASA Astrophysics Data System (ADS)

    Xiao, Jianyuan; Qin, Hong; Liu, Jian; He, Yang; Zhang, Ruili; Sun, Yajuan

    2015-11-01

    Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithms conserve a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a structure-preserving splitting method discovered by He et al. [preprint arXiv:1505.06076 (2015)], which produces five exactly soluble sub-systems, and high-order structure-preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom on massively parallel supercomputers. The algorithms have been tested and verified by the two physics problems, i.e., the nonlinear Landau damping and the electron Bernstein wave.

  10. Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules.

    PubMed

    Meinnel, T; Sacerdot, C; Graffe, M; Blanquet, S; Springer, M

    1999-07-23

    Translation initiation factor IF3, one of three factors specifically required for translation initiation in Escherichia coli, inhibits initiation on any codon other than the three canonical initiation codons, AUG, GUG, or UUG. This discrimination against initiation on non-canonical codons could be due to either direct recognition of the two last bases of the codon and their cognate bases on the anticodon or to some ability to "feel" codon-anticodon complementarity. To investigate the importance of codon-anticodon complementarity in the discriminatory role of IF3, we constructed a derivative of tRNALeuthat has all the known characteristics of an initiator tRNA except the CAU anticodon. This tRNA is efficiently formylated by methionyl-tRNAfMettransformylase and charged by leucyl-tRNA synthetase irrespective of the sequence of its anticodon. These initiator tRNALeuderivatives (called tRNALI) allow initiation at all the non-canonical codons tested, provided that the complementarity between the codon and the anticodon of the initiator tRNALeuis respected. More remarkably, the discrimination by IF3, normally observed with non-canonical codons, is neutralised if a tRNALIcarrying a complementary anticodon is used for initiation. This suggests that IF3 somehow recognises codon-anticodon complementarity, at least at the second and third position of the codon, rather than some specific bases in either the codon or the anticodon.

  11. Non-canonical Wnt signaling regulates cell polarity in female reproductive tract development via van gogh-like 2

    PubMed Central

    vandenBerg, Alysia L.; Sassoon, David A.

    2009-01-01

    Summary Wnt signaling effectors direct the development and adult remodeling of the female reproductive tract (FRT); however, the role of non-canonical Wnt signaling has not been explored in this tissue. The non-canonical Wnt signaling protein van gogh-like 2 is mutated in loop-tail (Lp) mutant mice (Vangl2Lp), which display defects in multiple tissues. We find that Vangl2Lp mutant uterine epithelium displays altered cell polarity, concommitant with changes in cytoskeletal actin and scribble (scribbled, Scrb1) localization. The postnatal mutant phenotype is an exacerbation of that seen at birth, exhibiting more smooth muscle and reduced stromal mesenchyme. These data suggest that early changes in cell polarity have lasting consequences for FRT development. Furthermore, Vangl2 is required to restrict Scrb1 protein to the basolateral epithelial membrane in the neonatal uterus, and an accumulation of fibrillar-like structures observed by electron microscopy in Vangl2Lp mutant epithelium suggests that mislocalization of Scrb1 in mutants alters the composition of the apical face of the epithelium. Heterozygous and homozygous Vangl2Lp mutant postnatal tissues exhibit similar phenotypes and polarity defects and display a 50% reduction in Wnt7a levels, suggesting that the Vangl2Lp mutation acts dominantly in the FRT. These studies demonstrate that the establishment and maintenance of cell polarity through non-canonical Wnt signaling are required for FRT development. PMID:19363157

  12. Non-canonical Wnt signaling regulates cell polarity in female reproductive tract development via van gogh-like 2.

    PubMed

    Vandenberg, Alysia L; Sassoon, David A

    2009-05-01

    Wnt signaling effectors direct the development and adult remodeling of the female reproductive tract (FRT); however, the role of non-canonical Wnt signaling has not been explored in this tissue. The non-canonical Wnt signaling protein van gogh-like 2 is mutated in loop-tail (Lp) mutant mice (Vangl2(Lp)), which display defects in multiple tissues. We find that Vangl2(Lp) mutant uterine epithelium displays altered cell polarity, concommitant with changes in cytoskeletal actin and scribble (scribbled, Scrb1) localization. The postnatal mutant phenotype is an exacerbation of that seen at birth, exhibiting more smooth muscle and reduced stromal mesenchyme. These data suggest that early changes in cell polarity have lasting consequences for FRT development. Furthermore, Vangl2 is required to restrict Scrb1 protein to the basolateral epithelial membrane in the neonatal uterus, and an accumulation of fibrillar-like structures observed by electron microscopy in Vangl2(Lp) mutant epithelium suggests that mislocalization of Scrb1 in mutants alters the composition of the apical face of the epithelium. Heterozygous and homozygous Vangl2(Lp) mutant postnatal tissues exhibit similar phenotypes and polarity defects and display a 50% reduction in Wnt7a levels, suggesting that the Vangl2(Lp) mutation acts dominantly in the FRT. These studies demonstrate that the establishment and maintenance of cell polarity through non-canonical Wnt signaling are required for FRT development.

  13. Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems

    SciTech Connect

    Xiao, Jianyuan; Qin, Hong; Liu, Jian; He, Yang; Zhang, Ruili; Sun, Yajuan

    2015-11-01

    Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithms conserve a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a structure-preserving splitting method discovered by He et al. [preprint arXiv: 1505.06076 (2015)], which produces five exactly soluble sub-systems, and high-order structure-preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom on massively parallel supercomputers. The algorithms have been tested and verified by the two physics problems, i.e., the nonlinear Landau damping and the electron Bernstein wave. (C) 2015 AIP Publishing LLC.

  14. Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting

    PubMed Central

    Loeb, Gabriel B.; Khan, Aly A.; Canner, David; Hiatt, Joseph B.; Shendure, Jay; Darnell, Robert B.; Leslie, Christina S.; Rudensky, Alexander Y.

    2012-01-01

    microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3′ untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA—miR-155—in a genetically controlled manner. We found that approximately forty percent of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these non-canonical sites feature extensive complementarity to the miRNA seed with one mismatch. These non-canonical sites confer regulation of gene expression albeit less potently than canonical sites. Thus, non-canonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation. PMID:23142080

  15. Reconstitution of a functional IS608 single-strand transpososome: role of non-canonical base pairing

    PubMed Central

    He, Susu; Hickman, Alison B.; Dyda, Fred; Johnson, Neil P.; Chandler, Michael; Ton-Hoang, Bao

    2011-01-01

    Single-stranded (ss) transposition, a recently identified mechanism adopted by members of the widespread IS200/IS605 family of insertion sequences (IS), is catalysed by the transposase, TnpA. The transposase of IS608, recognizes subterminal imperfect palindromes (IP) at both IS ends and cleaves at sites located at some distance. The cleavage sites, C, are not recognized directly by the protein but by short sequences 5′ to the foot of each IP, guide (G) sequences, using a network of canonical (‘Watson–Crick’) base interactions. In addition a set of non-canonical base interactions similar to those found in RNA structures are also involved. We have reconstituted a biologically relevant complex, the transpososome, including both left and right ends and TnpA, which catalyses excision of a ss DNA circle intermediate. We provide a detailed picture of the way in which the IS608 transpososome is assembled and demonstrate that both C and G sequences are essential for forming a robust transpososome detectable by EMSA. We also address several questions central to the organization and function of the ss transpososome and demonstrate the essential role of non-canonical base interactions in the IS608 ends for its stability by using point mutations which destroy individual non-canonical base interactions. PMID:21745812

  16. Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems

    SciTech Connect

    Xiao, Jianyuan; Liu, Jian; He, Yang; Zhang, Ruili; Qin, Hong; Sun, Yajuan

    2015-11-15

    Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithms conserve a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a structure-preserving splitting method discovered by He et al. [preprint http://arxiv.org/abs/arXiv:1505.06076 (2015)], which produces five exactly soluble sub-systems, and high-order structure-preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom on massively parallel supercomputers. The algorithms have been tested and verified by the two physics problems, i.e., the nonlinear Landau damping and the electron Bernstein wave.

  17. Non-canonical dynamic mechanisms of interaction between the p66Shc protein and Met receptor

    PubMed Central

    Landry, Mélissa; Pomerleau, Véronique; Saucier, Caroline

    2016-01-01

    Met receptor tyrosine kinase (RTK) is known to bind to the three distinct protein isoforms encoded by the ShcA (Shc) gene. Structure–function studies have unveiled critical roles for p52Shc-dependent signalling pathways in Met-regulated biological functions. The molecular basis of the interaction between the Met and p52Shc proteins is well-defined, but not for the longest protein isoform, p66Shc. In the present study, co-immunoprecipitation assays were performed in human embryonic kidney 293 (HEK293) cells, transiently co-transfected with Met and p66Shc mutants, in order to define the molecular determinants involved in mediating Met–p66Shc interaction. Our results show that p66Shc interacts constitutively with the receptor Met, and the Grb2 (growth factor receptor-bound protein-2) and Gab1 (Grb2-associated binder-1) adaptor proteins. Although its phosphotyrosine-binding domain (PTB) and Src homology 2 (SH2) domains co-ordinate p66Shc binding to non-activated Met receptor, these phosphotyrosine-binding modules, and its collagen homology domain 2 (CH2) region, exert negative constraints. In contrast, p66Shc interaction with the activated Met depends mainly on the integrity of its PTB domain, and to a lesser extent of its SH2 domain. Even though not required for the recruitment of p66Shc, tyrosine phosphorylation of p66Shc by activated Met enhances these interactions by mechanisms not reliant on the integrity of the Met multisubstrate-binding site. In turn, this increases phosphotyrosine-dependent p66Shc–Grb2–Gab1 complex formation away from the receptor, while blocking Grb2 and Gab1 recruitment to activated Met. In conclusion, we identify, for the first time, a novel non-canonical dynamic mode of interaction between Met and the p66 protein isoform of Shc and its effects on rewiring binding effector complexes according to the activation state of the receptor. PMID:27048591

  18. Novel non-canonical genetic rearrangements termed "complex structural variations" in HBV genome.

    PubMed

    Fujiwara, Kei; Matsunami, Kayoko; Iio, Etsuko; Nojiri, Shunsuke; Joh, Takashi

    2017-06-15

    WMHV and HBV from human and non-human primates showed that complex combinations of deletions and insertions accounted for their genetic differences. Non-canonical genetic rearrangements termed complex SVs were observed in HBV. Further, complex SVs accounted for the genetic differences of WMHV and HBV from human and non-human primates. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Non-canonical bases in the genome: The regulatory information layer in DNA.

    PubMed

    Carell, Thomas; Kurz, Matthias Q; Müller, Markus; Rossa, Martin; Spada, Fabio

    2017-09-21

    The sequence of the four canonical bases dA, dC, dG and dT forming two defined Watson-Crick base pairs (dT:dA, dG:dC), held together by H-bonding, establish the sequence information in the DNA double strand. The faithful replication of the sequence information during cell division, the transcription of the DNA information into RNA and the final translation of the sequence information into proteins is the basis for life on earth. Multicellular organisms developed the concept of specialized cells that perform specific functions. Examples are neurons and fibroblast to name just two out of more than 200. These cellular differences are established based on the same sequence information stored in the cell nucleus of all cells of an organism. The sequence information needs consequently different interpretations by the different cell types. During cellular development, when a zygote develops finally into a complex organism with its multitude of specialized cells, this interpretation of the genetic code has to be tightly regulated in space and time. Interpretation of the sequence information involves the controlled activation and silencing of specific genes so that certain proteins are made in one cell type but not in others. This involves an additional regulatory information layer beyond the pure base sequence. One aspect of this regulatory information layer relies on functional groups that are attached to the C(5) position of the canonical base dC. Currently four regulatory, non-canonical bases with a methyl (CH3)-, a hydroxymethyl (CH2OH)-, a formyl (CHO)- and a carboxyl (COOH)- group are known. While 5-methyl-cytidine is long recognized to be a regulatory base in the genome, the other three bases and the enzymes responsible for generating them, were just recently discovered. This review summarizes the discovery of the new bases and focusses at the chemical biology aspects associated with the regulatory DNA bases beyond Watson and Crick. © 2017 WILEY-VCH Verlag Gmb

  20. FZD6, targeted by miR-21, represses gastric cancer cell proliferation and migration via activating non-canonical wnt pathway.

    PubMed

    Yan, Jin; Liu, Tingyu; Zhou, Xiaoying; Dang, Yini; Yin, Chengqiang; Zhang, Guoxin

    2016-01-01

    FZD6 plays crucial roles in human tumorigenesis. However, its mechanism in regulating cancers has not been fully elucidated. In the study, we found that FZD6 repressed gastric cancer cell proliferation and migration via activating non-canonical wnt pathway. In addition, non-canonical wnt pathway ameliorated expression of canonical wnt pathway. We also demonstrated that the FZD6 was involved in miR-21-dependent effects in the canonical and non-canonical wnt pathways in gastric cancer. These findings provide a better understanding of the development and progression of gastric cancer and may be an important implication for future therapy.

  1. A Non-Canonical NRPS Is Involved in the Synthesis of Fungisporin and Related Hydrophobic Cyclic Tetrapeptides in Penicillium chrysogenum

    PubMed Central

    Lankhorst, Peter P.; van der Hoeven, Rob A. M.; Schouten, Olaf L.; Noga, Marek; Hankemeier, Thomas; van Peij, Noël N. M. E.; Bovenberg, Roel A. L.; Vreeken, Rob J.; Driessen, Arnold J. M.

    2014-01-01

    The filamentous fungus Penicillium chrysogenum harbors an astonishing variety of nonribosomal peptide synthetase genes, which encode proteins known to produce complex bioactive metabolites from simple building blocks. Here we report a novel non-canonical tetra-modular nonribosomal peptide synthetase (NRPS) with microheterogenicity of all involved adenylation domains towards their respective substrates. By deleting the putative gene in combination with comparative metabolite profiling various unique cyclic and derived linear tetrapeptides were identified which were associated with this NRPS, including fungisporin. In combination with substrate predictions for each module, we propose a mechanism for a ‘trans-acting’ adenylation domain. PMID:24887561

  2. A non-canonical NRPS is involved in the synthesis of fungisporin and related hydrophobic cyclic tetrapeptides in Penicillium chrysogenum.

    PubMed

    Ali, Hazrat; Ries, Marco I; Lankhorst, Peter P; van der Hoeven, Rob A M; Schouten, Olaf L; Noga, Marek; Hankemeier, Thomas; van Peij, Noël N M E; Bovenberg, Roel A L; Vreeken, Rob J; Driessen, Arnold J M

    2014-01-01

    The filamentous fungus Penicillium chrysogenum harbors an astonishing variety of nonribosomal peptide synthetase genes, which encode proteins known to produce complex bioactive metabolites from simple building blocks. Here we report a novel non-canonical tetra-modular nonribosomal peptide synthetase (NRPS) with microheterogenicity of all involved adenylation domains towards their respective substrates. By deleting the putative gene in combination with comparative metabolite profiling various unique cyclic and derived linear tetrapeptides were identified which were associated with this NRPS, including fungisporin. In combination with substrate predictions for each module, we propose a mechanism for a 'trans-acting' adenylation domain.

  3. RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

    PubMed

    Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

    2017-02-01

    Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

  4. RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

    2017-02-01

    Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

  5. Canonical and Non-Canonical Activation of NLRP3 Inflammasome at the Crossroad between Immune Tolerance and Intestinal Inflammation

    PubMed Central

    Pellegrini, Carolina; Antonioli, Luca; Lopez-Castejon, Gloria; Blandizzi, Corrado; Fornai, Matteo

    2017-01-01

    Several lines of evidence point out the relevance of nucleotide-binding oligomerization domain leucine rich repeat and pyrin domain-containing protein 3 (NLRP3) inflammasome as a pivotal player in regulating the integrity of intestinal homeostasis and shaping innate immune responses during bowel inflammation. Intensive research efforts are being made to achieve an integrated view about the protective/detrimental role of canonical and non-canonical NLRP3 inflammasome activation in the maintenance of intestinal microenvironment integrity. Evidence is also emerging that the pharmacological modulation of NLRP3 inflammasome could represent a promising molecular target for the therapeutic management of inflammatory immune-mediated gut diseases. The present review has been intended to provide a critical appraisal of the available knowledge about the role of canonical and non-canonical NLRP3 inflammasome activation in the dynamic interplay between microbiota, intestinal epithelium, and innate immune system, taken together as a whole integrated network regulating the maintenance/breakdown of intestinal homeostasis. Moreover, special attention has been paid to the pharmacological modulation of NLRP3 inflammasome, emphasizing the concept that this multiprotein complex could represent a suitable target for the management of inflammatory bowel diseases. PMID:28179906

  6. Src promotes castration-recurrent prostate cancer through androgen receptor-dependent canonical and non-canonical transcriptional signatures.

    PubMed

    Chattopadhyay, Indranil; Wang, Jianmin; Qin, Maochun; Gao, Lingqiu; Holtz, Renae; Vessella, Robert L; Leach, Robert W; Gelman, Irwin H

    2017-02-07

    Progression of prostate cancer (PC) to castration-recurrent growth (CRPC) remains dependent on sustained expression and transcriptional activity of the androgen receptor (AR). A major mechanism contributing to CRPC progression is through the direct phosphorylation and activation of AR by Src-family (SFK) and ACK1 tyrosine kinases. However, the AR-dependent transcriptional networks activated by Src during CRPC progression have not been elucidated. Here, we show that activated Src (Src527F) induces androgen-independent growth in human LNCaP cells, concomitant with its ability to induce proliferation/survival genes normally induced by dihydrotestosterone (DHT) in androgen-dependent LNCaP and VCaP cells. Src induces additional gene signatures unique to CRPC cell lines, LNCaP-C4-2 and CWR22Rv1, and to CRPC LuCaP35.1 xenografts. By comparing the Src-induced AR-cistrome and/or transcriptome in LNCaP to those in CRPC and LuCaP35.1 tumors, we identified an 11-gene Src-regulated CRPC signature consisting of AR-dependent, AR binding site (ARBS)-associated genes whose expression is altered by DHT in LNCaP[Src527F] but not in LNCaP cells. The differential expression of a subset (DPP4, BCAT1, CNTNAP4, CDH3) correlates with earlier PC metastasis onset and poorer survival, with the expression of BCAT1 required for Src-induced androgen-independent proliferation. Lastly, Src enhances AR binding to non-canonical ARBS enriched for FOXO1, TOP2B and ZNF217 binding motifs; cooperative AR/TOP2B binding to a non-canonical ARBS was both Src- and DHT-sensitive and correlated with increased levels of Src-induced phosphotyrosyl-TOP2B. These data suggest that CRPC progression is facilitated via Src-induced sensitization of AR to intracrine androgen levels, resulting in the engagement of canonical and non-canonical ARBS-dependent gene signatures.

  7. TTRAP Is a Novel Component of the Non-Canonical TRAF6-TAK1 TGF-β Signaling Pathway

    PubMed Central

    Várady, György; Sarkadi, Balázs; Fátyol, Károly

    2011-01-01

    Transforming growth factor-β (TGF-β) principally relays its effects through the Smad pathway however, accumulating evidence indicate that alternative signaling routes are also employed by this pleiotropic cytokine. For instance recently, we have demonstrated that ligand occupied TGF-β receptors can directly trigger the TRAF6-TAK1 signaling module, resulting in MAP kinase activation. Here we report identification of the adaptor molecule TTRAP as a novel component of this non-canonical TGF-β pathway. We show that the protein associates with TGF-β receptors and components of the TRAF6-TAK1 signaling module, resulting in differential regulation of TGF-β activated p38 and NF-κB responses. Modulation of cellular TTRAP level affects cell viability in the presence of TGF-β, suggesting that the protein is an important component of the TGF-β induced apoptotic process. PMID:21980489

  8. Recent Developments of Engineered Translational Machineries for the Incorporation of Non-Canonical Amino Acids into Polypeptides

    PubMed Central

    Terasaka, Naohiro; Iwane, Yoshihiko; Geiermann, Anna-Skrollan; Goto, Yuki; Suga, Hiroaki

    2015-01-01

    Genetic code expansion and reprogramming methodologies allow us to incorporate non-canonical amino acids (ncAAs) bearing various functional groups, such as fluorescent groups, bioorthogonal functional groups, and post-translational modifications, into a desired position or multiple positions in polypeptides both in vitro and in vivo. In order to efficiently incorporate a wide range of ncAAs, several methodologies have been developed, such as orthogonal aminoacyl-tRNA-synthetase (AARS)–tRNA pairs, aminoacylation ribozymes, frame-shift suppression of quadruplet codons, and engineered ribosomes. More recently, it has been reported that an engineered translation system specifically utilizes an artificially built genetic code and functions orthogonally to naturally occurring counterpart. In this review we summarize recent advances in the field of ribosomal polypeptide synthesis containing ncAAs. PMID:25803109

  9. Non-canonical NF-κB pathway activation predicts outcome in borderline oestrogen receptor positive breast carcinoma.

    PubMed

    Rojo, Federico; González-Pérez, Abel; Furriol, Jessica; Nicolau, Ma Jesús; Ferrer, Jaime; Burgués, Octavio; Sabbaghi, MohammadA; González-Navarrete, Irene; Cristobal, Ion; Serrano, Laia; Zazo, Sandra; Madoz, Juan; Servitja, Sonia; Tusquets, Ignasi; Albanell, Joan; Lluch, Ana; Rovira, Ana; Eroles, Pilar

    2016-07-26

    NF-κB signalling appears deregulated in breast tumours. The purpose of this study was to determine whether the non-canonical NF-κB pathway, is activated in oestrogen receptor positive (ER+) breast cancer, to identify any correlation between its activity and the clinico-pathological phenotype and to explore whether NF-κB2 and RelB subunits and/or any of their target genes might be used as a predictive marker. Two independent cohorts of ER+ early breast cancer patients treated with adjuvant endocrine therapy were included in the study. Activation of RelB and NF-κB2 subunits was determined in a training set of 121 patients by measuring DNA-binding activities in nuclear extracts from fresh frozen specimens by an ELISA-based assay. Samples of 15 ER- breast cancer patients were also included in the study. In a large validation cohort of 207 patients, nuclear immunostaining of RelB and NF-κB2 on formalin-fixed paraffin-embedded specimens was performed. Statistical correlation within clinico-pathological factors, disease-free survival (DFS) and overall survival (OS) was evaluated. Publicly available gene expression and survival data have been interrogated aimed to identify target genes. Activation of NF-κB2 and RelB was found in 53.7 and 49.2% of the 121 ER+ tumours analysed, with similar levels to ER- breast tumours analysed in parallel for comparisons. In the validation cohort, we obtained a similar proportion of cases with activation of NF-κB2 and RelB (59.9 and 32.4%), with a 39.6% of co-activation. Multiplexing immunofluorescence in breast cancer tissue confirmed an inverse spatial distribution of ER with NF-κB2 and RelB nuclear expression in tumour cells. Interestingly, NF-κB2 and RelB mRNA expression was inversely correlated with ER gene (ESR1) levels (P<0.001, both) and its activation was significantly associated with worse DFS (P=0.005 and P=0.035, respectively) in ER+ breast cancer. Moreover, the co-activation of both subunits showed a stronger

  10. Opinion: uracil DNA glycosylase (UNG) plays distinct and non-canonical roles in somatic hypermutation and class switch recombination.

    PubMed

    Yousif, Ashraf S; Stanlie, Andre; Begum, Nasim A; Honjo, Tasuku

    2014-10-01

    Activation-induced cytidine deaminase (AID) is essential to class switch recombination (CSR) and somatic hypermutation (SHM). Uracil DNA glycosylase (UNG), a member of the base excision repair complex, is required for CSR. The role of UNG in CSR and SHM is extremely controversial. AID deficiency in mice abolishes both CSR and SHM, while UNG-deficient mice have drastically reduced CSR but augmented SHM raising a possibility of differential functions of UNG in CSR and SHM. Interestingly, UNG has been associated with a CSR-specific repair adapter protein Brd4, which interacts with acetyl histone 4, γH2AX and 53BP1 to promote non-homologous end joining during CSR. A non-canonical scaffold function of UNG, but not the catalytic activity, can be attributed to the recruitment of essential repair proteins associated with the error-free repair during SHM, and the end joining during CSR.

  11. Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation

    PubMed Central

    Dobosz-Bartoszek, Malgorzata; Pinkerton, Mark H.; Otwinowski, Zbyszek; Chakravarthy, Srinivas; Söll, Dieter; Copeland, Paul R.; Simonović, Miljan

    2016-01-01

    Selenocysteine is the only proteinogenic amino acid encoded by a recoded in-frame UGA codon that does not operate as the canonical opal stop codon. A specialized translation elongation factor, eEFSec in eukaryotes and SelB in prokaryotes, promotes selenocysteine incorporation into selenoproteins by a still poorly understood mechanism. Our structural and biochemical results reveal that four domains of human eEFSec fold into a chalice-like structure that has similar binding affinities for GDP, GTP and other guanine nucleotides. Surprisingly, unlike in eEF1A and EF-Tu, the guanine nucleotide exchange does not cause a major conformational change in domain 1 of eEFSec, but instead induces a swing of domain 4. We propose that eEFSec employs a non-canonical mechanism involving the distinct C-terminal domain 4 for the release of the selenocysteinyl-tRNA during decoding on the ribosome. PMID:27708257

  12. Vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical Cys-His-Ser catalytic triad

    PubMed Central

    Sanchez-Pulido, Luis; Ponting, Chris P.

    2016-01-01

    Summary: Vasohibin-1 and Vasohibin-2 regulate angiogenesis, tumour growth and metastasis. Their molecular functions, however, were previously unknown, in large part owing to their perceived lack of homology to proteins of known structure and function. To identify their functional amino acids and domains, their molecular activity and their evolutionary history, we undertook an in-depth analysis of Vasohibin sequences. We find that Vasohibin proteins are previously undetected members of the transglutaminase-like cysteine protease superfamily, and all possess a non-canonical Cys-His-Ser catalytic triad. We further propose a calcium-dependent activation mechanism for Vasohibin proteins. These findings can now be used to design constructs for protein structure determination and to develop enzyme inhibitors as angiogenic regulators to treat metastasis and tumour growth. Contact: luis.sanchezpulido@dpag.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26794318

  13. The role of the non-canonical Wnt-planar cell polarity pathway in neural crest migration.

    PubMed

    Mayor, Roberto; Theveneau, Eric

    2014-01-01

    The neural crest is an embryonic stem cell population whose migratory behaviour has been likened to malignant invasion. The neural crest, as does cancer, undergoes an epithelial-to-mesenchymal transition and migrates to colonize almost all the tissues of the embryo. Neural crest cells exhibit collective cell migration, moving in streams of high directionality. The migratory neural crest streams are kept in shape by the presence of negative signals in their vicinity. The directionality of the migrating neural crest is achieved by contact-dependent cell polarization, in a phenomenon called contact inhibition of locomotion. Two cells experiencing contact inhibition of locomotion move away from each other after collision. However, if the cell density is high only cells exposed to a free edge can migrate away from the cluster leading to the directional migration of the whole group. Recent work performed in chicks, zebrafish and frogs has shown that the non-canonical Wnt-PCP (planar cell polarity) pathway plays a major role in neural crest migration. PCP signalling controls contact inhibition of locomotion between neural crest cells by localizing different PCP proteins at the site of cell contact during collision and locally regulating the activity of Rho GTPases. Upon collision RhoA (ras homologue family member A) is activated, whereas Rac1 is inhibited at the contact between two migrating neural crest cells, leading to the collapse of protrusions and the migration of cells away from one another. The present review summarizes the mechanisms that control neural crest migration and focuses on the role of non-canonical Wnt or PCP signalling in this process.

  14. A non-canonical secondary structure stabilizes mitochondrial tRNASer(UCN) by reducing the entropic cost of tertiary folding

    PubMed Central

    Mustoe, Anthony M.; Liu, Xin; Lin, Paul J.; Al-Hashimi, Hashim M.; Fierke, Carol A.; Brooks, Charles L.

    2015-01-01

    Mammalian mitochondrial tRNASer(UCN) (mt-tRNASer) and pyrrolysine tRNA (tRNAPyl) fold to near-canonical three-dimensional structures despite having non-canonical secondary structures with shortened interhelical loops that disrupt the conserved tRNA tertiary interaction network. How these non-canonical tRNAs compensate for their loss of tertiary interactions remains unclear. Furthermore, in human mt-tRNASer, lengthening the variable-loop by the 7472insC mutation reduces mt-tRNASer concentration in vivo through poorly understood mechanisms, and is strongly associated with diseases such as deafness and epilepsy. Using simulations of the TOPRNA coarse-grained model, we show that increased topological constraints encoded by the unique secondary structure of wild-type mt-tRNASer decrease the entropic cost of folding by ~2.5 kcal/mol compared to canonical tRNA, offsetting its loss of tertiary interactions. Further simulations show that the pathogenic 7472insC mutation disrupts topological constraints and hence destabilizes the mutant mt-tRNASer by ~0.6 kcal/mol relative to wild-type. UV melting experiments confirm that insertion mutations lower mt-tRNASer melting temperature by 6–9°C and increase the folding free energy by 0.8–1.7 kcal/mol in a largely sequence- and salt-independent manner, in quantitative agreement with our simulation predictions. Our results show that topological constraints provide a quantitative framework for describing key aspects of RNA folding behavior and also provide the first evidence of a pathogenic mutation that is due to disruption of topological constraints. PMID:25705930

  15. Canonical and non-canonical EcfG sigma factors control the general stress response in Rhizobium etli.

    PubMed

    Jans, Ann; Vercruysse, Maarten; Gao, Shanjun; Engelen, Kristof; Lambrichts, Ivo; Fauvart, Maarten; Michiels, Jan

    2013-12-01

    A core component of the α-proteobacterial general stress response (GSR) is the extracytoplasmic function (ECF) sigma factor EcfG, exclusively present in this taxonomic class. Half of the completed α-proteobacterial genome sequences contain two or more copies of genes encoding σ(EcfG) -like sigma factors, with the primary copy typically located adjacent to genes coding for a cognate anti-sigma factor (NepR) and two-component response regulator (PhyR). So far, the widespread occurrence of additional, non-canonical σ(EcfG) copies has not satisfactorily been explained. This study explores the hierarchical relation between Rhizobium etli σ(EcfG1) and σ(EcfG2) , canonical and non-canonical σ(EcfG) proteins, respectively. Contrary to reports in other species, we find that σ(EcfG1) and σ(EcfG2) act in parallel, as nodes of a complex regulatory network, rather than in series, as elements of a linear regulatory cascade. We demonstrate that both sigma factors control unique yet also shared target genes, corroborating phenotypic evidence. σ(EcfG1) drives expression of rpoH2, explaining the increased heat sensitivity of an ecfG1 mutant, while katG is under control of σ(EcfG2) , accounting for reduced oxidative stress resistance of an ecfG2 mutant. We also identify non-coding RNA genes as novel σ(EcfG) targets. We propose a modified model for GSR regulation in R. etli, in which σ(EcfG1) and σ(EcfG2) function largely independently. Based on a phylogenetic analysis and considering the prevalence of α-proteobacterial genomes with multiple σ(EcfG) copies, this model may also be applicable to numerous other species.

  16. New insights into transcription fidelity: thermal stability of non-canonical structures in template DNA regulates transcriptional arrest, pause, and slippage.

    PubMed

    Tateishi-Karimata, Hisae; Isono, Noburu; Sugimoto, Naoki

    2014-01-01

    The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts) from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG). Transcriptional arrest was induced when the stability of the G-quadruplex structure (-ΔG°37) in the presence of 20 wt% PEG was more than 8.2 kcal mol(-1). Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs.

  17. New Insights into Transcription Fidelity: Thermal Stability of Non-Canonical Structures in Template DNA Regulates Transcriptional Arrest, Pause, and Slippage

    PubMed Central

    Tateishi-Karimata, Hisae; Isono, Noburu; Sugimoto, Naoki

    2014-01-01

    The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts) from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG). Transcriptional arrest was induced when the stability of the G-quadruplex structure (−ΔGo37) in the presence of 20 wt% PEG was more than 8.2 kcal mol−1. Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs. PMID:24594642

  18. Non-canonical microRNAs miR-320 and miR-702 promote proliferation in Dgcr8-deficient embryonic stem cells

    SciTech Connect

    Kim, Byeong-Moo; Choi, Michael Y.

    2012-09-21

    Highlights: Black-Right-Pointing-Pointer Embryonic stem cells (ESCs) lacking non-canonical miRNAs proliferate slower. Black-Right-Pointing-Pointer miR-320 and miR-702 are two non-canonical miRNAs expressed in ESCs. Black-Right-Pointing-Pointer miR-320 and miR-702 promote proliferation of Dgcr8-deficient ESCs. Black-Right-Pointing-Pointer miR-320 targets p57 and helps to release Dgcr8-deficient ESCs from G1 arrest. Black-Right-Pointing-Pointer miR-702 targets p21 and helps to release Dgcr8-deficient ESCs from G1 arrest. -- Abstract: MicroRNAs are known to contribute significantly to stem cell phenotype by post-transcriptionally regulating gene expression. Most of our knowledge of microRNAs comes from the study of canonical microRNAs that require two sequential cleavages by the Drosha/Dgcr8 heterodimer and Dicer to generate mature products. In contrast, non-canonical microRNAs bypass the cleavage by the Drosha/Dgcr8 heterodimer within the nucleus but still require cytoplasmic cleavage by Dicer. The function of non-canonical microRNAs in embryonic stem cells (ESCs) remains obscure. It has been hypothesized that non-canonical microRNAs have important roles in ESCs based upon the phenotypes of ESC lines that lack these specific classes of microRNAs; Dicer-deficient ESCs lacking both canonical and non-canonical microRNAs have much more severe proliferation defect than Dgcr8-deficient ESCs lacking only canonical microRNAs. Using these cell lines, we identified two non-canonical microRNAs, miR-320 and miR-702, that promote proliferation of Dgcr8-deficient ESCs by releasing them from G1 arrest. This is accomplished by targeting the 3 Prime -untranslated regions of the cell cycle inhibitors p57 and p21 and thereby inhibiting their expression. This is the first report of the crucial role of non-canonical microRNAs in ESCs.

  19. TWEAK Activates the Non-Canonical NFκB Pathway in Murine Renal Tubular Cells: Modulation of CCL21

    PubMed Central

    Sanz, Ana B.; Sanchez-Niño, Maria D.; Izquierdo, Maria C.; Jakubowski, Aniela; Justo, Pilar; Blanco-Colio, Luis M.; Ruiz-Ortega, Marta; Selgas, Rafael; Egido, Jesús; Ortiz, Alberto

    2010-01-01

    TWEAK is a member of the TNF superfamily of cytokines that contribute to kidney tubulointerstitial injury. It has previously been reported that TWEAK induces transient nuclear translocation of RelA and expression of RelA-dependent cytokines in renal tubular cells. Additionally, TWEAK induced long-lasting NFκB activation suggestive of engagement of the non-canonical NFκB pathway. We now explore TWEAK-induced activation of NFκB2 and RelB, as well as expression of CCL21, a T-cell chemotactic factor, in cultured murine tubular epithelial cells and in healthy kidneys in vivo. In cultured tubular cells, TWEAK and TNFα activated different DNA-binding NFκB complexes. TWEAK-induced sustained NFκB activation was associated with NFκB2 p100 processing to p52 via proteasome and nuclear translocation and DNA-binding of p52 and RelB. TWEAK, but not TNFα used as control), induced a delayed increase in CCL21a mRNA (3.5±1.22-fold over control) and CCL21 protein (2.5±0.8-fold over control), which was prevented by inhibition of the proteasome, or siRNA targeting of NIK or RelB, but not by RelA inhibition with parthenolide. A second NFκB2-dependent chemokine, CCL19, was upregulates by TWEAK, but not by TNFα. However, both cytokines promoted chemokine RANTES expression (3-fold mRNA at 24 h). In vivo, TWEAK induced nuclear NFκB2 and RelB translocation and CCL21a mRNA (1.5±0.3-fold over control) and CCL21 protein (1.6±0.5-fold over control) expression in normal kidney. Increased tubular nuclear RelB and tubular CCL21 expression in acute kidney injury were decreased by neutralization (2±0.9 vs 1.3±0.6-fold over healthy control) or deficiency of TWEAK (2±0.9 vs 0.8±0.6-fold over healthy control). Moreover, anti-TWEAK treatment prevented the recruitment of T cells to the kidney in this model (4.1±1.4 vs 1.8±1-fold over healthy control). Our results thus identify TWEAK as a regulator of non-canonical NFκB activation and CCL21 expression in tubular cells thus promoting

  20. A Putative Non-Canonical Ras-Like GTPase from P. falciparum: Chemical Properties and Characterization of the Protein

    PubMed Central

    Przyborski, Jude; Kersting, David; Krüger, Mirko

    2015-01-01

    During its development the malaria parasite P. falciparum has to adapt to various different environmental contexts. Key cellular mechanisms involving G-protein coupled signal transduction chains are assumed to act at these interfaces. Heterotrimeric G-proteins are absent in Plasmodium. We here describe the first cloning and expression of a putative, non-canonical Ras-like G protein (acronym PfG) from Plasmodium. PfG reveals an open reading frame of 2736 bp encoding a protein of 912 amino acids with a theoretical pI of 8.68 and a molecular weight of 108.57 kDa. Transcript levels and expression are significantly increased in the erythrocytic phase in particular during schizont and gametocyte formation. Most notably, PfG has GTP binding capacity and GTPase activity due to an EngA2 domain present in small Ras-like GTPases in a variety of Bacillus species and Mycobacteria. By contrast, plasmodial PfG is divergent from any human alpha-subunit. PfG was expressed in E. coli as a histidine-tagged fusion protein and was stable only for 3.5 hours. Purification was only possible under native conditions by Nickel-chelate chromatography and subsequent separation by Blue Native PAGE. Binding of a fluorescent GTP analogue BODIPY® FL guanosine 5’O-(thiotriphosphate) was determined by fluorescence emission. Mastoparan stimulated GTP binding in the presence of Mg2+. GTPase activity was determined colorimetrically. Activity expressed as absolute fluorescence was 50% higher for the human paralogue than the activity of the parasitic enzyme. The PfG protein is expressed in the erythrocytic stages and binds GTP after immunoprecipitation. Immunofluorescence using specific antiserum suggests that PfG localizes to the parasite cytosol. The current data suggest that the putitative, Ras-like G-protein might be involved in a non-canonical signaling pathway in Plasmodium. Research on the function of PfG with respect to pathogenesis and antimalarial chemotherapy is currently under way. PMID

  1. The Processing of Non-Canonically Ordered Constituents in Long Distance Dependencies by Pre-School Children: A Real-Time Investigation

    ERIC Educational Resources Information Center

    Love, Tracy E.

    2007-01-01

    Four experiments were performed which had the goal of determining how and when young children acquire the ability to understand long distance dependencies. These studies examined the operations underlying the auditory processing of non-canonically ordered constituents in object-relative sentences. Children 4-6 years of age and an adult population…

  2. Zebrafish colgate/hdac1 functions in the non-canonical Wnt pathway during axial extension and in Wnt-independent branchiomotor neuron migration.

    PubMed

    Nambiar, Roopa M; Ignatius, Myron S; Henion, Paul D

    2007-01-01

    Vertebrate gastrulation involves the coordinated movements of populations of cells. These movements include cellular rearrangements in which cells polarize along their medio-lateral axes leading to cell intercalations that result in elongation of the body axis. Molecular analysis of this process has implicated the non-canonical Wnt/Frizzled signaling pathway that is similar to the planar cell polarity pathway (PCP) in Drosophila. Here we describe a zebrafish mutant, colgate (col), which displays defects in the extension of the body axis and the migration of branchiomotor neurons. Activation of the non-canonical Wnt/PCP pathway in these mutant embryos by overexpressing DeltaNdishevelled, rho kinase2 and van gogh-like protein 2 (vangl2) rescues the extension defects suggesting that col acts as a positive regulator of the non-canonical Wnt/PCP pathway. Further, we show that col normally regulates the caudal migration of nVII facial hindbrain branchiomotor neurons and that the mutant phenotype can be rescued by misexpression of vangl2 independent of the Wnt/PCP pathway. We cloned the col locus and found that it encodes histone deacetylase1 (hdac1). Our previous results and studies by others have implicated hdac1 in repressing the canonical Wnt pathway. Here, we demonstrate novel roles for zebrafish hdac1 in activating non-canonical Wnt/PCP signaling underlying axial extension and in promoting Wnt-independent caudal migration of a subset of hindbrain branchiomotor neurons.

  3. Statins activate the canonical hedgehog-signaling and aggravate non-cirrhotic portal hypertension, but inhibit the non-canonical hedgehog signaling and cirrhotic portal hypertension.

    PubMed

    Uschner, Frank E; Ranabhat, Ganesh; Choi, Steve S; Granzow, Michaela; Klein, Sabine; Schierwagen, Robert; Raskopf, Esther; Gautsch, Sebastian; van der Ven, Peter F M; Fürst, Dieter O; Strassburg, Christian P; Sauerbruch, Tilman; Diehl, Anna Mae; Trebicka, Jonel

    2015-09-28

    Liver cirrhosis but also portal vein obstruction cause portal hypertension (PHT) and angiogenesis. This study investigated the differences of angiogenesis in cirrhotic and non-cirrhotic PHT with special emphasis on the canonical (Shh/Gli) and non-canonical (Shh/RhoA) hedgehog pathway. Cirrhotic (bile duct ligation/BDL; CCl4 intoxication) and non-cirrhotic (partial portal vein ligation/PPVL) rats received either atorvastatin (15 mg/kg; 7d) or control chow before sacrifice. Invasive hemodynamic measurement and Matrigel implantation assessed angiogenesis in vivo. Angiogenesis in vitro was analysed using migration and tube formation assay. In liver and vessel samples from animals and humans, transcript expression was analyzed using RT-PCR and protein expression using Western blot. Atorvastatin decreased portal pressure, shunt flow and angiogenesis in cirrhosis, whereas atorvastatin increased these parameters in PPVL rats. Non-canonical Hh was upregulated in experimental and human liver cirrhosis and was blunted by atorvastatin. Moreover, atorvastatin blocked the non-canonical Hh-pathway RhoA dependently in activated hepatic steallate cells (HSCs). Interestingly, hepatic and extrahepatic Hh-pathway was enhanced in PPVL rats, which resulted in increased angiogenesis. In summary, statins caused contrary effects in cirrhotic and non-cirrhotic portal hypertension. Atorvastatin inhibited the non-canonical Hh-pathway and angiogenesis in cirrhosis. In portal vein obstruction, statins enhanced the canonical Hh-pathway and aggravated PHT and angiogenesis.

  4. The Processing of Non-Canonically Ordered Constituents in Long Distance Dependencies by Pre-School Children: A Real-Time Investigation

    ERIC Educational Resources Information Center

    Love, Tracy E.

    2007-01-01

    Four experiments were performed which had the goal of determining how and when young children acquire the ability to understand long distance dependencies. These studies examined the operations underlying the auditory processing of non-canonically ordered constituents in object-relative sentences. Children 4-6 years of age and an adult population…

  5. Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin.

    PubMed

    Wang, Yuxiao; Pascoe, Heath G; Brautigam, Chad A; He, Huawei; Zhang, Xuewu

    2013-10-01

    Plexins are cell surface receptors that bind semaphorins and transduce signals for regulating neuronal axon guidance and other processes. Plexin signaling depends on their cytoplasmic GTPase activating protein (GAP) domain, which specifically inactivates the Ras homolog Rap through an ill-defined non-canonical catalytic mechanism. The plexin GAP is activated by semaphorin-induced dimerization, the structural basis for which remained unknown. Here we present the crystal structures of the active dimer of zebrafish PlexinC1 cytoplasmic region in the apo state and in complex with Rap. The structures show that the dimerization induces a large-scale conformational change in plexin, which opens the GAP active site to allow Rap binding. Plexin stabilizes the switch II region of Rap in an unprecedented conformation, bringing Gln63 in Rap into the active site for catalyzing GTP hydrolysis. The structures also explain the unique Rap-specificity of plexins. Mutational analyses support that these mechanisms underlie plexin activation and signaling. DOI:http://dx.doi.org/10.7554/eLife.01279.001.

  6. Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin

    PubMed Central

    Wang, Yuxiao; Pascoe, Heath G; Brautigam, Chad A; He, Huawei; Zhang, Xuewu

    2013-01-01

    Plexins are cell surface receptors that bind semaphorins and transduce signals for regulating neuronal axon guidance and other processes. Plexin signaling depends on their cytoplasmic GTPase activating protein (GAP) domain, which specifically inactivates the Ras homolog Rap through an ill-defined non-canonical catalytic mechanism. The plexin GAP is activated by semaphorin-induced dimerization, the structural basis for which remained unknown. Here we present the crystal structures of the active dimer of zebrafish PlexinC1 cytoplasmic region in the apo state and in complex with Rap. The structures show that the dimerization induces a large-scale conformational change in plexin, which opens the GAP active site to allow Rap binding. Plexin stabilizes the switch II region of Rap in an unprecedented conformation, bringing Gln63 in Rap into the active site for catalyzing GTP hydrolysis. The structures also explain the unique Rap-specificity of plexins. Mutational analyses support that these mechanisms underlie plexin activation and signaling. DOI: http://dx.doi.org/10.7554/eLife.01279.001 PMID:24137545

  7. A role for NRAGE in NF-κB activation through the non-canonical BMP pathway

    PubMed Central

    2010-01-01

    Background Previous studies have linked neurotrophin receptor-interacting MAGE protein to the bone morphogenic protein signaling pathway and its effect on p38 mediated apoptosis of neural progenitor cells via the XIAP-Tak1-Tab1 complex. Its effect on NF-κB has yet to be explored. Results Herein we report that NRAGE, via the same XIAP-Tak1-Tab1 complex, is required for the phosphorylation of IKK -α/β and subsequent transcriptional activation of the p65 subunit of NF-κB. Ablation of endogenous NRAGE by siRNA inhibited NF-κB pathway activation, while ablation of Tak1 and Tab1 by morpholino inhibited overexpression of NRAGE from activating NF-κB. Finally, cytokine profiling of an NRAGE over-expressing stable line revealed the expression of macrophage migration inhibitory factor. Conclusion Modulation of NRAGE expression revealed novel roles in regulating NF-κB activity in the non-canonical bone morphogenic protein signaling pathway. The expression of macrophage migration inhibitory factor by bone morphogenic protein -4 reveals novel crosstalk between an immune cytokine and a developmental pathway. PMID:20100315

  8. A role for NRAGE in NF-kappaB activation through the non-canonical BMP pathway.

    PubMed

    Matluk, Nicholas; Rochira, Jennifer A; Karaczyn, Aldona; Adams, Tamara; Verdi, Joseph M

    2010-01-25

    Previous studies have linked neurotrophin receptor-interacting MAGE protein to the bone morphogenic protein signaling pathway and its effect on p38 mediated apoptosis of neural progenitor cells via the XIAP-Tak1-Tab1 complex. Its effect on NF-kappaB has yet to be explored. Herein we report that NRAGE, via the same XIAP-Tak1-Tab1 complex, is required for the phosphorylation of IKK -alpha/beta and subsequent transcriptional activation of the p65 subunit of NF-kappaB. Ablation of endogenous NRAGE by siRNA inhibited NF-kappaB pathway activation, while ablation of Tak1 and Tab1 by morpholino inhibited overexpression of NRAGE from activating NF-kappaB. Finally, cytokine profiling of an NRAGE over-expressing stable line revealed the expression of macrophage migration inhibitory factor. Modulation of NRAGE expression revealed novel roles in regulating NF-kappaB activity in the non-canonical bone morphogenic protein signaling pathway. The expression of macrophage migration inhibitory factor by bone morphogenic protein -4 reveals novel crosstalk between an immune cytokine and a developmental pathway.

  9. A Novel, Non-canonical Splice Variant of the Ikaros Gene Is Aberrantly Expressed in B-cell Lymphoproliferative Disorders

    PubMed Central

    Mancarelli, Maria Michela; Verzella, Daniela; Fischietti, Mariafausta; Di Tommaso, Ambra; Maccarone, Rita; Plebani, Sara; Di Ianni, Mauro; Gulino, Alberto; Alesse, Edoardo

    2013-01-01

    The Ikaros gene encodes a Krüppel-like zinc-finger transcription factor involved in hematopoiesis regulation. Ikaros has been established as one of the most clinically relevant tumor suppressors in several hematological malignancies. In fact, expression of dominant negative Ikaros isoforms is associated with adult B-cell acute lymphoblastic leukemia, myelodysplastic syndrome, acute myeloid leukemia and adult and juvenile chronic myeloid leukemia. Here, we report the isolation of a novel, non-canonical Ikaros splice variant, called Ikaros 11 (Ik11). Ik11 is structurally related to known dominant negative Ikaros isoforms, due to the lack of a functional DNA-binding domain. Interestingly, Ik11 is the first Ikaros splice variant missing the transcriptional activation domain. Indeed, we demonstrated that Ik11 works as a dominant negative protein, being able to dimerize with Ikaros DNA-binding isoforms and inhibit their functions, at least in part by retaining them in the cytoplasm. Notably, we demonstrated that Ik11 is the first dominant negative Ikaros isoform to be aberrantly expressed in B-cell lymphoproliferative disorders, such as chronic lymphocytic leukemia. Aberrant expression of Ik11 interferes with both proliferation and apoptotic pathways, providing a mechanism for Ik11 involvement in tumor pathogenesis. Thus, Ik11 could represent a novel marker for B-cell lymphoproliferative disorders. PMID:23874502

  10. DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana.

    PubMed

    Eamens, Andrew L; Wook Kim, Ki; Waterhouse, Peter M

    2012-10-01

    DOUBLE-STRANDED RNA BINDING (DRB) proteins have been functionally characterized in viruses, prokaryotes and eukaryotes and are involved in all aspects of RNA biology. Arabidopsis thaliana (Arabidopsis) encodes five closely related DRB proteins, DRB1 to DRB5. DRB1 and DRB4 are required by DICER-LIKE (DCL) proteins DCL1 and DCL4 to accurately and efficiently process structurally distinct double-stranded RNA (dsRNA) precursor substrates in the microRNA (miRNA) and trans-acting small-interfering RNA (tasiRNA) biogenesis pathways respectively. We recently reported that DRB2 is also involved in the biogenesis of specific miRNA subsets. ( 1) Furthermore, the severity of the developmental phenotype displayed by the drb235 triple mutant plant, compared with those expressed by either drb2, drb3 and drb5 single mutants, or double mutant combinations thereof, indicates that DRB3 and DRB5 function in the same non-canonical miRNA pathway as DRB2. Through the use of our artificial miRNA (amiRNA) plant expression vector, pBlueGreen ( 2) (,) ( 3) we demonstrate here that unlike DRB2, DRB3 and DRB5 are not involved in the dsRNA processing stages of the miRNA biogenesis pathway, but are required to mediate RNA silencing of target genes of DRB2-associated miRNAs.

  11. Non-canonical 3'-5' extension of RNA with prebiotically plausible ribonucleoside 2',3'-cyclic phosphates.

    PubMed

    Mutschler, Hannes; Holliger, Philipp

    2014-04-09

    Ribonucleoside 2',3'-cyclic phosphates (N>p's) are generated by multiple prebiotically plausible processes and are credible building blocks for the assembly of early RNA oligomers. While N>p's can be polymerized into short RNAs by non-enzymatic processes with variable efficiency and regioselectivity, no enzymatic route for RNA synthesis had been described. Here we report such a non-canonical 3'-5' nucleotidyl transferase activity. We engineered a variant of the hairpin ribozyme to catalyze addition of all four N>p's (2',3'-cyclic A-, G-, U-, and CMP) to the 5'-hydroxyl termini of RNA strands with 5' nucleotide addition enhanced in all cases by eutectic ice phase formation at -7 °C. We also observed 5' addition of 2',3'-cyclic phosphate-activated β-nicotinamide adenine dinucleotide (NAD>p) and ACA>p RNA trinucleotide, and multiple additions of GUCCA>p RNA pentamers. Our results establish a new mode of RNA 3'-5' extension with implications for RNA oligomer synthesis from prebiotic nucleotide pools.

  12. Deoxycholic acid mediates non-canonical EGFR-MAPK activation through the induction of calcium signaling in colon cancer cells.

    PubMed

    Centuori, Sara M; Gomes, Cecil J; Trujillo, Jesse; Borg, Jamie; Brownlee, Joshua; Putnam, Charles W; Martinez, Jesse D

    2016-07-01

    Obesity and a western diet have been linked to high levels of bile acids and the development of colon cancer. Specifically, increased levels of the bile acid deoxycholic acid (DCA), an established tumor promoter, has been shown to correlate with increased development of colorectal adenomas and progression to carcinoma. Herein we investigate the mechanism by which DCA leads to EGFR-MAPK activation, a candidate mechanism by which DCA may promote colorectal tumorigenesis. DCA treated colon cancer cells exhibited strong and prolonged activation of ERK1/2 when compared to EGF treatment alone. We also showed that DCA treatment prevents EGFR degradation as opposed to the canonical EGFR recycling observed with EGF treatment. Moreover, the combination of DCA and EGF treatment displayed synergistic activity, suggesting DCA activates MAPK signaling in a non-canonical manner. Further evaluation showed that DCA treatment increased intracellular calcium levels and CAMKII phosphorylation, and that blocking calcium with BAPTA-AM abrogated MAPK activation induced by DCA, but not by EGF. Finally we showed that DCA-induced CAMKII leads to MAPK activation through the recruitment of c-Src. Taken together, we demonstrated that DCA regulates MAPK activation through calcium signaling, an alternative mechanism not previously recognized in human colon cancer cells. Importantly, this mechanism allows for EGFR to escape degradation and thus achieve a constitutively active state, which may explain its tumor promoting effects. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. A non-canonical function of eukaryotic elongation factor 1A1: regulation of interleukin-6 expression.

    PubMed

    Schulz, Ingo; Engel, Claudia; Niestroj, André J; Kehlen, Astrid; Rahfeld, Jens-Ulrich; Kleinschmidt, Martin; Lehmann, Karola; Roßner, Steffen; Demuth, Hans-Ulrich

    2014-05-01

    Interleukin-6 is one of the most prominent triggers of inflammatory processes. We have shown recently that heteroarylketones (HAKs) interfere with stimulated interleukin-6 expression in astrocytes by suppression of STAT3 phosphorylation at serine 727. Surprisingly, this effect is not based on the inhibition of STAT3-relevant kinases. Therefore, we here used the structurally modified HAK compound biotin-HAK-3 in a reverse chemical approach to identify the relevant molecular target in UV-mediated cross-linking experiments. Employing streptavidin-specific 2D-immunoblotting followed by mass spectrometry we identified nine proteins putatively interacting with biotin-HAK-3. After co-immunoprecipitation, co-immunofluorescence, surface plasmon resonance analyses and RNAi-mediated knock-down, the eukaryotic elongation factor 1A1 (eEF1A1) was verified as the relevant target of HAK bioactivity. eEF1A1 forms complexes with STAT3 and PKCδ, which are crucial for STAT3(S727) phosphorylation and for NF-κB/STAT3-enhanced interleukin-6 expression. Furthermore, the intracellular HAK accumulation is strongly dependent on eEF1A1 expression. Taken together, the results reveal a novel molecular mechanism for a non-canonical role of eEF1A1 in signal transduction via direct modulation of kinase-dependent phosphorylation events.

  14. Canonical and Non-Canonical Aspects of JAK–STAT Signaling: Lessons from Interferons for Cytokine Responses

    PubMed Central

    Majoros, Andrea; Platanitis, Ekaterini; Kernbauer-Hölzl, Elisabeth; Rosebrock, Felix; Müller, Mathias; Decker, Thomas

    2017-01-01

    Janus kinase (JAK)–signal transducer and activator of transcription (STAT) signal transduction mediates cytokine responses. Canonical signaling is based on STAT tyrosine phosphorylation by activated JAKs. Downstream of interferon (IFN) receptors, activated JAKs cause the formation of the transcription factors IFN-stimulated gene factor 3 (ISGF3), a heterotrimer of STAT1, STAT2 and interferon regulatory factor 9 (IRF9) subunits, and gamma interferon-activated factor (GAF), a STAT1 homodimer. In recent years, several deviations from this paradigm were reported. These include kinase-independent JAK functions as well as extra- and intranuclear activities of U-STATs without phosphotyrosines. Additionally, transcriptional control by STAT complexes resembling neither GAF nor ISGF3 contributes to transcriptome changes in IFN-treated cells. Our review summarizes the contribution of non-canonical JAK–STAT signaling to the innate antimicrobial immunity imparted by IFN. Moreover, we touch upon functions of IFN pathway proteins beyond the IFN response. These include metabolic functions of IRF9 as well as the regulation of natural killer cell activity by kinase-dead TYK2 and different phosphorylation isoforms of STAT1. PMID:28184222

  15. The non-canonical mitochondrial inner membrane presequence translocase of trypanosomatids contains two essential rhomboid-like proteins

    PubMed Central

    Harsman, Anke; Oeljeklaus, Silke; Wenger, Christoph; Huot, Jonathan L.; Warscheid, Bettina; Schneider, André

    2016-01-01

    Mitochondrial protein import is essential for all eukaryotes. Here we show that the early diverging eukaryote Trypanosoma brucei has a non-canonical inner membrane (IM) protein translocation machinery. Besides TbTim17, the single member of the Tim17/22/23 family in trypanosomes, the presequence translocase contains nine subunits that co-purify in reciprocal immunoprecipitations and with a presequence-containing substrate that is trapped in the translocation channel. Two of the newly discovered subunits are rhomboid-like proteins, which are essential for growth and mitochondrial protein import. Rhomboid-like proteins were proposed to form the protein translocation pore of the ER-associated degradation system, suggesting that they may contribute to pore formation in the presequence translocase of T. brucei. Pulldown of import-arrested mitochondrial carrier protein shows that the carrier translocase shares eight subunits with the presequence translocase. This indicates that T. brucei may have a single IM translocase that with compositional variations mediates import of presequence-containing and carrier proteins. PMID:27991487

  16. Wnt3a regulates proliferation and migration of HUVEC via canonical and non-canonical Wnt signaling pathways

    SciTech Connect

    Samarzija, Ivana; Sini, Patrizia; Schlange, Thomas; MacDonald, Gwen; Hynes, Nancy E.

    2009-08-28

    Untangling the signaling pathways involved in endothelial cell biology is of central interest for the development of antiangiogenesis based therapies. Here we report that Wnt3a induces the proliferation and migration of HUVECs, but does not affect their survival. Wnt3a-induced proliferation was VEGFR signaling independent, but reduced upon CamKII inhibition. In a search for the downstream mediators of Wnt3a's effects on HUVEC biology, we found that Wnt3a treatment leads to phosphorylation of DVL3 and stabilization of {beta}-catenin. Moreover, under the same conditions we observed an upregulation in c-MYC, TIE-2 and GJA1 mRNA transcripts. Although treatment of HUVECs with Wnt5a induced DVL3 phosphorylation, we did not observe any of the other effects seen upon Wnt3a stimulation. Taken together, our data indicate that Wnt3a induces canonical and non-canonical Wnt signaling in HUVECs, and stimulates their proliferation and migration.

  17. Evidence for a non-canonical role of HDAC5 in regulation of the cardiac Ncx1 and Bnp genes

    PubMed Central

    Harris, Lillianne G.; Wang, Sabina H.; Mani, Santhosh K.; Kasiganesan, Harinath; Chou, C. James; Menick, Donald R.

    2016-01-01

    Class IIa histone deacetylases (HDACs) are very important for tissue specific gene regulation in development and pathology. Because class IIa HDAC catalytic activity is low, their exact molecular roles have not been fully elucidated. Studies have suggested that class IIa HDACs may serve as a scaffold to recruit the catalytically active class I HDAC complexes to their substrate. Here we directly address whether the class IIa HDAC, HDAC5 may function as a scaffold to recruit co-repressor complexes to promoters. We examined two well-characterized cardiac promoters, the sodium calcium exchanger (Ncx1) and the brain natriuretic peptide (Bnp) whose hypertrophic upregulation is mediated by both class I and IIa HDACs. Selective inhibition of class IIa HDACs did not prevent adrenergic stimulated Ncx1 upregulation, however HDAC5 knockout prevented pressure overload induced Ncx1 upregulation. Using the HDAC5(-/-) mouse we show that HDAC5 is required for the interaction of the HDAC1/2/Sin3a co-repressor complexes with the Nkx2.5 and YY1 transcription factors and critical for recruitment of the HDAC1/Sin3a co-repressor complex to either the Ncx1 or Bnp promoter. Our novel findings support a non-canonical role of class IIa HDACs in the scaffolding of transcriptional regulatory complexes, which may be relevant for therapeutic intervention for pathologies. PMID:26704971

  18. Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex.

    PubMed

    Xu, Jianqing; Tack, Drew; Hughes, Randall A; Ellington, Andrew D; Gray, Jeffrey J

    2014-02-01

    Engineering antibodies to utilize non-canonical amino acids (NCAA) should greatly expand the utility of an already important biological reagent. In particular, introducing crosslinking reagents into antibody complementarity determining regions (CDRs) should provide a means to covalently crosslink residues at the antibody-antigen interface. Unfortunately, finding the optimum position for crosslinking two proteins is often a matter of iterative guessing, even when the interface is known in atomic detail. Computer-aided antibody design can potentially greatly restrict the number of variants that must be explored in order to identify successful crosslinking sites. We have therefore used Rosetta to guide the introduction of an oxidizable crosslinking NCAA, l-3,4-dihydroxyphenylalanine (l-DOPA), into the CDRs of the anti-protective antigen scFv antibody M18, and have measured crosslinking to its cognate antigen, domain 4 of the anthrax protective antigen. Computed crosslinking distance, solvent accessibility, and interface energetics were three factors considered that could impact the efficiency of l-DOPA-mediated crosslinking. In the end, 10 variants were synthesized, and crosslinking efficiencies were generally 10% or higher, with the best variant crosslinking to 52% of the available antigen. The results suggest that computational analysis can be used in a pipeline for engineering crosslinking antibodies. The rules learned from l-DOPA crosslinking of antibodies may also be generalizable to the formation of other crosslinked interfaces and complexes.

  19. Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

    PubMed Central

    Laumont, Céline M.; Daouda, Tariq; Laverdure, Jean-Philippe; Bonneil, Éric; Caron-Lizotte, Olivier; Hardy, Marie-Pierre; Granados, Diana P.; Durette, Chantal; Lemieux, Sébastien; Thibault, Pierre; Perreault, Claude

    2016-01-01

    In view of recent reports documenting pervasive translation outside of canonical protein-coding sequences, we wished to determine the proportion of major histocompatibility complex (MHC) class I-associated peptides (MAPs) derived from non-canonical reading frames. Here we perform proteogenomic analyses of MAPs eluted from human B cells using high-throughput mass spectrometry to probe the six-frame translation of the B-cell transcriptome. We report that ∼10% of MAPs originate from allegedly noncoding genomic sequences or exonic out-of-frame translation. The biogenesis and properties of these ‘cryptic MAPs' differ from those of conventional MAPs. Cryptic MAPs come from very short proteins with atypical C termini, and are coded by transcripts bearing long 3′UTRs enriched in destabilizing elements. Relative to conventional MAPs, cryptic MAPs display different MHC class I-binding preferences and harbour more genomic polymorphisms, some of which are immunogenic. Cryptic MAPs increase the complexity of the MAP repertoire and enhance the scope of CD8 T-cell immunosurveillance. PMID:26728094

  20. The non-canonical NOTCH1 ligand Delta-like 1 homolog (DLK1) self interacts in mammals.

    PubMed

    Traustadóttir, Gunnhildur Ásta; Jensen, Charlotte Harken; Garcia Ramirez, Jose Javier; Beck, Hans Christian; Sheikh, Søren Paludan; Andersen, Ditte Caroline

    2017-04-01

    Delta-like 1 homolog (DLK1) is an imprinted gene, which is widely expressed during mammalian development and plays a pivotal role in differentiation of various tissue types. Most recently, we have shown that DLK1 interacts with NOTCH1, yet several Notch independent mechanisms have previously been suggested as well, but only poorly confirmed in a mammalian context. In the present study, we employed the mammalian two-hybrid (MTH) system, a genetic in vivo protein-protein interaction system, to show robust DLK1-DLK1, DLK1-FnI (Fibronectin) and DLK1-CFR (cysteine-rich FGF receptor) interactions, whereas the proposed DLK1-IGFBP1 interaction was not supported by MTH. Very little has previously been described on the DLK1 self-interaction. Herein, we showed by immunoprecipitation as well as Sulfo-SBED label transfer that the DLK1-DLK1 interaction likely is part of Dlk1's function in preadipocytes. Furthermore our data suggest that DLK1 interacts with itself through EGF domain 4 and 5, which is distinct from the recently described NOTCH1-DLK1 interaction, which occurs between EGF domain 5 and 6. This opens up the possibility that Notch independent mechanisms like the DLK1-DLK1 interaction may modulate the non-canonical NOTCH1-DLK1 interaction further complexing this system.

  1. Zinc-finger protein 91 plays a key role in LIGHT-induced activation of non-canonical NF-{kappa}B pathway

    SciTech Connect

    Jin, Hong Ri; Jin, Xuejun; Lee, Jung Joon

    2010-10-01

    Research highlights: {yields} LIGHT induces ZFP91expression and nuclear translocation of p65, p52, and RelB in LT{beta}R signaling. {yields} ZFP91 knock-down abolishes DNA-binding activity of p52 and RelB but not of p65. {yields} ZFP91 regulates LIGHT-induced stabilization and activation of NIK. {yields} ZFP91 is required for the expression of non-canonical NF-{kappa}B target genes. -- Abstract: LIGHT is a member of tumor necrosis factor (TNF) superfamily, and its function is mediated through lymphotoxin-{beta} receptor (LT{beta}R), which is known to play important roles in inflammatory and immune responses through activation of NF-{kappa}B signaling pathways. However, molecular mechanism of LT{beta}R ligation-induced NF-{kappa}B signaling remains incompletely understood. In this report we demonstrate that a novel zinc-finger protein 91 (ZFP91) is a critical regulator in LIGHT-induced activation of non-canonical NF-{kappa}B pathway. ZFP91 appears to be required for NF-{kappa}B2 (p100) processing to p52, nuclear translocation of p52 and RelB, and DNA-binding activity of NF-{kappa}B in LIGHT-induced activation of non-canonical NF-{kappa}B pathway. Furthermore, ZFP91 knock-down by RNA interference blocks the LIGHT-induced accumulation of NIK and p100 processing, as well as the expression of non-canonical NF-{kappa}B target genes. These data clearly indicate that ZFP91 is a key regulator in LIGHT-induced activation of non-canonical NF-{kappa}B pathway in LT{beta}R signaling.

  2. Lipopolysaccharide-induced activation of NF-{kappa}B non-canonical pathway requires BCL10 serine 138 and NIK phosphorylations

    SciTech Connect

    Bhattacharyya, Sumit; Borthakur, Alip; Dudeja, Pradeep K.; Tobacman, Joanne K.

    2010-11-15

    Background and aims: B-cell lymphoma/leukemia (BCL)-10 and reactive oxygen species mediate two pathways of NF-{kappa}B (RelA) activation by lipopolysaccharide (LPS) in human colonic epithelial cells. The pathway for LPS activation of RelB by the non-canonical pathway (RelB) in non-myeloid cells was not yet reported, but important for understanding the range of potential microbial LPS-induced effects in inflammatory bowel disease. Methods: Experiments were performed in human colonic epithelial cells and in mouse embryonic fibroblasts deficient in components of the IkappaB kinase (IKK) signalosome, in order to detect mediators of the non-canonical pathway of NF-{kappa}B activation, including nuclear RelB and p52 and phospho- and total NF-{kappa}B inducing kinase (NIK). BCL10 was silenced by siRNA and effects of mutations of specific phosphorylation sites of BCL10 (Ser138Gly and Ser218Gly) were determined. Results: By the non-canonical pathway, LPS exposure increased nuclear RelB and p52, and phospho-NIK, with no change in total NIK. Phosphorylation of BCL10 serine 138 was required for NIK phosphorylation, since mutation of this residue eliminated the increases in phospho-NIK and nuclear RelB and p52. Mutations of either serine 138 or serine 218 reduced RelA, p50, and phospho-I{kappa}B{alpha} of the canonical pathway. Effects of LPS stimulation and BCL10 silencing on NIK phosphorylation were demonstrated in confocal images. Conclusions: LPS induces activation of both canonical and non-canonical pathways of NF-{kappa}B in human colonic epithelial cells, and the non-canonical pathway requires phosphorylations of BCL10 (serine 138) and NIK. These findings demonstrate the important role of BCL10 in mediating LPS-induced inflammation in human colonic epithelial cells and may open new avenues for therapeutic interventions.

  3. Molecular cloning and characterization of a novel isoform of the non-canonical poly(A) polymerase PAPD7

    SciTech Connect

    Ogami, Koichi; Cho, Rihe; Hoshino, Shin-ichi

    2013-03-01

    Highlights: ► So far, only an enzymatically inactive isoform of PAPD7 was reported. ► The novel isoform: PAPD7 l shows robust nucleotidyl transferase activity. ► The newly identified amino terminal region is required for the activity. ► PAPD7 l localizes to the nucleoplasm. ► The N terminal region identified is also required for the nuclear localization. - Abstract: Non-canonical poly(A) polymerases (ncPAPs) catalyze the addition of poly(A) tail to the 3′ end of RNA to play pivotal roles in the regulation of gene expression and also in quality control. Here we identified a novel isoform of the 7th member of ncPAPs: PAPD7 (PAPD7 l), which contains 230 extra amino acids at the amino terminus of the previously identified PAPD7 (PAPD7 s). In sharp contrast to the inactive PAPD7 s, PAPD7 l showed robust nucleotidyl transferase activity when tethered to an RNA. A region required for the activity was localized to 187–219 aa, and this region was also required for the nuclear retention of PAPD7 l. Western blot analysis revealed that 94 kDa band (corresponding to PAPD7 l) but not 62 kDa band (corresponding to PAPD7 s) detected by PAPD7 antibody was specifically depleted by treatment with PAPD7 siRNA in both HeLa and U2OS cells. These results suggest that PAPD7 l is the major and active isoform of PAPD7 expressed in cells.

  4. Structure of Human Cytomegalovirus UL141 Binding to TRAIL-R2 Reveals Novel, Non-canonical Death Receptor Interactions

    PubMed Central

    Nemčovičová, Ivana; Benedict, Chris A.; Zajonc, Dirk M.

    2013-01-01

    The TRAIL (TNF-related apoptosis inducing ligand) death receptors (DRs) of the tumor necrosis factor receptor superfamily (TNFRSF) can promote apoptosis and regulate antiviral immunity by maintaining immune homeostasis during infection. In turn, human cytomegalovirus (HCMV) expresses immunomodulatory proteins that down-regulate cell surface expression of TNFRSF members as well as poliovirus receptor-related proteins in an effort to inhibit host immune effector pathways that would lead to viral clearance. The UL141 glycoprotein of human cytomegalovirus inhibits host defenses by blocking cell surface expression of TRAIL DRs (by retention in ER) and poliovirus receptor CD155, a nectin-like Ig-fold molecule. Here we show that the immunomodulatory function of HCMV UL141 is associated with its ability to bind diverse proteins, while utilizing at least two distinct binding sites to selectively engage TRAIL DRs or CD155. Binding studies revealed high affinity interaction of UL141 with both TRAIL-R2 and CD155 and low affinity binding to TRAIL-R1. We determined the crystal structure of UL141 bound to TRAIL-R2 at 2.1 Å resolution, which revealed that UL141 forms a homodimer that engages two TRAIL-R2 monomers 90° apart to form a heterotetrameric complex. Our structural and biochemical data reveal that UL141 utilizes its Ig-domain to facilitate non-canonical death receptor interactions while UL141 partially mimics the binding site of TRAIL on TRAIL-R2, which we found to be distinct from that of CD155. Moreover, UL141 also binds to an additional surface patch on TRAIL-R2 that is distinct from the TRAIL binding site. Therefore, the breadth of UL141-mediated effects indicates that HCMV has evolved sophisticated strategies to evade the immune system by modulating multiple effector pathways. PMID:23555243

  5. Non-canonical Smads phosphorylation induced by the glutamate release inhibitor, riluzole, through GSK3 activation in melanoma.

    PubMed

    Abushahba, Walid; Olabisi, Oyenike O; Jeong, Byeong-Seon; Boregowda, Rajeev K; Wen, Yu; Liu, Fang; Goydos, James S; Lasfar, Ahmed; Cohen-Solal, Karine A

    2012-01-01

    Riluzole, an inhibitor of glutamate release, has shown the ability to inhibit melanoma cell xenograft growth. A phase 0 clinical trial of riluzole as a single agent in patients with melanoma resulted in involution of tumors associated with inhibition of both the mitogen-activated protein kinase (MAPK) and phophoinositide-3-kinase/AKT (PI3K/AKT) pathways in 34% of patients. In the present study, we demonstrate that riluzole inhibits AKT-mediated glycogen synthase kinase 3 (GSK3) phosphorylation in melanoma cell lines. Because we have demonstrated that GSK3 is involved in the phosphorylation of two downstream effectors of transforming growth factor beta (TGFβ), Smad2 and Smad3, at their linker domain, our aim was to determine whether riluzole could induce GSK3β-mediated linker phosphorylation of Smad2 and Smad3. We present evidence that riluzole increases Smad2 and Smad3 linker phosphorylation at the cluster of serines 245/250/255 and serine 204 respectively. Using GSK3 inhibitors and siRNA knock-down, we demonstrate that the mechanism of riluzole-induced Smad phosphorylation involved GSK3β. In addition, GSK3β could phosphorylate the same linker sites in vitro. The riluzole-induced Smad linker phosphorylation is mechanistically different from the Smad linker phosphorylation induced by TGFβ. We also demonstrate that riluzole-induced Smad linker phosphorylation is independent of the expression of the metabotropic glutamate receptor 1 (GRM1), which is one of the glutamate receptors whose involvement in human melanoma has been documented. We further show that riluzole upregulates the expression of INHBB and PLAU, two genes associated with the TGFβ signaling pathway. The non-canonical increase in Smad linker phosphorylation induced by riluzole could contribute to the modulation of the pro-oncogenic functions of Smads in late stage melanomas.

  6. Prospects of In vivo Incorporation of Non-canonical Amino Acids for the Chemical Diversification of Antimicrobial Peptides

    PubMed Central

    Baumann, Tobias; Nickling, Jessica H.; Bartholomae, Maike; Buivydas, Andrius; Kuipers, Oscar P.; Budisa, Nediljko

    2017-01-01

    The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-nature AMPs, and can contribute to tackle the ongoing emergence of antibiotic resistance in pathogens. Especially from a pharmacological point of view, desirable improvements span pH and protease resistance, solubility, oral availability and circulation half-life. Although the primary focus of this report is on ribosomally synthesized and post-translationally modified peptides (RiPPs), we have included selected cases of peptides produced by solid phase peptide synthesis to comparatively show the potential and impact of ncAA introduction. Generally speaking, the introduction of ncAAs in recombinant AMPs delivers novel levels of chemical diversification. Cotranslationally incorporated, they can take part in AMP biogenesis either through direction interaction with elements of the post-translational modification (PTM) machinery or as untargeted sites with unique physicochemical properties and chemical handles for further modification. Together with genetic libraries, genome mining and processing by PTM machineries, ncAAs present not a mere addition to this process, but a highly diverse pool of building blocks to significantly broaden the chemical space of this valuable class of molecules. This perspective summarizes new developments of ncAA containing peptides. Challenges to be resolved in order to reach large-scale pharmaceutical production of these promising compounds and prospects for future developments are discussed. PMID:28210246

  7. CXCL12/CXCR4 Axis Activation Mediates Prostate Myofibroblast Phenoconversion through Non-Canonical EGFR/MEK/ERK Signaling

    PubMed Central

    Rodríguez-Nieves, José A.; Patalano, Susan C.; Almanza, Diego; Gharaee-Kermani, Mehrnaz; Macoska, Jill A.

    2016-01-01

    Benign prostate hyperplasia (BPH), an enlargement of the prostate common in aging in men, is associated with urinary voiding dysfunction manifest as Lower Urinary Tract Symptoms (LUTS). Although inflammation and abnormal smooth muscle contractions are known to play key roles in the development of LUTS, tissue fibrosis may also be an important and previously unrecognized contributing factor. Tissue fibrosis arises from the unregulated differentiation of fibroblasts or other precursor cell types into myofibroblasts, which is usually accomplished by activation of the TGFβ/TGFβR axis. Previously we reported that the CXC-type chemokines, CXCL5, CXCL8 and CXCL12, which are up-regulated in the aging in the prostate, can drive this differentiation process as well in the absence of TGFβ. Based on this data we sought to elucidate the molecular mechanisms employed by CXCL12, and its receptor CXCR4, during prostate myofibroblast phenoconversion. The results of these studies suggest that CXCL12/CXCR4-mediated signaling events in prostate myofibroblast phenoconversion may proceed through non-canonical pathways that do not depend on TGFβ/TGFβR axis activation or Smad signaling. Here we report that CXCL12/CXCR4 axis activation promotes signaling through the EGFR and downstream MEK/ERK and PI3K/Akt pathways during myofibroblast phenoconversion, but not through TGFβ/TGFβR and downstream Smad signaling, in prostate fibroblasts undergoing myofibroblast phenoconversion. We document that EGFR transactivation is required for CXCL12-mediated signaling and expression of genes associate with myofibroblast phenoconversion (α-SMA, COL1a1). Our study successfully identified TGFβ/TGFβR-independent molecular mechanisms that promote CXCL12/CXCR4-induced myofibroblast phenoconversion. This information may be crucial for the development of novel therapies and potential biomarkers for prostatic fibrosis. PMID:27434301

  8. Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions.

    PubMed

    Nemčovičová, Ivana; Benedict, Chris A; Zajonc, Dirk M

    2013-03-01

    The TRAIL (TNF-related apoptosis inducing ligand) death receptors (DRs) of the tumor necrosis factor receptor superfamily (TNFRSF) can promote apoptosis and regulate antiviral immunity by maintaining immune homeostasis during infection. In turn, human cytomegalovirus (HCMV) expresses immunomodulatory proteins that down-regulate cell surface expression of TNFRSF members as well as poliovirus receptor-related proteins in an effort to inhibit host immune effector pathways that would lead to viral clearance. The UL141 glycoprotein of human cytomegalovirus inhibits host defenses by blocking cell surface expression of TRAIL DRs (by retention in ER) and poliovirus receptor CD155, a nectin-like Ig-fold molecule. Here we show that the immunomodulatory function of HCMV UL141 is associated with its ability to bind diverse proteins, while utilizing at least two distinct binding sites to selectively engage TRAIL DRs or CD155. Binding studies revealed high affinity interaction of UL141 with both TRAIL-R2 and CD155 and low affinity binding to TRAIL-R1. We determined the crystal structure of UL141 bound to TRAIL-R2 at 2.1 Å resolution, which revealed that UL141 forms a homodimer that engages two TRAIL-R2 monomers 90° apart to form a heterotetrameric complex. Our structural and biochemical data reveal that UL141 utilizes its Ig-domain to facilitate non-canonical death receptor interactions while UL141 partially mimics the binding site of TRAIL on TRAIL-R2, which we found to be distinct from that of CD155. Moreover, UL141 also binds to an additional surface patch on TRAIL-R2 that is distinct from the TRAIL binding site. Therefore, the breadth of UL141-mediated effects indicates that HCMV has evolved sophisticated strategies to evade the immune system by modulating multiple effector pathways.

  9. Non-Canonical Smads Phosphorylation Induced by the Glutamate Release Inhibitor, Riluzole, through GSK3 Activation in Melanoma

    PubMed Central

    Jeong, Byeong-Seon; Boregowda, Rajeev K.; Wen, Yu; Liu, Fang; Goydos, James S.; Lasfar, Ahmed; Cohen-Solal, Karine A.

    2012-01-01

    Riluzole, an inhibitor of glutamate release, has shown the ability to inhibit melanoma cell xenograft growth. A phase 0 clinical trial of riluzole as a single agent in patients with melanoma resulted in involution of tumors associated with inhibition of both the mitogen-activated protein kinase (MAPK) and phophoinositide-3-kinase/AKT (PI3K/AKT) pathways in 34% of patients. In the present study, we demonstrate that riluzole inhibits AKT-mediated glycogen synthase kinase 3 (GSK3) phosphorylation in melanoma cell lines. Because we have demonstrated that GSK3 is involved in the phosphorylation of two downstream effectors of transforming growth factor beta (TGFβ), Smad2 and Smad3, at their linker domain, our aim was to determine whether riluzole could induce GSK3β-mediated linker phosphorylation of Smad2 and Smad3. We present evidence that riluzole increases Smad2 and Smad3 linker phosphorylation at the cluster of serines 245/250/255 and serine 204 respectively. Using GSK3 inhibitors and siRNA knock-down, we demonstrate that the mechanism of riluzole-induced Smad phosphorylation involved GSK3β. In addition, GSK3β could phosphorylate the same linker sites in vitro. The riluzole-induced Smad linker phosphorylation is mechanistically different from the Smad linker phosphorylation induced by TGFβ. We also demonstrate that riluzole-induced Smad linker phosphorylation is independent of the expression of the metabotropic glutamate receptor 1 (GRM1), which is one of the glutamate receptors whose involvement in human melanoma has been documented. We further show that riluzole upregulates the expression of INHBB and PLAU, two genes associated with the TGFβ signaling pathway. The non-canonical increase in Smad linker phosphorylation induced by riluzole could contribute to the modulation of the pro-oncogenic functions of Smads in late stage melanomas. PMID:23077590

  10. Loss of a membrane trafficking protein αSNAP induces non-canonical autophagy in human epithelia

    PubMed Central

    Naydenov, Nayden G.; Harris, Gianni; Morales, Victor; Ivanov, Andrei I.

    2012-01-01

    Autophagy is a catabolic process that sequesters intracellular proteins and organelles within membrane vesicles called autophagosomes with their subsequent delivery to lyzosomes for degradation. This process involves multiple fusions of autophagosomal membranes with different vesicular compartments; however, the role of vesicle fusion in autophagosomal biogenesis remains poorly understood. This study addresses the role of a key vesicle fusion regulator, soluble N-ethylmaleimide-sensitive factor attachment protein α (αSNAP), in autophagy. Small interfering RNA-mediated downregulation of αSNAP expression in cultured epithelial cells stimulated the autophagic flux, which was manifested by increased conjugation of microtubule-associated protein light chain 3 (LC3-II) and accumulation of LC3-positive autophagosomes. This enhanced autophagy developed via a non-canonical mechanism that did not require beclin1-p150-dependent nucleation, but involved Atg5 and Atg7-mediated elongation of autophagosomal membranes. Induction of autophagy in αSNAP-depleted cells was accompanied by decreased mTOR signaling but appeared to be independent of αSNAP-binding partners, N-ethylmaleimide-sensitive factor and BNIP1. Loss of αSNAP caused fragmentation of the Golgi and downregulation of the Golgi-specific GTP exchange factors, GBF1, BIG1 and BIG2. Pharmacological disruption of the Golgi and genetic inhibition of GBF1 recreated the effects of αSNAP depletion on the autophagic flux. Our study revealed a novel role for αSNAP as a negative regulator of autophagy that acts by enhancing mTOR signaling and regulating the integrity of the Golgi complex. PMID:23187805

  11. CXCL12/CXCR4 Axis Activation Mediates Prostate Myofibroblast Phenoconversion through Non-Canonical EGFR/MEK/ERK Signaling.

    PubMed

    Rodríguez-Nieves, José A; Patalano, Susan C; Almanza, Diego; Gharaee-Kermani, Mehrnaz; Macoska, Jill A

    2016-01-01

    Benign prostate hyperplasia (BPH), an enlargement of the prostate common in aging in men, is associated with urinary voiding dysfunction manifest as Lower Urinary Tract Symptoms (LUTS). Although inflammation and abnormal smooth muscle contractions are known to play key roles in the development of LUTS, tissue fibrosis may also be an important and previously unrecognized contributing factor. Tissue fibrosis arises from the unregulated differentiation of fibroblasts or other precursor cell types into myofibroblasts, which is usually accomplished by activation of the TGFβ/TGFβR axis. Previously we reported that the CXC-type chemokines, CXCL5, CXCL8 and CXCL12, which are up-regulated in the aging in the prostate, can drive this differentiation process as well in the absence of TGFβ. Based on this data we sought to elucidate the molecular mechanisms employed by CXCL12, and its receptor CXCR4, during prostate myofibroblast phenoconversion. The results of these studies suggest that CXCL12/CXCR4-mediated signaling events in prostate myofibroblast phenoconversion may proceed through non-canonical pathways that do not depend on TGFβ/TGFβR axis activation or Smad signaling. Here we report that CXCL12/CXCR4 axis activation promotes signaling through the EGFR and downstream MEK/ERK and PI3K/Akt pathways during myofibroblast phenoconversion, but not through TGFβ/TGFβR and downstream Smad signaling, in prostate fibroblasts undergoing myofibroblast phenoconversion. We document that EGFR transactivation is required for CXCL12-mediated signaling and expression of genes associate with myofibroblast phenoconversion (α-SMA, COL1a1). Our study successfully identified TGFβ/TGFβR-independent molecular mechanisms that promote CXCL12/CXCR4-induced myofibroblast phenoconversion. This information may be crucial for the development of novel therapies and potential biomarkers for prostatic fibrosis.

  12. Gremlin utilizes canonical and non-canonical TGFβ signaling to induce lysyl oxidase (LOX) genes in human trabecular meshwork cells☆

    PubMed Central

    Sethi, Anirudh; Wordinger, Robert J.; Clark, Abbot F.

    2013-01-01

    The TGFβ/BMP signaling pathways are involved in glaucomatous damage to the trabecular meshwork (TM) leading to elevated intraocular pressure (IOP), which is a major risk factor for the development and progression of glaucoma. The BMP antagonist gremlin is elevated in glaucomatous TM cells and tissues and can directly elevate IOP. Gremlin utilizes the TGFβ2/SMAD pathway to induce TM extracellular matrix (ECM) proteins. The purpose of this study is to determine whether expression of the ECM cross-linking lysyl oxidase (LOX) genes is regulated by gremlin in cultured human TM cells. Human TM cells were treated with recombinant gremlin, and expression of the LOX genes was examined by quantitative RT-PCR and western immunoblotting. TM cells were pretreated with TGFBR inhibitors (LY364947 or SB431542), an inhibitor of the SMAD signaling pathway (SIS3), or with JNK (SP600125) and p38 MAPK (SB203580) inhibitors to identify the signaling pathway(s) involved in gremlin induction of LOX protein expression. All five LOX genes (LOX and LOXL1–4) were induced by gremlin. Gremlin induction of LOX genes and protein expression was blocked by TGFBR inhibitors as well as by inhibitors of the SMAD3, JNK and p38 MAPK signaling pathways. We conclude that gremlin employs both canonical TGFβ/SMAD and the non-canonical JNK and p38 MAPK signaling pathways to induce LOX genes and proteins in cultured human TM cells. Increased LOX levels may be at least partially responsible for gremlin-mediated IOP elevation and increased aqueous humor outflow resistance leading to glaucoma. PMID:23748100

  13. Non-canonical Cajal bodies form in the nucleus of late stage avian oocytes lacking functional nucleolus.

    PubMed

    Khodyuchenko, Tatiana; Gaginskaya, Elena; Krasikova, Alla

    2012-07-01

    In the somatic cell nucleus, there are several universal domains such as nucleolus, SC35-domains, Cajal bodies (CBs) and histone locus bodies (HLBs). Among them, CBs were described more than 100 years ago; however, we still do not have a final understanding of their nature and biological significance. The giant nucleus of avian and amphibian growing oocytes represents an advantageous model for analysis of functions and biogenesis of various nuclear domains. Nevertheless, in large-sized avian oocytes that contain transcriptionally active lampbrush chromosomes, CB-like organelles have not been identified yet. Here we demonstrate that in the pigeon (Columba livia) oocyte nucleus, characterized by absence of any functional nucleoli, extrachromosomal spherical bodies contain TMG-capped spliceosomal snRNAs, core proteins of Sm snRNPs and the protein coilin typical for CBs, but not splicing factor SC35 nor the histone pre-mRNA 3'-end processing factor symplekin. The results establish that coilin-rich nuclear organelles in pigeon late-stage oocyte are not the equivalents of HLBs but belong to a group of CBs. At the same time, they do not contain the snoRNP/scaRNP protein fibrillarin involved in 2'-O-methylation of snoRNAs and snRNAs. Thus, the nucleus of late-stage pigeon oocytes houses CB-like organelles that have an unusual molecular composition and are implicated in the snRNP biogenesis pathway. These data demonstrate that snRNP-rich non-canonical CBs can form in the absence of nucleolus. We argue that pigeon oocytes represent a new promising model to investigate CB modular organization, functions and formation mechanism.

  14. Puerarin Attenuates Cardiac Hypertrophy Partly Through Increasing Mir-15b/195 Expression and Suppressing Non-Canonical Transforming Growth Factor Beta (Tgfβ) Signal Pathway

    PubMed Central

    Zhang, Xiuzhou; Liu, Yuxiang; Han, Qingliang

    2016-01-01

    Background Previous studies demonstrated that puerarin has therapeutic effects on cardiac hypertrophy. This study aimed to explore whether the effect of puerarin on attenuating cardiac hypertrophy is related to regulation of microRNAs (miRNAs) and the transforming growth factor beta (TGFβ) signal pathway. Material/Methods The therapeutic effect of puerarin was assessed using an angiotensin (Ang) II-induced heart hypertrophy model in mice. The primary cardiomyocytes were used as an in vitro model. MiR-15 family expression was quantified using qRT-PCR analysis. The expression of the genes involved in canonical and non-canonical TGFβ signal pathways was measured using qRT-PCR and Western blot analysis. In vitro cardiac hypertrophic features were assessed by quantifying cardiac hypertrophic genes and measurement of cell surface, protein synthesis, and total protein content. Results Puerarin attenuated cardiac hypertrophy and increased miR-15b and miR-195 expression in the mouse cardiac hypertrophy model and in primary cardiomyocytes. It suppressed both canonical and non-canonical TGFβ signal pathways, partially through miR-15b and miR-195. Puerarin reduced mRNA expression of cardiac hypertrophic genes, reduced cell surface area, and lowered the rate of protein synthesis and the total protein content induced by Ang II. Knockdown of endogenous miR-15b and miR-195 partly abrogated these effects. Knockdown of endogenous p38, but not Smad2/3/4, presented similar effects as miR-15b. Conclusions Puerarin administration enhances miR-15b and miR-195 expression in an Ang II-induced cardiac hypertrophy model, through which it suppresses both canonical and non-canonical TGFβ signal pathways at the same time. However, the effect of puerarin on attenuating cardiac hypertrophy is mainly through the non-canonical TGFβ pathway. PMID:27145790

  15. Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation

    PubMed Central

    Li, Yinghui; Zhou, Qi-Ling; Sun, Wenjie; Chandrasekharan, Prashant; Cheng, Hui Shan; Ying, Zhe; Lakshmanan, Manikandan; Raju, Anandhkumar; Tenen, Daniel G.; Cheng, Shi-Yuan; Chuang, Kai-Hsiang; Li, Jun; Prabhakar, Shyam; Li, Mengfeng; Tergaonkar, Vinay

    2016-01-01

    Transcriptional reactivation of TERT, the catalytic subunit of telomerase, is necessary for cancer progression in about 90% of human cancers. The recent discovery of two prevalent somatic mutations—C250T and C228T—in the TERT promoter in various cancers has provided insight into a plausible mechanism of TERT reactivation. Although the two hotspot mutations create a similar binding motif for E-twenty-six (ETS) transcription factors, we show that they are functionally distinct, in that the C250T unlike the C228T TERT promoter is driven by non-canonical NF-κB signalling. We demonstrate that binding of ETS to the mutant TERT promoter is insufficient in driving its transcription but this process requires non-canonical NF-κB signalling for stimulus responsiveness, sustained telomerase activity and hence cancer progression. Our findings highlight a previously unrecognized role of non-canonical NF-κB signalling in tumorigenesis and elucidate a fundamental mechanism for TERT reactivation in cancers, which if targeted could have immense therapeutic implications. PMID:26389665

  16. Galectin-1 induces invasion and the epithelial-mesenchymal transition in human gastric cancer cells via non-canonical activation of the hedgehog signaling pathway

    PubMed Central

    Chong, Yang; Tang, Dong; Gao, Jun; Jiang, Xuetong; Xu, Chuanqi; Xiong, Qingquan; Huang, Yuqin; Wang, Jie; Zhou, Huaicheng; Shi, Youquan; Wang, Daorong

    2016-01-01

    Galectin-1 (Gal-1) has been reported to be an independent prognostic indicator of poor survival in gastric cancer and overexpression of Gal-1 enhances the invasiveness of gastric cancer cells. However, the downstream mechanisms by which Gal-1 promotes invasion remains unclear. Moreover, the function of Gal-1 in the epithelial-mesenchymal transition (EMT) in gastric cancer has not yet been elucidated. In this study, we observed Gal-1 expression was upregulated and positively associated with metastasis and EMT markers in 162 human gastric cancer tissue specimens. In vitro studies showed Gal-1 induced invasion, the EMT phenotype and activated the non-canonical hedgehog (Hh) pathway in gastric cancer cell lines. Furthermore, our data revealed that Gal-1 modulated the non-canonical Hh pathway by increasing the transcription of glioma-associated oncogene-1 (Gli-1) via a Smoothened (SMO)-independent manner, and that upregulation of Gal-1 was strongly associated with gastric cancer metastasis. We conclude that Gal-1 promotes invasion and the EMT in gastric cancer cells via activation of the non-canonical Hh pathway, suggesting Gal-1 could represent a promising therapeutic target for the prevention and treatment of gastric cancer metastasis. PMID:27835885

  17. A novel non-canonical forkhead-associated (FHA) domain-binding interface mediates the interaction between Rad53 and Dbf4 proteins.

    PubMed

    Matthews, Lindsay A; Selvaratnam, Rajeevan; Jones, Darryl R; Akimoto, Madoka; McConkey, Brendan J; Melacini, Giuseppe; Duncker, Bernard P; Guarné, Alba

    2014-01-31

    Forkhead-associated (FHA) and BRCA1 C-terminal (BRCT) domains are overrepresented in DNA damage and replication stress response proteins. They function primarily as phosphoepitope recognition modules but can also mediate non-canonical interactions. The latter are rare, and only a few have been studied at a molecular level. We have identified a crucial non-canonical interaction between the N-terminal FHA1 domain of the checkpoint effector kinase Rad53 and the BRCT domain of the regulatory subunit of the Dbf4-dependent kinase that is critical to suppress late origin firing and to stabilize stalled forks during replication stress. The Rad53-Dbf4 interaction is phosphorylation-independent and involves a novel non-canonical interface on the FHA1 domain. Mutations within this surface result in hypersensitivity to genotoxic stress. Importantly, this surface is not conserved in the FHA2 domain of Rad53, suggesting that the FHA domains of Rad53 gain specificity by engaging additional interaction interfaces beyond their phosphoepitope-binding site. In general, our results point to FHA domains functioning as complex logic gates rather than mere phosphoepitope-targeting modules.

  18. Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation.

    PubMed

    Li, Yinghui; Zhou, Qi-Ling; Sun, Wenjie; Chandrasekharan, Prashant; Cheng, Hui Shan; Ying, Zhe; Lakshmanan, Manikandan; Raju, Anandhkumar; Tenen, Daniel G; Cheng, Shi-Yuan; Chuang, Kai-Hsiang; Li, Jun; Prabhakar, Shyam; Li, Mengfeng; Tergaonkar, Vinay

    2015-10-01

    Transcriptional reactivation of TERT, the catalytic subunit of telomerase, is necessary for cancer progression in about 90% of human cancers. The recent discovery of two prevalent somatic mutations-C250T and C228T-in the TERT promoter in various cancers has provided insight into a plausible mechanism of TERT reactivation. Although the two hotspot mutations create a similar binding motif for E-twenty-six (ETS) transcription factors, we show that they are functionally distinct, in that the C250T unlike the C228T TERT promoter is driven by non-canonical NF-κB signalling. We demonstrate that binding of ETS to the mutant TERT promoter is insufficient in driving its transcription but this process requires non-canonical NF-κB signalling for stimulus responsiveness, sustained telomerase activity and hence cancer progression. Our findings highlight a previously unrecognized role of non-canonical NF-κB signalling in tumorigenesis and elucidate a fundamental mechanism for TERT reactivation in cancers, which if targeted could have immense therapeutic implications.

  19. Prediction of two-photon absorption enhancement in red fluorescent protein chromophores made from non-canonical amino acids.

    PubMed

    Salem, M Alaraby; Twelves, Isaac; Brown, Alex

    2016-09-21

    Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool known for deep tissue penetration and little cellular damage. Being less sensitive than the one-photon microscopy alternatives, a protein with a large two-photon absorption (TPA) cross-section is needed. Here, we use time-dependent density functional theory (TD-DFT) at the B3LYP and CAM-B3LYP/6-31+G(d,p) levels of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the red fluorescent protein (RFP) chromophore with a non-canonical amino acid. The two-level model for TPA was used to assess the properties (i.e., transition dipole moment, permanent dipole moment difference, and the angle between them) leading to the TPA cross-sections determined via response theory. Computing TPA cross-sections with B3LYP and CAM-B3LYP yields similar overall trends. Results using both functionals agree that the RFP-derived model of the Gold Fluorescent Protein chromophore (Model 20) has the largest intrinsic TPA cross-section at the optimized geometry. TPA was further computed for selected chromophores following conformational changes: variation of both the dihedral angle of the acylimine moiety and the tilt and twist angles between the rings of the chromophore. The TPA cross-section assumed an oscillatory trend with the rotation of the acylimine dihedral, and the TPA is maximized in the planar conformation for almost all models. Model 21 (a hydroxyquinoline derivative) is shown to be comparable to Model 20 in terms of TPA cross-section. The conformational study on Model 21 shows that the acylimine angle has a much stronger effect on the TPA than its tilt and twist angles. Having an intrinsic TPA ability that is more than 7 times that of the native RFP chromophore, Models 20 and 21 appear to be very promising for future experimental investigation.

  20. Non-canonical mass laws in equilibrium isotopic fractionations: Evidence from the vapor pressure isotope effect of SF6

    NASA Astrophysics Data System (ADS)

    Eiler, John; Cartigny, Pierre; Hofmann, Amy E.; Piasecki, Alison

    2013-04-01

    We report experimental observations of the vapor pressure isotope effect, including 33S/32S and 34S/32S ratios, for SF6 ice between 137 and 173 K. The temporal evolution of observed fractionations, mass-balance of reactants and products, and reversal of the fractionation at one temperature (155 K) are consistent with a subset of our experiments having reached or closely approached thermodynamic equilibrium. That equilibrium involves a reversed vapor pressure isotope effect; i.e., vapor is between 2‰ and 3‰ higher in 34S/32S than co-existing ice, with the difference increasing with decreasing temperature. At the explored temperatures, the apparent equilibrium fractionation of 33S/32S ratios is 0.551 ± 0.010 times that for 34S/32S ratios—higher than the canonical ratio expected for mass dependent thermodynamic fractionations (˜0.515). Two experiments examining exchange between adsorbed and vapor SF6 suggest the sorbate-vapor fractionation at 180-188 K is similar to that for ice-vapor at ˜150 K. In contrast, the liquid-vapor fractionation at 228-300 K is negligibly small (˜0.1‰ for 34S/32S; the mass law is ill defined due to the low amplitude of fractionation). We hypothesize that the observed vapor pressure isotope for SF6 ice and sorbate is controlled by commonly understood effects of isotopic substitution on vibrational energies of molecules, but leads to both an exotic mass law and reversed fractionation due to the competition between isotope effects on intramolecular vibrations, which promote heavy isotope enrichment in vapor, and isotope effects on intermolecular (lattice) vibrations, which promote heavy isotope enrichment in ice. This explanation implies that a variety of naturally important compounds having diverse modes of vibration (i.e., varying greatly in frequency and particularly, reduced mass) could potentially exhibit similarly non-canonical mass laws for S and O isotope fractionations. We examined this hypothesis using a density function

  1. Disruption of the non-canonical Wnt gene PRICKLE2 leads to autism-like behaviors with evidence for hippocampal synaptic dysfunction

    PubMed Central

    Sowers, L. P.; Loo, L.; Wu, Y.; Campbell, E.; Ulrich, J. D.; Wu, S.; Paemka, L.; Wassink, T.; Meyer, K.; Bing, X.; El-Shanti, H.; Usachev, Y. M.; Ueno, N.; Manak, R. J.; Shepherd, A. J.; Ferguson, P. J.; Darbro, B. W.; Richerson, G. B.; Mohapatra, D. P.; Wemmie, J. A.; Bassuk, A. G.

    2014-01-01

    Autism spectrum disorders (ASDs) have been suggested to arise from abnormalities in the canonical and non-canonical Wnt signaling pathways. However, a direct connection between a human variant in a Wnt pathway gene and ASD-relevant brain pathology has not been established. Prickle2 (Pk2) is a post-synaptic non-canonical Wnt signaling protein shown to interact with post synaptic density 95 (PSD-95). Here we show that mice with disruption in Prickle2 display behavioral abnormalities including altered social interaction, learning abnormalities, and behavioral inflexibility. Prickle2 disruption in mouse hippocampal neurons led to reductions in dendrite branching, synapse number, and post-synaptic density size. Consistent with these findings, Prickle2 null neurons show decreased frequency and size of spontaneous miniature synaptic currents. These behavioral and physiological abnormalities in Prickle2 disrupted mice are consistent with ASD-like phenotypes present in other mouse models of ASDs. In 384 individuals with autism, we identified two with distinct, heterozygous, rare, non-synonymous PRICKLE2 variants (p.E8Q and p.V153I) that were shared by their affected siblings and inherited paternally. Unlike wild-type PRICKLE2, the PRICKLE2 variants found in ASD patients exhibit deficits in morphological and electrophysiological assays. These data suggest that these PRICKLE2 variants cause a critical loss of PRICKLE2 function. The data presented here provide new insight into the biological roles of Prickle2, its behavioral importance, and suggest disruptions in non-canonical Wnt genes such as PRICKLE2 may contribute to synaptic abnormalities underlying ASDs. PMID:23711981

  2. Disruption of the non-canonical Wnt gene PRICKLE2 leads to autism-like behaviors with evidence for hippocampal synaptic dysfunction.

    PubMed

    Sowers, L P; Loo, L; Wu, Y; Campbell, E; Ulrich, J D; Wu, S; Paemka, L; Wassink, T; Meyer, K; Bing, X; El-Shanti, H; Usachev, Y M; Ueno, N; Manak, J R; Manak, R J; Shepherd, A J; Ferguson, P J; Darbro, B W; Richerson, G B; Mohapatra, D P; Wemmie, J A; Bassuk, A G

    2013-10-01

    Autism spectrum disorders (ASDs) have been suggested to arise from abnormalities in the canonical and non-canonical Wnt signaling pathways. However, a direct connection between a human variant in a Wnt pathway gene and ASD-relevant brain pathology has not been established. Prickle2 (Pk2) is a post-synaptic non-canonical Wnt signaling protein shown to interact with post-synaptic density 95 (PSD-95). Here, we show that mice with disruption in Prickle2 display behavioral abnormalities including altered social interaction, learning abnormalities and behavioral inflexibility. Prickle2 disruption in mouse hippocampal neurons led to reductions in dendrite branching, synapse number and PSD size. Consistent with these findings, Prickle2 null neurons show decreased frequency and size of spontaneous miniature synaptic currents. These behavioral and physiological abnormalities in Prickle2 disrupted mice are consistent with ASD-like phenotypes present in other mouse models of ASDs. In 384 individuals with autism, we identified two with distinct, heterozygous, rare, non-synonymous PRICKLE2 variants (p.E8Q and p.V153I) that were shared by their affected siblings and inherited paternally. Unlike wild-type PRICKLE2, the PRICKLE2 variants found in ASD patients exhibit deficits in morphological and electrophysiological assays. These data suggest that these PRICKLE2 variants cause a critical loss of PRICKLE2 function. The data presented here provide new insight into the biological roles of Prickle2, its behavioral importance, and suggest disruptions in non-canonical Wnt genes such as PRICKLE2 may contribute to synaptic abnormalities underlying ASDs.

  3. Non-canonical NFκB mutations reinforce pro-survival TNF response in multiple myeloma through an autoregulatory RelB:p50 NFκB pathway

    PubMed Central

    Roy, P; Mukherjee, T; Chatterjee, B; Vijayaragavan, B; Banoth, B; Basak, S

    2017-01-01

    Environmental drug resistance constitutes a serious impediment for therapeutic intervention in multiple myeloma. Tumor-promoting cytokines, such as tumor necrosis factor (TNF), induce nuclear factor-κB (NFκB)- driven expression of pro-survival factors, which confer resistance in myeloma cells to apoptotic insults from TNF-related apoptosis-inducing ligand (TRAIL) and other chemotherapeutic drugs. It is thought that RelA:p50 dimer, activated from IκBα-inhibited complex in response to TNF-induced canonical NFκB signal, mediates the pro-survival NFκB function in cancerous cells. Myeloma cells additionally acquire gain-of-function mutations in the non-canonical NFκB module, which induces partial proteolysis of p100 into p52 to promote RelB:p52/NFκB activation from p100-inhibited complex during immune cell differentiation. However, role of non-canonical NFκB signaling in the drug resistance in multiple myeloma remains unclear. Here we report that myeloma-associated non-canonical aberrations reinforce pro-survival TNF signaling in producing a protracted TRAIL-refractory state. These mutations did not act through a typical p52 NFκB complex, but completely degraded p100 to reposition RelB under IκBα control, whose degradation during TNF signaling induced an early RelB:p50 containing NFκB activity. More so, autoregulatory RelB synthesis prolonged this TNF-induced RelB:p50 activity in myeloma cells harboring non-canonical mutations. Intriguingly, TNF-activated RelB:p50 dimer was both necessary and sufficient, and RelA was not required, for NFκB-dependent pro-survival gene expressions and suppression of apoptosis. Indeed, high RelB mRNA expressions in myeloma patients correlated with the augmented level of pro-survival factors and resistance to therapeutic intervention. In sum, we provide evidence that cancer-associated mutations perpetuate TNF-induced pro-survival NFκB activity through autoregulatory RelB control and thereby exacerbate environmental drug

  4. p53 in the mitochondria, as a trans-acting protein, provides error-correction activities during the incorporation of non-canonical dUTP into DNA.

    PubMed

    Bonda, Elad; Rahav, Galia; Kaya, Angelina; Bakhanashvili, Mary

    2016-11-08

    Mutations in mitochondrial DNA is an outcome of errors produced by DNA polymerase γ during replication and failure of the repair mechanism. Misincorporation of non-canonical dUTP leads to mutagenesis or apoptosis, and may contribute to the cytotoxic effects of 5'-fluorouracil chemotherapy. Tumor suppressor p53 protein in the mitochondria displays physical and functional interactions with mitochondrial DNA and polymerase γ, and by its intrinsic 3'→5' exonuclease activity can diminish the polymerization errors. Here we demonstrate the impact of p53 on incorporation of uracil into DNA examined with mitochondrial fractions, as the source of polymerase γ. p53 in mitochondria facilitates DNA damage repair functions resulting from uracil-DNA misincorporation. Our biochemical studies revealed that the procession of U:A and mismatched U:G lesions enhances in the presence of recombinant or endogenous cytoplasmic p53. p53 in mitochondria can function as an exonuclease/proofreader for polymerase γ by either decreasing the incorporation of non-canonical dUTP into DNA or by promoting the excision of incorporated nucleotide from nascent DNA, thus expanding the spectrum of DNA damage sites exploited for proofreading as a trans-acting protein. The data suggest that p53 may contribute to defense of the cells from consequences of dUTP misincorporation in both normal and tumor cells.

  5. Mono and trimethine cyanines Cyan 40 and Cyan 2 as probes for highly selective fluorescent detection of non-canonical DNA structures.

    PubMed

    Kovalska, Vladyslava B; Losytskyy, Mykhaylo Yu; Yarmoluk, Sergiy M; Lubitz, Irit; Kotlyar, Alexander B

    2011-01-01

    Two of earlier reported dsDNA sensitive cyanine dyes-monomethine Cyan 40 and meso-substituted trimethine Cyan 2 were studied for their ability to interact with non-canonical DNA conformations. These dyes were characterized by spectral-luminescent methods in the presence of G-quadruplex, triplex and dsDNA motifs. We have demonstrated that Cyan 2 binds strongly and preferentially to triple- and quadruple-stranded DNA forms that results in a strong enhancement of the dye fluorescence, as compared to dsDNA, while Cyan 40 form fluorescent complexes preferentially only with the triplex form. Highly fluorescent complexes of Cyan 2 with DNA triplexes and G-quadruplexes and Cyan 40 with DNA triplexes are very stable and do not dissociate during gel electrophoresis, leading to preferential staining of the above DNA forms in gels. The data presented point to the intercalation mechanism of the Cyan 2 binding to G4-DNA, while the complexes of Cyan 40 and Cyan 2 with triplex DNA are believed to be formed via groove binding mode. The Cyan dyes can provide a highly sensitive method for detection and quantification of non-canonical structures in genome.

  6. Canonical Wnt signaling protects hippocampal neurons from Aβ oligomers: role of non-canonical Wnt-5a/Ca2+ in mitochondrial dynamics

    PubMed Central

    Silva-Alvarez, Carmen; Arrázola, Macarena S.; Godoy, Juan A.; Ordenes, Daniela; Inestrosa, Nibaldo C.

    2013-01-01

    Alzheimer's disease (AD) is the most common type of age-related dementia. The disease is characterized by a progressive loss of cognitive abilities, severe neurodegeneration, synaptic loss and mitochondrial dysfunction. The Wnt signaling pathway participates in the development of the central nervous system and growing evidence indicates that Wnts also regulate the function of the adult nervous system. We report here, that indirect activation of canonical Wnt/β-catenin signaling using Bromoindirubin-30-Oxime (6-BIO), an inhibitor of glycogen synthase kinase-3β, protects hippocampal neurons from amyloid-β (Aβ) oligomers with the concomitant blockade of neuronal apoptosis. More importantly, activation with Wnt-5a, a non-canonical Wnt ligand, results in the modulation of mitochondrial dynamics, preventing the changes induced by Aβ oligomers (Aβo) in mitochondrial fission-fusion dynamics and modulates Bcl-2 increases induced by oligomers. The canonical Wnt-3a ligand neither the secreted Frizzled-Related Protein (sFRP), a Wnt scavenger, did not prevent these effects. In contrast, some of the Aβ oligomer effects were blocked by Ryanodine. We conclude that canonical Wnt/β-catenin signaling controls neuronal survival, and that non-canonical Wnt/Ca2+signaling modulates mitochondrial dysfunction. Since mitochondrial dysfunction is present in neurodegenerative diseases, the therapeutic possibilities of the activation of Wnt signaling are evident. PMID:23805073

  7. Canonical Wnt signaling protects hippocampal neurons from Aβ oligomers: role of non-canonical Wnt-5a/Ca(2+) in mitochondrial dynamics.

    PubMed

    Silva-Alvarez, Carmen; Arrázola, Macarena S; Godoy, Juan A; Ordenes, Daniela; Inestrosa, Nibaldo C

    2013-01-01

    Alzheimer's disease (AD) is the most common type of age-related dementia. The disease is characterized by a progressive loss of cognitive abilities, severe neurodegeneration, synaptic loss and mitochondrial dysfunction. The Wnt signaling pathway participates in the development of the central nervous system and growing evidence indicates that Wnts also regulate the function of the adult nervous system. We report here, that indirect activation of canonical Wnt/β-catenin signaling using Bromoindirubin-30-Oxime (6-BIO), an inhibitor of glycogen synthase kinase-3β, protects hippocampal neurons from amyloid-β (Aβ) oligomers with the concomitant blockade of neuronal apoptosis. More importantly, activation with Wnt-5a, a non-canonical Wnt ligand, results in the modulation of mitochondrial dynamics, preventing the changes induced by Aβ oligomers (Aβo) in mitochondrial fission-fusion dynamics and modulates Bcl-2 increases induced by oligomers. The canonical Wnt-3a ligand neither the secreted Frizzled-Related Protein (sFRP), a Wnt scavenger, did not prevent these effects. In contrast, some of the Aβ oligomer effects were blocked by Ryanodine. We conclude that canonical Wnt/β-catenin signaling controls neuronal survival, and that non-canonical Wnt/Ca(2+)signaling modulates mitochondrial dysfunction. Since mitochondrial dysfunction is present in neurodegenerative diseases, the therapeutic possibilities of the activation of Wnt signaling are evident.

  8. Interaction between the N-terminal SH3 domain of Nck-alpha and CD3-epsilon-derived peptides: non-canonical and canonical recognition motifs.

    PubMed

    Santiveri, Clara M; Borroto, Aldo; Simón, Luis; Rico, Manuel; Alarcón, Balbino; Jiménez, M Angeles

    2009-01-01

    The first SH3 domain (SH3.1) of Nckalpha specifically recognizes the proline-rich region of CD3varepsilon, a subunit of the T cell receptor complex. We have solved the NMR structure of Nckalpha SH3.1 that shows the characteristic SH3 fold consisting of two antiparallel beta-sheets tightly packed against each other. According to chemical shift mapping analysis, a peptide encompassing residues 150-166 of CD3varepsilon binds at the canonical SH3 binding site. An exhaustive comparison with the structures of other SH3 domains able and unable to bind CD3varepsilon reveals that Nckalpha SH3.1 recognises a non-canonical PxxPxxDY motif that orientates at the binding site as a class II ligand. A positively charged residue (K/R) at position -2 relative to the WW sequence at the beginning of strand beta3 is crucial for PxxDY recognition. A 14-mer optimised Nckalpha SH3.1 ligand was found using a multi-substitution approach. Based on NMR data, this improved ligand binds Nckalpha SH3.1 through a PxxPxRDY motif that combines specific stabilising interactions corresponding to both canonical class II, PxxPx(K/R), and non-canonical PxxPxxDY motifs. This explains its higher capacity for Nckalpha SH3.1 binding relative to the wild type sequence.

  9. p53 in the mitochondria, as a trans-acting protein, provides error-correction activities during the incorporation of non-canonical dUTP into DNA

    PubMed Central

    Bonda, Elad; Rahav, Galia; Kaya, Angelina; Bakhanashvili, Mary

    2016-01-01

    Mutations in mitochondrial DNA is an outcome of errors produced by DNA polymerase γ during replication and failure of the repair mechanism. Misincorporation of non-canonical dUTP leads to mutagenesis or apoptosis, and may contribute to the cytotoxic effects of 5′-fluorouracil chemotherapy. Tumor suppressor p53 protein in the mitochondria displays physical and functional interactions with mitochondrial DNA and polymerase γ, and by its intrinsic 3′→5′ exonuclease activity can diminish the polymerization errors. Here we demonstrate the impact of p53 on incorporation of uracil into DNA examined with mitochondrial fractions, as the source of polymerase γ. p53 in mitochondria facilitates DNA damage repair functions resulting from uracil–DNA misincorporation. Our biochemical studies revealed that the procession of U:A and mismatched U:G lesions enhances in the presence of recombinant or endogenous cytoplasmic p53. p53 in mitochondria can function as an exonuclease/proofreader for polymerase γ by either decreasing the incorporation of non-canonical dUTP into DNA or by promoting the excision of incorporated nucleotide from nascent DNA, thus expanding the spectrum of DNA damage sites exploited for proofreading as a trans-acting protein. The data suggest that p53 may contribute to defense of the cells from consequences of dUTP misincorporation in both normal and tumor cells. PMID:27689337

  10. Chimeric Vaccine Stimulation of Human Dendritic Cell Indoleamine 2, 3-Dioxygenase Occurs via the Non-Canonical NF-κB Pathway.

    PubMed

    Kim, Nan-Sun; Mbongue, Jacques C; Nicholas, Dequina A; Esebanmen, Grace E; Unternaehrer, Juli J; Firek, Anthony F; Langridge, William H R

    2016-01-01

    A chimeric protein vaccine composed of the cholera toxin B subunit fused to proinsulin (CTB-INS) was shown to suppress type 1 diabetes onset in NOD mice and upregulate biosynthesis of the tryptophan catabolic enzyme indoleamine 2, 3-dioxygenase (IDO1) in human dendritic cells (DCs). Here we demonstrate siRNA inhibition of the NF-κB-inducing kinase (NIK) suppresses vaccine-induced IDO1 biosynthesis as well as IKKα phosphorylation. Chromatin immunoprecipitation (ChIP) analysis of CTB-INS inoculated DCs showed that RelB bound to NF-κB consensus sequences in the IDO1 promoter, suggesting vaccine stimulation of the non-canonical NF-κB pathway activates IDO1 expression in vivo. The addition of Tumor Necrosis Factor Associated Factors (TRAF) TRAF 2, 3 and TRAF6 blocking peptides to vaccine inoculated DCs was shown to inhibit IDO1 biosynthesis. This experimental outcome suggests vaccine activation of the TNFR super-family receptor pathway leads to upregulation of IDO1 biosynthesis in CTB-INS inoculated dendritic cells. Together, our experimental data suggest the CTB-INS vaccine uses a TNFR-dependent signaling pathway of the non-canonical NF-κB signaling pathway resulting in suppression of dendritic cell mediated type 1 diabetes autoimmunity.

  11. The impairment of HCCS leads to MLS syndrome by activating a non-canonical cell death pathway in the brain and eyes

    PubMed Central

    Indrieri, Alessia; Conte, Ivan; Chesi, Giancarlo; Romano, Alessia; Quartararo, Jade; Tatè, Rosarita; Ghezzi, Daniele; Zeviani, Massimo; Goffrini, Paola; Ferrero, Ileana; Bovolenta, Paola; Franco, Brunella

    2013-01-01

    Mitochondrial-dependent (intrinsic) programmed cell death (PCD) is an essential homoeostatic mechanism that selects bioenergetically proficient cells suitable for tissue/organ development. However, the link between mitochondrial dysfunction, intrinsic apoptosis and developmental anomalies has not been demonstrated to date. Now we provide the evidence that non-canonical mitochondrial-dependent apoptosis explains the phenotype of microphthalmia with linear skin lesions (MLS), an X-linked developmental disorder caused by mutations in the holo-cytochrome c-type synthase (HCCS) gene. By taking advantage of a medaka model that recapitulates the MLS phenotype we demonstrate that downregulation of hccs, an essential player of the mitochondrial respiratory chain (MRC), causes increased cell death via an apoptosome-independent caspase-9 activation in brain and eyes. We also show that the unconventional activation of caspase-9 occurs in the mitochondria and is triggered by MRC impairment and overproduction of reactive oxygen species (ROS). We thus propose that HCCS plays a key role in central nervous system (CNS) development by modulating a novel non-canonical start-up of cell death and provide the first experimental evidence for a mechanistic link between mitochondrial dysfunction, intrinsic apoptosis and developmental disorders. PMID:23239471

  12. The impairment of HCCS leads to MLS syndrome by activating a non-canonical cell death pathway in the brain and eyes.

    PubMed

    Indrieri, Alessia; Conte, Ivan; Chesi, Giancarlo; Romano, Alessia; Quartararo, Jade; Tatè, Rosarita; Ghezzi, Daniele; Zeviani, Massimo; Goffrini, Paola; Ferrero, Ileana; Bovolenta, Paola; Franco, Brunella

    2013-02-01

    Mitochondrial-dependent (intrinsic) programmed cell death (PCD) is an essential homoeostatic mechanism that selects bioenergetically proficient cells suitable for tissue/organ development. However, the link between mitochondrial dysfunction, intrinsic apoptosis and developmental anomalies has not been demonstrated to date. Now we provide the evidence that non-canonical mitochondrial dependent apoptosis explains the phenotype of microphthalmia with linear skin lesions (MLS), an X-linked developmental disorder caused by mutations in the holocytochrome c-type synthase (HCCS)gene [corrected]. By taking advantage of a medaka model that recapitulates the MLS phenotype we demonstrate that downregulation of hccs, an essential player of the mitochondrial respiratory chain (MRC), causes increased cell death via an apoptosome-independent caspase-9 activation in brain and eyes. We also show that the unconventional activation of caspase-9 occurs in the mitochondria and is triggered by MRC impairment and overproduction of reactive oxygen species (ROS). We thus propose that HCCS plays a key role in central nervous system (CNS) development by modulating a novel non-canonical start-up of cell death and provide the first experimental evidence for a mechanistic link between mitochondrial dysfunction, intrinsic apoptosis and developmental disorders. Copyright © 2013 The Authors. Published by John Wiley and Sons, Ltd on behalf of EMBO.

  13. Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes.

    PubMed

    Hall, Amanda C; Ostrowski, Lauren A; Pietrobon, Violena; Mekhail, Karim

    2017-03-04

    Cells have evolved intricate mechanisms to maintain genome stability despite allowing mutational changes to drive evolutionary adaptation. Repetitive DNA sequences, which represent the bulk of most genomes, are a major threat to genome stability often driving chromosome rearrangements and disease. The major source of repetitive DNA sequences and thus the most vulnerable constituents of the genome are the rDNA (rDNA) repeats, telomeres, and transposable elements. Maintaining the stability of these loci is critical to overall cellular fitness and lifespan. Therefore, cells have evolved mechanisms to regulate rDNA copy number, telomere length and transposon activity, as well as DNA repair at these loci. In addition, non-canonical structure-forming DNA motifs can also modulate the function of these repetitive DNA loci by impacting their transcription, replication, and stability. Here, we discuss key mechanisms that maintain rDNA repeats, telomeres, and transposons in yeast and human before highlighting emerging roles for non-canonical DNA structures at these repetitive loci.

  14. Genome-wide mapping of embedded ribonucleotides and other non-canonical nucleotides using emRiboSeq and EndoSeq

    PubMed Central

    Ding, James; Taylor, Martin S.; Jackson, Andrew P.; Reijns, Martin A. M.

    2016-01-01

    Ribonucleotides are the most common non-canonical nucleotides incorporated into the genome of replicating cells. They are efficiently removed by ribonucleotide excision repair initiated by Ribonuclease (RNase) H2 cleavage. In the absence of RNase H2, such embedded ribonucleotides can be used to track DNA polymerase activity in vivo. To determine their precise location in Saccharomyces cerevisiae we developed embedded Ribonucleotide Sequencing (emRiboSeq), which uses recombinant RNase H2 to selectively create ligatable 3’-hydroxyl groups, in contrast to alternative methods that utilize alkaline hydrolysis. EmRiboSeq allows reproducible, strand-specific and potentially quantitative detection of embedded ribonucleotides at single-nucleotide resolution. This protocol can be adapted for the genome-wide mapping of other non-canonical bases by replacing RNase H2 with specific nicking endonucleases, a method we term Endonuclease Sequencing (EndoSeq). With the protocol taking <5 days to complete, these methods allow the in vivo study of DNA replication and repair, including the identification of replication origins and termination regions. PMID:26313479

  15. Induction of CXC chemokines in human mesenchymal stem cells by stimulation with secreted frizzled-related proteins through non-canonical Wnt signaling

    PubMed Central

    Bischoff, David S; Zhu, Jian-Hua; Makhijani, Nalini S; Yamaguchi, Dean T

    2015-01-01

    AIM: To investigate the effect of secreted frizzled-related proteins (sFRPs) on CXC chemokine expression in human mesenchymal stem cells (hMSCs). METHODS: CXC chemokines such as CXCL5 and CXCL8 are induced in hMSCs during differentiation with osteogenic differentiation medium (OGM) and may be involved in angiogenic stimulation during bone repair. hMSCs were treated with conditioned medium (CM) from L-cells expressing non-canonical Wnt5a protein, or with control CM from wild type L-cells, or directly with sFRPs for up to 10 d in culture. mRNA expression levels of both CXCL5 and CXCL8 were quantitated by real-time reverse transcriptase-polymerase chain reaction and secreted protein levels of these proteins determined by ELISA. Dose- (0-500 ng/mL) and time-response curves were generated for treatment with sFRP1. Signal transduction pathways were explored by western blot analysis with pan- or phosphorylation-specific antibodies, through use of specific pathway inhibitors, and through use of siRNAs targeting specific frizzled receptors (Fzd)-2 and 5 or the receptor tyrosine kinase-like orphan receptor-2 (RoR2) prior to treatment with sFRPs. RESULTS: CM from L-cells expressing Wnt5a, a non-canonical Wnt, stimulated an increase in CXCL5 mRNA expression and protein secretion in comparison to control L-cell CM. sFRP1, which should inhibit both canonical and non-canonical Wnt signaling, surprisingly enhanced the expression of CXCL5 at 7 and 10 d. Dickkopf1, an inhibitor of canonical Wnt signaling prevented the sFRP-stimulated induction of CXCL5 and actually inhibited basal levels of CXCL5 expression at 7 but not at 10 d post treatment. In addition, all four sFRPs isoforms induced CXCL8 expression in a dose- and time-dependent manner with maximum expression at 7 d with treatment at 150 ng/mL. The largest increases in CXCL5 expression were seen from stimulation with sFRP1 or sFRP2. Analysis of mitogen-activated protein kinase signaling pathways in the presence of OGM showed s

  16. The Meckel-Gruber syndrome protein TMEM67 controls basal body positioning and epithelial branching morphogenesis in mice via the non-canonical Wnt pathway.

    PubMed

    Abdelhamed, Zakia A; Natarajan, Subaashini; Wheway, Gabrielle; Inglehearn, Christopher F; Toomes, Carmel; Johnson, Colin A; Jagger, Daniel J

    2015-06-01

    Ciliopathies are a group of developmental disorders that manifest with multi-organ anomalies. Mutations in TMEM67 (MKS3) cause a range of human ciliopathies, including Meckel-Gruber and Joubert syndromes. In this study we describe multi-organ developmental abnormalities in the Tmem67(tm1Dgen/H1) knockout mouse that closely resemble those seen in Wnt5a and Ror2 knockout mice. These include pulmonary hypoplasia, ventricular septal defects, shortening of the body longitudinal axis, limb abnormalities, and cochlear hair cell stereociliary bundle orientation and basal body/kinocilium positioning defects. The basal body/kinocilium complex was often uncoupled from the hair bundle, suggesting aberrant basal body migration, although planar cell polarity and apical planar asymmetry in the organ of Corti were normal. TMEM67 (meckelin) is essential for phosphorylation of the non-canonical Wnt receptor ROR2 (receptor-tyrosine-kinase-like orphan receptor 2) upon stimulation with Wnt5a-conditioned medium. ROR2 also colocalises and interacts with TMEM67 at the ciliary transition zone. Additionally, the extracellular N-terminal domain of TMEM67 preferentially binds to Wnt5a in an in vitro binding assay. Cultured lungs of Tmem67 mutant mice failed to respond to stimulation of epithelial branching morphogenesis by Wnt5a. Wnt5a also inhibited both the Shh and canonical Wnt/β-catenin signalling pathways in wild-type embryonic lung. Pulmonary hypoplasia phenotypes, including loss of correct epithelial branching morphogenesis and cell polarity, were rescued by stimulating the non-canonical Wnt pathway downstream of the Wnt5a-TMEM67-ROR2 axis by activating RhoA. We propose that TMEM67 is a receptor that has a main role in non-canonical Wnt signalling, mediated by Wnt5a and ROR2, and normally represses Shh signalling. Downstream therapeutic targeting of the Wnt5a-TMEM67-ROR2 axis might, therefore, reduce or prevent pulmonary hypoplasia in ciliopathies and other congenital conditions.

  17. The Meckel-Gruber syndrome protein TMEM67 controls basal body positioning and epithelial branching morphogenesis in mice via the non-canonical Wnt pathway

    PubMed Central

    Abdelhamed, Zakia A.; Natarajan, Subaashini; Wheway, Gabrielle; Inglehearn, Christopher F.; Toomes, Carmel; Johnson, Colin A.; Jagger, Daniel J.

    2015-01-01

    ABSTRACT Ciliopathies are a group of developmental disorders that manifest with multi-organ anomalies. Mutations in TMEM67 (MKS3) cause a range of human ciliopathies, including Meckel-Gruber and Joubert syndromes. In this study we describe multi-organ developmental abnormalities in the Tmem67tm1Dgen/H1 knockout mouse that closely resemble those seen in Wnt5a and Ror2 knockout mice. These include pulmonary hypoplasia, ventricular septal defects, shortening of the body longitudinal axis, limb abnormalities, and cochlear hair cell stereociliary bundle orientation and basal body/kinocilium positioning defects. The basal body/kinocilium complex was often uncoupled from the hair bundle, suggesting aberrant basal body migration, although planar cell polarity and apical planar asymmetry in the organ of Corti were normal. TMEM67 (meckelin) is essential for phosphorylation of the non-canonical Wnt receptor ROR2 (receptor-tyrosine-kinase-like orphan receptor 2) upon stimulation with Wnt5a-conditioned medium. ROR2 also colocalises and interacts with TMEM67 at the ciliary transition zone. Additionally, the extracellular N-terminal domain of TMEM67 preferentially binds to Wnt5a in an in vitro binding assay. Cultured lungs of Tmem67 mutant mice failed to respond to stimulation of epithelial branching morphogenesis by Wnt5a. Wnt5a also inhibited both the Shh and canonical Wnt/β-catenin signalling pathways in wild-type embryonic lung. Pulmonary hypoplasia phenotypes, including loss of correct epithelial branching morphogenesis and cell polarity, were rescued by stimulating the non-canonical Wnt pathway downstream of the Wnt5a-TMEM67-ROR2 axis by activating RhoA. We propose that TMEM67 is a receptor that has a main role in non-canonical Wnt signalling, mediated by Wnt5a and ROR2, and normally represses Shh signalling. Downstream therapeutic targeting of the Wnt5a-TMEM67-ROR2 axis might, therefore, reduce or prevent pulmonary hypoplasia in ciliopathies and other congenital

  18. Identification of p62/SQSTM1 as a component of non-canonical Wnt VANGL2-JNK signalling in breast cancer.

    PubMed

    Puvirajesinghe, Tania M; Bertucci, François; Jain, Ashish; Scerbo, Pierluigi; Belotti, Edwige; Audebert, Stéphane; Sebbagh, Michael; Lopez, Marc; Brech, Andreas; Finetti, Pascal; Charafe-Jauffret, Emmanuelle; Chaffanet, Max; Castellano, Rémy; Restouin, Audrey; Marchetto, Sylvie; Collette, Yves; Gonçalvès, Anthony; Macara, Ian; Birnbaum, Daniel; Kodjabachian, Laurent; Johansen, Terje; Borg, Jean-Paul

    2016-01-12

    The non-canonical Wnt/planar cell polarity (Wnt/PCP) pathway plays a crucial role in embryonic development. Recent work has linked defects of this pathway to breast cancer aggressiveness and proposed Wnt/PCP signalling as a therapeutic target. Here we show that the archetypal Wnt/PCP protein VANGL2 is overexpressed in basal breast cancers, associated with poor prognosis and implicated in tumour growth. We identify the scaffold p62/SQSTM1 protein as a novel VANGL2-binding partner and show its key role in an evolutionarily conserved VANGL2-p62/SQSTM1-JNK pathway. This proliferative signalling cascade is upregulated in breast cancer patients with shorter survival and can be inactivated in patient-derived xenograft cells by inhibition of the JNK pathway or by disruption of the VANGL2-p62/SQSTM1 interaction. VANGL2-JNK signalling is thus a potential target for breast cancer therapy.

  19. Evidence of non-canonical NOTCH signaling: Delta-like 1 homolog (DLK1) directly interacts with the NOTCH1 receptor in mammals.

    PubMed

    Traustadóttir, Gunnhildur Ásta; Jensen, Charlotte H; Thomassen, Mads; Beck, Hans Christian; Mortensen, Sussi B; Laborda, Jorge; Baladrón, Victoriano; Sheikh, Søren P; Andersen, Ditte C

    2016-04-01

    Canonical NOTCH signaling, known to be essential for tissue development, requires the Delta-Serrate-LAG2 (DSL) domain for NOTCH to interact with its ligand. However, despite lacking DSL, Delta-like 1 homolog (DLK1), a protein that plays a significant role in mammalian development, has been suggested to interact with NOTCH1 and act as an antagonist. This non-canonical interaction is, however controversial, and evidence for a direct interaction, still lacking in mammals. In this study, we elucidated the putative DLK1-NOTCH1 interaction in a mammalian context. Taking a global approach and using Dlk1(+/+) and Dlk1(-/-) mouse tissues at E16.5, we demonstrated that several NOTCH signaling pathways indeed are affected by DLK1 during tissue development, and this was supported by a lower activation of NOTCH1 protein in Dlk1(+/+) embryos. Likewise, but using a distinct Dlk1-manipulated (siRNA) setup in a mammalian cell line, NOTCH signaling was substantially inhibited by DLK1. Using a mammalian two-hybrid system, we firmly established that the effect of DLK1 on NOTCH signaling was due to a direct interaction between DLK1 and NOTCH1. By careful dissection of this mechanism, we found this interaction to occur between EGF domains 5 and 6 of DLK1 and EGF domains 10-15 of NOTCH1. Thus, our data provide the first evidence for a direct interaction between DLK1 and NOTCH1 in mammals, and substantiate that non-canonical NOTCH ligands exist, adding to the complexity of NOTCH signaling.

  20. TGF-β1 prevents simulated ischemia/reperfusion-induced cardiac fibroblast apoptosis by activation of both canonical and non-canonical signaling pathways.

    PubMed

    Vivar, Raúl; Humeres, Claudio; Ayala, Pedro; Olmedo, Ivonne; Catalán, Mabel; García, Lorena; Lavandero, Sergio; Díaz-Araya, Guillermo

    2013-06-01

    Ischemia/reperfusion injury is a major cause of myocardial death. In the heart, cardiac fibroblasts play a critical role in healing post myocardial infarction. TGF-β1 has shown cardioprotective effects in cardiac damage; however, if TGF-β1 can prevent cardiac fibroblast death triggered by ischemia/reperfusion is unknown. Therefore, we test this hypothesis, and whether the canonical and/or non-canonical TGF-β1 signaling pathways are involved in this protective effect. Cultured rat cardiac fibroblasts were subjected to simulated ischemia/reperfusion. Cell viability was analyzed by trypan blue exclusion and propidium iodide by flow cytometry. The processing of procaspases 8, 9 and 3 to their active forms was assessed by Western blot, whereas subG1 population was evaluated by flow cytometry. Levels of total and phosphorylated forms of ERK1/2, Akt and Smad2/3 were determined by Western blot. The role of these signaling pathways on the protective effect of TGF-β1 was studied using specific chemical inhibitors. Simulated ischemia over 8h triggers a significant cardiac fibroblast death, which increased by reperfusion, with apoptosis actively involved. These effects were only prevented by the addition of TGF-β1 during reperfusion. TGF-β1 pretreatment increased the levels of phosphorylated forms of ERK1/2, Akt and Smad2/3. The inhibition of ERK1/2, Akt and Smad3 also blocked the preventive effects of TGF-β1 on cardiac fibroblast apoptosis induced by simulated ischemia/reperfusion. Overall, our data suggest that TGF-β1 prevents cardiac fibroblast apoptosis induced by simulated ischemia-reperfusion through the canonical (Smad3) and non canonical (ERK1/2 and Akt) signaling pathways. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. A Phenotypic Screen in Zebrafish Identifies a Novel Small-Molecule Inducer of Ectopic Tail Formation Suggestive of Alterations in Non-Canonical Wnt/PCP Signaling

    PubMed Central

    Gebruers, Evelien; Cordero-Maldonado, María Lorena; Gray, Alexander I.; Clements, Carol; Harvey, Alan L.; Edrada-Ebel, Ruangelie; de Witte, Peter A. M.; Crawford, Alexander D.; Esguerra, Camila V.

    2013-01-01

    Zebrafish have recently emerged as an attractive model for the in vivo bioassay-guided isolation and characterization of pharmacologically active small molecules of natural origin. We carried out a zebrafish-based phenotypic screen of over 3000 plant-derived secondary metabolite extracts with the goal of identifying novel small-molecule modulators of the BMP and Wnt signaling pathways. One of the bioactive plant extracts identified in this screen – Jasminum gilgianum, an Oleaceae species native to Papua New Guinea – induced ectopic tails during zebrafish embryonic development. As ectopic tail formation occurs when BMP or non-canonical Wnt signaling is inhibited during the tail protrusion process, we suspected a constituent of this extract to act as a modulator of these pathways. A bioassay-guided isolation was carried out on the basis of this zebrafish phenotype, identifying para-coumaric acid methyl ester (pCAME) as the active compound. We then performed an in-depth phenotypic analysis of pCAME-treated zebrafish embryos, including a tissue-specific marker analysis of the secondary tails. We found pCAME to synergize with the BMP-inhibitors dorsomorphin and LDN-193189 in inducing ectopic tails, and causing convergence-extension defects in compound-treated embryos. These results indicate that pCAME may interfere with non-canonical Wnt signaling. Inhibition of Jnk, a downstream target of Wnt/PCP signaling (via morpholino antisense knockdown and pharmacological inhibition with the kinase inhibitor SP600125) phenocopied pCAME-treated embryos. However, immunoblotting experiments revealed pCAME to not directly inhibit Jnk-mediated phosphorylation of c-Jun, suggesting additional targets of SP600125, and/or other pathways, as possibly being involved in the ectopic tail formation activity of pCAME. Further investigation of pCAME’s mechanism of action will help determine this compound’s pharmacological utility. PMID:24349481

  2. Estrogen receptor α regulates non-canonical autophagy that provides stress resistance to neuroblastoma and breast cancer cells and involves BAG3 function

    PubMed Central

    Felzen, V; Hiebel, C; Koziollek-Drechsler, I; Reißig, S; Wolfrum, U; Kögel, D; Brandts, C; Behl, C; Morawe, T

    2015-01-01

    Breast cancer is a heterogeneous disease and approximately 70% of newly diagnosed breast cancers are estrogen receptor (ER) positive. Out of the two ER types, α and β, ERα is the only ER that is detectable by immunohistochemistry in breast cancer biopsies and is the predominant subtype expressed in breast tumor tissue. ER-positive tumors are currently treated with anti-hormone therapy to inhibit ER signaling. It is well known that breast cancer cells can develop endocrine resistance and resistance to anti-hormone therapy and this can be facilitated via the autophagy pathway, but so far the description of a detailed autophagy expression profile of ER-positive cancer cells is missing. In the present study, we characterized tumor cell lines ectopically expressing ERα or ERβ as well as the breast cancer-derived MCF-7 cell line endogenously expressing ERα but being ERβ negative. We could show that ERα-expressing cells have a higher autophagic activity than cells expressing ERβ and cells lacking ER expression. Additionally, for autophagy-related gene expression we describe an ERα-specific ‘autophagy-footprint' that is fundamentally different to tumor cells expressing ERβ or lacking ER expression. This newly described ERα-mediated and estrogen response element (ERE)-independent non-canonical autophagy pathway, which involves the function of the co-chaperone Bcl2-associated athanogene 3 (BAG3), is independent of classical mammalian target of rapamycin (mTOR) and phosphatidylinositol 3 kinase (PI3K) signaling networks and provides stress resistance in our model systems. Altogether, our study uncovers a novel non-canonical autophagy pathway that might be an interesting target for personalized medicine and treatment of ERα-positive breast cancer cells that do not respond to anti-hormone therapy and classical autophagy inhibitors. PMID:26158518

  3. A phenotypic screen in zebrafish identifies a novel small-molecule inducer of ectopic tail formation suggestive of alterations in non-canonical Wnt/PCP signaling.

    PubMed

    Gebruers, Evelien; Cordero-Maldonado, María Lorena; Gray, Alexander I; Clements, Carol; Harvey, Alan L; Edrada-Ebel, Ruangelie; de Witte, Peter A M; Crawford, Alexander D; Esguerra, Camila V

    2013-01-01

    Zebrafish have recently emerged as an attractive model for the in vivo bioassay-guided isolation and characterization of pharmacologically active small molecules of natural origin. We carried out a zebrafish-based phenotypic screen of over 3000 plant-derived secondary metabolite extracts with the goal of identifying novel small-molecule modulators of the BMP and Wnt signaling pathways. One of the bioactive plant extracts identified in this screen - Jasminum gilgianum, an Oleaceae species native to Papua New Guinea - induced ectopic tails during zebrafish embryonic development. As ectopic tail formation occurs when BMP or non-canonical Wnt signaling is inhibited during the tail protrusion process, we suspected a constituent of this extract to act as a modulator of these pathways. A bioassay-guided isolation was carried out on the basis of this zebrafish phenotype, identifying para-coumaric acid methyl ester (pCAME) as the active compound. We then performed an in-depth phenotypic analysis of pCAME-treated zebrafish embryos, including a tissue-specific marker analysis of the secondary tails. We found pCAME to synergize with the BMP-inhibitors dorsomorphin and LDN-193189 in inducing ectopic tails, and causing convergence-extension defects in compound-treated embryos. These results indicate that pCAME may interfere with non-canonical Wnt signaling. Inhibition of Jnk, a downstream target of Wnt/PCP signaling (via morpholino antisense knockdown and pharmacological inhibition with the kinase inhibitor SP600125) phenocopied pCAME-treated embryos. However, immunoblotting experiments revealed pCAME to not directly inhibit Jnk-mediated phosphorylation of c-Jun, suggesting additional targets of SP600125, and/or other pathways, as possibly being involved in the ectopic tail formation activity of pCAME. Further investigation of pCAME's mechanism of action will help determine this compound's pharmacological utility.

  4. TWEAK favors phosphate-induced calcification of vascular smooth muscle cells through canonical and non-canonical activation of NFκB

    PubMed Central

    Hénaut, L; Sanz, A B; Martin-Sanchez, D; Carrasco, S; Villa-Bellosta, R; Aldamiz-Echevarria, G; Massy, Z A; Sanchez-Nino, M D; Ortiz, A

    2016-01-01

    Vascular calcification (VC) is associated with increased cardiovascular mortality in aging, chronic kidney disease (CKD), type 2 diabetes mellitus (T2DM) and atherosclerosis. TNF-like weak inducer of apoptosis (TWEAK) recently emerged as a new biomarker for the diagnosis and prognosis of cardiovascular diseases. TWEAK binding to its functional receptor Fn14 was reported to promote several steps of atherosclerotic plaque progression. However, no information is currently available on the role of TWEAK/Fn14 on the development of medial calcification, which is highly prevalent in aging, CKD and T2DM. This study explored the involvement of TWEAK in human vascular smooth muscle cells (h-VSMCs) calcification in vitro. We report that TWEAK binding to Fn14 promotes inorganic phosphate-induced h-VSMCs calcification, favors h-VSMCs osteogenic transition, decreasing acta2 and myh11 and increasing bmp2 mRNA and tissue non-specific alkaline phosphatase (TNAP), and increases MMP9 activity. Blockade of the canonical NFκB pathway reduced by 80% TWEAK pro-calcific properties and decreased osteogenic transition, TNAP and MMP9 activity. Blockade of non-canonical NFκB signaling by a siRNA targeting RelB reduced by 20% TWEAK pro-calcific effects and decreased TWEAK-induced loss of h-VSMCs contractile phenotype and MMP9 activity, without modulating bmp2 mRNA or TNAP activity. Inhibition of ERK1/2 activation by a MAPK kinase inhibitor did not influence TWEAK pro-calcific properties. Our results suggest that TWEAK/Fn14 directly favors inorganic phosphate-induced h-VSMCs calcification by activation of both canonical and non-canonical NFκB pathways. Given the availability of neutralizing anti-TWEAK strategies, our study sheds light on the TWEAK/Fn14 axis as a novel therapeutic target in the prevention of VC. PMID:27441657

  5. The cross-talk between canonical and non-canonical Wnt-dependent pathways regulates P-glycoprotein expression in human blood–brain barrier cells

    PubMed Central

    Pinzón-Daza, Martha L; Salaroglio, Iris C; Kopecka, Joanna; Garzòn, Ruth; Couraud, Pierre-Olivier; Ghigo, Dario; Riganti, Chiara

    2014-01-01

    In this work, we investigate if and how transducers of the ‘canonical' Wnt pathway, i.e., Wnt/glycogen synthase kinase 3 (GSK3)/β-catenin, and transducers of the ‘non-canonical' Wnt pathway, i.e., Wnt/RhoA/RhoA kinase (RhoAK), cooperate to control the expression of P-glycoprotein (Pgp) in blood–brain barrier (BBB) cells. By analyzing human primary brain microvascular endothelial cells constitutively activated for RhoA, silenced for RhoA or treated with the RhoAK inhibitor Y27632, we found that RhoAK phosphorylated and activated the protein tyrosine phosphatase 1B (PTP1B), which dephosphorylated tyrosine 216 of GSK3, decreasing the GSK3-mediated inhibition of β-catenin. By contrast, the inhibition of RhoA/RhoAK axis prevented the activation of PTP1B, enhanced the GSK3-induced phosphorylation and ubiquitination of β-catenin, and reduced the β-catenin-driven transcription of Pgp. The RhoAK inhibition increased the delivery of Pgp substrates like doxorubicin across the BBB and improved the doxorubicin efficacy against glioblastoma cells co-cultured under a BBB monolayer. Our data demonstrate that in human BBB cells the expression of Pgp is controlled by a cross-talk between canonical and non-canonical Wnt pathways. The disruption of this cross-talk, e.g., by inhibiting RhoAK, downregulates Pgp and increases the delivery of Pgp substrates across the BBB. PMID:24896565

  6. Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.

    PubMed

    Krepl, Miroslav; Réblová, Kamila; Koča, Jaroslav; Sponer, Jiří

    2013-05-09

    The L1 stalk is a prominent mobile element of the large ribosomal subunit. We explore the structure and dynamics of its non-canonical rRNA elements, which include two kink-turns, an internal loop, and a tetraloop. We use bioinformatics to identify the L1 stalk RNA conservation patterns and carry out over 11.5 μs of MD simulations for a set of systems ranging from isolated RNA building blocks up to complexes of L1 stalk rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk tetraloop has an unusual GNNA or UNNG conservation pattern deviating from major GNRA and YNMG RNA tetraloop families. We suggest that this deviation is related to a highly conserved tertiary contact within the L1 stalk. The available X-ray structures contain only UCCG tetraloops which in addition differ in orientation (anti vs syn) of the guanine. Our analysis suggests that the anti orientation might be a mis-refinement, although even the anti interaction would be compatible with the sequence pattern and observed tertiary interaction. Alternatively, the anti conformation may be a real substate whose population could be pH-dependent, since the guanine syn orientation requires protonation of cytosine in the tertiary contact. In absence of structural data, we use molecular modeling to explore the GCCA tetraloop that is dominant in bacteria and suggest that the GCCA tetraloop is structurally similar to the YNMG tetraloop. Kink-turn Kt-77 is unusual due to its 11-nucleotide bulge. The simulations indicate that the long bulge is a stalk-specific eight-nucleotide insertion into consensual kink-turn only subtly modifying its structural dynamics. We discuss a possible evolutionary role of helix H78 and a mechanism of L1 stalk interaction with tRNA. We also assess the simulation methodology. The simulations provide a good description of the studied systems with the latest bsc0χOL3 force field showing improved performance. Still, even bsc0χOL3 is unable to fully stabilize an essential

  7. Targeting non-canonical nuclear factor-κB signalling attenuates neovascularization in a novel 3D model of rheumatoid arthritis synovial angiogenesis.

    PubMed

    Maracle, Chrissta X; Kucharzewska, Paulina; Helder, Boy; van der Horst, Corine; Correa de Sampaio, Pedro; Noort, Ae-Ri; van Zoest, Katinka; Griffioen, Arjan W; Olsson, Henric; Tas, Sander W

    2017-02-01

    Angiogenesis is crucial in RA disease progression. Lymphotoxin β receptor (LTβR)-induced activation of the non-canonical nuclear factor-κB (NF-κB) pathway via NF-κB-inducing kinase (NIK) has been implicated in this process. Consequently, inhibition of this pathway may hold therapeutic potential in RA. We describe a novel three-dimensional (3D) model of synovial angiogenesis incorporating endothelial cells (ECs), RA fibroblast-like synoviocytes (RAFLSs) and RA synovial fluid (RASF) to further investigate the contributions of NF-κB in this process. Spheroids consisting of RAFLSs and ECs were stimulated with RASF, the LTβR ligands LTβ and LIGHT, or growth factor bFGF and VEGF, followed by quantification of EC sprouting using confocal microscopy and digital image analysis. Next, the effects of anginex, NIK-targeting siRNA (siNIK), LTβR-Ig fusion protein (baminercept) and a novel pharmacological NIK inhibitor were investigated. RASF significantly promoted sprout formation, which was blocked by the established angiogenesis inhibitor anginex (P < 0.05). LTβ and LIGHT induced significant sprouting (P < 0.05), as did bFGF/VEGF (P < 0.01). siNIK pre-treatment of ECs led to reductions in LTβR-induced vessel formation (P < 0.05). LTβR-Ig not only blocked LTβ- or LIGHT-induced sprouting, but also RASF-induced sprouting (P < 0.05). The NIK inhibitor blocked angiogenesis induced by LTβ, LIGHT, growth factors (P < 0.05) and RASF (P < 0.01). We present a novel 3D model of synovial angiogenesis incorporating RAFLSs, ECs and RASF that mimics the in vivo situation. Using this system, we demonstrate that non-canonical NF-κB signalling promotes neovascularization and show that this model is useful for dissecting relative contributions of signalling pathways in specific cell types to angiogenic responses and for testing pharmacological inhibitors of angiogenesis. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All

  8. Identification of canonical tyrosine-dependent and non-canonical tyrosine-independent STAT3 activation sites in the intracellular domain of the interleukin 23 receptor.

    PubMed

    Floss, Doreen M; Mrotzek, Simone; Klöcker, Tobias; Schröder, Jutta; Grötzinger, Joachim; Rose-John, Stefan; Scheller, Jürgen

    2013-07-05

    Signaling of interleukin 23 (IL-23) via the IL-23 receptor (IL-23R) and the shared IL-12 receptor β1 (IL-12Rβ1) controls innate and adaptive immune responses and is involved in the differentiation and expansion of IL-17-producing CD4(+) T helper (TH17) cells. Activation of signal transducer and activator of transcription 3 (STAT3) appears to be the major signaling pathway of IL-23, and STAT binding sites were predicted in the IL-23R but not in the IL-12Rβ1 chain. Using site-directed mutagenesis and deletion variants of the murine and human IL-23R, we showed that the predicted STAT binding sites (pYXXQ; including Tyr-504 and Tyr-626 in murine IL-23R and Tyr-484 and Tyr-611 in human IL-23R) mediated STAT3 activation. Furthermore, we identified two uncommon STAT3 binding/activation sites within the murine IL-23R. First, the murine IL-23R carried the Y(542)PNFQ sequence, which acts as an unusual Src homology 2 (SH2) domain-binding protein activation site of STAT3. Second, we identified a non-canonical, phosphotyrosine-independent STAT3 activation motif within the IL-23R. A third predicted site, Tyr-416 in murine and Tyr-397 in human IL-23R, is involved in the activation of PI3K/Akt and the MAPK pathway leading to STAT3-independent proliferation of Ba/F3 cells upon stimulation with IL-23. In contrast to IL-6-induced short term STAT3 phosphorylation, cellular activation by IL-23 resulted in a slower but long term STAT3 phosphorylation, indicating that the IL-23R might not be a major target of negative feedback inhibition by suppressor of cytokine signaling (SOCS) proteins. In summary, we characterized IL-23-dependent signal transduction with a focus on STAT3 phosphorylation and identified canonical tyrosine-dependent and non-canonical tyrosine-independent STAT3 activation sites in the IL-23R.

  9. Identification of Canonical Tyrosine-dependent and Non-canonical Tyrosine-independent STAT3 Activation Sites in the Intracellular Domain of the Interleukin 23 Receptor*

    PubMed Central

    Floss, Doreen M.; Mrotzek, Simone; Klöcker, Tobias; Schröder, Jutta; Grötzinger, Joachim; Rose-John, Stefan; Scheller, Jürgen

    2013-01-01

    Signaling of interleukin 23 (IL-23) via the IL-23 receptor (IL-23R) and the shared IL-12 receptor β1 (IL-12Rβ1) controls innate and adaptive immune responses and is involved in the differentiation and expansion of IL-17-producing CD4+ T helper (TH17) cells. Activation of signal transducer and activator of transcription 3 (STAT3) appears to be the major signaling pathway of IL-23, and STAT binding sites were predicted in the IL-23R but not in the IL-12Rβ1 chain. Using site-directed mutagenesis and deletion variants of the murine and human IL-23R, we showed that the predicted STAT binding sites (pYXXQ; including Tyr-504 and Tyr-626 in murine IL-23R and Tyr-484 and Tyr-611 in human IL-23R) mediated STAT3 activation. Furthermore, we identified two uncommon STAT3 binding/activation sites within the murine IL-23R. First, the murine IL-23R carried the Y542PNFQ sequence, which acts as an unusual Src homology 2 (SH2) domain-binding protein activation site of STAT3. Second, we identified a non-canonical, phosphotyrosine-independent STAT3 activation motif within the IL-23R. A third predicted site, Tyr-416 in murine and Tyr-397 in human IL-23R, is involved in the activation of PI3K/Akt and the MAPK pathway leading to STAT3-independent proliferation of Ba/F3 cells upon stimulation with IL-23. In contrast to IL-6-induced short term STAT3 phosphorylation, cellular activation by IL-23 resulted in a slower but long term STAT3 phosphorylation, indicating that the IL-23R might not be a major target of negative feedback inhibition by suppressor of cytokine signaling (SOCS) proteins. In summary, we characterized IL-23-dependent signal transduction with a focus on STAT3 phosphorylation and identified canonical tyrosine-dependent and non-canonical tyrosine-independent STAT3 activation sites in the IL-23R. PMID:23673666

  10. A hierarchical cascade activated by non-canonical Notch signaling and the mTOR-Rictor complex regulates neglect-induced death in mammalian cells.

    PubMed

    Perumalsamy, L R; Nagala, M; Banerjee, P; Sarin, A

    2009-06-01

    The regulation of cellular metabolism and survival by trophic factors is not completely understood. Here, we describe a signaling cascade activated by the developmental regulator Notch, which inhibits apoptosis triggered by neglect in mammalian cells. In this pathway, the Notch intracellular domain (NIC), which is released after interaction with ligand, converges on the kinase mammalian target of rapamycin (mTOR) and the substrate-defining protein rapamycin independent companion of mTOR (Rictor), culminating in the activation of the kinase Akt/PKB. Biochemical and molecular approaches using site-directed mutants identified AktS473 as a key downstream target in the antiapoptotic pathway activated by NIC. Despite the demonstrated requirement for Notch processing and its predominant nuclear localization, NIC function was independent of CBF1/RBP-J, an essential DNA-binding component required for canonical signaling. In experiments that placed spatial constraints on NIC, enforced nuclear retention abrogated antiapoptotic activity and a membrane-anchored form of NIC-blocked apoptosis through mTOR, Rictor and Akt-dependent signaling. We show that the NIC-mTORC2-Akt cascade blocks the apoptotic response triggered by removal of medium or serum deprivation. Consistently, membrane-tethered NIC, and AktS473 inhibited apoptosis triggered by cytokine deprivation in activated T cells. Thus, this study identifies a non-canonical signaling cascade wherein NIC integrates with multiple pathways to regulate cell survival.

  11. The bHLH/Per-Arnt-Sim transcription factor SIM2 regulates muscle transcript myomesin2 via a novel, non-canonical E-box sequence

    PubMed Central

    Woods, Susan; Farrall, Alexandra; Procko, Carl; Whitelaw, Murray L.

    2008-01-01

    Despite a growing number of descriptive studies that show Single-minded 2 (Sim2) is not only essential for murine survival, but also upregulated in colon, prostate and pancreatic tumours, there is a lack of direct target genes identified for this basic helix–loop–helix/PAS transcription factor. We have performed a set of microarray experiments aimed at identifying genes that are differentially regulated by SIM2, and successfully verified that the Myomesin2 (Myom2) gene is SIM2-responsive. Although SIM2 has been reported to be a transcription repressor, we find that SIM2 induces transcription of Myom2 and activates the Myom2 promoter sequence when co-expressed with the heterodimeric partner protein, ARNT1, in human embryonic kidney cells. Truncation and mutation of the Myom2 promoter sequence, combined with chromatin immunoprecipitation studies in cells, has lead to the delineation of a non-canonical E-box sequence 5′-AACGTG-3′ that is bound by SIM2/ARNT1 heterodimers. Interestingly, in immortalized human myoblasts knock down of Sim2 results in increased levels of Myom2 RNA, suggesting that SIM2 is acting as a repressor in these cells and so its activity is likely to be highly context dependent. This is the first report of a direct SIM2/ARNT1 target gene with accompanying analysis of a functional response element. PMID:18480125

  12. Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects

    PubMed Central

    Sang, Yi; Silva-Ortega, Claudia O.; Wu, Shuang; Yamaguchi, Nobutoshi; Wu, Miin-Feng; Pfluger, Jennifer; Gillmor, C. Stewart; Gallagher, Kimberly L.; Wagner, Doris

    2012-01-01

    Summary SWI2/SNF2 chromatin remodeling ATPases play important roles in plant and metazoan development. While metazoans generally encode one or two SWI2/SNF2 ATPase genes, Arabidopsis encodes four such chromatin regulators: the well-studied BRAHMA and SPLAYED ATPases as well as two closely related non-canonical SWI2/SNF2 ATPases, CHR12 and CHR23. No developmental role has as yet been described for CHR12 and CHR23. Here we show that while strong single chr12 or chr23 mutants are morphologically indistinguishable from the wild type, chr12 chr23 double mutants cause embryonic lethality. The double mutant embryos fail to initiate root and shoot meristems and display few and aberrant cell division. Weak double mutant embryos give rise to viable seedlings with dramatic defects in the maintenance of both the shoot and the root stem cell populations. Paradoxically, the stem cell defects are correlated with increased expression of the stem cell markers WUSCHEL and WOX5. During subsequent development, the meristem defects are partially overcome to allow for the formation of very small, bushy adult plants. Based on the observed morphological defects we named the two chromatin remodelers MINUSCULE 1 and 2. Possible links between minu1 minu2 defects and defects in hormone signaling and replication-coupled chromatin assembly are discussed. PMID:23062007

  13. An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins.

    PubMed

    Singh-Blom, Amrita; Hughes, Randall A; Ellington, Andrew D

    2014-05-20

    Residue-specific incorporation of non-canonical amino acids into proteins is usually performed in vivo using amino acid auxotrophic strains and replacing the natural amino acid with an unnatural amino acid analog. Herein, we present an efficient amino acid depleted cell-free protein synthesis system that can be used to study residue-specific replacement of a natural amino acid by an unnatural amino acid analog. This system combines a simple methodology and high protein expression titers with a high-efficiency analog substitution into a target protein. To demonstrate the productivity and efficacy of a cell-free synthesis system for residue-specific incorporation of unnatural amino acids in vitro, we use this system to show that 5-fluorotryptophan and 6-fluorotryptophan substituted streptavidin retain the ability to bind biotin despite protein-wide replacement of a natural amino acid for the amino acid analog. We envisage this amino acid depleted cell-free synthesis system being an economical and convenient format for the high-throughput screening of a myriad of amino acid analogs with a variety of protein targets for the study and functional characterization of proteins substituted with unnatural amino acids when compared to the currently employed in vivo methodologies. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. STAT3 cooperates with the non-canonical NF-κB signaling to regulate pro-labor genes in the human placenta.

    PubMed

    Yu, L J; Wang, B; Parobchak, N; Roche, N; Rosen, T

    2015-05-01

    Our recent studies have shown that constitutively activated non-canonical RelB/NF-κB2 (p52) in the human placenta positively regulates the pro-labor genes CRH and COX-2. STAT3 regulates NF-κB2 (p100) processing to active p52, and in turn, nuclear activation of RelB/p52, by directly binding to p100/p52 in a variety of cancer cells. In the current study, we tested the hypothesis that STAT3 is involved in regulation of pro-labor genes by associating with RelB/p52 heterodimers in the human placenta. We used a variety of techniques including immunohistochemical staining, gene silencing, ectopic expression, chromatin immunoprecipitation, Western blot, RT-qPCR, and immunofluorescence assays in primary culture of cytotrophoblast and placental tissues. We found that knockdown of STAT3 led to down-regulation of both CRH and COX-2 in a dose-dependent manner. By using chromatin immunoprecipitation, we further showed that interaction of RelB with the CRH or COX-2 gene promoters decreased when STAT3 was depleted. Immunofluorescence demonstrated co-localization of STAT3 with RelB or p100/p52 in both the cytoplasm and nucleus of term cytotrophoblasts. Collectively, these results suggest that STAT3 constitutes part of the RelB/p52-containing activator complex that positively regulates pro-labor genes in the human placenta. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. PAPERCLIP identifies microRNA targets and a role of CstF64/64tau in promoting non-canonical poly(A) site usage

    PubMed Central

    Hwang, Hun-Way; Park, Christopher Y.; Goodarzi, Hani; Fak, John J.; Mele, Aldo; Moore, Michael J.; Saito, Yuhki; Darnell, Robert B.

    2016-01-01

    Accurate and precise annotation of the 3′ untranslated regions (3′ UTRs) is critical in understanding how mRNAs are regulated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). Here we describe a method, PAPERCLIP (Poly(A) binding Protein-mediated mRNA 3′ End Retrieval by CrossLinking ImmunoPrecipitation), which shows high specificity for the mRNA 3′ ends and compares favorably to existing 3′ end mapping methods. PAPERCLIP uncovers a previously unrecognized role of CstF64/64tau in promoting the usage of a selected group of non-canonical poly(A) sites, the majority of them containing a downstream GUKKU motif. Furthermore, in mouse brain, PAPERCLIP discovers extended 3′ UTR sequences harboring functional miRNA binding sites and reveals developmentally regulated APA shifts including one in Atp2b2 that is evolutionarily conserved in human and results in a gain of a functional binding site of miR-137. PAPERCLIP provides a powerful tool to decipher post-transcriptional regulation of mRNAs through APA in vivo. PMID:27050522

  16. Activation of non-canonical NF-kappaB pathway mediated by STP-A11, an oncoprotein of Herpesvirus saimiri.

    PubMed

    Cho, Il-Rae; Jeong, Sunam; Jhun, Byung Hak; An, Won G; Lee, BokSoo; Kwak, Youn-Tae; Lee, Sun-Hwa; Jung, Jae U; Chung, Young-Hwa

    2007-03-01

    Although Saimiri Transforming Protein (STP)-A11, an oncoprotein of Herpesvirus saimiri, has been known to activate NF-kappaB signaling pathway, the detailed mechanism has not been reported yet. We herein report that STP-A11 activates non-canonical NF-kappaB pathway, resulting in p100 processing to p52. In addition, translocation of p52 protein (NF-kappaB2) into the nucleus is observed by the expression of STP-A11. STP-A11-mediated processing of p100 to p52 protein requires proteosome-mediated proteolysis because MG132 treatment clearly blocked p52 production in spite of the expression of STP-A11. Analysis of STP-A11 mutants to activate NF-kappaB2 pathway discloses the requirement of TRAF6-binding site not Src-binding site for STP-A11-mediated NF-kappaB2 pathway. Blockage of STP-A11-mediated p52 production using siRNA against p52 enhanced a chemotherapeutic drug-mediated cell death, suggesting that p52 production induced by the expression of STP-A11 would contribute to cellular transformation, which results from a resistance to cell death.

  17. Non-canonical antagonism of PI3K by the kinase Itpkb delays thymocyte β-selection and renders it Notch-dependent

    PubMed Central

    Westernberg, Luise; Conche, Claire; Huang, Yina Hsing; Rigaud, Stephanie; Deng, Yisong; Siegemund, Sabine; Mukherjee, Sayak; Nosaka, Lyn'Al; Das, Jayajit; Sauer, Karsten

    2016-01-01

    β-selection is the most pivotal event determining αβ T cell fate. Here, surface-expression of a pre-T cell receptor (pre-TCR) induces thymocyte metabolic activation, proliferation, survival and differentiation. Besides the pre-TCR, β-selection also requires co-stimulatory signals from Notch receptors - key cell fate determinants in eukaryotes. Here, we show that this Notch-dependence is established through antagonistic signaling by the pre-TCR/Notch effector, phosphoinositide 3-kinase (PI3K), and by inositol-trisphosphate 3-kinase B (Itpkb). Canonically, PI3K is counteracted by the lipid-phosphatases Pten and Inpp5d/SHIP-1. In contrast, Itpkb dampens pre-TCR induced PI3K/Akt signaling by producing IP4, a soluble antagonist of the Akt-activating PI3K-product PIP3. Itpkb-/- thymocytes are pre-TCR hyperresponsive, hyperactivate Akt, downstream mTOR and metabolism, undergo an accelerated β-selection and can develop to CD4+CD8+ cells without Notch. This is reversed by inhibition of Akt, mTOR or glucose metabolism. Thus, non-canonical PI3K-antagonism by Itpkb restricts pre-TCR induced metabolic activation to enforce coincidence-detection of pre-TCR expression and Notch-engagement. DOI: http://dx.doi.org/10.7554/eLife.10786.001 PMID:26880557

  18. PfAP2Tel, harbouring a non-canonical DNA-binding AP2 domain, binds to Plasmodium falciparum telomeres.

    PubMed

    Sierra-Miranda, Miguel; Vembar, Shruthi S; Delgadillo, Dulce María; Ávila-López, P A; Vargas, Miguel; Hernandez-Rivas, Rosaura

    2017-04-04

    The telomeres of the malaria parasite Plasmodium falciparum are essential not only for chromosome end maintenance during blood stage development in humans but also to generate genetic diversity by facilitating homologous recombination of subtelomeric, multigene virulence families such as var and rifin. However, other than the telomerase PfTERT, proteins that act at P. falciparum telomeres are poorly characterized. To isolate components that bind to telomeres, we performed oligonucleotide pulldowns and electromobility shift assays with a telomeric DNA probe and identified a non-canonical member of the ApiAP2 family of transcription factors, PfAP2Tel (encoded by PF3D7_0622900), as a component of the P. falciparum telomere-binding protein complex. PfAP2Tel is expressed throughout the intra-erythrocytic life cycle and localizes to the nuclear periphery, co-localizing with telomeric clusters. Furthermore, EMSAs using the recombinant protein demonstrated direct binding of PfAP2Tel to telomeric repeats in vitro, while genome-wide chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) corroborated the high specificity of this protein to telomeric ends of all 14 chromosomes in vivo. Taken together, our data describe a novel function for ApiAP2 proteins at chromosome ends and open new avenues to study the molecular machinery that regulates telomere function in P. falciparum.

  19. Regulation of natural competence by the orphan two-component system sensor kinase ChiS involves a non-canonical transmembrane regulator in Vibrio cholerae.

    PubMed

    Yamamoto, Shouji; Mitobe, Jiro; Ishikawa, Takahiko; Wai, Sun Nyunt; Ohnishi, Makoto; Watanabe, Haruo; Izumiya, Hidemasa

    2014-01-01

    In Vibrio cholerae, 41 chitin-inducible genes, including the genes involved in natural competence for DNA uptake, are governed by the orphan two-component system (TCS) sensor kinase ChiS. However, the mechanism by which ChiS controls the expression of these genes is currently unknown. Here, we report the involvement of a novel transcription factor termed 'TfoS' in this process. TfoS is a transmembrane protein that contains a large periplasmic domain and a cytoplasmic AraC-type DNA-binding domain, but lacks TCS signature domains. Inactivation of tfoS abolished natural competence as well as transcription of the tfoR gene encoding a chitin-induced small RNA essential for competence gene expression. A TfoS fragment containing the DNA-binding domain specifically bound to and activated transcription from the tfoR promoter. Intracellular TfoS levels were unaffected by disruption of chiS and coexpression of TfoS and ChiS in Escherichia coli recovered transcription of the chromosomally integrated tfoR::lacZ gene, suggesting that TfoS is post-translationally modulated by ChiS during transcriptional activation; however, this regulation persisted when the canonical phosphorelay residues of ChiS were mutated. The results presented here suggest that ChiS operates a chitin-induced non-canonical signal transduction cascade through TfoS, leading to transcriptional activation of tfoR.

  20. Two-photon absorption of fluorescent protein chromophores incorporating non-canonical amino acids: TD-DFT screening and classical dynamics.

    PubMed

    Alaraby Salem, M; Brown, Alex

    2015-10-14

    Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool characterized by deep tissue penetration and little damage. However, two-photon spectroscopy has lower sensitivity than one-photon microscopy alternatives and hence a protein with a large two-photon absorption cross-section is needed. We use time-dependent density functional theory (TD-DFT) at the B3LYP/6-31+G(d,p) level of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the green fluorescent protein (GFP) chromophore with a non-canonical amino acid. A proposed chromophore with a nitro substituent was found to have a large two-photon absorption cross-section (29 GM) compared to other fluorescent protein chromophores as determined at the same level of theory. Classical molecular dynamics are then performed on a nitro-modified fluorescent protein to test its stability and study the effect of the conformational flexibility of the chromophore on its two-photon absorption cross-section. The theoretical results show that the large cross-section is primarily due to the difference between the permanent dipole moments of the excited and ground states of the nitro-modified chromophore. This large difference is maintained through the various conformations assumed by the chromophore in the protein cavity. The nitro-derived protein appears to be very promising as a two-photon absorption probe.

  1. A conserved non-canonical docking mechanism regulates the binding of dual specificity phosphatases to cell integrity mitogen-activated protein kinases (MAPKs) in budding and fission yeasts.

    PubMed

    Sacristán-Reviriego, Almudena; Madrid, Marisa; Cansado, José; Martín, Humberto; Molina, María

    2014-01-01

    Dual-specificity MAPK phosphatases (MKPs) are essential for the negative regulation of MAPK pathways. Similar to other MAPK-interacting proteins, most MKPs bind MAPKs through specific docking domains known as D-motifs. However, we found that the Saccharomyces cerevisiae MKP Msg5 binds the MAPK Slt2 within the cell wall integrity (CWI) pathway through a distinct motif (IYT). Here, we demonstrate that the IYT motif mediates binding of the Msg5 paralogue Sdp1 to Slt2 as well as of the MKP Pmp1 to its CWI MAPK counterpart Pmk1 in the evolutionarily distant yeast Schizosaccharomyces pombe. As a consequence, removal of the IYT site in Msg5, Sdp1 and Pmp1 reduces MAPK trapping caused by the overexpression of catalytically inactive versions of these phosphatases. Accordingly, an intact IYT site is necessary for inactive Sdp1 to prevent nuclear accumulation of Slt2. We also show that both Ile and Tyr but not Thr are essential for the functionality of the IYT motif. These results provide mechanistic insight into MKP-MAPK interplay and stress the relevance of this conserved non-canonical docking site in the regulation of the CWI pathway in fungi.

  2. Non-Canonical Binding Of An Antibody Resembling A Naïve B Cell Receptor Immunoglobin To Hepatitis B Virus Capsids

    PubMed Central

    Watts, Norman R.; Cardone, Giovanni; Vethanayagam, Joe G.; Cheng, Naiqian; Hultgren, Catharina; Stahl, Stephen J.; Steven, Alasdair C.; Sällberg, Matti; Wingfield, Paul T.

    2008-01-01

    The hepatitis B virus capsid (core antigen) is able to bind to and activate naïve B cells whereby these become efficient primary antigen-presenting cells for the priming of T cells. We have investigated this interaction by using cryo-electron microscopy, three-dimensional image reconstruction, and molecular modeling to visualize capsids decorated with Fab fragments of a receptor immunoglobulin, and surface plasmon resonance to measure the binding affinity. By both criteria, the mode of binding differs from those of the six monoclonal anti-core antigen antibodies that have been previously characterized. The Fab interacts with two sites, ~ 30 Å apart. One interaction is canonical, whereby the CDR loops engage the tip of one of the 25 Å-long spikes that protrude from the capsid surface. The second interaction is non-canonical; in it, the Fab framework contacts the tip of an adjacent spike. The binding affinity of this Fab for capsids, KD ~ 4 × 10−7 M, is relatively low for an antibody-antigen interaction, but is ~150-fold lower still (~ 2.5 × 10−5 M) for unassembled capsid protein dimers. The latter observation indicates that both of the observed interactions are required to achieve stable binding of capsids by this receptor immunoglobulin. Considerations of conserved sequence motifs in other such molecules suggest that other naïve B cells may interact with HBV capsids in much the same way. PMID:18486949

  3. MCL-1V, a novel mouse antiapoptotic MCL-1 variant, generated by RNA splicing at a non-canonical splicing pair.

    PubMed

    Kojima, Shogo; Hyakutake, Akira; Koshikawa, Nobuko; Nakagawara, Akira; Takenaga, Keizo

    2010-01-01

    Myeloid cell leukemia-1 (MCL-1) that belongs to BCL-2 family is essential for survival of hematopoietic stem cells. It is upregulated in various types of cancer and promotes cancer cell metastasis. It is known that human MCL-1 gene undergoes differential splicing and yields three mRNAs encoding antiapoptotic MCL-1L and proapoptotic MCL-1S and MCL-1ES. However, no MCL-1 variants have been reported in mouse cells. We report here a new splicing variant of mouse Mcl-1, Mcl-1V, that is expressed in a variety of mouse normal and tumor cell lines and tissues. Comparative sequence analysis of the full-length Mcl-1 and Mcl-1V cDNAs suggested that Mcl-1V mRNA results from splicing within the first coding exon of Mcl-1 gene at a non-canonical donor-acceptor pair. MCL-1V lacks 46 amino acid residues within the N-terminal region of MCL-1. It localizes in mitochondria and inhibits anoxia- and anticancer drug-induced apoptosis as potent as MCL-1, and decayed less rapidly than MCL-1 in the cells undergoing apoptosis. Collectively, our results show that mouse cells ubiquitously express antiapoptotic MCL-1V that may play a role in mitochondrial cell death. Copyright 2009 Elsevier Inc. All rights reserved.

  4. An Appraisal of Human Mitochondrial DNA Instability: New Insights into the Role of Non-Canonical DNA Structures and Sequence Motifs

    PubMed Central

    Oliveira, Pedro H.; Lobato da Silva, Cláudia; Cabral, Joaquim M. S.

    2013-01-01

    Mitochondrial DNA (mtDNA) deletion mutations are frequently observed in aged postmitotic tissues and are the cause of a wide range of human disorders. Presently, the molecular bases underlying mtDNA deletion formation remain a matter of intense debate, and it is commonly accepted that several mechanisms contribute to the spectra of mutations in the mitochondrial genome. In this work we performed an extensive screening of human mtDNA deletions and evaluated the association between breakpoint density and presence of non-canonical DNA elements and over-represented sequence motifs. Our observations support the involvement of helix-distorting intrinsically curved regions and long G-tetrads in eliciting instability events. In addition, higher breakpoint densities were consistently observed within GC-skewed regions and in the close vicinity of the degenerate sequence motif YMMYMNNMMHM. A parallelism is also established with hot spot motifs previously identified in the nuclear genome, as well as with the minimal binding site for the mitochondrial transcription termination factor mTERF. This study extends the current knowledge on the mechanisms driving mitochondrial rearrangements and opens up exciting avenues for further research. PMID:23555828

  5. EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling

    PubMed Central

    Zhang, Fan; Qi, Bin; Wang, Likai; Zhao, Bo; Rode, Siddharth; Riggan, Nathaniel D.; Ecker, Joseph R.; Qiao, Hong

    2016-01-01

    Ethylene gas is essential for many developmental processes and stress responses in plants. EIN2 plays a key role in ethylene signalling but its function remains enigmatic. Here, we show that ethylene specifically elevates acetylation of histone H3K14 and the non-canonical acetylation of H3K23 in etiolated seedlings. The up-regulation of these two histone marks positively correlates with ethylene-regulated transcription activation, and the elevation requires EIN2. Both EIN2 and EIN3 interact with a SANT domain protein named EIN2 nuclear associated protein 1 (ENAP1), overexpression of which results in elevation of histone acetylation and enhanced ethylene-inducible gene expression in an EIN2-dependent manner. On the basis of these findings we propose a model where, in the presence of ethylene, the EIN2 C terminus contributes to downstream signalling via the elevation of acetylation at H3K14 and H3K23. ENAP1 may potentially mediate ethylene-induced histone acetylation via its interactions with EIN2 C terminus. PMID:27694846

  6. Dengue Virus Uses a Non-Canonical Function of the Host GBF1-Arf-COPI System for Capsid Protein Accumulation on Lipid Droplets.

    PubMed

    Iglesias, Nestor G; Mondotte, Juan A; Byk, Laura A; De Maio, Federico A; Samsa, Marcelo M; Alvarez, Cecilia; Gamarnik, Andrea V

    2015-09-01

    Dengue viruses cause the most important human viral disease transmitted by mosquitoes. In recent years, a great deal has been learned about molecular details of dengue virus genome replication; however, little is known about genome encapsidation and the functions of the viral capsid protein. During infection, dengue virus capsid progressively accumulates around lipid droplets (LDs) by an unknown mechanism. Here, we examined the process by which the viral capsid is transported from the endoplasmic reticulum (ER) membrane, where the protein is synthesized, to LDs. Using different methods of intervention, we found that the GBF1-Arf1/Arf4-COPI pathway is necessary for capsid transport to LDs, while the process is independent of both COPII components and Golgi integrity. The transport was sensitive to Brefeldin A, while a drug resistant form of GBF1 was sufficient to restore capsid subcellular distribution in infected cells. The mechanism by which LDs gain or lose proteins is still an open question. Our results support a model in which the virus uses a non-canonical function of the COPI system for capsid accumulation on LDs, providing new ideas for antiviral strategies. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. The malate sensing two-component system MaeKR is a non-canonical class of sensory complex for C4-dicarboxylates.

    PubMed

    Miguel-Romero, L; Casino, P; Landete, J M; Monedero, V; Zúñiga, M; Marina, A

    2017-06-02

    Microbial colonization of different environments is enabled to a great extent by the plasticity of their sensory mechanisms, among them, the two-component signal transduction systems (TCS). Here, an example of TCS plasticity is presented: the regulation of L-malate catabolism via malic enzyme by MaeRK in Lactobacillales. MaeKR belongs to the citrate family of TCS as the Escherichia coli DcuSR system. We show that the Lactobacillus casei histidine-kinase MaeK is defective in autophosphorylation activity as it lacks a functional catalytic and ATP binding domain. The cognate response regulator MaeR was poorly phosphorylated at its phosphoacceptor Asp in vitro. This phosphorylation, however, enhanced MaeR binding in vitro to its target sites and it was required for induction of regulated genes in vivo. Elucidation of the MaeR structure revealed that response regulator dimerization is accomplished by the swapping of α4-β5-α5 elements between two monomers, generating a phosphoacceptor competent conformation. Sequence and phylogenetic analyses showed that the MaeKR peculiarities are not exclusive to L. casei as they are shared by the rest of orthologous systems of Lactobacillales. Our results reveal MaeKR as a non-canonical TCS displaying distinctive features: a swapped response regulator and a sensor histidine kinase lacking ATP-dependent kinase activity.

  8. A Conserved Non-Canonical Docking Mechanism Regulates the Binding of Dual Specificity Phosphatases to Cell Integrity Mitogen-Activated Protein Kinases (MAPKs) in Budding and Fission Yeasts

    PubMed Central

    Sacristán-Reviriego, Almudena; Madrid, Marisa; Cansado, José; Martín, Humberto; Molina, María

    2014-01-01

    Dual-specificity MAPK phosphatases (MKPs) are essential for the negative regulation of MAPK pathways. Similar to other MAPK-interacting proteins, most MKPs bind MAPKs through specific docking domains known as D-motifs. However, we found that the Saccharomyces cerevisiae MKP Msg5 binds the MAPK Slt2 within the cell wall integrity (CWI) pathway through a distinct motif (IYT). Here, we demonstrate that the IYT motif mediates binding of the Msg5 paralogue Sdp1 to Slt2 as well as of the MKP Pmp1 to its CWI MAPK counterpart Pmk1 in the evolutionarily distant yeast Schizosaccharomyces pombe. As a consequence, removal of the IYT site in Msg5, Sdp1 and Pmp1 reduces MAPK trapping caused by the overexpression of catalytically inactive versions of these phosphatases. Accordingly, an intact IYT site is necessary for inactive Sdp1 to prevent nuclear accumulation of Slt2. We also show that both Ile and Tyr but not Thr are essential for the functionality of the IYT motif. These results provide mechanistic insight into MKP-MAPK interplay and stress the relevance of this conserved non-canonical docking site in the regulation of the CWI pathway in fungi. PMID:24465549

  9. Non-canonical 3′-5′ Extension of RNA with Prebiotically Plausible Ribonucleoside 2′,3′-Cyclic Phosphates

    PubMed Central

    2014-01-01

    Ribonucleoside 2′,3′-cyclic phosphates (N>p’s) are generated by multiple prebiotically plausible processes and are credible building blocks for the assembly of early RNA oligomers. While N>p’s can be polymerized into short RNAs by non-enzymatic processes with variable efficiency and regioselectivity, no enzymatic route for RNA synthesis had been described. Here we report such a non-canonical 3′-5′ nucleotidyl transferase activity. We engineered a variant of the hairpin ribozyme to catalyze addition of all four N>p’s (2′,3′-cyclic A-, G-, U-, and CMP) to the 5′-hydroxyl termini of RNA strands with 5′ nucleotide addition enhanced in all cases by eutectic ice phase formation at −7 °C. We also observed 5′ addition of 2′,3′-cyclic phosphate-activated β-nicotinamide adenine dinucleotide (NAD>p) and ACA>p RNA trinucleotide, and multiple additions of GUCCA>p RNA pentamers. Our results establish a new mode of RNA 3′-5′ extension with implications for RNA oligomer synthesis from prebiotic nucleotide pools. PMID:24660752

  10. Identification of p62/SQSTM1 as a component of non-canonical Wnt VANGL2–JNK signalling in breast cancer

    PubMed Central

    Puvirajesinghe, Tania M.; Bertucci, François; Jain, Ashish; Scerbo, Pierluigi; Belotti, Edwige; Audebert, Stéphane; Sebbagh, Michael; Lopez, Marc; Brech, Andreas; Finetti, Pascal; Charafe-Jauffret, Emmanuelle; Chaffanet, Max; Castellano, Rémy; Restouin, Audrey; Marchetto, Sylvie; Collette, Yves; Gonçalvès, Anthony; Macara, Ian; Birnbaum, Daniel; Kodjabachian, Laurent; Johansen, Terje; Borg, Jean-Paul

    2016-01-01

    The non-canonical Wnt/planar cell polarity (Wnt/PCP) pathway plays a crucial role in embryonic development. Recent work has linked defects of this pathway to breast cancer aggressiveness and proposed Wnt/PCP signalling as a therapeutic target. Here we show that the archetypal Wnt/PCP protein VANGL2 is overexpressed in basal breast cancers, associated with poor prognosis and implicated in tumour growth. We identify the scaffold p62/SQSTM1 protein as a novel VANGL2-binding partner and show its key role in an evolutionarily conserved VANGL2–p62/SQSTM1–JNK pathway. This proliferative signalling cascade is upregulated in breast cancer patients with shorter survival and can be inactivated in patient-derived xenograft cells by inhibition of the JNK pathway or by disruption of the VANGL2–p62/SQSTM1 interaction. VANGL2–JNK signalling is thus a potential target for breast cancer therapy. PMID:26754771

  11. MIF inhibits monocytic movement through a non-canonical receptor and disruption of temporal Rho GTPase activities in U-937 cells.

    PubMed

    DiCosmo-Ponticello, Crystal J; Hoover, Daniel; Coffman, Frederick D; Cohen, Stanley; Cohen, Marion C

    2014-09-01

    Macrophage migration inhibitory factor (MIF) is a pro-inflammatory cytokine that was initially identified by its ability to inhibit the movement of macrophages. Cell migration is a highly complex process involving changes to the cytoskeleton and cell adhesion molecules, and is regulated by the Rho GTPases. A simple model using human monocytic U-937 cells to elicit the classic MIF response was implemented to examine the mechanism of MIF-induced migration inhibition. Our results demonstrate that MIF inhibits migration of these U-937 cells through a non-canonical receptor, CXCR4, in the absence of the putative primary MIF receptor CD74. Migration inhibition is dependent upon a series of temporal perturbations of the activities of the Rho GTPases: initial activation followed by subsequent inactivation of RhoA, inactivation of Rac1, and cyclic activation of Cdc42. MIF-mediated changes in the activities of the Rho GTPases jointly contributed to migration inhibition in these cells. Collectively, these data suggest that the MIF-mediated migration inhibition is mediated by the outcome of G-protein signaling, and in less adherent cells such as those of the monocyte/macrophage lineage, RhoA directly affects net translocation through its ability to induce cell body contraction. These findings demonstrate that CXCR4 can mediate MIF signaling in the absence of CD74 in addition to serving as a MIF co-receptor along with CD74. These results correlate MIF activity to specific and sequential Rho GTPase activity perturbations, and given that CXCR4 functions in numerous processes, suggests potential roles for the modulation of cell movement in those events including development, cell survival and viral infection.

  12. The Structure of Treponema pallidum Tp0751 (Pallilysin) Reveals a Non-canonical Lipocalin Fold That Mediates Adhesion to Extracellular Matrix Components and Interactions with Host Cells

    PubMed Central

    Pětrošová, Helena; Lithgow, Karen V.; Hof, Rebecca; Wetherell, Charmaine; Kao, Wei-Chien; Lin, Yi-Pin; Ebady, Rhodaba; Cameron, Caroline E.

    2016-01-01

    Syphilis is a chronic disease caused by the bacterium Treponema pallidum subsp. pallidum. Treponema pallidum disseminates widely throughout the host and extravasates from the vasculature, a process that is at least partially dependent upon the ability of T. pallidum to interact with host extracellular matrix (ECM) components. Defining the molecular basis for the interaction between T. pallidum and the host is complicated by the intractability of T. pallidum to in vitro culturing and genetic manipulation. Correspondingly, few T. pallidum proteins have been identified that interact directly with host components. Of these, Tp0751 (also known as pallilysin) displays a propensity to interact with the ECM, although the underlying mechanism of these interactions remains unknown. Towards establishing the molecular mechanism of Tp0751-host ECM attachment, we first determined the crystal structure of Tp0751 to a resolution of 2.15 Å using selenomethionine phasing. Structural analysis revealed an eight-stranded beta-barrel with a profile of short conserved regions consistent with a non-canonical lipocalin fold. Using a library of native and scrambled peptides representing the full Tp0751 sequence, we next identified a subset of peptides that showed statistically significant and dose-dependent interactions with the ECM components fibrinogen, fibronectin, collagen I, and collagen IV. Intriguingly, each ECM-interacting peptide mapped to the lipocalin domain. To assess the potential of these ECM-coordinating peptides to inhibit adhesion of bacteria to host cells, we engineered an adherence-deficient strain of the spirochete Borrelia burgdorferi to heterologously express Tp0751. This engineered strain displayed Tp0751 on its surface and exhibited a Tp0751-dependent gain-of-function in adhering to human umbilical vein endothelial cells that was inhibited in the presence of one of the ECM-interacting peptides (p10). Overall, these data provide the first structural insight into the

  13. Identification of a non-canonical E-box motif as a regulatory element in the proximal promoter region of the apolipoprotein E gene.

    PubMed Central

    Salero, Enrique; Giménez, Cecilio; Zafra, Francisco

    2003-01-01

    We have used the yeast one-hybrid system to identify transcription factors with binding capability to specific sequences in proximal regions of the apolipoprotein E gene ( APOE ) promoter. The sequence between -113 and -80 nt, which contains regulatory elements in various cell types, was used as a bait to screen a human brain cDNA library. Four cDNA clones that encoded portions of the human upstream-stimulatory-factor (USF) transcription factor were isolated. Electrophoretic-mobility-shift assays ('EMSAs') using nuclear extracts from various human cell lines as well as from rat brain and liver revealed the formation of two DNA-protein complexes within the sequence CACCTCGTGAC (region -101/-91 of the APOE promoter) that show similarity to the E-box element. The retarded complexes contained USF1, as deduced from competition and supershift assays. Functional experiments using different APOE promoter-luciferase reporter constructs transiently transfected into U87, HepG2 or HeLa cell lines showed that mutations that precluded the formation of complexes decreased the basal activity of the promoter by about 50%. Overexpression of USF1 in U87 glioblastoma cells led to an increased activity of the promoter that was partially mediated by the atypical E-box. The stimulatory effect of USF1 was cell-type specific, as it was not observed in hepatoma HepG2 cells. Similarly, overexpression of a USF1 dominant-negative mutant decreased the basal activity of the promoter in glioblastoma, but not in hepatoma, cells. These data indicated that USF, and probably other related transcription factors, might be involved in the basal transcriptional machinery of APOE by binding to a non-canonical E-box motif within the proximal promoter. PMID:12444925

  14. Arjunolic acid, a peroxisome proliferator-activated receptor α agonist, regresses cardiac fibrosis by inhibiting non-canonical TGF-β signaling.

    PubMed

    Bansal, Trisha; Chatterjee, Emeli; Singh, Jasdeep; Ray, Arjun; Kundu, Bishwajit; Thankamani, V; Sengupta, Shantanu; Sarkar, Sagartirtha

    2017-10-06

    Cardiac hypertrophy and associated heart fibrosis remain a major cause of death worldwide. Phytochemicals have gained attention as alternative therapeutics for managing cardiovascular diseases. These include the extract from the plant Terminalia arjuna, which is a popular cardioprotectant and may prevent or slow progression of pathological hypertrophy to heart failure. Here, we investigated the mode of action of a principal bioactive T. arjuna compound, arjunolic acid (AA), in ameliorating hemodynamic load-induced cardiac fibrosis and identified its intracellular target. Our data revealed that AA significantly represses collagen expression and improves cardiac function during hypertrophy. We found that AA binds to and stabilizes the ligand-binding domain of peroxisome proliferator-activated receptor α (PPARα) and increases its expression during cardiac hypertrophy. PPARα knockdown during AA treatment in hypertrophy samples, including angiotensin II-treated adult cardiac fibroblasts and renal artery-ligated rat heart, suggests that AA-driven cardioprotection primarily arises from PPARα agonism. Moreover, AA-induced PPARα up-regulation leads to repression of TGF-β signaling, specifically by inhibiting TGF-β-activated kinase1 (TAK1) phosphorylation. We observed that PPARα directly interacts with TAK1, predominantly via PPARα N-terminal transactivation domain (AF-1) thereby masking the TAK1 kinase domain. The AA-induced PPARα-bound TAK1 level thereby shows inverse correlation with the phosphorylation level of TAK1 and subsequent reduction in p38 MAPK and NF-κBp65 activation, ultimately culminating in amelioration of excess collagen synthesis in cardiac hypertrophy. In conclusion, our findings unravel the mechanism of AA action in regressing hypertrophy-associated cardiac fibrosis by assigning a role of AA as a PPARα agonist that inactivates non-canonical TGF-β signaling. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Identification of TBK1 and IKKε, the non-canonical IκB kinases, as crucial pro-survival factors in HTLV-1-transformed T lymphocytes.

    PubMed

    Zhang, Huan; Chen, Li; Cai, Shao-Hui; Cheng, Hua

    2016-07-01

    Persistent activation of NF-κB is a prerequisite for development of adult T cell leukemia-lymphoma (ATL) caused by human T cell leukemia virus type 1 (HTLV-1). HTLV-1 genome encodes a viral transforming protein named Tax, which constitutively activates the canonical IκB kinases (IKK), the central regulator of NF-κB signaling. However, the role of the non-canonical IκB kinases, TBK1 and IKKε, in the pathogenesis of HTLV-1-associated leukemia has not been evaluated. We here show that TBK1/IKKε are crucial pro-survival molecules by maintaining persistent activity of Stat3. Consistent with this finding, silencing Stat3 by the specific shRNA or by the chemical inhibitor ruxolitinib results in drastic impediment of leukemia cell growth. We further find that in HTLV-1-transformed T cells expressing Tax, TBK1 co-localizes with the canonical IκB kinases and Tax in the lipid raft microdomains. The wild type Tax, but not the Tax mutant defective in activating the canonical IKK, promotes the lipid raft translocation of TBK1. This phenomenon correlates with Tax activation of both NF-κB and Stat3. Tax does not interact directly with TBK1/IKKε, and it rather engages a molecular crosstalk between the canonical IKKs and TBK1/IKKε. Our data, therefore, demonstrate a key role of TBK1/IKKε in the survival and proliferation of HTLV-1-transformed T cells and implicate a potential therapy targeting TBK1/IKKε and Stat3 in controlling HTLV-1-mediated oncogenesis.

  16. Swiss Cheese, a protein involved in progressive neurodegeneration acts as a non-canonical regulatory subunit for PKA-C3

    PubMed Central

    da Cruz, Alexandre Bettencourt; Wentzell, Jill; Kretzschmar, Doris

    2008-01-01

    The Drosophila Swiss Cheese (SWS) protein and its vertebrate orthologue Neuropathy Target Esterase (NTE) are required for neuronal survival and glial integrity. In humans, NTE is the target of organophosphorous compounds which cause a paralyzing axonal degeneration and recently mutations in NTE have been shown to cause a Hereditary Spastic Paraplegia called NTE-related Motor-Neuron Disorder. SWS and NTE are concentrated in the endoplasmic reticulum and both have been shown to have an esterase function against an artificial substrate. However, the functional mechanisms and the pathways in which SWS/NTE are involved in are still widely unknown. Here we show that SWS interacts specifically with the C3 catalytic subunit of cAMP activated protein kinase (PKA-C3) which together with orthologues in mouse (Pkare) and human (PrKX) forms a novel class of catalytic subunits of unknown function. This interaction requires a domain of SWS which shows homology to regulatory subunits of PKA and, like conventional regulatory subunits, the binding of SWS to the PKA-C3 inhibits is function. Consistent with this result, expression of additional PKA-C3 induces degeneration and enhances the neurodegenerative phenotype in sws mutants. We also show that the complex formation with the membrane-bound SWS tethers PKA-C3 to membranes. We therefore propose a model in which SWS acts as a non-canonical subunit for PKA-C3, whereby the complex formation regulates the localization and kinase activity of PKA-C3, and that disruption of this regulation can induce neurodegeneration. PMID:18945896

  17. Structure and specificity of a new class of Ca(2+) independent housekeeping sortase from Streptomyces avermitilis provides insights into its non-canonical substrate preference.

    PubMed

    Das, Sreetama; Pawale, Vijaykumar S; Dadireddy, Venkatareddy; Singh, Avinash Kumar; Ramakumar, Suryanarayanarao; Roy, Rajendra P

    2017-03-07

    Surface proteins in Gram-positive bacteria are incorporated into the cell wall through a peptide ligation reaction catalyzed by transpeptidase sortase. Six main classes (A-F) of sortase have been identified of which class A sortase is meant for housekeeping functions. The prototypic housekeeping sortase A (SaSrtA) from Staphylococcus aureus cleaves LPXTG-containing proteins at the scissile T-G peptide bond and ligates Protein-LPXT to the terminal Gly residue of the nascent cross-bridge of peptidoglycan Lipid II precursor. Sortase-mediated ligation ('sortagging') of LPXTG-containing substrates and Gly-terminated nucleophiles occurs in vitro as well as in cellulo in the presence of Ca(2+) and has been applied extensively for protein conjugations. Although majority of applications emanate from SaSrtA, low catalytic efficiency, LPXTG specificity restriction, and Ca(2+) requirement (particularly for in cellulo applications) remains a drawback. Given that Gram-positive bacterial genomes encode a variety of sortases, natural sortase mining can be a viable complementary approach akin to engineering of wild type SaSrtA. Here we describe the structure and specificity of a new class E sortase (SavSrtE) annotated to perform housekeeping roles in Streptomyces avermitilis Biochemical experiments define the attributes of an optimum peptide substrate, demonstrate Ca(2+)-independent activity and provide insights about contrasting functional characteristics of SavSrtE and SaSrtA. Crystal structure, substrate docking and mutagenesis experiments have identified a critical residue that dictates the preference for a non-canonical LAXTG recognition motif over LPXTG. These results have implications for rational tailoring of substrate tolerance in sortases. Besides, Ca(2+) independent orthogonal specificity of SavSrtE is likely to expand the sortagging toolkit.

  18. Non-canonical WNT5A signaling up-regulates the expression of the tumor suppressor 15-PGDH and induces differentiation of colon cancer cells.

    PubMed

    Mehdawi, Lubna M; Prasad, Chandra Prakash; Ehrnström, Roy; Andersson, Tommy; Sjölander, Anita

    2016-11-01

    The tumor suppressor 15-hydroxyprostaglandin dehydrogenase (15-PGDH) is the key enzyme in prostaglandin E2 catabolism and is down-regulated in colorectal cancer (CRC) tissue. Canonical Wnt signaling is frequently elevated in colon cancers and has been shown to down-regulate 15-PGDH expression. Therefore, we have in the current study investigated if the non-canonical ligand WNT5A relates to increased expression of 15-PGDH in colon cancer cells. In the same cohort of patients, we demonstrated a parallel and significant loss of 15-PGDH and WNT5A protein expression in CRC tissues compared with matched normal colon tissues. Furthermore, patients with low 15-PGDH/WNT5A expression in their tumors showed reduced survival compared with patients with high 15-PGDH/WNT5A expression. To investigate if WNT5A signaling directly affects 15-PGDH expression, we performed in vitro analyses of colon cancer cells (HT-29 and Caco-2). Both cell lines, when treated with recombinant WNT5A (rWNT5A) or Foxy-5, a WNT5A-mimicking peptide, responded by increasing their expression of 15-PGDH mRNA and protein. Our investigations showed that rWNT5A and Foxy-5 induced this increased expression of 15-PGDH through reduced β-catenin signaling as well as increased JNK/AP-1 signaling in colon cancer cells. WNT5A signaling also induced increased 15-PGDH expression in a breast cancer cell line both in vitro and in vivo. In agreement, WNT5A signaling also increased the expression of the differentiation markers sucrose-isomaltase and mucin-2 in colon cancer cells. Our results show that WNT5A signaling regulates 15-PGDH expression, thus uncovering a novel mechanism by which WNT5A acts as a tumor suppressor and suggests that increased 15-PGDH expression could be used as an indicator of a positive response to Foxy-5 in patients treated with this WNT5A agonist.

  19. Netrin-1 acts as a non-canonical angiogenic factor produced by human Wharton's jelly mesenchymal stem cells (WJ-MSC).

    PubMed

    Prieto, Catalina P; Ortiz, María Carolina; Villanueva, Andrea; Villarroel, Cynthia; Edwards, Sandra S; Elliott, Matías; Lattus, José; Aedo, Sócrates; Meza, Daniel; Lois, Pablo; Palma, Verónica

    2017-02-28

    Angiogenesis, the process in which new blood vessels are formed from preexisting ones, is highly dependent on the presence of classical angiogenic factors. Recent evidence suggests that axonal guidance proteins and their receptors can also act as angiogenic regulators. Netrin, a family of laminin-like proteins, specifically Netrin-1 and 4, act via DCC/Neogenin-1 and UNC5 class of receptors to promote or inhibit angiogenesis, depending on the physiological context. Mesenchymal stem cells secrete a broad set of classical angiogenic factors. However, little is known about the expression of non-canonical angiogenic factors such as Netrin-1. The aim was to characterize the possible secretion of Netrin ligands by Wharton's jelly-derived mesenchymal stem cells (WJ-MSC). We evaluated if Netrin-1 presence in the conditioned media from these cells was capable of inducing angiogenesis both in vitro and in vivo, using human umbilical vein endothelial cells (HUVEC) and chicken chorioallantoic membrane (CAM), respectively. In addition, we investigated if the RhoA/ROCK pathway is responsible for the integration of Netrin signaling to control vessel formation. The paracrine angiogenic effect of the WJ-MSC-conditioned media is mediated at least in part by Netrin-1 given that pharmacological blockage of Netrin-1 in WJ-MSC resulted in diminished angiogenesis on HUVEC. When HUVEC were stimulated with exogenous Netrin-1 assayed at physiological concentrations (10-200 ng/mL), endothelial vascular migration occurred in a concentration-dependent manner. In line with our determination of Netrin-1 present in WJ-MSC-conditioned media we were able to obtain endothelial tubule formation even in the pg/mL range. Through CAM assays we validated that WJ-MSC-secreted Netrin-1 promotes an increased angiogenesis in vivo. Netrin-1, secreted by WJ-MSC, might mediate its angiogenic effect through specific cell surface receptors on the endothelium, such as UNC5b and/or integrin α6β1, expressed in

  20. [Non-canonical Wnt signaling contributes to development of non-alcoholic steatohepatitis in a rat model of type 2 diabetes mellitus].

    PubMed

    Tian, Feng; Zhang, Ya-jie; Wang, Lin

    2013-07-01

    To investigate the role of the non-canonical Wnt signaling pathway in development of non-alcoholic steatohepatitis (NASH) related to type 2 diabetes mellitus (T2DM) using a rat model. Twenty-four male Sprague-Dawley rats were randomly divided into two equal groups: control group, fed a stand diet; T2DM-NASH model group, fed a high sucrose and fat diet for 4 weeks and intraperitoneally injected with streptozotocin (30 mg/kg). Twelve weeks after model establishment, all rats were sacrificed. Serum levels of glucose, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were detected by biochemical analysis. Liver pathological changes were assessed microscopically by hematoxylin-eosin and oil red O staining. The liver expression of Wnt5a and NF-kB p65 were detected by immunohistochemistry and western blotting (protein), and quantitative real-time PCR (mRNA). The T2DM-NASH model group showed significantly higher levels of glucose (control group: 6.25 +/- 1.28 vs. 31.21 +/- 0.86 mmol/L, t = -36.204, P less than 0.01), ALT (31.00 +/- 3.69 vs. 301.50 +/- 8.62 U/L, t = -99.94, P less than 0.01), and AST (77.58 +/- 1.83 vs. 344.75 +/- 1.82 U/L, t = -358.85, P less than 0.01). The T2DM-NASH group also showed remarkable signs of steatosis and inflammation in hepatic tissues. The T2DM-NASH group had significantly higher integral optical density (IOD) detection of Wnt5a (control group: 1.15E4 +/- 577.45 vs. 4.04E5 +/- 2.42E4, t = -56.24, P less than 0.01) and NF-kB p65 (1.28E4 +/- 1.59E3 vs. 4.21E5 +/- 1.68E4, t = -83.895, P less than 0.01), as well as protein levels detected by western blot (Wnt5a: 4.21 +/- 0.34 vs. 1.00 +/- 0.25, t = 17.030, P less than 0.01; NF-kB p65: 4.93 +/- 0.76 vs. 1 +/- 0.13, t = 11.438, P less than 0.01). The hepatic mRNA levels followed the same trend (Wnt5a: 9.53 +/- 0.64 vs. 1.04 +/- 0.35, t = 20.165, P less than 0.01; NF-kB p65: 0.60 +/- 0.13 vs. 0.74 +/- 0.10, t = -1.802, P = 0.125). In the T2DM-NASH group, hepatic Wnt5a protein

  1. The distribution of Elongation Factor-1 Alpha (EF-1alpha), Elongation Factor-Like (EFL), and a non-canonical genetic code in the ulvophyceae: discrete genetic characters support a consistent phylogenetic framework.

    PubMed

    Gile, Gillian H; Novis, Philip M; Cragg, David S; Zuccarello, Giuseppe C; Keeling, Patrick J

    2009-01-01

    The systematics of the green algal class Ulvophyceae have been difficult to resolve with ultrastructural and molecular phylogenetic analyses. Therefore, we investigated relationships among ulvophycean orders by determining the distribution of two discrete genetic characters previously identified only in the order Dasycladales. First, Acetabularia acetabulum uses the core translation GTPase Elongation Factor 1alpha (EF-1alpha) while most Chlorophyta instead possess the related GTPase Elongation Factor-Like (EFL). Second, the nuclear genomes of dasycladaleans A. acetabulum and Batophora oerstedii use a rare non-canonical genetic code in which the canonical termination codons TAA and TAG instead encode glutamine. Representatives of Ulvales and Ulotrichales were found to encode EFL, while Caulerpales, Dasycladales, Siphonocladales, and Ignatius tetrasporus were found to encode EF-1alpha, in congruence with the two major lineages previously proposed for the Ulvophyceae. The EF-1alpha of I. tetrasporus supports its relationship with Caulerpales/Dasycladales/Siphonocladales, in agreement with ultrastructural evidence, but contrary to certain small subunit rRNA analyses that place it with Ulvales/Ulotrichales. The same non-canonical genetic code previously described in A. acetabulum was observed in EF-1alpha sequences from Parvocaulis pusillus (Dasycladales), Chaetomorpha coliformis, and Cladophora cf. crinalis (Siphonocladales), whereas Caulerpales use the universal code. This supports a sister relationship between Siphonocladales and Dasycladales and further refines our understanding of ulvophycean phylogeny.

  2. Cosmology with dynamical extra dimensions

    NASA Astrophysics Data System (ADS)

    Erickson, Joel K.

    Nearly every attempt to unify the fundamental forces incorporates the idea of compact extra dimensions. The notion was introduced by Kaluza and Klein in the 1920s and is an essential part of contemporary string theory and M-theory. In most treatments the extra dimensions are static. We consider the consequences of extra dimensions with time-varying radii. The radii are modeled by light scalar fields. These may have unusual properties which produce observable effects, such as non-canonical kinetic energies, couplings to matter and radiation, and non-minimal coupling to gravity. Extra dimensions may be responsible for dark energy in the late universe. The simplest model of dark energy is characterized by its equation of state. We show that constraints placed on realistic models by the universality of free fall, variation of fundamental constants and metric tests of gravity are often stricter than bounds on the equation of state. Testing the equivalence principle maybe an effective way of distinguishing some quintessence models from a cosmological constant. In certain dark energy models the speed of sound is much less than the speed of light. We calculate how this affects the cosmic microwave background and show that the speed of sound may be measurable, provided dark energy is sufficiently dense at decoupling. This is another possible signature of quintessence. Dynamical extra dimensions may have consequences for the early universe. In the cyclic model, the universe is described in terms of a series of contractions and expansions of an extra dimension. The big bang is preceded by a big crunch and quantum fluctuations of the scalar field produce structure in universe. We consider how the fluctuations evolve and build over many cycles and show that there are no observable instabilities or adverse effects. In the cyclic model extra dimensions act as both dark energy and as an agent to cause contraction and a big crunch. Previous theorems suggested that contraction

  3. HER2-encoded mir-4728 forms a receptor-independent circuit with miR-21-5p through the non-canonical poly(A) polymerase PAPD5

    PubMed Central

    Newie, Inga; Søkilde, Rolf; Persson, Helena; Jacomasso, Thiago; Gorbatenko, Andrej; Borg, Åke; de Hoon, Michiel; Pedersen, Stine F.; Rovira, Carlos

    2016-01-01

    We previously reported that the human HER2 gene encodes the intronic microRNA mir-4728, which is overexpressed together with its oncogenic host gene and may act independently of the HER2 receptor. More recently, we also reported that the oncogenic miR-21-5p is regulated by 3′ tailing and trimming by the non-canonical poly(A) polymerase PAPD5 and the ribonuclease PARN. Here we demonstrate a dual function for the HER2 locus in upregulation of miR-21-5p; while HER2 signalling activates transcription of mir-21, miR-4728-3p specifically stabilises miR-21-5p through inhibition of PAPD5. Our results establish a new and unexpected oncogenic role for the HER2 locus that is not currently being targeted by any anti-HER2 therapy. PMID:27752128

  4. Canonical and Non-canonical Reelin Signaling

    PubMed Central

    Bock, Hans H.; May, Petra

    2016-01-01

    Reelin is a large secreted glycoprotein that is essential for correct neuronal positioning during neurodevelopment and is important for synaptic plasticity in the mature brain. Moreover, Reelin is expressed in many extraneuronal tissues; yet the roles of peripheral Reelin are largely unknown. In the brain, many of Reelin’s functions are mediated by a molecular signaling cascade that involves two lipoprotein receptors, apolipoprotein E receptor-2 (Apoer2) and very low density-lipoprotein receptor (Vldlr), the neuronal phosphoprotein Disabled-1 (Dab1), and members of the Src family of protein tyrosine kinases as crucial elements. This core signaling pathway in turn modulates the activity of adaptor proteins and downstream protein kinase cascades, many of which target the neuronal cytoskeleton. However, additional Reelin-binding receptors have been postulated or described, either as coreceptors that are essential for the activation of the “canonical” Reelin signaling cascade involving Apoer2/Vldlr and Dab1, or as receptors that activate alternative or additional signaling pathways. Here we will give an overview of canonical and alternative Reelin signaling pathways, molecular mechanisms involved, and their potential physiological roles in the context of different biological settings. PMID:27445693

  5. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies

    PubMed Central

    Karamitros, Timokratis; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

    2016-01-01

    Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from <1% to 53% of amino acids in each gene exhibiting at least one substitution within the pool of samples. The UL23 gene had one of the highest genetic variabilities at 35.2% in keeping with its role in development of drug resistance. The assembly of accurate, full-length HHV-1 genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal. PMID:27309375

  6. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

    PubMed

    Karamitros, Timokratis; Harrison, Ian; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

    2016-01-01

    Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from <1% to 53% of amino acids in each gene exhibiting at least one substitution within the pool of samples. The UL23 gene had one of the highest genetic variabilities at 35.2% in keeping with its role in development of drug resistance. The assembly of accurate, full-length HHV-1 genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal.

  7. Non-canonical interleukin 23 receptor complex assembly: p40 protein recruits interleukin 12 receptor β1 via site II and induces p19/interleukin 23 receptor interaction via site III.

    PubMed

    Schröder, Jutta; Moll, Jens M; Baran, Paul; Grötzinger, Joachim; Scheller, Jürgen; Floss, Doreen M

    2015-01-02

    IL-23, composed of the cytokine subunit p19 and the soluble α receptor subunit p40, binds to a receptor complex consisting of the IL-23 receptor (IL-23R) and the IL-12 receptor β1 (IL-12Rβ1). Complex formation was hypothesized to follow the "site I-II-III" architectural paradigm, with site I of p19 being required for binding to p40, whereas sites II and III of p19 mediate binding to IL-12Rβ1 and IL-23R, respectively. Here we show that the binding mode of p19 to p40 and of p19 to IL-23R follow the canonical site I and III paradigm but that interaction of IL-23 to IL-12Rβ1 is independent of site II in p19. Instead, binding of IL-23 to the cytokine binding module of IL-12Rβ1 is mediated by domains 1 and 2 of p40 via corresponding site II amino acids of IL-12Rβ1. Moreover, domains 2 and 3 of p40 were sufficient for complex formation with p19 and to induce binding of p19 to IL-23R. The Fc-tagged fusion protein of p40_D2D3/p19 did, however, not act as a competitive IL-23 antagonist but, at higher concentrations, induced proliferation via IL-23R but independent of IL-12Rβ1. On the basis of our experimental validation, we propose a non-canonical topology of the IL-23·IL-23R·IL-12Rβ1 complex. Furthermore, our data help to explain why p40 is an antagonist of IL-23 and IL-12 signaling and show that site II of p19 is dispensable for IL-23 signaling. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. In-Frame Amber Stop Codon Replacement Mutagenesis for the Directed Evolution of Proteins Containing Non-Canonical Amino Acids: Identification of Residues Open to Bio-Orthogonal Modification

    PubMed Central

    Arpino, James A. J.; Baldwin, Amy J.; McGarrity, Adam R.; Tippmann, Eric M.; Jones, D. Dafydd

    2015-01-01

    Expanded genetic code approaches are a powerful means to add new and useful chemistry to proteins at defined residues positions. One such use is the introduction of non-biological reactive chemical handles for site-specific biocompatible orthogonal conjugation of proteins. Due to our currently limited information on the impact of non-canonical amino acids (nAAs) on the protein structure-function relationship, rational protein engineering is a “hit and miss” approach to selecting suitable sites. Furthermore, dogma suggests surface exposed native residues should be the primary focus for introducing new conjugation chemistry. Here we describe a directed evolution approach to introduce and select for in-frame codon replacement to facilitate engineering proteins with nAAs. To demonstrate the approach, the commonly reprogrammed amber stop codon (TAG) was randomly introduced in-frame in two different proteins: the bionanotechnologically important cyt b562 and therapeutic protein KGF. The target protein is linked at the gene level to sfGFP via a TEV protease site. In absence of a nAA, an in-frame TAG will terminate translation resulting in a non-fluorescent cell phenotype. In the presence of a nAA, TAG will encode for nAA incorporation so instilling a green fluorescence phenotype on E. coli. The presence of endogenously expressed TEV proteases separates in vivo target protein from its fusion to sfGFP if expressed as a soluble fusion product. Using this approach, we incorporated an azide reactive handle and identified residue positions amenable to conjugation with a fluorescence dye via strain-promoted azide-alkyne cycloaddition (SPAAC). Interestingly, best positions for efficient conjugation via SPAAC were residues whose native side chain were buried through analysis of their determined 3D structures and thus may not have been chosen through rational protein engineering. Molecular modeling suggests these buried native residues could become partially exposed on

  9. Dynamical system of scalar field from 2-dimension to 3-D and its cosmological implications

    NASA Astrophysics Data System (ADS)

    Fang, Wei; Tu, Hong; Huang, Jiasheng; Shu, Chenggang

    2016-09-01

    We give the three-dimensional dynamical autonomous systems for most of the popular scalar field dark energy models including (phantom) quintessence, (phantom) tachyon, K-essence, and general non-canonical scalar field models, change the dynamical variables from variables (x, y, λ ) to observable related variables (w_{φ }, Ω _{φ }, λ ), and show the intimate relationships between those scalar fields that the three-dimensional system of K-essence can reduce to (phantom) tachyon, general non-canonical scalar field can reduce to (phantom) quintessence and K-essence can also reduce to (phantom) quintessence for some special cases. For the applications of the three-dimensional dynamical systems, we investigate several special cases and give the exactly dynamical solutions in detail. In the end of this paper, we argue that it is more convenient and also has more physical meaning to express the differential equations of dynamical systems in (w_{φ }, Ω _{φ }, λ ) instead of variables (x, y, λ ) and to investigate the dynamical system in three dimensions instead of two dimensions. We also raise a question about the possibility of the chaotic behavior in the spatially flat single scalar field FRW cosmological models in the presence of ordinary matter.

  10. Extra Dimensions

    SciTech Connect

    Hewett, J.

    2004-10-05

    The large separation between the weak scale {approx} 10{sup 3} GeV and the traditional scale of gravity--the Planck scale with M{sub PI} {approx} 10{sup 19} GeV--is one of the most puzzling aspects of nature. The origin of this large ratio, as well as its stability under radiative corrections, demands explanation. This is known as the hierarchy problem. One theoretical means of solving this problem is to introduce Supersymmetry. Alternatively one may hope to address the hierarchy by exploiting the geometry of space time. Specifically, recent theories involve the idea that the 3-spatial dimensions in which we live could be a 3-spatial-dimensional ''membrane'' embedded in a much larger extra dimensional space, and that the hierarchy is generated by the geometry of the additional dimensions. Such ideas have led to extra dimensional theories which have verifiable consequences at the TeV scale. Our knowledge of the weak and strong forces extends down to scales of {approx} (100 GeV){sup -1} (or of order 10{sup -15} mm). On the other hand, we have almost no knowledge of gravity at distances less than roughly a millimeter, as direct tests of the gravitational force at the smallest distances are based on torsion-balance experiments, which are mechanically limited. It is thus conceivable that gravity may behave quite differently from the 3-dimensional Newtonian theory at small distances. This leads to the possibility that matter and non-gravitational forces are confined to our 3-dimensional subspace, whereas gravity may propagate throughout a higher dimensional volume. In this case, the gauge forces are trapped within our 3-dimensional space, unaware of the extra dimensions, and maintain their usual behavior. Gravity, on the other hand, would no longer follow the inverse-square force law at distances smaller than the size of the extra dimensions, as the gravitational equivalent of Gauss' Law mandates that the gravitational field spreads out into the full spatial volume

  11. Rad and Rem are non-canonical G-proteins with respect to the regulatory role of guanine nucleotide binding in Ca(V)1.2 channel regulation.

    PubMed

    Chang, Donald D; Colecraft, Henry M

    2015-12-01

    Rad and Rem are Ras-like G-proteins linked to diverse cardiovascular functions and pathophysiology. Understanding how Rad and Rem are regulated is important for deepened insights into their pathophysiological roles. As in other Ras-like G-proteins, Rad and Rem contain a conserved guanine-nucleotide binding domain (G-domain). Canonically, G-domains are key control modules, functioning as nucleotide-regulated switches of G-protein activity. Whether Rad and Rem G-domains conform to this canonical paradigm is ambiguous. Here, we used multiple functional measurements in HEK293 cells and cardiomyocytes (Ca(V)1.2 currents, Ca(2+) transients, Ca(V)β binding) as biosensors to probe the role of the G-domain in regulation of Rad and Rem function. We utilized Rad(S105N) and Rem(T94N), which are the cognate mutants to Ras(S17N), a dominant-negative variant of Ras that displays decreased nucleotide binding affinity. In HEK293 cells, over-expression of either Rad(S105N) or Rem(T94N) strongly inhibited reconstituted Ca(V)1.2 currents to the same extent as their wild-type (wt) counterparts, contrasting with reports that Rad(S105N) is functionally inert in HEK293 cells. Adenovirus-mediated expression of either wt Rad or Rad(S105N) in cardiomyocytes dramatically blocked L-type calcium current (I(Ca,L)) and inhibited Ca(2+)-induced Ca(2+) release, contradicting reports that Rad(S105N) acts as a dominant negative in heart. By contrast, Rem(T94N) was significantly less effective than wt Rem at inhibiting I(Ca,L) and Ca(2+) transients in cardiomyocytes. FRET analyses in cardiomyocytes revealed that both Rad(S105N) and Rem(T94N) had moderately reduced binding affinity for Ca(V)βs relative to their wt counterparts. The results indicate Rad and Rem are non-canonical G-proteins with respect to the regulatory role of their G-domain in Ca(V)1.2 regulation. © 2015 The Authors. The Journal of Physiology © 2015 The Physiological Society.

  12. Dimension stone

    USGS Publications Warehouse

    Dolley, T.P.

    2003-01-01

    Dimension stone can be defined as natural rock material quarried to obtain blocks or slabs that meet specifications as to size (width, length and thickness) and shape for architectural or engineering purposes. Color, grain texture and pattern, and surface finish of the stone are also normal requirements. Other important selection criteria are durability (based on mineral composition, hardness and past performance), strength and the ability of the stone to take a polish.

  13. Dimension of chaotic attractors

    SciTech Connect

    Farmer, J.D.; Ott, E.; Yorke, J.A.

    1982-09-01

    Dimension is perhaps the most basic property of an attractor. In this paper we discuss a variety of different definitions of dimension, compute their values for a typical example, and review previous work on the dimension of chaotic attractors. The relevant definitions of dimension are of two general types, those that depend only on metric properties, and those that depend on probabilistic properties (that is, they depend on the frequency with which a typical trajectory visits different regions of the attractor). Both our example and the previous work that we review support the conclusion that all of the probabilistic dimensions take on the same value, which we call the dimension of the natural measure, and all of the metric dimensions take on a common value, which we call the fractal dimension. Furthermore, the dimension of the natural measure is typically equal to the Lyapunov dimension, which is defined in terms of Lyapunov numbers, and thus is usually far easier to calculate than any other definition. Because it is computable and more physically relevant, we feel that the dimension of the natural measure is more important than the fractal dimension.

  14. Doing without dimensions

    NASA Astrophysics Data System (ADS)

    Spurgin, C. B.

    1986-03-01

    The author discusses the concept of dimensions of a physical quantity, and the relationship between derived units (expressed in terms of their base units) and the dimensions of the derived quantities. He calls for the replacement of 'dimensions' by base units in the GCE A-level syllabus and provides some recommendations to GCE examining boards.

  15. Dimensions of Educational Need.

    ERIC Educational Resources Information Center

    Johns, Roe L., Ed.; And Others

    Roe L. Johns and J. Alan Thomas survey the problem of educational need; and Kern Alexander considers the implications of the dimensions of educational need for school financing. Dimensions of need in the following areas are defined: early childhood and basic elementary and secondary education, by William P. McLure; educational programs for…

  16. Navigating between the Dimensions

    ERIC Educational Resources Information Center

    Fleron, Julian F.; Ecke, Volker

    2011-01-01

    Generations have been inspired by Edwin A. Abbott's profound tour of the dimensions in his novella "Flatland: A Romance of Many Dimensions" (1884). This well-known satire is the story of a flat land inhabited by geometric shapes trying to navigate the subtleties of their geometric, social, and political positions. In this article, the authors…

  17. Navigating between the Dimensions

    ERIC Educational Resources Information Center

    Fleron, Julian F.; Ecke, Volker

    2011-01-01

    Generations have been inspired by Edwin A. Abbott's profound tour of the dimensions in his novella "Flatland: A Romance of Many Dimensions" (1884). This well-known satire is the story of a flat land inhabited by geometric shapes trying to navigate the subtleties of their geometric, social, and political positions. In this article, the authors…

  18. The Qualitative Dimension.

    ERIC Educational Resources Information Center

    Lodge-Peters, Dianne S.

    The qualitative dimension of educational research methodology is explored, and the literature of qualitative methodology is reviewed so researchers may (1) understand more fully the qualitative dimension as it, in turn, fits within the parameters of educational research as a whole, and (2) have more informed access to the sometimes daunting array…

  19. A non-canonical mismatch repair pathway in prokaryotes

    PubMed Central

    Castañeda-García, A.; Prieto, A. I.; Rodríguez-Beltrán, J.; Alonso, N.; Cantillon, D.; Costas, C.; Pérez-Lago, L.; Zegeye, E. D.; Herranz, M.; Plociński, P.; Tonjum, T.; García de Viedma, D.; Paget, M.; Waddell, S. J.; Rojas, A. M.; Doherty, A. J.; Blázquez, J.

    2017-01-01

    Mismatch repair (MMR) is a near ubiquitous pathway, essential for the maintenance of genome stability. Members of the MutS and MutL protein families perform key steps in mismatch correction. Despite the major importance of this repair pathway, MutS–MutL are absent in almost all Actinobacteria and many Archaea. However, these organisms exhibit rates and spectra of spontaneous mutations similar to MMR-bearing species, suggesting the existence of an alternative to the canonical MutS–MutL-based MMR. Here we report that Mycobacterium smegmatis NucS/EndoMS, a putative endonuclease with no structural homology to known MMR factors, is required for mutation avoidance and anti-recombination, hallmarks of the canonical MMR. Furthermore, phenotypic analysis of naturally occurring polymorphic NucS in a M. smegmatis surrogate model, suggests the existence of M. tuberculosis mutator strains. The phylogenetic analysis of NucS indicates a complex evolutionary process leading to a disperse distribution pattern in prokaryotes. Together, these findings indicate that distinct pathways for MMR have evolved at least twice in nature. PMID:28128207

  20. Nonlinear superhorizon perturbations of non-canonical scalar field

    SciTech Connect

    Takamizu, Yu-ichi; Mukohyama, Shinji E-mail: shinji.mukohyama@ipmu.jp

    2009-01-15

    We develop a theory of non-linear cosmological perturbations at superhorizon scales for a scalar field with a Lagrangian of the form P(X,{phi}), where X = -{partial_derivative}{sup {mu}}{phi}{partial_derivative}{sub {mu}}{phi} and {phi} is the scalar field. We employ the ADM formalism and the spatial gradient expansion approach to obtain general solutions valid up to the second order in the gradient expansion. This formulation can be applied to, for example, DBI inflation models to investigate superhorizon evolution of non-Gaussianities. With slight modification, we also obtain general solutions valid up to the same order for a perfect fluid with a general equation of state P = P({rho})

  1. A non-canonical mismatch repair pathway in prokaryotes.

    PubMed

    Castañeda-García, A; Prieto, A I; Rodríguez-Beltrán, J; Alonso, N; Cantillon, D; Costas, C; Pérez-Lago, L; Zegeye, E D; Herranz, M; Plociński, P; Tonjum, T; García de Viedma, D; Paget, M; Waddell, S J; Rojas, A M; Doherty, A J; Blázquez, J

    2017-01-27

    Mismatch repair (MMR) is a near ubiquitous pathway, essential for the maintenance of genome stability. Members of the MutS and MutL protein families perform key steps in mismatch correction. Despite the major importance of this repair pathway, MutS-MutL are absent in almost all Actinobacteria and many Archaea. However, these organisms exhibit rates and spectra of spontaneous mutations similar to MMR-bearing species, suggesting the existence of an alternative to the canonical MutS-MutL-based MMR. Here we report that Mycobacterium smegmatis NucS/EndoMS, a putative endonuclease with no structural homology to known MMR factors, is required for mutation avoidance and anti-recombination, hallmarks of the canonical MMR. Furthermore, phenotypic analysis of naturally occurring polymorphic NucS in a M. smegmatis surrogate model, suggests the existence of M. tuberculosis mutator strains. The phylogenetic analysis of NucS indicates a complex evolutionary process leading to a disperse distribution pattern in prokaryotes. Together, these findings indicate that distinct pathways for MMR have evolved at least twice in nature.

  2. Activation of B cells by non-canonical helper signals.

    PubMed

    Cerutti, Andrea; Cols, Montserrat; Puga, Irene

    2012-09-01

    Cognate interaction between T and B lymphocytes of the adaptive immune system is essential for the production of high-affinity antibodies against microbes, and for the establishment of long-term immunological memory. Growing evidence shows that--in addition to presenting antigens to T and B cells--macrophages, dendritic cells and other cells of the innate immune system provide activating signals to B cells, as well as survival signals to antibody-secreting plasma cells. Here, we discuss how these innate immune cells contribute to the induction of highly diversified and temporally sustained antibody responses, both systemically and at mucosal sites of antigen entry.

  3. The dimensions of indexing.

    PubMed

    Wilbur, W John; Kim, Won

    2003-01-01

    Indexing of documents is an important strategy intended to make the literature more readily available to the user. Here we describe several dimensions of indexing that are important if indexing is to be optimal. These dimensions are coverage, predictability, and transparency. MeSH terms and text words are compared in MEDLINE in regard to these dimensions. Part of our analysis consists in applying AdaBoost with decisions trees as the weak learners to estimate how reliably index terms are being assigned and how complex the criteria are by which they are being assigned. Our conclusions are that MeSH terms are more predictable and more transparent than text words.

  4. On universal quantum dimensions

    NASA Astrophysics Data System (ADS)

    Mkrtchyan, R. L.

    2017-08-01

    We represent in the universal form restricted one-instanton partition function of supersymmetric Yang-Mills theory. It is based on the derivation of universal expressions for quantum dimensions (universal characters) of Cartan powers of adjoint and some other series of irreps of simple Lie algebras. These formulae also provide a proof of formulae for universal quantum dimensions for low-dimensional representations, needed in derivation of universal knot polynomials (i.e. colored Wilson averages of Chern-Simons theory on 3d sphere). As a check of the (complicated) formulae for universal quantum dimensions we prove numerically Deligne's hypothesis on universal characters for symmetric cube of adjoint representation.

  5. Dimensions of Aesthetic Perception.

    ERIC Educational Resources Information Center

    Biaggio, Mary Kay; Supplee, Katherine A.

    1983-01-01

    Examines the validity of three dimensions of aesthetic perception: hedonic value, arousal, and uncertainty. Hedonic interest and arousal factors were found to differ from factors previously reported, while the uncertainty factor paralleled that previously reported. (Author/RH)

  6. Polyhedra and Higher Dimensions.

    ERIC Educational Resources Information Center

    Scott, Paul

    1988-01-01

    Describes the definition and characteristics of a regular polyhedron, tessellation, and pseudopolyhedra with diagrams. Discusses the nature of simplex, hypercube, and cross-polytope in the fourth dimension and beyond. (YP)

  7. Dimensions of Aesthetic Perception.

    ERIC Educational Resources Information Center

    Biaggio, Mary Kay; Supplee, Katherine A.

    1983-01-01

    Examines the validity of three dimensions of aesthetic perception: hedonic value, arousal, and uncertainty. Hedonic interest and arousal factors were found to differ from factors previously reported, while the uncertainty factor paralleled that previously reported. (Author/RH)

  8. Phenylalanine ammonia lyase from Arabidopsis thaliana (AtPAL2): a potent enzyme for the synthesis of non-canonical aromatic alpha-amino acids: Part I: Comparative characterization to the enzymes from Petroselinum crispum (PcPAL1) and Rhodosporidium toruloides (RtPAL).

    PubMed

    Dreßen, Alana; Hilberath, Thomas; Mackfeld, Ursula; Billmeier, Arne; Rudat, Jens; Pohl, Martina

    2017-04-06

    Phenylalanine ammonia lyase (PAL) from Arabidopsis thaliana (AtPAL2) was comparatively characterized to the well-studied enzyme from parsley (PcPAL1) and Rhodosporidium toruloides (RtPAL) with respect to kinetic parameters for the deamination and the amination reaction, pH- and temperature optima and the substrate range of the amination reaction. Whereas both plant enzymes are specific for phenylalanine, the bifunctional enzyme from Rhodosporidium toruloides shows KM-values for L-Phe and L-Tyr in the same order of magnitude and, compared to both plant enzymes, a 10-15-fold higher activity. At 30°C all enzymes were sufficiently stable with half-lives of 3.4days (PcPAL1), 4.6days (AtPAL2) and 9.7days (RtPAL/TAL). Very good results for the amination of various trans-cinnamic acid derivatives were obtained using E. coli cells as whole cell biocatalysts in ammonium carbonate buffer. Investigation of the substrate ranges gave interesting results for the newly tested enzymes from A. thaliana and R. toruloides. Only the latter accepts besides 4-hydroxy-CA also 3-methoxy-4-hydroxy-CA as a substrate, which is an interesting intermediate for the formation of pharmaceutically relevant L-Dopa. AtPAL2 is a very good catalyst for the formation of (S)-3-F-Phe, (S)-4-F-Phe and (S)-2-Cl-Phe. Such non-canonical amino acids are valuable building blocks for the formation of various drug molecules.

  9. Rokhlin Dimension for Flows

    NASA Astrophysics Data System (ADS)

    Hirshberg, Ilan; Szabó, Gábor; Winter, Wilhelm; Wu, Jianchao

    2016-10-01

    We introduce a notion of Rokhlin dimension for one parameter automorphism groups of {C^*} -algebras. This generalizes Kishimoto's Rokhlin property for flows, and is analogous to the notion of Rokhlin dimension for actions of the integers and other discrete groups introduced by the authors and Zacharias in previous papers. We show that finite nuclear dimension and absorption of a strongly self-absorbing {C^*} -algebra are preserved under forming crossed products by flows with finite Rokhlin dimension, and that these crossed products are stable. Furthermore, we show that a flow on a commutative {C^*} -algebra arising from a free topological flow has finite Rokhlin dimension, whenever the spectrum is a locally compact metrizable space with finite covering dimension. For flows that are both free and minimal, this has strong consequences for the associated crossed product {C^{*}} -algebras: Those containing a non-zero projection are classified by the Elliott invariant (for compact manifolds this consists of topological {K} -theory together with the space of invariant probability measures and a natural pairing given by the Ruelle-Sullivan map).

  10. Rokhlin Dimension for Flows

    NASA Astrophysics Data System (ADS)

    Hirshberg, Ilan; Szabó, Gábor; Winter, Wilhelm; Wu, Jianchao

    2017-07-01

    We introduce a notion of Rokhlin dimension for one parameter automorphism groups of {C^*}-algebras. This generalizes Kishimoto's Rokhlin property for flows, and is analogous to the notion of Rokhlin dimension for actions of the integers and other discrete groups introduced by the authors and Zacharias in previous papers. We show that finite nuclear dimension and absorption of a strongly self-absorbing {C^*}-algebra are preserved under forming crossed products by flows with finite Rokhlin dimension, and that these crossed products are stable. Furthermore, we show that a flow on a commutative {C^*}-algebra arising from a free topological flow has finite Rokhlin dimension, whenever the spectrum is a locally compact metrizable space with finite covering dimension. For flows that are both free and minimal, this has strong consequences for the associated crossed product {C^{*}}-algebras: Those containing a non-zero projection are classified by the Elliott invariant (for compact manifolds this consists of topological {K}-theory together with the space of invariant probability measures and a natural pairing given by the Ruelle-Sullivan map).

  11. Perceptual dimensions differentiate emotions.

    PubMed

    Cavanaugh, Lisa A; MacInnis, Deborah J; Weiss, Allen M

    2015-08-26

    Individuals often describe objects in their world in terms of perceptual dimensions that span a variety of modalities; the visual (e.g., brightness: dark-bright), the auditory (e.g., loudness: quiet-loud), the gustatory (e.g., taste: sour-sweet), the tactile (e.g., hardness: soft vs. hard) and the kinaesthetic (e.g., speed: slow-fast). We ask whether individuals use perceptual dimensions to differentiate emotions from one another. Participants in two studies (one where respondents reported on abstract emotion concepts and a second where they reported on specific emotion episodes) rated the extent to which features anchoring 29 perceptual dimensions (e.g., temperature, texture and taste) are associated with 8 emotions (anger, fear, sadness, guilt, contentment, gratitude, pride and excitement). Results revealed that in both studies perceptual dimensions differentiate positive from negative emotions and high arousal from low arousal emotions. They also differentiate among emotions that are similar in arousal and valence (e.g., high arousal negative emotions such as anger and fear). Specific features that anchor particular perceptual dimensions (e.g., hot vs. cold) are also differentially associated with emotions.

  12. The Dimensions of Indexing

    PubMed Central

    Wilbur, W. John; Kim, Won

    2003-01-01

    Indexing of documents is an important strategy intended to make the literature more readily available to the user. Here we describe several dimensions of indexing that are important if indexing is to be optimal. These dimensions are coverage, predictability, and transparency. MeSH® terms and text words are compared in MEDLINE® in regard to these dimensions. Part of our analysis consists in applying AdaBoost with decision trees as the weak learners to estimate how reliably index terms are being assigned and how complex the criteria are by which they are being assigned. Our conclusions are that MeSH terms are more predictable and more transparent than text words. PMID:14728266

  13. Selective Attention to Perceptual Dimensions and Switching between Dimensions

    ERIC Educational Resources Information Center

    Meiran, Nachshon; Dimov, Eduard; Ganel, Tzvi

    2013-01-01

    In the present experiments, the question being addressed was whether switching attention between perceptual dimensions and selective attention to dimensions are processes that compete over a common resource? Attention to perceptual dimensions is usually studied by requiring participants to ignore a never-relevant dimension. Selection failure…

  14. Selective Attention to Perceptual Dimensions and Switching between Dimensions

    ERIC Educational Resources Information Center

    Meiran, Nachshon; Dimov, Eduard; Ganel, Tzvi

    2013-01-01

    In the present experiments, the question being addressed was whether switching attention between perceptual dimensions and selective attention to dimensions are processes that compete over a common resource? Attention to perceptual dimensions is usually studied by requiring participants to ignore a never-relevant dimension. Selection failure…

  15. Dimensions of Dialect.

    ERIC Educational Resources Information Center

    Evertts, Eldonna L., Ed.

    This collection of articles discusses social dialects, the problems that dialects cause the disadvantaged, and how these problems can be overcome in curriculum planning and classroom practice. Articles are (1) "English: New Dimensions and New Demands" by Muriel Crosby, (2) "A Checklist of Significant Features for Discriminating Social Dialects" by…

  16. Physics in One Dimension

    ERIC Educational Resources Information Center

    Bertel, Erminald

    2013-01-01

    Due to progress in nanotechnology high-quality quantum wires can nowadays be fabricated. The behavior of particles in one dimension differs significantly from that in three-dimensional (3D) systems, yet the physics of such low-dimensional systems is generally not very well represented in standard undergraduate or graduate curricula. For instance,…

  17. Constructing gravitational dimensions

    NASA Astrophysics Data System (ADS)

    Schwartz, Matthew

    2003-07-01

    It would be extremely useful to know whether a particular low energy effective theory might have come from a compactification of a higher dimensional space. Here, this problem is approached from the ground up by considering theories with multiple interacting massive gravitons. It is actually very difficult to construct discrete gravitational dimensions which have a local continuum limit. In fact, any model with only nearest neighbor interactions is doomed. If we could find a non-linear extension for the Fierz-Pauli Lagrangian for a graviton of mass mg, which does not break down until the scale Λ2=(mgMPl), this could be used to construct a large class of models whose continuum limit is local in the extra dimension. But this is shown to be impossible: a theory with a single graviton must break down by Λ3=(m2gMPl)1/3. Next, we look at how the discretization prescribed by the truncation of the Kaluza-Klein tower of an honest extra dimension raises the scale of strong coupling. It dictates an intricate set of interactions among various fields which conspire to soften the strongest scattering amplitudes and allow for a local continuum limit, at least at the tree level. A number of candidate symmetries associated with locality in the discretized dimension are also discussed.

  18. Dimensions of Nonverbal Communication.

    ERIC Educational Resources Information Center

    Overmier, Mary; And Others

    After a brief description of the dimensions of nonverbal communication, this booklet presents 21 activities that deal with nonverbal communication. Activities in the booklet involve body movements (kinesics), facial expressions, eye movements, perception and use of space (proxemics), haptics (touch), paralinguistics (vocal elements that accompany…

  19. Moving between Dimensions

    ERIC Educational Resources Information Center

    Stephenson, Paul

    2012-01-01

    The first word of this item is "imagine". This instruction has the potential to signal a journey through a world of geometry that might leave you spellbound. On the other hand, it could be the start of a roller-coaster ride through three dimensions that will tax both your imagination, and your powers of visualisation. It is likely that you will…

  20. Dimensions of Delinquency.

    ERIC Educational Resources Information Center

    Wunderlich, Richard A.

    1985-01-01

    In response to research questioning the utility of the Jesness Inventory in predicting and differentiating delinquency, this study isolated the personality dimensions of 422 adjudicated, noninstitutionalized adolescents by item level factor analysis. The resulting three factors--Mistrust, Social Pessimism, and Hypersensitivity--were compared with…

  1. Moving between Dimensions

    ERIC Educational Resources Information Center

    Stephenson, Paul

    2012-01-01

    The first word of this item is "imagine". This instruction has the potential to signal a journey through a world of geometry that might leave you spellbound. On the other hand, it could be the start of a roller-coaster ride through three dimensions that will tax both your imagination, and your powers of visualisation. It is likely that you will…

  2. Extra Dimensions of Space

    ERIC Educational Resources Information Center

    Lincoln, Don

    2013-01-01

    They say that there is no such thing as a stupid question. In a pedagogically pure sense, that's probably true. But some questions do seem to flirt dangerously close to being really quite ridiculous. One such question might well be, "How many dimensions of space are there?" I mean, it's pretty obvious that there are three:…

  3. Big Mysteries: Extra Dimensions

    SciTech Connect

    Lincoln, Don

    2014-06-10

    The weakness of gravity compared to the other subatomic forces is a real mystery. While nobody knows the answer, one credible solution is that gravity has access to more spatial dimensions than the other three known forces. In this video, Fermilab's Dr. Don Lincoln describes this idea, with the help of some very urbane characters.

  4. Extra Dimensions of Space

    ERIC Educational Resources Information Center

    Lincoln, Don

    2013-01-01

    They say that there is no such thing as a stupid question. In a pedagogically pure sense, that's probably true. But some questions do seem to flirt dangerously close to being really quite ridiculous. One such question might well be, "How many dimensions of space are there?" I mean, it's pretty obvious that there are three:…

  5. Big Mysteries: Extra Dimensions

    ScienceCinema

    Lincoln, Don

    2016-07-12

    The weakness of gravity compared to the other subatomic forces is a real mystery. While nobody knows the answer, one credible solution is that gravity has access to more spatial dimensions than the other three known forces. In this video, Fermilab's Dr. Don Lincoln describes this idea, with the help of some very urbane characters.

  6. Cultural dimensions of learning

    NASA Astrophysics Data System (ADS)

    Eyford, Glen A.

    1990-06-01

    How, what, when and where we learn is frequently discussed, as are content versus process, or right brain versus left brain learning. What is usually missing is the cultural dimension. This is not an easy concept to define, but various aspects can be identified. The World Decade for Cultural Development emphasizes the need for a counterbalance to a quantitative, economic approach. In the last century poets also warned against brutalizing materialism, and Sorokin and others have described culture more recently in terms of cohesive basic values expressed through aesthetics and institutions. Bloom's taxonomy incorporates the category of affective learning, which internalizes values. If cultural learning goes beyond knowledge acquisition, perhaps the surest way of understanding the cultural dimension of learning is to examine the aesthetic experience. This can use myths, metaphors and symbols, and to teach and learn by using these can help to unlock the human potential for vision and creativity.

  7. Introduction to Extra Dimensions

    SciTech Connect

    Rizzo, Thomas G.; /SLAC

    2010-04-29

    Extra dimensions provide a very useful tool in addressing a number of the fundamental problems faced by the Standard Model. The following provides a very basic introduction to this very broad subject area as given at the VIII School of the Gravitational and Mathematical Physics Division of the Mexican Physical Society in December 2009. Some prospects for extra dimensional searches at the 7 TeV LHC with {approx}1 fb{sup -1} of integrated luminosity are provided.

  8. Introduction to Extra Dimensions

    SciTech Connect

    Rizzo, Thomas G.

    2010-07-12

    Extra dimensions provide a very useful tool in addressing a number of the fundamental problems faced by the Standard Model. The following provides a very basic introduction to this very broad subject area as given at the VIII School of the Gravitational and Mathematical Physics Division of the Mexican Physical Society in December 2009. Some prospects for extra dimensional searches at the 7 TeV LHC with {approx}1 fb{sup -1} of integrated luminosity are provided.

  9. Infinitely Large New Dimensions

    SciTech Connect

    Arkani-Hamed, Nima; Dimopoulos, Savas; Dvali, Gia; Kaloper, Nemanja

    1999-07-29

    We construct intersecting brane configurations in Anti-de-Sitter space localizing gravity to the intersection region, with any number n of extra dimensions. This allows us to construct two kinds of theories with infinitely large new dimensions, TeV scale quantum gravity and sub-millimeter deviations from Newton's Law. The effective 4D Planck scale M{sub Pl} is determined in terms of the fundamental Planck scale M{sub *} and the AdS radius of curvature L via the familiar relation M{sub Pl}{sup 2} {approx} M{sub *}{sup 2+n} L{sup n}; L acts as an effective radius of compactification for gravity on the intersection. Taking M{sub *} {approx} TeV and L {approx} sub-mm reproduces the phenomenology of theories with large extra dimensions. Alternately, taking M{sub *} {approx} L{sup -1} {approx} M{sub Pl}, and placing our 3-brane a distance {approx} 100M{sub Pl}{sup -1} away from the intersection gives us a theory with an exponential determination of the Weak/Planck hierarchy.

  10. Inhomogeneous compact extra dimensions

    NASA Astrophysics Data System (ADS)

    Bronnikov, K. A.; Budaev, R. I.; Grobov, A. V.; Dmitriev, A. E.; Rubin, Sergey G.

    2017-10-01

    We show that an inhomogeneous compact extra space possesses two necessary features— their existence does not contradict the observable value of the cosmological constant Λ4 in pure f(R) theory, and the extra dimensions are stable relative to the "radion mode" of perturbations, the only mode considered. For a two-dimensional extra space, both analytical and numerical solutions for the metric are found, able to provide a zero or arbitrarily small Λ4. A no-go theorem has also been proved, that maximally symmetric compact extra spaces are inconsistent with 4D Minkowski space in the framework of pure f(R) gravity.

  11. Extra Dimensions of Space

    NASA Astrophysics Data System (ADS)

    Lincoln, Don

    2013-09-01

    They say that there is no such thing as a stupid question. In a pedagogically pure sense, that's probably true. But some questions do seem to flirt dangerously close to being really quite ridiculous. One such question might well be, "How many dimensions of space are there?" I mean, it's pretty obvious that there are three: left/right, up/down, and forward/backward. No matter how you express an object's coordinate, be it Cartesian, spherical, cylindrical, or something exotic, it's eminently clear that we live in a three-dimensional universe.

  12. Bond percolation in higher dimensions

    NASA Astrophysics Data System (ADS)

    Corwin, Eric I.; Stinchcombe, Robin; Thorpe, M. F.

    2013-07-01

    We collect results for bond percolation on various lattices from two to fourteen dimensions that, in the limit of large dimension d or number of neighbors z, smoothly approach a randomly diluted Erdős-Rényi graph. We include results on bond-diluted hypersphere packs in up to nine dimensions, which show the mean coordination, excess kurtosis, and skewness evolving smoothly with dimension towards the Erdős-Rényi limit.

  13. Flying in Two Dimensions

    NASA Astrophysics Data System (ADS)

    Prakash, Manu; Bardon, Thibaut

    2012-11-01

    It has long been proposed that insect flight might have evolved on a fluid interface. Surface of a pond provides an ecological niche which is exploited by a large number of species capable of locomotion on a fluid interface. Here we describe the discovery of constrained flight in two dimensions as a novel mode of locomotion used by water lily beetles (genus Galerucella). Because water lily beetles are also capable of three-dimensional free flight, this novel two-dimensional locomotion provides us with a unique model system to explore both the transition between two and three dimensional flight and the associated energetics. Here we present a comparative analysis of this transition in terms of wing stroke angles associated with two and three dimensional flight, as well as modeling surface tension forces on both the horizontal and vertical axes. Special attention is paid to the dynamics and energetics of flight in two-dimensions, focusing on the interaction of the wing strokes with the fluid interface and the capillary-gravity wave drag associated with two-dimensional propulsion. Current Address: Ecole Polytechnique, France.

  14. Correlation dimension of financial market

    NASA Astrophysics Data System (ADS)

    Nie, Chun-Xiao

    2017-05-01

    In this paper, correlation dimension is applied to financial data analysis. We calculate the correlation dimensions of some real market data and find that the dimensions are significantly smaller than those of the simulation data based on geometric Brownian motion. Based on the analysis of the Chinese and US stock market data, the main results are as follows. First, by calculating three data sets for the Chinese and US market, we find that large market volatility leads to a significant decrease in the dimensions. Second, based on 5-min stock price data, we find that the Chinese market dimension is significantly larger than the US market; this shows a significant difference between the two markets for high frequency data. Third, we randomly extract stocks from a stock set and calculate the correlation dimensions, and find that the average value of these dimensions is close to the dimension of the original set. In addition, we analyse the intuitional meaning of the relevant dimensions used in this paper, which are directly related to the average degree of the financial threshold network. The dimension measures the speed of the average degree that varies with the threshold value. A smaller dimension means that the rate of change is slower.

  15. FRACTAL DIMENSION OF GALAXY ISOPHOTES

    SciTech Connect

    Thanki, Sandip; Rhee, George; Lepp, Stephen E-mail: grhee@physics.unlv.edu

    2009-09-15

    In this paper we investigate the use of the fractal dimension of galaxy isophotes in galaxy classification. We have applied two different methods for determining fractal dimensions to the isophotes of elliptical and spiral galaxies derived from CCD images. We conclude that fractal dimension alone is not a reliable tool but that combined with other parameters in a neural net algorithm the fractal dimension could be of use. In particular, we have used three parameters to segregate the ellipticals and lenticulars from the spiral galaxies in our sample. These three parameters are the correlation fractal dimension D {sub corr}, the difference between the correlation fractal dimension and the capacity fractal dimension D {sub corr} - D {sub cap}, and, thirdly, the B - V color of the galaxy.

  16. Action languages: Dimensions, effects

    NASA Technical Reports Server (NTRS)

    Hayes, Daniel G.; Streeter, Gordon

    1989-01-01

    Dimensions of action languages are discussed for communication between humans and machines, and the message handling capabilities of object oriented programming systems are examined. Design of action languages is seen to be very contextual. Economical and effective design will depend on features of situations, the tasks intended to be accomplished, and the nature of the devices themselves. Current object oriented systems turn out to have fairly simple and straightforward message handling facilities, which in themselves do little to buffer action or even in some cases to handle competing messages. Even so, it is possible to program a certain amount of discretion about how they react to messages. Such thoughtfulness and perhaps relative autonomy of program modules seems prerequisite to future systems to handle complex interactions in changing situations.

  17. Phenomenology of Extra Dimensions

    SciTech Connect

    Hewett, J.L.; /SLAC

    2006-11-07

    If the structure of spacetime is different than that readily observed, gravitational physics, particle physics and cosmology are all immediately affected. The physics of extra dimensions offers new insights and solutions to fundamental questions arising in these fields. Novel ideas and frameworks are continuously born and evolved. They make use of string theoretical features and tools and they may reveal if and how the 11-dimensional string theory is relevant to our four-dimensional world. We have outlined some of the experimental observations in particle and gravitational physics as well as astrophysical and cosmological considerations that can constrain or confirm these scenarios. These developing ideas and the wide interdisciplinary experimental program that is charted out to investigate them mark a renewed effort to describe the dynamics behind spacetime. We look forward to the discovery of a higher dimensional spacetime.

  18. The Dimension of Information

    NASA Astrophysics Data System (ADS)

    Preuss, Lucien

    2008-11-01

    To implement Jaynes' vision [1] of applications of Shannon's ideas outside Communication Theory proper, the dimension of information must be clarified, mainly because general applications provide no ready-made set of discrete, mutually exclusive and exhaustive "events" which could play a rôle similar to that of the alphabet which communication theory implicitely supposes known from the outset. For instance, a doctor's "alphabet" may be said to consist of readily distinguishable bundles of symptoms, cures, etc., each of which he considers specific enough to describe an illness of interest. Setting up an appropriate alphabet requires learning, in the same way as a child painfully learns to read letters, and a quantitative assessment of this task depends crucially on the dimension of information. Information is an extensive property, as explicited by the standard equation I = N.H for the amount of information delivered by a succession of N events. All other things remaining equal, doubling the length of a message doubles the amount of information. But by definition, Shannon's uncertainty H on the right-hand side of the equation is a rate, i.e. an intensive property, as illustrated by the fact that the simultaneous throw of two true and identical dice removes less than twice the uncertainty removed by the throw of a single die, as is well-known to poker-players. If the above equation is to be dimensionally consistent, N can not be a pure number, but must have an extensive dimension of its own. The obvious question "which?" was swept under the rug by von Neumann's famous quip [3], which advised to call H an entropy, thereby suggesting improperly that H by itself-without the factor N-is an extensive property like physical entropy. But H only evaluates an amount of information when multiplied by N, which measures an amount of order akin to the chronological order without which any message becomes garbage. In analogy with the decomposition E S.T of energy E into the pair

  19. Scientific Visualization of Extra Dimensions

    NASA Astrophysics Data System (ADS)

    Black, Don V.

    2010-10-01

    In the 21st Century, many theoretical physicists claim that higher dimensions may indeed exist. Arkani-Hamed, Dimopoulos, & Dvali (ADD) and Randall-Sundrum (RS), in addition to Kaluza-Klein (KK) and M-string theorists, have introduced reasonable explanations for the existence of heretofore ``invisible'' higher dimensions. Whether or not these extra dimensions actually exist is irrelevant to their contributions to the visionary conceptualization associated with novel and improved mathematical and physical analysis. Envisioning extra dimensions beyond the three of common experience is a daunting challenge for three dimensional observers. Intuition relies on experience gained in a three dimensional environment. Gaining experience with virtual four dimensional objects and virtual three manifolds in four-space on a personal computer may provide the basis for an intuitive grasp of four dimensions. This presentation is a video ``outtake'' of the author's research into ``Visualizing Extra Spatial Dimensions'' at the University of California at Irvine.

  20. Johannes Kepler and Extra Dimensions

    NASA Astrophysics Data System (ADS)

    Hendry, Archibald W.

    2004-02-01

    How many dimensions are there? The answer used to be four — three spatial and one time dimension. Maybe it still is, though nowadays we hear that the answer may be more, perhaps many more. Many of our students have heard about this on television or read about it. They want to know more. Why do physicists think we need more than three spatial dimensions? What's the point of it all?

  1. Endogeneity in High Dimensions

    PubMed Central

    Fan, Jianqing; Liao, Yuan

    2014-01-01

    Most papers on high-dimensional statistics are based on the assumption that none of the regressors are correlated with the regression error, namely, they are exogenous. Yet, endogeneity can arise incidentally from a large pool of regressors in a high-dimensional regression. This causes the inconsistency of the penalized least-squares method and possible false scientific discoveries. A necessary condition for model selection consistency of a general class of penalized regression methods is given, which allows us to prove formally the inconsistency claim. To cope with the incidental endogeneity, we construct a novel penalized focused generalized method of moments (FGMM) criterion function. The FGMM effectively achieves the dimension reduction and applies the instrumental variable methods. We show that it possesses the oracle property even in the presence of endogenous predictors, and that the solution is also near global minimum under the over-identification assumption. Finally, we also show how the semi-parametric efficiency of estimation can be achieved via a two-step approach. PMID:25580040

  2. Electrons in one dimension

    PubMed Central

    Berggren, K.-F.; Pepper, M.

    2010-01-01

    In this article, we present a summary of the current status of the study of the transport of electrons confined to one dimension in very low disorder GaAs–AlGaAs heterostructures. By means of suitably located gates and application of a voltage to ‘electrostatically squeeze’ the electronic wave functions, it is possible to produce a controllable size quantization and a transition from two-dimensional transport. If the length of the electron channel is sufficiently short, then transport is ballistic and the quantized subbands each have a conductance equal to the fundamental quantum value 2e2/h, where the factor of 2 arises from the spin degeneracy. This mode of conduction is discussed, and it is shown that a number of many-body effects can be observed. These effects are discussed as in the spin-incoherent regime, which is entered when the separation of the electrons is increased and the exchange energy is less than kT. Finally, results are presented in the regime where the confinement potential is decreased and the electron configuration relaxes to minimize the electron–electron repulsion to move towards a two-dimensional array. It is shown that the ground state is no longer a line determined by the size quantization alone, but becomes two distinct rows arising from minimization of the electrostatic energy and is the precursor of a two-dimensional Wigner lattice. PMID:20123751

  3. Physics in one dimension

    NASA Astrophysics Data System (ADS)

    van Houselt, A.; Schäfer, J.; Zandvliet, H. J. W.; Claessen, R.

    2013-01-01

    With modern microelectronics moving towards smaller and smaller length scales on the (sub-) nm scale, quantum effects (apart from band structure and band gaps) have begun to play an increasingly important role. This especially concerns dimensional confinement to 2D (high electron mobility transistors and integer/fractional quantum Hall effect physics, graphene and topological insulators) and 1D (with electrical connections eventually reaching the quantum limit). Recent developments in the above-mentioned areas have revealed that the properties of electron systems become increasingly exotic as one progresses from the 3D case into lower dimensions. As compared to 2D electron systems, much less experimental progress has been achieved in the field of 1D electron systems. The main reason for the lack of experimental results in this field is related to the difficulty of realizing 1D electron systems. Atom chains created in quantum mechanical break junction set-ups are too short to exhibit the typically 1D signatures. As an alternative, atomic chains can be produced on crystal surfaces, either via assembling them one-by-one using a scanning tunnelling microscope or via self-assembly. The drawback of the latter systems is that the atomic chains are not truly 1D since they are coupled to the underlying crystal and sometimes even to the neighbouring chains. In retrospect, this coupling turns out to be an absolute necessity in the experiment since true 1D systems are disordered at any non-zero temperature [1]. The coupling to the crystal and/or neighbouring chains shifts the phase transition, for example, a Peierls instability, to a non-zero temperature and thus allows experiments to be performed in the ordered state. Here, we want to emphasize that the electronic properties of the 1D electron system are fundamentally different from its 2D and 3D counterparts. The Fermi liquid theory, which is applicable to 2D and 3D electron systems, breaks down spectacularly in the 1D case

  4. Nonminimal universal extra dimensions

    SciTech Connect

    Flacke, Thomas; Menon, A.; Phalen, Daniel J.

    2009-03-01

    In this paper, we investigate the phenomenological implications of boundary localized terms (BLTs) in the model of universal extra dimensions (UED). In particular, we study the electroweak Kaluza-Klein mass spectrum resulting from BLTs and their effect on electroweak symmetry breaking via the five-dimensional Higgs mechanism. We find that the addition of BLTs to massive five-dimensional fields induces a nontrivial extra-dimensional profile for the zero and nonzero Kaluza-Klein (KK) modes. Hence BLTs generically lead to a modification of standard model parameters and are therefore experimentally constrained, even at tree level. We study standard model constraints on three representative nonminimal UED models in detail and find that the constraints on BLTs are weak. On the contrary, nonzero BLTs have a major impact on the spectrum and couplings of nonzero KK modes. For example, there are regions of parameter space where the lightest Kaluza-Klein particle is either the Kaluza-Klein Higgs boson or the first KK mode of the W{sup 3}.

  5. Exterior dimension of fat fractals

    NASA Technical Reports Server (NTRS)

    Grebogi, C.; Mcdonald, S. W.; Ott, E.; Yorke, J. A.

    1985-01-01

    Geometric scaling properties of fat fractal sets (fractals with finite volume) are discussed and characterized via the introduction of a new dimension-like quantity which is called the exterior dimension. In addition, it is shown that the exterior dimension is related to the 'uncertainty exponent' previously used in studies of fractal basin boundaries, and it is shown how this connection can be exploited to determine the exterior dimension. Three illustrative applications are described, two in nonlinear dynamics and one dealing with blood flow in the body. Possible relevance to porous materials and ballistic driven aggregation is also noted.

  6. Thermal dimension of quantum spacetime

    NASA Astrophysics Data System (ADS)

    Amelino-Camelia, Giovanni; Brighenti, Francesco; Gubitosi, Giulia; Santos, Grasiele

    2017-04-01

    Recent results suggest that a crucial crossroad for quantum gravity is the characterization of the effective dimension of spacetime at short distances, where quantum properties of spacetime become significant. This is relevant in particular for various scenarios of "dynamical dimensional reduction" which have been discussed in the literature. We are here concerned with the fact that the related research effort has been based mostly on analyses of the "spectral dimension", which involves an unphysical Euclideanization of spacetime and is highly sensitive to the off-shell properties of a theory. As here shown, different formulations of the same physical theory can have wildly different spectral dimension. We propose that dynamical dimensional reduction should be described in terms of the "thermal dimension" which we here introduce, a notion that only depends on the physical content of the theory. We analyze a few models with dynamical reduction both of the spectral dimension and of our thermal dimension, finding in particular some cases where thermal and spectral dimension agree, but also some cases where the spectral dimension has puzzling properties while the thermal dimension gives a different and meaningful picture.

  7. Deconstructing Dimensions: Adventures in Theory Space (Large Extra Dimension)

    SciTech Connect

    Arkani-Hamed, Nima

    2009-11-28

    Theories of gravity and gauge forces in more than four dimensions offer a new paradigm for physics beyond the standard model. We present some of the most interesting recent ideas, and explain how signals for extra dimensions could appear in experiments at a linear e+e- collider.

  8. Dimensions of temperament: an analysis.

    PubMed

    Lorr, M; Stefic, E C

    1976-01-01

    The TDOT recast into a single stimulus format was administered to 150 college Ss. A factor analysis of the items followed by an analysis of item clusters that define each factor indicated the presence of 14 dimensions. Of the 10 bipolar scales of the TDOT, 3 were confirmed as independent dimensions, and 5 were confirmed in part or split into unipolar factors.

  9. The Dimensions of Maltreatment: Introduction

    ERIC Educational Resources Information Center

    English, Diana J.; Bangdiwala, Shrikant I.; Runyan, Desmond K.

    2005-01-01

    This special issue includes an introduction and seven papers exploring dimensions of maltreatment including type, severity, chronicity, and substantiation status of referrals to CPS, utilizing a subsample of the LONGSCAN studies. Each paper examines one of the dimensions of maltreatment from various perspectives to determine if different…

  10. String universality in ten dimensions.

    PubMed

    Adams, Allan; Taylor, Washington; Dewolfe, Oliver

    2010-08-13

    We show that the N=1 supergravity theories in ten dimensions with gauge groups U(1){496} and E{8}×U(1){248} are not consistent quantum theories. Cancellation of anomalies cannot be made compatible with supersymmetry and Abelian gauge invariance. Thus, in ten dimensions all supersymmetric theories of gravity without known inconsistencies are realized in string theory.

  11. Mathematics Teachers' Criteria of Dimension

    ERIC Educational Resources Information Center

    Ural, Alattin

    2014-01-01

    The aim of the study is to determine mathematics teachers' decisions about dimensions of the geometric figures, criteria of dimension and consistency of decision-criteria. The research is a qualitative research and the model applied in the study is descriptive method on the basis of general scanning model. 15 mathematics teachers attended the…

  12. Mathematics Teachers' Criteria of Dimension

    ERIC Educational Resources Information Center

    Ural, Alattin

    2014-01-01

    The aim of the study is to determine mathematics teachers' decisions about dimensions of the geometric figures, criteria of dimension and consistency of decision-criteria. The research is a qualitative research and the model applied in the study is descriptive method on the basis of general scanning model. 15 mathematics teachers attended the…

  13. The dimension of product spaces

    PubMed Central

    Wage, Michael L.

    1978-01-01

    The covering dimension of a product space can exceed the sum of the dimensions of its factors. A separable metric space X and a paracompact space Y are constructed such that dim X + dim Y = 0 < 1 = dim(X × Y). Related results are also discussed. PMID:16592575

  14. The dimension of product spaces.

    PubMed

    Wage, M L

    1978-10-01

    The covering dimension of a product space can exceed the sum of the dimensions of its factors. A separable metric space X and a paracompact space Y are constructed such that dim X + dim Y = 0 < 1 = dim(X x Y). Related results are also discussed.

  15. Dimensioning, Tolerancing, and Machine Finishes.

    ERIC Educational Resources Information Center

    Adams, George C.

    Intended for use with the vocational education student interested in technical drawing, this guide provides answers to questions relating to dimensioning and tolerancing machine drawings. It also gives examples of standard dimensioning practices, tolerancing applications, and finish applications. The problems and examples presented are based on…

  16. Inflation from periodic extra dimensions

    NASA Astrophysics Data System (ADS)

    Higaki, Tetsutaro; Tatsuta, Yoshiyuki

    2017-07-01

    We discuss a realization of a small field inflation based on string inspired supergravities. In theories accompanying extra dimensions, compactification of them with small radii is required for realistic situations. Since the extra dimension can have a periodicity, there will appear (quasi-)periodic functions under transformations of moduli of the extra dimensions in low energy scales. Such a periodic property can lead to a UV completion of so-called multi-natural inflation model where inflaton potential consists of a sum of multiple sinusoidal functions with a decay constant smaller than the Planck scale. As an illustration, we construct a SUSY breaking model, and then show that such an inflaton potential can be generated by a sum of world sheet instantons in intersecting brane models on extra dimensions containing orbifold. We show also predictions of cosmic observables by numerical analyzes.

  17. The Dimensions of Creative Prose

    ERIC Educational Resources Information Center

    Miller, Melvin H.

    1975-01-01

    The thesis in this paper centered around the meaning of "effective" speaking and "effective" writing. The dimensions of effective prose are analyzed as one method of determining what is involved. (Author/RK)

  18. Fourier dimension of random images

    NASA Astrophysics Data System (ADS)

    Ekström, Fredrik

    2016-10-01

    Given a compact set of real numbers, a random C^{m + α}-diffeomorphism is constructed such that the image of any measure concentrated on the set and satisfying a certain condition involving a real number s, almost surely has Fourier dimension greater than or equal to s / (m + α). This is used to show that every Borel subset of the real numbers of Hausdorff dimension s is C^{m + α}-equivalent to a set of Fourier dimension greater than or equal to s / (m + α ). In particular every Borel set is diffeomorphic to a Salem set, and the Fourier dimension is not invariant under Cm-diffeomorphisms for any m.

  19. Bubble dynamics in N dimensions

    NASA Astrophysics Data System (ADS)

    Klotz, Alexander R.

    2013-08-01

    Cavitation and bubble dynamics are central concepts in engineering, the natural sciences, and the mathematics of fluid mechanics. Due to the nonlinear nature of their dynamics, the governing equations are not fully solvable. Here, the dynamics of a spherical bubble in an N-dimensional fluid are discussed in the hope that examining bubble behavior in N dimensions will add insight to their behavior in three dimensions. Several canonical results in bubble dynamics are re-derived, including the Rayleigh collapse time, the Rayleigh-Plesset equation, and the Minnaert frequency. Recent analytical approximations to the Rayleigh collapse are discussed, and the N-dimensional generalization is used to resolve a known discrepancy. Numerical simulations are used to examine the onset of nonlinear behavior. Overall, the dynamics of bubbles are faster at higher dimensions, with nonlinear behavior occurring at lower strain. Several features are found to be unique to three dimensions, including the trend of nonlinear behavior and apparent coincidences in timescales.

  20. Timbre Dimensions for Musical Control

    NASA Astrophysics Data System (ADS)

    Giese, Gregory Roy

    This dissertation addresses the folowing question: Given the technologies to develop and implement any kind of sound generating and controlling device, what will the instrument designer, the composer, and the performer need to know in order to more fully utilize the dimensions of timbre in music and musical performance? This question is approached from the standpoint of music theory. Definitions of timbre and a few examples of related physical and perceptual research are reviewed. Included is a discussion of the essential elements of musical control and of intelligent organization of sound in music. This discussion raises more questions than can be answered simply. It is an attempt to unravel the nature of sound clues and sound qualities as they convey sound identities and musical gesture. A theoretical simplification of sound dimensions for musical use is proposed. Sounds which can be sustained indefinitely consist of steady-state acoustical dimensions. These dimensions rely upon the perceptual phenomenon of simultaneous fusion (synance). Sounds which can not be sustained indefinitely consist of transitions. Transitions may cause successive fusion (sonance). The discussion of steady-state and transition dimensions includes a review of a few informal experiments. This work reveals problems that will influence the musical use of timbre dimensions. It also leads to a theory for the organization and control of timbre dimensions in music. Among the timbre dimensions discussed are: spectral envelope, harmonic content, brightness, phase, inharmonicity, aperiodicity, and temporal transitions. Questions are raised regarding the perception of harmonic content. The effect of register on perception of tones consisting of from two to nine partials is explored and discussed. The size of interval between partials determines a unique quality. This is most apparent with tones consisting of only two or three partials (dions or trions).

  1. Phenomenology of universal extra dimensions

    SciTech Connect

    Kong, Kyoungchul; Matchev, Konstantin T.; /Florida U.

    2006-10-01

    In this proceeding, the phenomenology of Universal Extra Dimensions (UED), in which all the Standard Model fields propagate, is explored. We focus on models with one universal extra dimension, compactified on an S{sub 1}/Z{sub 2} orbifold. We revisit calculations of Kaluza-Klein (KK) dark matter without an assumption of the KK mass degeneracy including all possible coannihilations. We then contrast the experimental signatures of low energy supersymmetry and UED.

  2. The Sirens of Eleven Dimensions

    NASA Astrophysics Data System (ADS)

    Ramond, Pierre

    While most theorists are tied to the mast of four dimensions, some have found it irresistible to speculate about eleven dimensions, the domain of M-theory. We outline a program which starts from the light-cone description of supergravity, and tracks its divergences to suggest the existence of an infinite component theory which in the lightcone relies on the coset F4/SO(9), long known to be linked to the Exceptional Jordan Algebra

  3. Collider Phenomenology of Extra Dimensions

    SciTech Connect

    Lillie, Benjamin Huntington; /Stanford U., Phys. Dept. /SLAC

    2006-03-10

    In recent years there has been much interest in the possibility that there exist more spacetime dimensions than the usual four. Models of particle physics beyond the Standard Model that incorporate these extra dimensions can solve the gauge hierarchy problem and explain why the fermion masses a spread over many orders of magnitude. In this thesis we explore several possibilities for models with extra dimensions. First we examine constraints on the proposal of Arkani-Hamed and Schmaltz that the Standard Model fermions are localized to different positions in an extra dimension, thereby generating the hierarchy in fermion masses. We find strong constraints on the compactification scale of such models arising from flavor-changing neutral currents. Next we investigate the phenomenology of the Randall-Sundrum model, where the hierarchy between the electroweak and Planck scales is generated by the warping in a five-dimensional anti-de Sitter space. In particular, we investigate the ''Higgsless'' model of electroweak symmetry breaking due to Csaki et. al., where the Higgs has been decoupled from the spectrum by taking its vacuum expectation value to infinity. We find that this model produces many distinctive features at the LHC. However, we also find that it is strongly constrained by precision electroweak observables and the requirement that gauge-boson scattering be perturbative. We then examine the model with a finite vacuum expectation value, and find that there are observable shifts to the Higgs scalar properties. Finally, in the original large extra dimension scenario of Arkani-Hamed, Dimopoulos, and Dvali, the hierarchy problem is solved by allowing gravity to propagate in a large extra dimensional volume, while the Standard Model fields are confined to 4 dimensions. We consider the case where there are a large number of extra dimensions (n {approx} 20). This model can solve the hierarchy problem without introducing a exponentially large radii for the extra

  4. Fractal dimension of alumina aggregates grown in two dimensions

    NASA Technical Reports Server (NTRS)

    Larosa, Judith L.; Cawley, James D.

    1992-01-01

    The concepts of fractal geometry are applied to the analysis of 0.4-micron alumina constrained to agglomerate in two dimensions. Particles were trapped at the bottom surface of a drop of a dilute suspension, and the agglomeration process was directly observed, using an inverted optical microscope. Photographs were digitized and analyzed, using three distinct approaches. The results indicate that the agglomerates are fractal, having a dimension of approximately 1.5, which agrees well with the predictions of the diffusion-limited cluster-cluster aggregation model.

  5. Dimension of fractal basin boundaries

    SciTech Connect

    Park, B.S.

    1988-01-01

    In many dynamical systems, multiple attractors coexist for certain parameter ranges. The set of initial conditions that asymptotically approach each attractor is its basin of attraction. These basins can be intertwined on arbitrary small scales. Basin boundary can be either smooth or fractal. Dynamical systems that have fractal basin boundary show final state sensitivity of the initial conditions. A measure of this sensitivity (uncertainty exponent {alpha}) is related to the dimension of the basin boundary d = D - {alpha}, where D is the dimension of the phase space and d is the dimension of the basin boundary. At metamorphosis values of the parameter, there might happen a conversion from smooth to fractal basin boundary (smooth-fractal metamorphosis) or a conversion from fractal to another fractal basin boundary characteristically different from the previous fractal one (fractal-fractal metamorphosis). The dimension changes continuously with the parameter except at the metamorphosis values where the dimension of the basin boundary jumps discontinuously. We chose the Henon map and the forced damped pendulum to investigate this. Scaling of the basin volumes near the metamorphosis values of the parameter is also being studied for the Henon map. Observations are explained analytically by using low dimensional model map.

  6. Collider searches for extra dimensions

    SciTech Connect

    Landsberg, Greg; /Brown U.

    2004-12-01

    Searches for extra spatial dimensions remain among the most popular new directions in our quest for physics beyond the Standard Model. High-energy collider experiments of the current decade should be able to find an ultimate answer to the question of their existence in a variety of models. Until the start of the LHC in a few years, the Tevatron will remain the key player in this quest. In this paper, we review the most recent results from the Tevatron on searches for large, TeV{sup -1}-size, and Randall-Sundrum extra spatial dimensions, which have reached a new level of sensitivity and currently probe the parameter space beyond the existing constraints. While no evidence for the existence of extra dimensions has been found so far, an exciting discovery might be just steps away.

  7. Correlated Electrons in Reduced Dimensions

    SciTech Connect

    Bonesteel, Nicholas E

    2015-01-31

    This report summarizes the work accomplished under the support of US DOE grant # DE-FG02-97ER45639, "Correlated Electrons in Reduced Dimensions." The underlying hypothesis of the research supported by this grant has been that studying the unique behavior of correlated electrons in reduced dimensions can lead to new ways of understanding how matter can order and how it can potentially be used. The systems under study have included i) fractional quantum Hall matter, which is realized when electrons are confined to two-dimensions and placed in a strong magnetic field at low temperature, ii) one-dimensional chains of spins and exotic quasiparticle excitations of topologically ordered matter, and iii) electrons confined in effectively ``zero-dimensional" semiconductor quantum dots.

  8. Image Segmentation via Fractal Dimension

    DTIC Science & Technology

    1987-12-01

    statistical expectation K = a proportionality constant H = the Hurst exponent , in interval [0,1] (14:249) Eq (4) is a mathematical generalization of...ease, negatively correlated (24:16). The Hurst exponent is directly related to the fractal diment.ion of the process being modelled by the relation (24...24) DzE.I -H (5) where D = the fractal dimension E m the Euclidean dimension H = the Hurst exponent The effect of N1 on a typical trace can be seen

  9. Maximal cuts in arbitrary dimension

    NASA Astrophysics Data System (ADS)

    Bosma, Jorrit; Sogaard, Mads; Zhang, Yang

    2017-08-01

    We develop a systematic procedure for computing maximal unitarity cuts of multiloop Feynman integrals in arbitrary dimension. Our approach is based on the Baikov representation in which the structure of the cuts is particularly simple. We examine several planar and nonplanar integral topologies and demonstrate that the maximal cut inherits IBPs and dimension shift identities satisfied by the uncut integral. Furthermore, for the examples we calculated, we find that the maximal cut functions from different allowed regions, form the Wronskian matrix of the differential equations on the maximal cut.

  10. Topological insulators in three dimensions.

    PubMed

    Fu, Liang; Kane, C L; Mele, E J

    2007-03-09

    We study three-dimensional generalizations of the quantum spin Hall (QSH) effect. Unlike two dimensions, where a single Z2 topological invariant governs the effect, in three dimensions there are 4 invariants distinguishing 16 phases with two general classes: weak (WTI) and strong (STI) topological insulators. The WTI are like layered 2D QSH states, but are destroyed by disorder. The STI are robust and lead to novel "topological metal" surface states. We introduce a tight binding model which realizes the WTI and STI phases, and we discuss its relevance to real materials, including bismuth.

  11. Topological Insulators in Three Dimensions

    NASA Astrophysics Data System (ADS)

    Fu, Liang; Kane, C. L.; Mele, E. J.

    2007-03-01

    We study three-dimensional generalizations of the quantum spin Hall (QSH) effect. Unlike two dimensions, where a single Z2 topological invariant governs the effect, in three dimensions there are 4 invariants distinguishing 16 phases with two general classes: weak (WTI) and strong (STI) topological insulators. The WTI are like layered 2D QSH states, but are destroyed by disorder. The STI are robust and lead to novel “topological metal” surface states. We introduce a tight binding model which realizes the WTI and STI phases, and we discuss its relevance to real materials, including bismuth.

  12. Dimension independence in exterior algebra.

    PubMed

    Hawrylycz, M

    1995-03-14

    The identities between homogeneous expressions in rank 1 vectors and rank n - 1 covectors in a Grassmann-Cayley algebra of rank n, in which one set occurs multilinearly, are shown to represent a set of dimension-independent identities. The theorem yields an infinite set of nontrivial geometric identities from a given identity.

  13. The Feeling Dimension in Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    The feeling dimension of students cannot be ignored in teaching and learning situations. Feelings are there and must not be ignored. Reading stresses word recognition, comprehension of subject matter at diverse levels of complexity, and application of what has been learned. A major ingredient so frequently left out is student appreciation of the…

  14. Pedagogical Introduction to Extra Dimensions

    SciTech Connect

    Rizzo, T

    2004-09-27

    Extra dimensions provide a new window on a number of problems faced by the Standard Model. The following provides an introduction to this very broad subject aimed at experimental graduate students and post-docs based on a lecture given at the 2004 SLAC Summer Institute.

  15. The European Dimension in Education.

    ERIC Educational Resources Information Center

    Council of Europe, Strasbourg (France). Directorate of Education, Culture and Sport, Documentation Section.

    This paper addresses concerns about a European dimension in education that has been created by the enlargement of the European Union (EU) (the inclusion of Austria, Finland, and Sweden) and the gradual transformations of institutions into a future federal state. Sections of the paper include: (1) "Introduction"; (2) "Defining the…

  16. Heat conduction in three dimensions

    NASA Technical Reports Server (NTRS)

    Danza, T. M.; Fesler, L. W.; Mongan, R. D.

    1980-01-01

    Multidimensional heat conduction program computes transient temperature history and steady state temperatures of complex body geometries in three dimensions. Emphasis is placed on type of problems associated with Space Shuttle thermal protection system, but program could be used in thermal analysis of most three dimensional systems.

  17. Investigation of a Creativity Dimension.

    ERIC Educational Resources Information Center

    Murphy, Richard T.

    This thesis provides evidence for the existence of a creativity dimension containing figural and verbal subfactors which is independent of intelligence and marginally related to school achievement. The original data of Wallach and Kogan, as well as the data from the Ward, Cropley and Maslany and Wallach and Wing studies were reanalyzed using…

  18. The Visuospatial Dimension of Writing

    ERIC Educational Resources Information Center

    Olive, Thierry; Passerault, Jean-Michel

    2012-01-01

    The authors suggest that writing should be conceived of not only as a verbal activity but also as a visuospatial activity, in which writers process and construct visuospatial mental representations. After briefly describing research on visuospatial cognition, they look at how cognitive researchers have investigated the visuospatial dimension of…

  19. The Visuospatial Dimension of Writing

    ERIC Educational Resources Information Center

    Olive, Thierry; Passerault, Jean-Michel

    2012-01-01

    The authors suggest that writing should be conceived of not only as a verbal activity but also as a visuospatial activity, in which writers process and construct visuospatial mental representations. After briefly describing research on visuospatial cognition, they look at how cognitive researchers have investigated the visuospatial dimension of…

  20. The European Dimension in Education.

    ERIC Educational Resources Information Center

    Council of Europe, Strasbourg (France). Directorate of Education, Culture and Sport, Documentation Section.

    This paper addresses concerns about a European dimension in education that has been created by the enlargement of the European Union (EU) (the inclusion of Austria, Finland, and Sweden) and the gradual transformations of institutions into a future federal state. Sections of the paper include: (1) "Introduction"; (2) "Defining the…

  1. Dimension independence in exterior algebra.

    PubMed Central

    Hawrylycz, M

    1995-01-01

    The identities between homogeneous expressions in rank 1 vectors and rank n - 1 covectors in a Grassmann-Cayley algebra of rank n, in which one set occurs multilinearly, are shown to represent a set of dimension-independent identities. The theorem yields an infinite set of nontrivial geometric identities from a given identity. PMID:11607520

  2. Charged polymers in high dimensions

    NASA Technical Reports Server (NTRS)

    Kantor, Yacov

    1990-01-01

    A Monte Carlo study of charged polymers with either homogeneously distributed frozen charges or with mobile charges has been performed in four and five space dimensions. The results are consistent with the renormalization-group predictions and contradict the predictions of Flory-type theory. Introduction of charge mobility does not modify the behavior of the polymers.

  3. Heat conduction in three dimensions

    NASA Technical Reports Server (NTRS)

    Danza, T. M.; Fesler, L. W.; Mongan, R. D.

    1980-01-01

    Multidimensional heat conduction program computes transient temperature history and steady state temperatures of complex body geometries in three dimensions. Emphasis is placed on type of problems associated with Space Shuttle thermal protection system, but program could be used in thermal analysis of most three dimensional systems.

  4. Warping the universal extra dimensions

    SciTech Connect

    McDonald, Kristian L.

    2009-07-15

    We develop the necessary ingredients for the construction of realistic models with warped universal extra dimensions. Our investigations are based on the seven-dimensional (7D) spacetime AdS{sub 5}xT{sup 2}/Z{sub 2} and we derive the Kaluza-Klein (KK) spectra for gravitons, bulk vectors, and the TeV brane localized Higgs boson. We show that, starting with a massive 7D fermion, one may obtain a single chiral massless mode whose profile is readily localized towards the Planck or TeV brane. This allows one to place the standard model fermions in the bulk and construct models of flavor as in Randall-Sundrum models. Our solution also admits the familiar KK parity of models with universal extra dimensions so that the lightest odd KK state is stable and may be a dark matter candidate. As an additional feature the AdS{sub 5} warping ensures that the excited modes on the torus, including the dark matter candidate, appear at TeV energies (as is usually assumed in models with universal extra dimensions) even though the Planck scale sets the dimensions for the torus.

  5. Interpretation and the Aesthetic Dimension

    ERIC Educational Resources Information Center

    Mortensen, Charles O.

    1976-01-01

    The author, utilizing a synthesis of philosophic comments on aesthetics, provides a discourse on the aesthetic dimension and offers examples of how interpreters can nurture the innate sense of beauty in man. Poetic forms, such as haiku, are used to relate the aesthetic relationship between man and the environment. (BT)

  6. Compactified Vacuum in Ten Dimensions.

    NASA Astrophysics Data System (ADS)

    Wurmser, Daniel

    1987-09-01

    Since the 1920's, theories which unify gravity with the other fundamental forces have called for more than the four observed dimensions of space-time. According to such a theory, the vacuum consists of flat four-dimensional space-time described by the Minkowski metric M ^4 and a "compactified" space B. The dimensions of B are small, and the space can only be observed at distance scales smaller than the present experimental limit. These theories have had serious difficulties. The equations of gravity severely restrict the possible choices for the space B. The allowed spaces are complicated and difficult to study. The vacuum is furthermore unstable in the sense that a small perturbation causes the compactified dimensions to expand indefinitely. There is an addition a semi-classical argument which implies that the compactified vacuum be annihilated by virtual black holes. It follows that a universe with compactified extra dimensions could not have survived to the present. These results were derived by applying the equations of general relativity to spaces of more than four dimensions. The form of these equations was assumed to be unchanged by an increase in the number of dimensions. Recently, it has been proposed that gravity in more than four dimensions may involve terms of higher order in the curvature as well as the linear terms present in ordinary general relativity. I illustrate the effect of such terms by considering the example B = S^6 where S ^6 is the six-dimensional sphere. Only when the extra terms are included is this choice of the compactified space allowed. I explore the effect of a small perturbation on such a vacuum. The ten-dimensional spherically symmetric potential is examined, and I determine conditions under which the formation of virtual black holes is forbidden. The example M^4 times S^6 is still plagued by the semi -classical instability, but this result does not hold in general. The requirement that virtual black holes be forbidden provides a

  7. Supersymmetric unification requires extra dimensions

    SciTech Connect

    Chen, Mu-Chun; Fallbacher, Maximilian; Ratz, Michael

    2013-05-23

    We discuss settings that predict precision gauge unification in the minimal supersymmetric standard model. We show that, if one requires anomaly freedom and fermion masses while demanding that unification is not an accident, only R symmetries can forbid the supersymmetric Higgs mass term {mu}. We then review the proof that R symmetries are not available in conventional grand unified theories (GUTs) and argue that this prevents natural solutions to the doublet-triplet splitting problem in four dimensions. On the other hand, higher-dimensional GUTs do not suffer from this problem. We briefly comment on an explicit string-derived model in which the {mu} and dimension five proton decay problems are solved by an order four discrete R symmetry, and comment on the higher-dimensional origin of this symmetry.

  8. Black Holes in Higher Dimensions

    NASA Astrophysics Data System (ADS)

    Horowitz, Gary T.

    2012-04-01

    List of contributors; Preface; Part I. Introduction: 1. Black holes in four dimensions Gary Horowitz; Part II. Five Dimensional Kaluza-Klein Theory: 2. The Gregory-Laflamme instability Ruth Gregory; 3. Final state of Gregory-Laflamme instability Luis Lehner and Frans Pretorius; 4. General black holes in Kaluza-Klein theory Gary Horowitz and Toby Wiseman; Part III. Higher Dimensional Solutions: 5. Myers-Perry black holes Rob Myers; 6. Black rings Roberto Emparan and Harvey Reall; Part IV. General Properties: 7. Constraints on the topology of higher dimensional black holes Greg Galloway; 8. Blackfolds Roberto Emparan; 9. Algebraically special solutions in higher dimensions Harvey Reall; 10. Numerical construction of static and stationary black holes Toby Wiseman; Part V. Advanced Topics: 11. Black holes and branes in supergravity Don Marolf; 12. The gauge/gravity duality Juan Maldacena; 13. The fluid/gravity correspondence Veronika Hubeny, Mukund Rangamani and Shiraz Minwalla; 14. Horizons, holography and condensed matter Sean Hartnoll; Index.

  9. Critical gravity in four dimensions.

    PubMed

    Lü, H; Pope, C N

    2011-05-06

    We study four-dimensional gravity theories that are rendered renormalizable by the inclusion of curvature-squared terms to the usual Einstein action with a cosmological constant. By choosing the parameters appropriately, the massive scalar mode can be eliminated and the massive spin-2 mode can become massless. This "critical" theory may be viewed as a four-dimensional analogue of chiral topologically massive gravity, or of critical "new massive gravity" with a cosmological constant, in three dimensions. We find that the on-shell energy for the remaining massless gravitons vanishes. There are also logarithmic spin-2 modes, which have positive energy. The mass and entropy of standard Schwarzschild-type black holes vanish. The critical theory might provide a consistent toy model for quantum gravity in four dimensions.

  10. Critical Gravity in Four Dimensions

    SciTech Connect

    Lue, H.; Pope, C. N.

    2011-05-06

    We study four-dimensional gravity theories that are rendered renormalizable by the inclusion of curvature-squared terms to the usual Einstein action with a cosmological constant. By choosing the parameters appropriately, the massive scalar mode can be eliminated and the massive spin-2 mode can become massless. This ''critical'' theory may be viewed as a four-dimensional analogue of chiral topologically massive gravity, or of critical 'new massive gravity' with a cosmological constant, in three dimensions. We find that the on-shell energy for the remaining massless gravitons vanishes. There are also logarithmic spin-2 modes, which have positive energy. The mass and entropy of standard Schwarzschild-type black holes vanish. The critical theory might provide a consistent toy model for quantum gravity in four dimensions.

  11. Dimension Reduction for Object Ranking

    NASA Astrophysics Data System (ADS)

    Kamishima, Toshihiro; Akaho, Shotaro

    Ordered lists of objects are widely used as representational forms. Such ordered objects include Web search results and bestseller lists. Techniques for processing such ordinal data are being developed, particularly methods for an object ranking task: i.e., learning functions used to sort objects from sample orders. In this article, we propose two dimension reduction methods specifically designed to improve prediction performance in an object ranking task.

  12. Economic Dimensions of Civil Conflicts

    DTIC Science & Technology

    2012-09-01

    CODE 13. ABSTRACT (maximum 200 words) The thesis has five chapters: (1) an introduction, (2) the economic risk factors causing civil conflicts...3) the economic dimensions of peace building (4) a Kosovo case study, and (5) the conclusion. Chapter II discusses the economic risk factors that...provide development. 14. SUBJECT TERMS Civil conflict, insurgency, armed groups, economic risk factors , war economies, post-conflict

  13. Robust large dimension terahertz cloaking.

    PubMed

    Liang, Dachuan; Gu, Jianqiang; Han, Jiaguang; Yang, Yuanmu; Zhang, Shuang; Zhang, Weili

    2012-02-14

    A large scale homogenous invisibility cloak functioning at terahertz frequencies is reported. The terahertz invisibility device features a large concealed volume, low loss, and broad bandwidth. In particular, it is capable of hiding objects with a dimension nearly an order of magnitude larger than that of its lithographic counterpart, but without involving complex and time-consuming cleanroom processing. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Wormholes leading to extra dimensions

    NASA Astrophysics Data System (ADS)

    Bronnikov, K. A.; Skvortsova, M. V.

    2016-10-01

    In 6D general relativity with a scalar field as a source of gravity, a new type of static wormhole solutions is presented: such wormholes connect our universe with a small 2D extra subspace with a universe where this extra subspace is large, and the whole space-time is effectively 6-dimensional. We consider manifolds with the structure M0 x M1 x M2 , where M0 is 2D Lorentzian space-time while each of M1 an M2 can be a 2-sphere or a 2-torus. After selecting possible asymptotic behaviors of the metric functions compatible with the field equations, we give two explicit examples of wormhole solutions with spherical symmetry in our space-time and toroidal extra dimensions. In one example, with a massless scalar field (it is a special case of a well-known more general solution), the extra dimensions have a large constant size at the "far end"; the other example contains a nonzero potential $V(\\phi)$ which provides a 6D anti-de Sitter asymptotic, where all spatial dimensions are infinite.

  15. Gardner transition in finite dimensions

    NASA Astrophysics Data System (ADS)

    Urbani, Pierfrancesco; Biroli, Giulio

    2015-03-01

    Recent works on hard spheres in the limit of infinite dimensions revealed that glass states, envisioned as metabasins in configuration space, can break up in a multitude of separate basins at low enough temperature or high enough pressure, leading to the emergence of new kinds of soft-modes and unusual properties. In this paper we study by perturbative renormalization group techniques the critical properties of this transition, which has been discovered in disordered mean-field models in the 1980s. We find that the upper-critical dimension du, above which mean-field results hold, is strictly larger than six and apparently nonuniversal, i.e., system dependent. Below du, we do not find any perturbative attractive fixed point (except for a tiny region of the one-step replica symmetry breaking parameter), thus showing that the transition in three dimensions either is governed by a nonperturbative fixed point unrelated to the Gaussian mean-field one or becomes first order or does not exist. We also discuss possible relationships with the behavior of spin glasses in a field.

  16. Search for Extra Dimensions at CDF

    SciTech Connect

    Wynne, Sara-Madge; /Liverpool U.

    2007-08-01

    This poster, presented at the 2006 Duke Hadron Collider Symposium, presents the results from searches for large extra dimensions, as proposed by Arkani-Hamed, Dimopoulos and Dvali (ADD), and Randall-Sundrum (RS) model warped extra dimensions, at CDF.

  17. A Short Existence Proof for Correlation Dimension

    NASA Astrophysics Data System (ADS)

    Manning, Anthony; Simon, Károly

    1998-02-01

    The Grassberger-Hentschel-Procaccia correlation dimension has been put on a rigorous basis by Pesin and Tempelman. We simplify their proof that this dimension is given in terms of the measure of neighborhoods of the diagonal.

  18. Fractal dimension of bioconvection patterns

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1990-01-01

    Shallow cultures of the motile algal strain, Euglena gracilis, were concentrated to 2 x 10 to the 6th organisms per ml and placed in constant temperature water baths at 24 and 38 C. Bioconvective patterns formed an open two-dimensional structure with random branches, similar to clusters encountered in the diffusion-limited aggregation (DLA) model. When averaged over several example cultures, the pattern was found to have no natural length scale, self-similar branching, and a fractal dimension (d about 1.7). These agree well with the two-dimensional DLA.

  19. Fractal Dimension of Bioconvection Patterns

    NASA Astrophysics Data System (ADS)

    Noever, David A.

    1990-10-01

    Shallow cultures of the motile algal strain, Euglena gracilis, were concentrated to 2× 106 organisms per ml and placed in constant temperature water baths at 24 and 38 C. Bioconvective patterns formed an open two-dimensional structure with random branches, similar to clusters encountered in the diffusion-limited aggregation (DLA) model. When averaged over several example cultures, the pattern was found to have no natural length scale, self-similar branching and a fractal dimension (d˜1.7). These agree well with the two-dimensional DLA.

  20. Complex dimensions and their observability

    NASA Astrophysics Data System (ADS)

    Calcagni, Gianluca

    2017-08-01

    We show that the dimension of spacetime becomes complex-valued when its short-scale geometry is invariant under a discrete scaling symmetry. This characteristic can generically arise in quantum gravities, for instance, in those based on combinatorial or multifractal structures or as the partial breaking of continuous dilation symmetry in any conformal-invariant theory. With its infinite scale hierarchy, discrete scale invariance overlaps with the traditional separation between ultraviolet and infrared physics and it can leave an all-range observable imprint, such as a pattern of log oscillations and sharp features in the cosmic microwave background primordial power spectrum.

  1. Equientangled bases in arbitrary dimensions

    SciTech Connect

    Karimipour, V.; Memarzadeh, L.

    2006-01-15

    For the space of two identical systems of arbitrary dimensions, we introduce a continuous family of bases with the following properties: (i) the bases are orthonormal (ii) in each basis, all the states have the same values of entanglement, and (iii) they continuously interpolate between the product basis and the maximally entangled basis. The states thus constructed may find applications in many areas related to the quantum information science including quantum cryptography, optimal Bell tests, and the investigation of the enhancement of channel capacity due to entanglement.

  2. Model Pores of Molecular Dimension

    PubMed Central

    Quinn, J. A.; Anderson, J. L.; Ho, W. S.; Petzny, W. J.

    1972-01-01

    Extremely uniform pores of near molecular dimension can be formed by the irradiation-etching technique first demonstrated by Price and Walker. The technique has now been developed to the stage where it can be used to fabricate model membranes for examining the various steric, hydrodynamic, and electrodynamic phenomena encountered in transport through molecular-size pores. Methods for preparing and characterizing membranes with pores as small as 25 A (radius) are described in this paper. Results on pore size determination via Knudsen gas flow and electrolyte conduction are compared. Pore wall modification by monolayer deposition is also discussed. PMID:4339801

  3. Localized instanton in four dimensions

    SciTech Connect

    O'Brien, G.M.; Tchrakian, D.H.

    1987-02-15

    A family of generalized Yang-Mills- (GYM) Higgs (H) systems is proposed as phenomenological models giving rise to localized instantons in four dimensions. An argument in favor of the (qualified) uniqueness of this system, which features a fundamental-representation Higgs field, is given. Two ''radial'' Ansa$auml: tze are made, and the compatibility of one of them with the field equation is analyzed in detail. It is suggested that such GYMH systems can be used in the computation of the confining potential.

  4. Localized instanton in four dimensions

    NASA Astrophysics Data System (ADS)

    O'brien, G. M.; Tchrakian, D. H.

    1987-02-01

    A family of generalized Yang-Mills- (GYM) Higgs (H) systems is proposed as phenomenological models giving rise to localized instantons in four dimensions. An argument in favor of the (qualified) uniqueness of this system, which features a fundamental-representation Higgs field, is given. Two ``radial'' Ansa$auml-tze are made, and the compatibility of one of them with the field equation is analyzed in detail. It is suggested that such GYMH systems can be used in the computation of the confining potential.

  5. Correlation dimension of complex networks.

    PubMed

    Lacasa, Lucas; Gómez-Gardeñes, Jesús

    2013-04-19

    We propose a new measure to characterize the dimension of complex networks based on the ergodic theory of dynamical systems. This measure is derived from the correlation sum of a trajectory generated by a random walker navigating the network, and extends the classical Grassberger-Procaccia algorithm to the context of complex networks. The method is validated with reliable results for both synthetic networks and real-world networks such as the world air-transportation network or urban networks, and provides a computationally fast way for estimating the dimensionality of networks which only relies on the local information provided by the walkers.

  6. BMS Modules in Three Dimensions

    NASA Astrophysics Data System (ADS)

    Campoleoni, A.; González, H. A.; Oblak, B.; Riegler, M.

    We build unitary representations of the BMS algebra and its higher-spin extensions in three dimensions, using induced representations as a guide. Our prescription naturally emerges from an ultrarelativistic limit of highest-weight representations of Virasoro and 𝒲 algebras, which is to be contrasted with nonrelativistic limits that typically give non-unitary representations. To support this dichotomy, we also point out that the ultrarelativistic and non-relativistic limits of generic 𝒲 algebras differ in the structure of their non-linear terms.

  7. Massive gravity in three dimensions.

    PubMed

    Bergshoeff, Eric A; Hohm, Olaf; Townsend, Paul K

    2009-05-22

    A particular higher-derivative extension of the Einstein-Hilbert action in three spacetime dimensions is shown to be equivalent at the linearized level to the (unitary) Pauli-Fierz action for a massive spin-2 field. A more general model, which also includes "topologically-massive" gravity as a special case, propagates the two spin-2 helicity states with different masses. We discuss the extension to massive N-extended supergravity, and we present a "cosmological" extension that admits an anti-de Sitter vacuum.

  8. Quantum cosmology near two dimensions

    NASA Astrophysics Data System (ADS)

    Bautista, Teresa; Dabholkar, Atish

    2016-08-01

    We consider a Weyl-invariant formulation of gravity with a cosmological constant in d -dimensional spacetime and show that near two dimensions the classical action reduces to the timelike Liouville action. We show that the renormalized cosmological term leads to a nonlocal quantum momentum tensor which satisfies the Ward identities in a nontrivial way. The resulting evolution equations for an isotropic, homogeneous universe lead to slowly decaying vacuum energy and power-law expansion. We outline the implications for the cosmological constant problem, inflation, and dark energy.

  9. Extended scaling in high dimensions

    NASA Astrophysics Data System (ADS)

    Berche, B.; Chatelain, C.; Dhall, C.; Kenna, R.; Low, R.; Walter, J.-C.

    2008-11-01

    We apply and test the recently proposed 'extended scaling' scheme in an analysis of the magnetic susceptibility of Ising systems above the upper critical dimension. The data are obtained by Monte Carlo simulations using both the conventional Wolff cluster algorithm and the Prokof'ev-Svistunov worm algorithm. As already observed for other models, extended scaling is shown to extend the high-temperature critical scaling regime over a range of temperatures much wider than that achieved conventionally. It allows for an accurate determination of leading and sub-leading scaling indices, critical temperatures and amplitudes of the confluent corrections.

  10. Noncentrosymmetric superconductors in one dimension

    NASA Astrophysics Data System (ADS)

    Samokhin, K. V.

    2017-02-01

    We study the fermionic boundary modes (Andreev bound states) in a time-reversal invariant one-dimensional superconductor. In the presence of a substrate, spatial inversion symmetry is broken and the electronic properties are strongly affected by an antisymmetric spin-orbit coupling. We assume an arbitrary even number of nondegenerate bands crossing the Fermi level. We show that there is only one possible pairing symmetry in one dimension, an analog of s -wave pairing. The zero-energy Andreev bound states are present if the sign of the gap function in an odd number of the bands is different from all other bands.

  11. Calculation of the dimension of strange attractors

    NASA Astrophysics Data System (ADS)

    Malinetskii, G. G.; Potapov, A. B.

    1988-07-01

    Algorithms for calculating the dimension of strange attractors of dynamic systems are presented. Algorithms proposed for calculating the capacity, information dimension, and correlation index make it possible to reduce the amount of computations and the memory size. Calculations of the dimension of a Kantor set and a Feigenbaum attractor are considered as tests. Examples of calculations of the dimension of attractors of certain systems of ordinary differential equations are also considered.

  12. 15 CFR 241.5 - Standard dimensions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Standard dimensions. 241.5 Section 241..., VEGETABLES AND OTHER DRY COMMODITIES, AND FOR CRANBERRIES § 241.5 Standard dimensions. Whenever in the rules and regulations in this part the error on a dimension is mentioned, this error shall be determined by...

  13. 15 CFR 241.5 - Standard dimensions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Standard dimensions. 241.5 Section 241..., VEGETABLES AND OTHER DRY COMMODITIES, AND FOR CRANBERRIES § 241.5 Standard dimensions. Whenever in the rules and regulations in this part the error on a dimension is mentioned, this error shall be determined by...

  14. NEW DIMENSIONS IN JUNIOR COLLEGE PLANNING.

    ERIC Educational Resources Information Center

    BOYCE, R. DUDLEY; AND OTHERS

    THIS REPORT CONSISTS OF A SERIES OF DISCUSSIONS BY MANY AUTHORS IN FOUR BROAD DIMENSIONS RELATIVE TO JUNIOR COLLEGES. THE FIRST DIMENSION IS PURPOSES AND DEALS WITH THE UNIQUE ROLE OF THE COMMUNITY JUNIOR COLLEGE, PROVISIONS FOR FACILITIES, PROBLEMS, AND POTENTIALITIES. THE SECOND DIMENSION FOCUSES ON PLANNING AND REPORTS ON STUDIES IN PLANNING…

  15. 16 CFR 1508.3 - Dimensions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Dimensions. 1508.3 Section 1508.3 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR FULL-SIZE BABY CRIBS § 1508.3 Dimensions. Full-size baby cribs shall have dimensions as follows:...

  16. 15 CFR 241.5 - Standard dimensions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Standard dimensions. 241.5 Section 241..., VEGETABLES AND OTHER DRY COMMODITIES, AND FOR CRANBERRIES § 241.5 Standard dimensions. Whenever in the rules and regulations in this part the error on a dimension is mentioned, this error shall be determined by...

  17. 15 CFR 241.5 - Standard dimensions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 15 Commerce and Foreign Trade 1 2014-01-01 2014-01-01 false Standard dimensions. 241.5 Section 241..., VEGETABLES AND OTHER DRY COMMODITIES, AND FOR CRANBERRIES § 241.5 Standard dimensions. Whenever in the rules and regulations in this part the error on a dimension is mentioned, this error shall be determined by...

  18. 15 CFR 241.5 - Standard dimensions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 15 Commerce and Foreign Trade 1 2012-01-01 2012-01-01 false Standard dimensions. 241.5 Section 241..., VEGETABLES AND OTHER DRY COMMODITIES, AND FOR CRANBERRIES § 241.5 Standard dimensions. Whenever in the rules and regulations in this part the error on a dimension is mentioned, this error shall be determined by...

  19. Deconstructing signaling in three dimensions.

    PubMed

    Rubashkin, Matthew G; Ou, Guanqing; Weaver, Valerie M

    2014-04-08

    Cells in vivo exist within the context of a multicellular tissue, where their behavior is governed by homo- and heterotypic cell-cell interactions, the material properties of the extracellular matrix, and the distribution of various soluble and physical factors. Most methods currently used to study and manipulate cellular behavior in vitro, however, sacrifice physiological relevance for experimental expediency. The fallacy of such approaches has been highlighted by the recent development and application of three-dimensional culture models to cell biology, which has revealed striking phenotypic differences in cell survival, migration, and differentiation in genetically identical cells simply by varying culture conditions. These perplexing findings beg the question of what constitutes a three-dimensional culture and why cells behave so differently in two- and three-dimensional culture formats. In the following review, we dissect the fundamental differences between two- and three-dimensional culture conditions. We begin by establishing a basic definition of what "three dimensions" means at different biological scales and discuss how dimensionality influences cell signaling across different length scales. We identify which three-dimensional features most potently influence intracellular signaling and distinguish between conserved biological principles that are maintained across culture conditions and cellular behaviors that are sensitive to microenvironmental context. Finally, we highlight state-of-the-art molecular tools amenable to the study of signaling in three dimensions under conditions that facilitate deconstruction of signaling in a more physiologically relevant manner.

  20. Reflections from the fourth dimension

    NASA Astrophysics Data System (ADS)

    Lefranc, Marc

    2013-01-01

    The knot-theoretic characterization of three-dimensional strange attractors has proved an invaluable tool for comparing models to experiments, understanding the structure of bifurcation diagrams, constructing symbolic encodings or obtaining signatures of chaos. In four dimensions and above, however, all closed curves can be deformed into each other without crossing themselves. Therefore, the fundamental idea of topological analysis, namely that the topological structure of a strange attractor provides signatures of the stretching and folding mechanisms which organize it, must be translated into a different formalism. Here, we discuss two modest attempts to make progress in this direction. First, we illustrate the relevance of catastrophe theory in the analysis of higher-dimensional systems by describing experimental signatures of cusps in weakly coupled chaotic systems. Second, we note that determinism not only precludes intersection of two trajectories but also orientation reversal of phase space volume elements. Enforcing this principle on dynamical triangulations of periodic points advected by the flow leads to higher-dimensional analogues of braids, which in three dimensions appear to provide the same information as usual approaches.

  1. Topological Insulators in Three Dimensions

    NASA Astrophysics Data System (ADS)

    Fu, Liang; Kane, Charles; Mele, Eugene

    2007-03-01

    We study three dimensional generalizations of the quantum spin Hall (QSH) effect. Unlike two dimensions, where the QSH effect is distinguished by a single Z2 topological invariant, in three dimensions there are 4 invariants distinguishing 16 ``topological insulator'' phases. There are two general classes: weak (WTI) and strong (STI) topological insulators. The WTI states are equivalent to layered 2D QSH states, but are fragile because disorder continuously connects them to band insulators. The STI states are robust and have surface states that realize the 2+1 dimensional parity anomaly without fermion doubling, giving rise to a novel ``topological metal'' surface phase. We show that the Z2 invariants can be easily determined for systems with inversion symmetry. This allows us to predict specific materials are STI's, including semiconducting alloy Bi1-x Sbx as well as α-Sn and HgTe under uniaxial strain.1. Liang Fu, C.L. Kane, E.J. Mele, cond-mat/0607699. 2. Liang Fu, C.L. Kane, cond- mat/0611341.

  2. Double shrinking sparse dimension reduction.

    PubMed

    Zhou, Tianyi; Tao, Dacheng

    2013-01-01

    Learning tasks such as classification and clustering usually perform better and cost less (time and space) on compressed representations than on the original data. Previous works mainly compress data via dimension reduction. In this paper, we propose "double shrinking" to compress image data on both dimensionality and cardinality via building either sparse low-dimensional representations or a sparse projection matrix for dimension reduction. We formulate a double shrinking model (DSM) as an l(1) regularized variance maximization with constraint ||x||(2)=1, and develop a double shrinking algorithm (DSA) to optimize DSM. DSA is a path-following algorithm that can build the whole solution path of locally optimal solutions of different sparse levels. Each solution on the path is a "warm start" for searching the next sparser one. In each iteration of DSA, the direction, the step size, and the Lagrangian multiplier are deduced from the Karush-Kuhn-Tucker conditions. The magnitudes of trivial variables are shrunk and the importances of critical variables are simultaneously augmented along the selected direction with the determined step length. Double shrinking can be applied to manifold learning and feature selections for better interpretation of features, and can be combined with classification and clustering to boost their performance. The experimental results suggest that double shrinking produces efficient and effective data compression.

  3. Generalized dimensions applied to speaker identification

    NASA Astrophysics Data System (ADS)

    Hou, Limin; Wang, Shuozhong

    2004-08-01

    This paper describes an application of fractal dimensions to speech processing and speaker identification. There are several dimensions that can be used to characterize speech signals such as box dimension, correlation dimension, etc. We are mainly concerned with the generalized dimensions of speech signals as they provide more information than individual dimensions. Generalized dimensions of arbitrary orders are used in speaker identification in this work. Based on the experimental data, the artificial phase space is generated and smooth behavior of correlation integral is obtained in a straightforward and accurate analysis. Using the dimension D(2) derived from the correlation integral, the generalized dimension D(q) of an arbitrary order q is calculated. Moreover, experiments applying the generalized dimension in speaker identification have been carried out. A speaker recognition dedicated Chinese language speech corpus with PKU-SRSC, recorded by Peking University, was used in the experiments. The results are compared to a baseline speaker identification that uses MFCC features. Experimental results have indicated the usefulness of fractal dimensions in characterizing speaker's identity.

  4. Psychophysical dimensions of tactile perception of textures.

    PubMed

    Okamoto, Shogo; Nagano, Hikaru; Yamada, Yoji

    2013-01-01

    This paper reviews studies on the tactile dimensionality of physical properties of materials in order to determine a common structure for these dimensions. Based on the commonality found in a number of studies and known mechanisms for the perception of physical properties of textures, we conclude that tactile textures are composed of three prominent psychophysical dimensions that are perceived as roughness/smoothness, hardness/softness, and coldness/warmness. The roughness dimension may be divided into two dimensions: macro and fine roughness. Furthermore, it is reasonable to consider that a friction dimension that is related to the perception of moistness/dryness and stickiness/slipperiness exists. Thus, the five potential dimensions of tactile perception are macro and fine roughness, warmness/coldness, hardness/softness, and friction (moistness/dryness, stickiness/slipperiness). We also summarize methods such as psychological experiments and mathematical approaches for structuring tactile dimensions and their limitations.

  5. Dirac Semimetals in Two Dimensions.

    PubMed

    Young, Steve M; Kane, Charles L

    2015-09-18

    Graphene is famous for being a host of 2D Dirac fermions. However, spin-orbit coupling introduces a small gap, so that graphene is formally a quantum spin Hall insulator. Here we present symmetry-protected 2D Dirac semimetals, which feature Dirac cones at high-symmetry points that are not gapped by spin-orbit interactions and exhibit behavior distinct from both graphene and 3D Dirac semimetals. Using a two-site tight-binding model, we construct representatives of three possible distinct Dirac semimetal phases and show that single symmetry-protected Dirac points are impossible in two dimensions. An essential role is played by the presence of nonsymmorphic space group symmetries. We argue that these symmetries tune the system to the boundary between a 2D topological and trivial insulator. By breaking the symmetries we are able to access trivial and topological insulators as well as Weyl semimetal phases.

  6. Plasma torches dimensioning and optimization

    NASA Astrophysics Data System (ADS)

    Muller, S.

    A set of codes which enable dimensioning and optimization of non transferred plasma torches made up of two coaxial cylindrical electrodes cooled up in the 100 kW power range is described. These torches are used in ballistic, space and industrial fields. The sharp model of exchanges between the electric arc and the plasma producing gas requires a thorough knowledge of the physical properties of this plasma producing gas so a specific study was carried out on the air. Equations taken into account include mass conservation, Navier-Stokes and energy conservation equations. An experimental data bank gathers the plasma torches performances described. The modular structure of the package and its continuous feedback between theoretical and experimental data bank improves constantly with new experimentation.

  7. Accessible solitons of fractional dimension

    SciTech Connect

    Zhong, Wei-Ping; Belić, Milivoj; Zhang, Yiqi

    2016-05-15

    We demonstrate that accessible solitons described by an extended Schrödinger equation with the Laplacian of fractional dimension can exist in strongly nonlocal nonlinear media. The soliton solutions of the model are constructed by two special functions, the associated Legendre polynomials and the Laguerre polynomials in the fraction-dimensional space. Our results show that these fractional accessible solitons form a soliton family which includes crescent solitons, and asymmetric single-layer and multi-layer necklace solitons. -- Highlights: •Analytic solutions of a fractional Schrödinger equation are obtained. •The solutions are produced by means of self-similar method applied to the fractional Schrödinger equation with parabolic potential. •The fractional accessible solitons form crescent, asymmetric single-layer and multilayer necklace profiles. •The model applies to the propagation of optical pulses in strongly nonlocal nonlinear media.

  8. [Temporal dimensions of suicide: hypothesis].

    PubMed

    Carbonell-Camós, Eliseu

    2008-01-01

    In this article, the author examines the temporal dimensions of suicide by taking into account the multiple existing approaches-circadian physiology, psychiatric or sociological epidemiology of suicide-however promoting a socio-anthropological perspective. From this perspective, suicide is examined as a social phenomenon inscribed in time. By beginning with a concern that is characteristic of anthropology of time, knowingly the relation between time of nature and time of society, the author addresses a key issue of the study of suicide already elaborated by Durkheim, in the relation between change that is a basic expression of the passage of time and suicide. After presenting different scientific contributions on the subject, the author proposes an hypothesis allowing integration of the influence of time related to natural phenomenon (cosmobiological rhythms) and the relation of time to social phenomenon (politico-economic rhythms) in relation with suicide and this, according to Gabennesch's theory of "failed promises."

  9. Kolmogorov Flow in Three Dimensions

    NASA Technical Reports Server (NTRS)

    Shebalin, John V.; Woodruff, Stephen L.

    1996-01-01

    A numerical study of the long-time evolution of incompressible Navier-Stokes turbulence forced at a single long-wavelength Fourier mode, i.e., a Kolmogorov flow, has been completed. The boundary conditions are periodic in three dimensions and the forcing is effected by imposing a steady, two-dimensional, sinusoidal shear velocity which is directed along the x-direction and varies along the z-direction. A comparison with experimental data shows agreement with measured cross-correlations of the turbulent velocity components which lie in the mean-flow plane. A statistical analysis reveals that the shear-driven turbulence studied here has significant spectral anisotropy which increases with wave number.

  10. Ambitwistor Strings in Four Dimensions

    NASA Astrophysics Data System (ADS)

    Geyer, Yvonne; Lipstein, Arthur E.; Mason, Lionel

    2014-08-01

    We develop ambitwistor string theories for four dimensions to obtain new formulas for tree-level gauge and gravity amplitudes with arbitrary amounts of supersymmetry. Ambitwistor space is the space of complex null geodesics in complexified Minkowski space, and in contrast to earlier ambitwistor strings, we use twistors rather than vectors to represent this space. Although superficially similar to the original twistor string theories of Witten, Berkovits, and Skinner, these theories differ in the assignment of world sheet spins of the fields, rely on both twistor and dual twistor representatives for the vertex operators, and use the ambitwistor procedure for calculating correlation functions. Our models are much more flexible, no longer requiring maximal supersymmetry, and the resulting formulas for amplitudes are simpler, having substantially reduced moduli. These are supported on the solutions to the scattering equations refined according to helicity and can be checked by comparison with corresponding formulas of Witten and of Cachazo and Skinner.

  11. Grand unification in higher dimensions

    NASA Astrophysics Data System (ADS)

    Hall, Lawrence J.; Nomura, Yasunori

    2003-07-01

    We have recently proposed an alternative picture for the physics at the scale of gauge coupling unification, where the unified symmetry is realized in higher dimensions but is broken locally by a symmetry breaking defect. Gauge coupling unification, the quantum numbers of quarks and leptons and the longevity of the proton arise as phenomena of the symmetrical bulk, while the lightness of the Higgs doublets and the masses of the light quarks and leptons probe the symmetry breaking defect. Moreover, the framework is extremely predictive if the effective higher dimensional theory is valid over a large energy interval up to the scale of strong coupling. Precise agreement with experiments is obtained in the simplest theory— SU(5) in five dimensions with two Higgs multiplets propagating in the bulk. The weak mixing angle is predicted to be sin 2θw=0.2313±0.0004, which fits the data with extraordinary accuracy. The compactification scale and the strong coupling scale are determined to be M c≃5×10 14 GeV and M s≃1×10 17 GeV, respectively. Proton decay with a lifetime of order 10 34 years is expected with a variety of final states such as e+π0, and several aspects of flavor, including large neutrino mixing angles, are understood by the geometrical locations of the matter fields. When combined with a particular supersymmetry breaking mechanism, the theory predicts large lepton flavor violating μ→ e and τ→ μ transitions, with all superpartner masses determined by only two free parameters. The predicted value of the bottom quark mass from Yukawa unification agrees well with the data. This paper is mainly a review of the work presented in hep-ph/0103125, hep-ph/0111068, and hep-ph/0205067 [1-3].

  12. Dimensioning of Aeronautical Satellite Services

    NASA Astrophysics Data System (ADS)

    Holzbock, M.; Jahn, A.; Werner, M.

    2002-01-01

    This paper will provide a generalised baseline for a systematic AirCom design process and address in particular the dimensioning of satellite systems for aeronautical services. These services will roll out soon in medium- and long-haul aircraft. The offered services will range from low rate telephony, internet access, and streaming applications for video and audio. The aggregate bit rates on up- and downlink will certainly be statistically time-dependent and asymmetric in forward and backward direction. A tool will be described that is able to model this traffic. Furthermore the dimensioning of satellite constellations can be done. Due to the stochastic nature of the traffic, multi-service models for the traffic generation of different services will be described. Furthermore, the traffic will be affected by the available bit rate and shaping or blocking will equalize the peak loads. If fleets with many aircraft are considered, aeronautical traffic models must be based on actual aircraft routes, flight schedules, location and time of day, as well as seats per aircraft and type of aircraft (charter, business etc.). The regionally distributed traffic has to be served by several satellites and appropriate sharing of the serving satellites may spread the traffic in hot zones and yield a better load distribution. When aeronautical services will spread out, the capacity demand will grow quickly and the capacity of existing Ku-band GEO satellites will soon be exceeded. Changing to higher frequency bands will provide large spectrum portions and smaller spotbeams will allow better frequency reuse. Even constellations with non-geostationary satellites could be re-advent to serve better the higher latitude regions. Then, another mobility component for the fast changing satellite topology need to be addressed, and routing issues of the traffic must be considered. The paper will describe solutions for the mapping of satellites and traffic demand as well as routing algorithms

  13. Space: The Hunt for Hidden Dimensions

    SciTech Connect

    Hewett, JoAnne

    2006-04-25

    Extra dimensions of space may be present in our universe. Their discovery would dramatically change our view of the cosmos and would prompt many questions. How do they hide? What is their shape? How many are there? How big are they? Do particles and forces feel their presence? This lecture will explain the concept of dimensions and show that current theoretical models predict the existence of extra spatial dimensions which could be in the discovery reach of present and near-term experiments. The manner by which these additional dimensions reveal their existence will be described. Searches for modifications of the gravitational force, astrophysical effects, and collider signatures already constrain the size of extra dimensions and will be summarized. Once new dimensions are discovered, the technology by which the above questions can be answered will be discussed.

  14. On some trees having partition dimension four

    NASA Astrophysics Data System (ADS)

    Ida Bagus Kade Puja Arimbawa, K.; Baskoro, Edy Tri

    2016-02-01

    In 1998, G. Chartrand, E. Salehi and P. Zhang introduced the notion of partition dimension of a graph. Since then, the study of this graph parameter has received much attention. A number of results have been obtained to know the values of partition dimensions of various classes of graphs. However, for some particular classes of graphs, finding of their partition dimensions is still not completely solved, for instances a class of general tree. In this paper, we study the properties of trees having partition dimension 4. In particular, we show that, for olive trees O(n), its partition dimension is equal to 4 if and only if 8 ≤ n ≤ 17. We also characterize all centipede trees having partition dimension 4.

  15. The Hausdorff and dynamical dimensions of self-affine sponges: a dimension gap result

    NASA Astrophysics Data System (ADS)

    Das, Tushar; Simmons, David

    2017-10-01

    We construct a self-affine sponge in $\\mathbb R^3$ whose dynamical dimension, i.e. the supremum of the Hausdorff dimensions of its invariant measures, is strictly less than its Hausdorff dimension. This resolves a long-standing open problem in the dimension theory of dynamical systems, namely whether every expanding repeller has an ergodic invariant measure of full Hausdorff dimension. More generally we compute the Hausdorff and dynamical dimensions of a large class of self-affine sponges, a problem that previous techniques could only solve in two dimensions. The Hausdorff and dynamical dimensions depend continuously on the iterated function system defining the sponge, implying that sponges with a dimension gap represent a nonempty open subset of the parameter space.

  16. Non-canonical features of the Golgi apparatus in bipolar epithelial neural stem cells.

    PubMed

    Taverna, Elena; Mora-Bermúdez, Felipe; Strzyz, Paulina J; Florio, Marta; Icha, Jaroslav; Haffner, Christiane; Norden, Caren; Wilsch-Bräuninger, Michaela; Huttner, Wieland B

    2016-02-16

    Apical radial glia (aRG), the stem cells in developing neocortex, are unique bipolar epithelial cells, extending an apical process to the ventricle and a basal process to the basal lamina. Here, we report novel features of the Golgi apparatus, a central organelle for cell polarity, in mouse aRGs. The Golgi was confined to the apical process but not associated with apical centrosome(s). In contrast, in aRG-derived, delaminating basal progenitors that lose apical polarity, the Golgi became pericentrosomal. The aRG Golgi underwent evolutionarily conserved, accordion-like compression and extension concomitant with cell cycle-dependent nuclear migration. Importantly, in line with endoplasmic reticulum but not Golgi being present in the aRG basal process, its plasma membrane contained glycans lacking Golgi processing, consistent with direct ER-to-cell surface membrane traffic. Our study reveals hitherto unknown complexity of neural stem cell polarity, differential Golgi contribution to their specific architecture, and fundamental Golgi re-organization upon cell fate change.

  17. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    DOE PAGES

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; ...

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active sitemore » metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.« less

  18. Fancd2 in vivo interaction network reveals a non-canonical role in mitochondrial function

    PubMed Central

    Zhang, Tingting; Du, Wei; Wilson, Andrew F.; Namekawa, Satoshi H.; Andreassen, Paul R.; Meetei, Amom Ruhikanta; Pang, Qishen

    2017-01-01

    Fancd2 is a component of the Fanconi anemia (FA) DNA repair pathway, which is frequently found defective in human cancers. The full repertoire of Fancd2 functions in normal development and tumorigenesis remains to be determined. Here we developed a Flag- and hemagglutinin-tagged Fancd2 knock-in mouse strain that allowed a high throughput mass spectrometry approach to search for Fancd2-binding proteins in different mouse organs. In addition to DNA repair partners, we observed that many Fancd2-interacting proteins are mitochondrion-specific. Fancd2 localizes in the mitochondrion and associates with the nucleoid complex components Atad3 and Tufm. The Atad3-Tufm complex is disrupted in Fancd2−/− mice and those deficient for the FA core component Fanca. Fancd2 mitochondrial localization requires Atad3. Collectively, these findings provide evidence for Fancd2 as a crucial regulator of mitochondrion biosynthesis, and of a molecular link between FA and mitochondrial homeostasis. PMID:28378742

  19. A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage.

    PubMed

    Yakunina, Maria; Artamonova, Tatyana; Borukhov, Sergei; Makarova, Kira S; Severinov, Konstantin; Minakhin, Leonid

    2015-12-02

    The infection of Pseudomonas aeruginosa by the giant bacteriophage phiKZ is resistant to host RNA polymerase (RNAP) inhibitor rifampicin. phiKZ encodes two sets of polypeptides that are distantly related to fragments of the two largest subunits of cellular multisubunit RNAPs. Polypeptides of one set are encoded by middle phage genes and are found in the phiKZ virions. Polypeptides of the second set are encoded by early phage genes and are absent from virions. Here, we report isolation of a five-subunit RNAP from phiKZ-infected cells. Four subunits of this enzyme are cellular RNAP subunits homologs of the non-virion set; the fifth subunit is a protein of unknown function. In vitro, this complex initiates transcription from late phiKZ promoters in rifampicin-resistant manner. Thus, this enzyme is a non-virion phiKZ RNAP responsible for transcription of late phage genes. The phiKZ RNAP lacks identifiable assembly and promoter specificity subunits/factors characteristic for eukaryal, archaeal and bacterial RNAPs and thus provides a unique model for comparative analysis of the mechanism, regulation and evolution of this important class of enzymes.

  20. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    SciTech Connect

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  1. Canonical and non-canonical Wnt signaling control the regeneration of amputated rodent vibrissae follicles.

    PubMed

    Yuan, Yan-Ping; Huang, Keng; Xu, Yan-Min; Chen, Xian-Cai; Li, Hai-Hong; Cai, Bo-Zhi; Liu, Yang; Zhang, Huan; Li, Yu; Lin, Chang-Min

    2016-02-01

    Although mammals are notoriously poor at regeneration compared with many lower-order species, the hair follicle, particular to mammals, is capable of regeneration following partial amputation. The detailed internal mechanism of this phenomenon is still unclear. Development and regrowth of the hair follicle depends on dermal-epidermal interaction within the hair follicle. Previous studies have shown that Wnt/β-catenin, Shh, Bmp, PDGF, TGF and Notch signals all take part in the development and growth of the hair follicle, and the Wnt/β-catenin signaling additionally plays an indispensable role in hair follicle morphogenesis and regrowth. In this study, we investigated the localization, as well as, protein levels of Wnt/β-catenin signaling molecules during amputated whisker follicle regeneration.

  2. To ~P or Not to ~P? Non-canonical activation by two-component response regulators

    PubMed Central

    Desai, Stuti K.; Kenney, Linda J.

    2016-01-01

    Summary Bacteria sense and respond to their environment through the use of two-component regulatory systems. The ability to adapt to a wide range of environmental stresses is directly related to the number of two-component systems an organism possesses. Recent advances in this area have identified numerous variations on the archetype systems that employ a sensor kinase and a response regulator. It is now evident that many orphan regulators that lack cognate kinases do not rely on phosphorylation for activation and new roles for unphosphorylated response regulators have been identified. The significance of recent findings and suggestions for further research are discussed. PMID:27656860

  3. A Non-canonical Melanin Biosynthesis Pathway Protects Aspergillus terreus Conidia from Environmental Stress.

    PubMed

    Geib, Elena; Gressler, Markus; Viediernikova, Iuliia; Hillmann, Falk; Jacobsen, Ilse D; Nietzsche, Sandor; Hertweck, Christian; Brock, Matthias

    2016-05-19

    Melanins are ubiquitous pigments found in all kingdoms of life. Most organisms use them for protection from environmental stress, although some fungi employ melanins as virulence determinants. The human pathogenic fungus Aspergillus fumigatus and related Ascomycetes produce dihydroxynaphthalene- (DHN) melanin in their spores, the conidia, and use it to inhibit phagolysosome acidification. However, biosynthetic origin of melanin in a related fungus, Aspergillus terreus, has remained a mystery because A. terreus lacks genes for synthesis of DHN-melanin. Here we identify genes coding for an unusual NRPS-like enzyme (MelA) and a tyrosinase (TyrP) that A. terreus expressed under conidiation conditions. We demonstrate that MelA produces aspulvinone E, which is activated for polymerization by TyrP. Functional studies reveal that this new pigment, Asp-melanin, confers resistance against UV light and hampers phagocytosis by soil amoeba. Unexpectedly, Asp-melanin does not inhibit acidification of phagolysosomes, thus likely contributing specifically to survival of A. terreus conidia in acidic environments. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Planck limits on non-canonical generalizations of large-field inflation models

    NASA Astrophysics Data System (ADS)

    Stein, Nina K.; Kinney, William H.

    2017-04-01

    In this paper, we consider two case examples of Dirac-Born-Infeld (DBI) generalizations of canonical large-field inflation models, characterized by a reduced sound speed, cS < 1. The reduced speed of sound lowers the tensor-scalar ratio, improving the fit of the models to the data, but increases the equilateral-mode non-Gaussianity, fequil.NL, which the latest results from the Planck satellite constrain by a new upper bound. We examine constraints on these models in light of the most recent Planck and BICEP/Keck results, and find that they have a greatly decreased window of viability. The upper bound on fequil.NL corresponds to a lower bound on the sound speed and a corresponding lower bound on the tensor-scalar ratio of r ~ 0.01, so that near-future Cosmic Microwave Background observations may be capable of ruling out entire classes of DBI inflation models. The result is, however, not universal: infrared-type DBI inflation models, where the speed of sound increases with time, are not subject to the bound.

  5. [The frame of non-canonical theory of heredity: from genes to epigenes].

    PubMed

    Churaev, R N

    2005-01-01

    Particular theory of heredity that exceeds the limits of mendelian genetics is suggested. The model based on five sufficiently obvious assumptions (accepted as axioms) As consequence of these axioms the strict statements concerningfunctional heredity memory were formulated in mathematical terms. Molecular-genetic realization of the memory cells appears as new class of heredity units--epigenes. In the epigenes part f hereditary information is contained, encoded and transmitted beyond the primary structure of DNA molecules of genome. Epigenes capable to conserve sequences of genes functional states in the course of ontogenesis and provide transmission of information contained in this states throw consequent generations. It was shown that epigenes differ from genes at least by encoding method of heredity information. There are three functional-equivalent classes of really existing epigenes mechanisms: dynamic, modificational and transpositional; and there is one hypothetical class--invertional. It was shown that a lot of experimental data concerning epigenetic mechanism of heredity is in accord with theoretical conclusions concerning epigenes existence. Moreover, we constructed an artificial epigenes by genetic engineering methods. The existence of epigenes means that obtaining complete genome sequence, its physical and genetic maps, as well as distinguishing the rules of genes function encoding by its primary structure do not provide complete decoding of hereditary information. The role of epigenes in ontogenesis and phylogenesis was examined. It was shown that even elementary epigenetic systems could determine key ontogenesis events. Epigenetic system could serve as the basis of non-darwinian evolutionary strategies by means of "memorization of rather unsuccessfully steps of evolution" and conservation of alternative variants of ontogenesis. Teleonomic hypothesis on functional heredity memory was formulated. This theory provides explanation of phenomena of acquired features inheritance and molecular mechanisms of stress-induced evolution.

  6. Non-canonical ribosomal DNA segments in the human genome, and nucleoli functioning.

    PubMed

    Kupriyanova, Natalia S; Netchvolodov, Kirill K; Sadova, Anastasia A; Cherepanova, Marina D; Ryskov, Alexei P

    2015-11-10

    Ribosomal DNA (rDNA) in the human genome is represented by tandem repeats of 43 kb nucleotide sequences that form nucleoli organizers (NORs) on each of five pairs of acrocentric chromosomes. RDNA-similar segments of different lengths are also present on (NOR)(-) chromosomes. Many of these segments contain nucleotide substitutions, supplementary microsatellite clusters, and extended deletions. Recently, it was shown that, in addition to ribosome biogenesis, nucleoli exhibit additional functions, such as cell-cycle regulation and response to stresses. In particular, several stress-inducible loci located in the ribosomal intergenic spacer (rIGS) produce stimuli-specific noncoding nucleolus RNAs. By mapping the 5'/3' ends of the rIGS segments scattered throughout (NOR)(-) chromosomes, we discovered that the bonds in the rIGS that were most often susceptible to disruption in the rIGS were adjacent to, or overlapped with stimuli-specific inducible loci. This suggests the interconnection of the two phenomena - nucleoli functioning and the scattering of rDNA-like sequences on (NOR)(-) chromosomes. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. The core spliceosome as target and effector of non-canonical ATM signaling

    PubMed Central

    Tresini, Maria; Warmerdam, Daniël O.; Kolovos, Petros; Snijder, Loes; Vrouwe, Mischa G.; Demmers, Jeroen A.A.; van IJcken, Wilfred F.J.; Grosveld, Frank G.; Medema, René H.; Hoeijmakers, Jan H.J.; Mullenders, Leon H.F.; Vermeulen, Wim; Marteijn, Jurgen A.

    2015-01-01

    In response to DNA damage tissue homoeostasis is ensured by protein networks promoting DNA repair, cell cycle arrest or apoptosis. DNA damage response signaling pathways coordinate these processes, partly by propagating gene expression-modulating signals. DNA damage influences not only abundance of mRNAs, but also their coding information through alternative splicing. Here we show that transcription-blocking DNA lesions promote chromatin displacement of late-stage spliceosomes and initiate a positive feedback loop centered on the signaling kinase ATM. We propose that initial spliceosome displacement and subsequent R-loop formation is triggered by pausing of RNA polymerase at DNA lesions. In turn, R-loops activate ATM which signals to further impede spliceosome organization and augment UV-triggered alternative splicing at genome-wide level. Our findings define the R-loop-dependent ATM activation by transcription-blocking lesions as an important event in the DNA damage response of non-replicating cells and highlight a key role for spliceosome displacement in this process. PMID:26106861

  8. Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli

    PubMed Central

    Mukai, Takahito; Yamaguchi, Atsushi; Ohtake, Kazumasa; Takahashi, Mihoko; Hayashi, Akiko; Iraha, Fumie; Kira, Satoshi; Yanagisawa, Tatsuo; Yokoyama, Shigeyuki; Hoshi, Hiroko; Kobayashi, Takatsugu; Sakamoto, Kensaku

    2015-01-01

    The immutability of the genetic code has been challenged with the successful reassignment of the UAG stop codon to non-natural amino acids in Escherichia coli. In the present study, we demonstrated the in vivo reassignment of the AGG sense codon from arginine to l-homoarginine. As the first step, we engineered a novel variant of the archaeal pyrrolysyl-tRNA synthetase (PylRS) able to recognize l-homoarginine and l-N6-(1-iminoethyl)lysine (l-NIL). When this PylRS variant or HarRS was expressed in E. coli, together with the AGG-reading tRNAPylCCU molecule, these arginine analogs were efficiently incorporated into proteins in response to AGG. Next, some or all of the AGG codons in the essential genes were eliminated by their synonymous replacements with other arginine codons, whereas the majority of the AGG codons remained in the genome. The bacterial host's ability to translate AGG into arginine was then restricted in a temperature-dependent manner. The temperature sensitivity caused by this restriction was rescued by the translation of AGG to l-homoarginine or l-NIL. The assignment of AGG to l-homoarginine in the cells was confirmed by mass spectrometric analyses. The results showed the feasibility of breaking the degeneracy of sense codons to enhance the amino-acid diversity in the genetic code. PMID:26240376

  9. Fancd2 in vivo interaction network reveals a non-canonical role in mitochondrial function.

    PubMed

    Zhang, Tingting; Du, Wei; Wilson, Andrew F; Namekawa, Satoshi H; Andreassen, Paul R; Meetei, Amom Ruhikanta; Pang, Qishen

    2017-04-05

    Fancd2 is a component of the Fanconi anemia (FA) DNA repair pathway, which is frequently found defective in human cancers. The full repertoire of Fancd2 functions in normal development and tumorigenesis remains to be determined. Here we developed a Flag- and hemagglutinin-tagged Fancd2 knock-in mouse strain that allowed a high throughput mass spectrometry approach to search for Fancd2-binding proteins in different mouse organs. In addition to DNA repair partners, we observed that many Fancd2-interacting proteins are mitochondrion-specific. Fancd2 localizes in the mitochondrion and associates with the nucleoid complex components Atad3 and Tufm. The Atad3-Tufm complex is disrupted in Fancd2-/- mice and those deficient for the FA core component Fanca. Fancd2 mitochondrial localization requires Atad3. Collectively, these findings provide evidence for Fancd2 as a crucial regulator of mitochondrion biosynthesis, and of a molecular link between FA and mitochondrial homeostasis.

  10. Interferon Gamma Induces Protective Non-Canonical Signaling Pathways in Primary Neurons

    PubMed Central

    O'Donnell, Lauren A.; Henkins, Kristen M.; Kulkarni, Apurva; Matullo, Christine M.; Balachandran, Siddharth; Pattisapu, Anil K.; Rall, Glenn F.

    2016-01-01

    The signal transduction molecule, Stat1, is critical for the expression of type I and II interferon (IFN)-responsive genes in most cells; however, we previously showed that primary hippocampal mouse neurons express low basal Stat1, with delayed and attenuated expression of IFN-responsive genes. Moreover, IFNγ-dependent resolution of a neurotropic viral challenge in permissive mice is Stat1-independent. Here, we show that exogenous INFγ has no deleterious impact on neuronal viability, and staurosporine-induced apoptosis in neurons is significantly blunted by the addition of INFγ, suggesting that INFγ confers a pro-survival signal in neurons. To identify the pathways induced by INFγ in neurons, the activation of alternative signal transducers associated with INFγ signaling was assessed. Rapid and pronounced activation of extracellular signal regulated kinase (Erk1/2) was observed in neurons, compared to a modest response in fibroblasts. Moreover, the absence of Stat1 in primary fibroblasts led to enhanced Erk activation following IFNγ addition, implying that the cell-specific availability of signal transducers can diversify the cellular response following IFN engagement. PMID:26190522

  11. A non canonical subtilase attenuates the transcriptional activation of defence responses in Arabidopsis thaliana

    PubMed Central

    Serrano, Irene; Buscaill, Pierre; Audran, Corinne; Pouzet, Cécile; Jauneau, Alain; Rivas, Susana

    2016-01-01

    Proteases play crucial physiological functions in all organisms by controlling the lifetime of proteins. Here, we identified an atypical protease of the subtilase family [SBT5.2(b)] that attenuates the transcriptional activation of plant defence independently of its protease activity. The SBT5.2 gene produces two distinct transcripts encoding a canonical secreted subtilase [SBT5.2(a)] and an intracellular protein [SBT5.2(b)]. Concomitant to SBT5.2(a) downregulation, SBT5.2(b) expression is induced after bacterial inoculation. SBT5.2(b) localizes to endosomes where it interacts with and retains the defence-related transcription factor MYB30. Nuclear exclusion of MYB30 results in its reduced transcriptional activation and, thus, suppressed resistance. sbt5.2 mutants, with abolished SBT5.2(a) and SBT5.2(b) expression, display enhanced defence that is suppressed in a myb30 mutant background. Moreover, overexpression of SBT5.2(b), but not SBT5.2(a), in sbt5.2 plants reverts the phenotypes displayed by sbt5.2 mutants. Overall, we uncover a regulatory mode of the transcriptional activation of defence responses previously undescribed in eukaryotes. DOI: http://dx.doi.org/10.7554/eLife.19755.001 PMID:27685353

  12. Reelin Induces Erk1/2 Signaling in Cortical Neurons Through a Non-canonical Pathway*

    PubMed Central

    Lee, Gum Hwa; Chhangawala, Zinal; von Daake, Sventja; Savas, Jeffrey N.; Yates, John R.; Comoletti, Davide; D'Arcangelo, Gabriella

    2014-01-01

    Reelin is an extracellular protein that controls many aspects of pre- and postnatal brain development and function. The molecular mechanisms that mediate postnatal activities of Reelin are not well understood. Here, we first set out to express and purify the full length Reelin protein and a biologically active central fragment. Second, we investigated in detail the signal transduction mechanisms elicited by these purified Reelin proteins in cortical neurons. Unexpectedly, we discovered that the full-length Reelin moiety, but not the central fragment, is capable of activating Erk1/2 signaling, leading to increased p90RSK phosphorylation and the induction of immediate-early gene expression. Remarkably, Erk1/2 activation is not mediated by the canonical signal transduction pathway, involving ApoER2/VLDLR and Dab1, that mediates other functions of Reelin in early brain development. The activation of Erk1/2 signaling likely contributes to the modulation of neuronal maturation and synaptic plasticity by Reelin in the postnatal and adult brain. PMID:24876378

  13. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    PubMed Central

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-01-01

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5′-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies. PMID:25813242

  14. Non-canonical features of the Golgi apparatus in bipolar epithelial neural stem cells

    PubMed Central

    Taverna, Elena; Mora-Bermúdez, Felipe; Strzyz, Paulina J.; Florio, Marta; Icha, Jaroslav; Haffner, Christiane; Norden, Caren; Wilsch-Bräuninger, Michaela; Huttner, Wieland B.

    2016-01-01

    Apical radial glia (aRG), the stem cells in developing neocortex, are unique bipolar epithelial cells, extending an apical process to the ventricle and a basal process to the basal lamina. Here, we report novel features of the Golgi apparatus, a central organelle for cell polarity, in mouse aRGs. The Golgi was confined to the apical process but not associated with apical centrosome(s). In contrast, in aRG-derived, delaminating basal progenitors that lose apical polarity, the Golgi became pericentrosomal. The aRG Golgi underwent evolutionarily conserved, accordion-like compression and extension concomitant with cell cycle-dependent nuclear migration. Importantly, in line with endoplasmic reticulum but not Golgi being present in the aRG basal process, its plasma membrane contained glycans lacking Golgi processing, consistent with direct ER-to-cell surface membrane traffic. Our study reveals hitherto unknown complexity of neural stem cell polarity, differential Golgi contribution to their specific architecture, and fundamental Golgi re-organization upon cell fate change. PMID:26879757

  15. A non-canonical pathway from cochlea to brain signals tissue-damaging noise.

    PubMed

    Flores, Emma N; Duggan, Anne; Madathany, Thomas; Hogan, Ann K; Márquez, Freddie G; Kumar, Gagan; Seal, Rebecca P; Edwards, Robert H; Liberman, M Charles; García-Añoveros, Jaime

    2015-03-02

    Intense noise damages the cochlear organ of Corti, particularly the outer hair cells (OHCs) [1]; however, this epithelium is not innervated by nociceptors of somatosensory ganglia, which detect damage elsewhere in the body. The only sensory neurons innervating the organ of Corti originate from the spiral ganglion, roughly 95% of which innervate exclusively inner hair cells (IHCs) [2-4]. Upon sound stimulation, IHCs release glutamate to activate AMPA-type receptors on these myelinated type-I neurons, which carry the neuronal signals to the cochlear nucleus. The remaining spiral ganglion cells (type IIs) are unmyelinated and contact OHCs [2-4]. Their function is unknown. Using immunoreactivity to cFos, we documented neuronal activation in the brainstem of Vglut3(-/-) mice, in which the canonical auditory pathway (activation of type-I afferents by glutamate released from inner hair cells) is silenced [5, 6]. In these deaf mice, we found responses to noxious noise, which damages hair cells, but not to innocuous noise, in neurons of the cochlear nucleus, but not in the vestibular or trigeminal nuclei. This response originates in the cochlea and not in other areas also stimulated by intense noise (middle ear and vestibule) as it was absent in CD1 mice with selective cochlear degeneration but normal vestibular and somatosensory function. These data imply the existence of an alternative neuronal pathway from cochlea to brainstem that is activated by tissue-damaging noise and does not require glutamate release from IHCs. This detection of noise-induced tissue damage, possibly by type-II cochlear afferents, represents a novel form of sensation that we term auditory nociception.

  16. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    NASA Astrophysics Data System (ADS)

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-01

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5‧-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  17. A Non-canonical Pathway from Cochlea to Brain Signals Tissue-damaging Noise

    PubMed Central

    Flores, Emma N.; Duggan, Anne; Madathany, Thomas; Hogan, Ann K.; Márquez, Freddie; Kumar, Gagan; Seal, Rebecca; Edwards, Robert; Liberman, M. Charles; García-Añoveros, Jaime

    2015-01-01

    Summary Intense noise damages the cochlear organ of Corti, particularly the outer hair cells (OHCs)[1], however this epithelium is not innervated by nociceptors of somatosensory ganglia, which detect damage elsewhere in the body. The only sensory neurons innervating the organ of Corti originate from the spiral ganglion, roughly 95% of which innervate exclusively inner hair cells (IHCs)[2-4]. Upon sound stimulation, IHCs release glutamate to activate AMPA-type receptors on these myelinated type-I neurons, which carry the neuronal signals to the cochlear nucleus. The remaining spiral ganglion cells (type-IIs) are unmyelinated and contact OHCs[2-4]. Their function is unknown. Using immunoreactivity to cFos, we documented neuronal activation in the brainstem of Vglut3−/− mice, in which the canonical auditory pathway (activation of type-I afferents by glutamate released from inner hair cells) is silenced[5, 6]. In these deaf mice, we found responses to noxious noise, that damages hair cells, but not to innocuous noise, in neurons of the cochlear nucleus, but not in the vestibular or trigeminal nuclei. This response originates in the cochlea and not in other areas also stimulated by intense noise (middle ear and vestibule) as it was absent in CD1 mice with selective cochlear degeneration but normal vestibular and somatosensory function. These data imply the existence of an alternative neuronal pathway from cochlea to brainstem that is activated by tissue-damaging noise and does not require glutamate release from IHCs. This detection of noise-induced tissue damage, possibly by type-II cochlear afferents, represents a novel form of sensation we term auditory nociception. PMID:25639244

  18. A non canonical subtilase attenuates the transcriptional activation of defence responses in Arabidopsis thaliana.

    PubMed

    Serrano, Irene; Buscaill, Pierre; Audran, Corinne; Pouzet, Cécile; Jauneau, Alain; Rivas, Susana

    2016-09-29

    Proteases play crucial physiological functions in all organisms by controlling the lifetime of proteins. Here, we identified an atypical protease of the subtilase family [SBT5.2(b)] that attenuates the transcriptional activation of plant defence independently of its protease activity. The SBT5.2 gene produces two distinct transcripts encoding a canonical secreted subtilase [SBT5.2(a)] and an intracellular protein [SBT5.2(b)]. Concomitant to SBT5.2(a) downregulation, SBT5.2(b) expression is induced after bacterial inoculation. SBT5.2(b) localizes to endosomes where it interacts with and retains the defence-related transcription factor MYB30. Nuclear exclusion of MYB30 results in its reduced transcriptional activation and, thus, suppressed resistance. sbt5.2 mutants, with abolished SBT5.2(a) and SBT5.2(b) expression, display enhanced defence that is suppressed in a myb30 mutant background. Moreover, overexpression of SBT5.2(b), but not SBT5.2(a), in sbt5.2 plants reverts the phenotypes displayed by sbt5.2 mutants. Overall, we uncover a regulatory mode of the transcriptional activation of defence responses previously undescribed in eukaryotes.

  19. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.

    PubMed

    Fenwick, Michael K; Mehta, Angad P; Zhang, Yang; Abdelwahed, Sameh H; Begley, Tadhg P; Ealick, Steven E

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  20. Non-canonical integration events in Pichia pastoris encountered during standard transformation analysed with genome sequencing

    PubMed Central

    Schwarzhans, Jan-Philipp; Wibberg, Daniel; Winkler, Anika; Luttermann, Tobias; Kalinowski, Jörn; Friehs, Karl

    2016-01-01

    The non-conventional yeast Pichia pastoris is a popular host for recombinant protein production in scientific research and industry. Typically, the expression cassette is integrated into the genome via homologous recombination. Due to unknown integration events, a large clonal variability is often encountered consisting of clones with different productivities as well as aberrant morphological or growth characteristics. In this study, we analysed several clones with abnormal colony morphology and discovered unpredicted integration events via whole genome sequencing. These include (i) the relocation of the locus targeted for replacement to another chromosome (ii) co-integration of DNA from the E. coli plasmid host and (iii) the disruption of untargeted genes affecting colony morphology. Most of these events have not been reported so far in literature and present challenges for genetic engineering approaches in this yeast. Especially, the presence and independent activity of E. coli DNA elements in P. pastoris is of concern. In our study, we provide a deeper insight into these events and their potential origins. Steps preventing or reducing the risk for these phenomena are proposed and will help scientists working on genetic engineering of P. pastoris or similar non-conventional yeast to better understand and control clonal variability. PMID:27958335

  1. Oestrogen receptor-alpha regulates non-canonical Hedgehog-signalling in the mammary gland

    PubMed Central

    Okolowsky, Nadia; Furth, Priscilla A.; Hamel, Paul A.

    2014-01-01

    Mesenchymal dysplasia (mes) mice harbour a truncation in the C-terminal region of the Hh-ligand receptor, Patched-1 (mPtch1). While the mes variant of mPtch1 binds to Hh-ligands with an affinity similar to that of wild type mPtch1 and appears to normally regulate canonical Hh-signalling via smoothened, the mes mutation causes, among other non-lethal defects, a block to mammary ductal elongation at puberty. We demonstrated previously Hh-signalling induces the activation of Erk1/2 and c-src independently of its control of smo activity. Furthermore, mammary epithelial cell-directed expression of an activated allele of c-src rescued the block to ductal elongation in mes mice, albeit with delayed kinetics. Given that this rescue was accompanied by an induction in estrogen receptor-alpha (ERα) expression and that complex regulatory interactions between ERα and c-src are required for normal mammary gland development, it was hypothesized that expression of ERα would also overcome the block to mammary ductal elongation at puberty in the mes mouse. We demonstrate here that conditional expression of ERα in luminal mammary epithelial cells on the mes background facilitates ductal morphogenesis with kinetics similar to that of the MMTV-c-srcAct mice. We demonstrate further that Erk1/2 is activated in primary mammary epithelial cells by Shh-ligand and that this activation is blocked by the inhibitor of c-src, PP2, is partially blocked by the ERα inhibitor, ICI 182780 but is not blocked by the smo-inhibitor, SANT-1. These data reveal an apparent Hh-signalling cascade operating through c-src and ERα that is required for mammary gland morphogenesis at puberty. PMID:24769368

  2. Non-canonical WOX11-mediated root branching contributes to plasticity in Arabidopsis root system architecture.

    PubMed

    Sheng, Lihong; Hu, Xiaomei; Du, Yujuan; Zhang, Guifang; Huang, Hai; Scheres, Ben; Xu, Lin

    2017-09-01

    Lateral roots (LRs), which originate from the growing root, and adventitious roots (ARs), which are formed from non-root organs, are the main contributors to the post-embryonic root system in Arabidopsis However, our knowledge of how formation of the root system is altered in response to diverse inductive cues is limited. Here, we show that WOX11 contributes to root system plasticity. When seedlings are grown vertically on medium, WOX11 is not expressed in LR founder cells. During AR initiation, WOX11 is expressed in AR founder cells and activates LBD16LBD16 also functions in LR formation and is activated in that context by ARF7/19 and not by WOX11 This indicates that divergent initial processes that lead to ARs and LRs may converge on a similar mechanism for primordium development. Furthermore, we demonstrated that when plants are grown in soil or upon wounding on medium, the primary root is able to produce both WOX11-mediated and non-WOX11-mediated roots. The discovery of WOX11-mediated root-derived roots reveals a previously uncharacterized pathway that confers plasticity during the generation of root system architecture in response to different inductive cues. © 2017. Published by The Company of Biologists Ltd.

  3. Ethanol Effects Involve Non-canonical Unfolded Protein Response Activation in Yeast Cells

    PubMed Central

    Navarro-Tapia, Elisabet; Pérez-Torrado, Roberto; Querol, Amparo

    2017-01-01

    The unfolded protein response (UPR) is a conserved intracellular signaling pathway that controls transcription of endoplasmic reticulum (ER) homeostasis related genes. Ethanol stress has been recently described as an activator of the UPR response in yeast Saccharomyces cerevisiae, but very little is known about the causes of this activation. Although some authors ensure that the UPR is triggered by the unfolded proteins generated by ethanol in the cell, there are studies which demonstrate that protein denaturation occurs at higher ethanol concentrations than those used to trigger the UPR. Here, we studied UPR after ethanol stress by three different approaches and we concluded that unfolded proteins do not accumulate in the ER under. We also ruled out inositol depletion as an alternative mechanism to activate the UPR under ethanol stress discarding that ethanol effects on the cell decreased inositol levels by different methods. All these data suggest that ethanol, at relatively low concentrations, does not cause unfolded proteins in the yeasts and UPR activation is likely due to other unknown mechanism related with a restructuring of ER membrane due to the effect of ethanol. PMID:28326077

  4. Non-canonical transcription initiation: the expanding universe of transcription initiating substrates.

    PubMed

    Barvík, Ivan; Rejman, Dominik; Panova, Natalya; Šanderová, Hana; Krásný, Libor

    2017-03-01

    RNA polymerase (RNAP) is the central enzyme of transcription of the genetic information from DNA into RNA. RNAP recognizes four main substrates: ATP, CTP, GTP and UTP. Experimental evidence from the past several years suggests that, besides these four NTPs, other molecules can be used to initiate transcription: (i) ribooligonucleotides (nanoRNAs) and (ii) coenzymes such as NAD+, NADH, dephospho-CoA and FAD. The presence of these molecules at the 5΄ ends of RNAs affects the properties of the RNA. Here, we discuss the expanding portfolio of molecules that can initiate transcription, their mechanism of incorporation, effects on RNA and cellular processes, and we present an outlook toward other possible initiation substrates.

  5. Ciliary intraflagellar transport protein 80 balances canonical versus non-canonical hedgehog signaling for osteoblast differentiation

    USDA-ARS?s Scientific Manuscript database

    Mutation of different IFT proteins cause numerous different clinical bone disorders accompanied with or without the disruption of cilia formation. Currently, there is no any effective treatment for these disorders due to lack of understanding in the function and mechanism of these proteins. IFT80 is...

  6. Psychological Dimensions of Cross-Cultural Differences

    DTIC Science & Technology

    2013-05-01

    AFRL-OSR-VA-TR-2013-0214 Psychological Dimensions of Cross- Cultural Differences Saucier, Gerard University of Oregon May...Psychological Dimensions of Cross- Cultural Differences Grant Research Final Performance Report – February 2013 prepared by Gerard Saucier, Principal...Psychological Dimensions of Cross- Cultural Differences Contract/Grant Number: FA9550-09-1-0398 Reporting period: June 1, 2009 to November 30, 2012

  7. The Cultural Dimension of Army Transition

    DTIC Science & Technology

    2012-12-06

    TITLE AND SUBTITLE THE CULTURAL DIMENSION OF ARMY TRANSITION 5. FUNDING NUMBERS 6. AUTHOR( S ) ANGUS M. A. TILNEY 7. PERFORMING ORGANIZATION...armies. Furthermore, according to the well-recognized “ dimensions of national culture ” studied by Geert Hofstede , Britain and the United States share...Approved for Public Release; Distribution is Unlimited The Cultural Dimension of Army Transition A Monograph by Major Angus Myles Arthur Tilney

  8. Contagion Shocks in One Dimension

    NASA Astrophysics Data System (ADS)

    Bertozzi, Andrea L.; Rosado, Jesus; Short, Martin B.; Wang, Li

    2015-02-01

    We consider an agent-based model of emotional contagion coupled with motion in one dimension that has recently been studied in the computer science community. The model involves movement with a speed proportional to a "fear" variable that undergoes a temporal consensus averaging based on distance to other agents. We study the effect of Riemann initial data for this problem, leading to shock dynamics that are studied both within the agent-based model as well as in a continuum limit. We examine the behavior of the model under distinguished limits as the characteristic contagion interaction distance and the interaction timescale both approach zero. The limiting behavior is related to a classical model for pressureless gas dynamics with "sticky" particles. In comparison, we observe a threshold for the interaction distance vs. interaction timescale that produce qualitatively different behavior for the system - in one case particle paths do not cross and there is a natural Eulerian limit involving nonlocal interactions and in the other case particle paths can cross and one may consider only a kinetic model in the continuum limit.

  9. Optoacoustic imaging in five dimensions

    NASA Astrophysics Data System (ADS)

    Deán-Ben, X. L.; Gottschalk, Sven; Fehm, Thomas F.; Razansky, Daniel

    2015-03-01

    We report on an optoacoustic imaging system capable of acquiring volumetric multispectral optoacoustic data in real time. The system is based on simultaneous acquisition of optoacoustic signals from 256 different tomographic projections by means of a spherical matrix array. Thereby, volumetric reconstructions can be done at high frame rate, only limited by the pulse repetition rate of the laser. The developed tomographic approach presents important advantages over previously reported systems that use scanning for attaining volumetric optoacoustic data. First, dynamic processes, such as the biodistribution of optical biomarkers, can be monitored in the entire volume of interest. Second, out-of-plane and motion artifacts that could degrade the image quality when imaging living specimens can be avoided. Finally, real-time 3D performance can obviously save time required for experimental and clinical observations. The feasibility of optoacoustic imaging in five dimensions, i.e. real time acquisition of volumetric datasets at multiple wavelengths, is reported. In this way, volumetric images of spectrally resolved chromophores are rendered in real time, thus offering an unparallel imaging performance among the current bio-imaging modalities. This performance is subsequently showcased by video-rate visualization of in vivo hemodynamic changes in mouse brain and handheld visualization of blood oxygenation in deep human vessels. The newly discovered capacities open new prospects for translating the optoacoustic technology into highly performing imaging modality for biomedical research and clinical practice with multiple applications envisioned, from cardiovascular and cancer diagnostics to neuroimaging and ophthalmology.

  10. THE INTERNATIONAL DIMENSIONS OF NEUROETHICS

    PubMed Central

    LOMBERA, SOFIA; ILLES, JUDY

    2008-01-01

    Neuroethics, in its modern form, investigates the impact of brain science in four basic dimensions: the self, social policy, practice and discourse. In this study, we analyzed a set of 461 peer-reviewed articles with neuroethics content, published by authors from 32 countries. We analyzed the data for: (1) trends in the development of international neuroethics over time, and (2) how challenges at the intersection of ethics and neuroscience are viewed in countries that are considered developed by International Monetary Fund (IMF) standards, and in those that are developing. Our results demonstrate a steady increase in global participation in neuroethics from 1989 to 2005, characterized by an increase in numbers of articles published specifically on neuroethics, journals publishing these articles, and countries contributing to the literature. The focus from all countries was on the practice of brain science and the amelioration of neurological disease. Indicators of technology creation and diffusion in developing countries were specifically correlated with increases in publications concerning policy implications of brain science. Neuroethics is an international endeavor and, as such, should be sensitive to the impact that context has on acceptance and use of technological innovation. PMID:18445073

  11. Deconstructing Signaling in Three Dimensions

    PubMed Central

    2015-01-01

    Cells in vivo exist within the context of a multicellular tissue, where their behavior is governed by homo- and heterotypic cell–cell interactions, the material properties of the extracellular matrix, and the distribution of various soluble and physical factors. Most methods currently used to study and manipulate cellular behavior in vitro, however, sacrifice physiological relevance for experimental expediency. The fallacy of such approaches has been highlighted by the recent development and application of three-dimensional culture models to cell biology, which has revealed striking phenotypic differences in cell survival, migration, and differentiation in genetically identical cells simply by varying culture conditions. These perplexing findings beg the question of what constitutes a three-dimensional culture and why cells behave so differently in two- and three-dimensional culture formats. In the following review, we dissect the fundamental differences between two- and three-dimensional culture conditions. We begin by establishing a basic definition of what “three dimensions” means at different biological scales and discuss how dimensionality influences cell signaling across different length scales. We identify which three-dimensional features most potently influence intracellular signaling and distinguish between conserved biological principles that are maintained across culture conditions and cellular behaviors that are sensitive to microenvironmental context. Finally, we highlight state-of-the-art molecular tools amenable to the study of signaling in three dimensions under conditions that facilitate deconstruction of signaling in a more physiologically relevant manner. PMID:24649923

  12. The international dimensions of neuroethics.

    PubMed

    Lombera, Sofia; Illes, Judy

    2009-08-01

    Neuroethics, in its modern form, investigates the impact of brain science in four basic dimensions: the self, social policy, practice and discourse. In this study, we analyzed a set of 461 peer-reviewed articles with neuroethics content, published by authors from 32 countries. We analyzed the data for: (1) trends in the development of international neuroethics over time, and (2) how challenges at the intersection of ethics and neuroscience are viewed in countries that are considered developed by International Monetary Fund (IMF) standards, and in those that are developing. Our results demonstrate a steady increase in global participation in neuroethics from 1989 to 2005, characterized by an increase in numbers of articles published specifically on neuroethics, journals publishing these articles, and countries contributing to the literature. The focus from all countries was on the practice of brain science and the amelioration of neurological disease. Indicators of technology creation and diffusion in developing countries were specifically correlated with increases in publications concerning policy implications of brain science. Neuroethics is an international endeavor and, as such, should be sensitive to the impact that context has on acceptance and use of technological innovation.

  13. Dimensions of vehicle sounds perception.

    PubMed

    Wagner, Verena; Kallus, K Wolfgang; Foehl, Ulrich

    2017-10-01

    Vehicle sounds play an important role concerning customer satisfaction and can show another differentiating factor of brands. With an online survey of 1762 German and American customers, the requirement characteristics of high-quality vehicle sounds were determined. On the basis of these characteristics, a requirement profile was generated for every analyzed sound. These profiles were investigated in a second study with 78 customers using real vehicles. The assessment results of the vehicle sounds can be represented using the dimensions "timbre", "loudness", and "roughness/sharpness". The comparison of the requirement profiles and the assessment results show that the sounds which are perceived as pleasant and high-quality, more often correspond to the requirement profile. High-quality sounds are characterized by the fact that they are rather gentle, soft and reserved, rich, a bit dark and not too rough. For those sounds which are assessed worse by the customers, recommendations for improvements can be derived. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Ising spin glasses in dimension five

    NASA Astrophysics Data System (ADS)

    Lundow, P. H.; Campbell, I. A.

    2017-01-01

    Ising spin-glass models with bimodal, Gaussian, uniform, and Laplacian interaction distributions in dimension five are studied through detailed numerical simulations. The data are analyzed in both the finite-size scaling regime and the thermodynamic limit regime. It is shown that the values of critical exponents and of dimensionless observables at criticality are model dependent. Models in a single universality class have identical values for each of these critical parameters, so Ising spin-glass models in dimension five with different interaction distributions each lie in different universality classes. This result confirms conclusions drawn from measurements in dimension four and dimension two.

  15. Ising spin glasses in dimension five.

    PubMed

    Lundow, P H; Campbell, I A

    2017-01-01

    Ising spin-glass models with bimodal, Gaussian, uniform, and Laplacian interaction distributions in dimension five are studied through detailed numerical simulations. The data are analyzed in both the finite-size scaling regime and the thermodynamic limit regime. It is shown that the values of critical exponents and of dimensionless observables at criticality are model dependent. Models in a single universality class have identical values for each of these critical parameters, so Ising spin-glass models in dimension five with different interaction distributions each lie in different universality classes. This result confirms conclusions drawn from measurements in dimension four and dimension two.

  16. Spontaneous symmetry breaking in quasi one dimension

    SciTech Connect

    Satpathi, Urbashi Deo, P. Singha

    2015-06-24

    Electronic charge and spin separation leading to charge density wave and spin density wave is well established in one dimension in the presence and absence of Coulomb interaction. We start from quasi one dimension and show the possibility of such a transition in quasi one dimension as well as in two dimensions by going to a regime where it can be shown for electrons that just interact via Fermi statistics. Such density waves arise due to internal symmetry breaking in a many fermion quantum system. We can extend this result to very wide rings with infinitely many electrons including Coulomb interaction.

  17. Transformation equations for the fifth dimension

    NASA Astrophysics Data System (ADS)

    Said, M. Helmy

    2017-07-01

    Scientists have been arguing for a long time if there are particles faster than the speed of light or not. Those who denied the existence of particles faster than light speed always refer to Lorentz equation. This equation deals with particles in only four dimensions. In this paper, we show what would happen if we add one more dimension to this equation to make it deals with five dimensions instead of four. The addition of this fifth dimension will greatly help us understand the state of particles before, near, at, and above the speed of light.

  18. Origin of Everything and the 21 Dimensions of the Universe

    NASA Astrophysics Data System (ADS)

    Loev, Mark

    2009-03-01

    The Dimensions of the Universe correspond with the Dimensions of the human body. The emotion that is a positive for every dimension is Love. The negative emotion that effects each dimension are listed. All seven negative emotions effect Peace, Love and Happiness. 21st Dimension: Happiness Groin & Heart 20th Dimension: Love Groin & Heart 19th Dimension: Peace Groin & heart 18th Dimension: Imagination Wave Eyes Anger 17th Dimension: Z Wave / Closed Birth 16th Dimension: Electromagnetic Wave Ears Anger 15th Dimension: Universal Wave Skin Worry 14th Dimension: Lover Wave Blood Hate 13th Dimension: Disposal Wave Buttocks Fear 12th Dimension: Builder Wave Hands Hate 11th Dimension: Energy Wave Arms Fear 10th Dimension: Time Wave Brain Pessimism 9th Dimension: Gravity Wave Legs Fear 8th Dimension: Sweet Wave Pancreas Fear 7th Dimension: File Wave Left Lung Fear 6th Dimension: Breathing Wave Right Lung Fear 5th Dimension: Digestive Wave Stomach Fear 4th Dimension: Swab Wave Liver Guilt 3rd Dimension: Space Wave Face Sadness 2nd Dimension: Line Wave Mouth Revenge 1st Dimension: Dot Wave Nose Sadness The seven deadly sins correspond: Anger Hate Sadness Fear Worry Pessimism Revenge Note: Guilt is fear

  19. Neuroanatomical profiles of alexithymia dimensions and subtypes.

    PubMed

    Goerlich-Dobre, Katharina Sophia; Votinov, Mikhail; Habel, Ute; Pripfl, Juergen; Lamm, Claus

    2015-10-01

    Alexithymia, a major risk factor for a range of psychiatric and neurological disorders, has been recognized to comprise two dimensions, a cognitive dimension (difficulties identifying, analyzing, and verbalizing feelings) and an affective one (difficulties emotionalizing and fantasizing). Based on these dimensions, the existence of four distinct alexithymia subtypes has been proposed, but never empirically tested. In this study, 125 participants were assigned to four groups corresponding to the proposed alexithymia subtypes: Type I (impairment on both dimensions), Type II (impairment on the cognitive, but not the affective dimension), Type III (impairment on the affective, but not the cognitive dimension), and Lexithymics (no impairment on either dimension). By means of voxel-based morphometry, associations of the alexithymia dimensions and subtypes with gray and white matter volumes were analyzed. Type I and Type II alexithymia were characterized by gray matter volume reductions in the left amygdala and the thalamus. The cognitive dimension was further linked to volume reductions in the right amygdala, left posterior insula, precuneus, caudate, hippocampus, and parahippocampus. Type III alexithymia was marked by volume reduction in the MCC only, and the affective dimension was further characterized by larger sgACC volume. Moreover, individuals with the intermediate alexithymia Types II and III showed gray matter volume reductions in distinct regions, and had larger corpus callosum volumes compared to Lexithymics. These results substantiate the notion of a differential impact of the cognitive and affective alexithymia dimensions on brain morphology and provide evidence for separable neuroanatomical representations of the different alexithymia subtypes. © 2015 Wiley Periodicals, Inc.

  20. Dimensions of health system reform.

    PubMed

    Frenk, J

    1994-01-31

    During recent years there has been a growth of worldwide interest in health system reform. Countries at all levels of economic development are engaged in a creative search for better ways of organizing and financing health care, while promoting the goals of equity, effectiveness, and efficiency. Together with economic, political, and ideological reasons, this search has been fueled by the need to find answers to the complexities posed by the epidemiologic transition, whereby many nations are facing the simultaneous burdens of old, unresolved problems and new, emerging challenges. In order to better understand reform attempts, it is necessary to develop a clear conception of the object of reform: the health system. This paper presents the health system as a set of relationships among five major groups of actors: the health care providers, the population, the state as a collective mediator, the organizations that generate resources, and the other sectors that produce services with health effects. The relationships among providers, population, and the state form the basis for a typology of health care modalities. The type and number of modalities present in a country make it possible to characterize its health system. In the last part, the paper proposes that health system reform operates at four policy levels: systemic, which deals with the institutional arrangements for regulation, financing, and delivery of services; programmatic, which specifies the priorities of the system, by defining a universal package of health care interventions; organizational, which is concerned with the actual production of services by focusing on issues of quality assurance and technical efficiency; and instrumental, which generates the institutional intelligence for improving system performance through information, research, technological innovation, and human resource development. The dimensions of reform offer a repertoire of policy options, which need to be enriched by cross

  1. 49 CFR 178.360-3 - Dimensions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false Dimensions. 178.360-3 Section 178.360-3 Transportation Other Regulations Relating to Transportation PIPELINE AND HAZARDOUS MATERIALS SAFETY... Specifications for Packagings for Class 7 (Radioactive) Materials § 178.360-3 Dimensions. (a) The inside diameter...

  2. 49 CFR 178.360-3 - Dimensions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 3 2011-10-01 2011-10-01 false Dimensions. 178.360-3 Section 178.360-3 Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY... Packagings for Class 7 (Radioactive) Materials § 178.360-3 Dimensions. (a) The inside diameter of the vessel...

  3. Physics of Extra Dimensions Final Report

    SciTech Connect

    Csaba Csaki

    2007-12-19

    We provide the final report for Csaba Csaki's OJI project on "Physics of extra dimensions". It includes the summary of results of higgsless electroweak symmetry breaking, gauge-higgs unification, AdS/QCD and holographic technicolor, and chiral lattice theories from warped extra dimensions.

  4. Understanding Dimensions of Organizational Evaluation Capacity

    ERIC Educational Resources Information Center

    Bourgeois, Isabelle; Cousins, J. Bradley

    2013-01-01

    Organizational evaluation capacity building has been a topic of increasing interest in recent years. However, the actual dimensions of evaluation capacity have not been clearly articulated through empirical research. This study sought to address this gap by identifying the key dimensions of evaluation capacity in Canadian federal government…

  5. Quantum Field Theory in (0 + 1) Dimensions

    ERIC Educational Resources Information Center

    Boozer, A. D.

    2007-01-01

    We show that many of the key ideas of quantum field theory can be illustrated simply and straightforwardly by using toy models in (0 + 1) dimensions. Because quantum field theory in (0 + 1) dimensions is equivalent to quantum mechanics, these models allow us to use techniques from quantum mechanics to gain insight into quantum field theory. In…

  6. Four Essential Dimensions of Workplace Learning

    ERIC Educational Resources Information Center

    Hopwood, Nick

    2014-01-01

    Purpose: This conceptual paper aims to argue that times, spaces, bodies and things constitute four essential dimensions of workplace learning. It examines how practices relate or hang together, taking Gherardi's texture of practices or connectedness in action as the foundation for making visible essential but often overlooked dimensions of…

  7. Feature binding across different visual dimensions.

    PubMed

    Ward, Robert; Arend, Isabel

    2012-10-01

    The human brain represents different kinds of visual feature dimensions in different ways. For example, surface features exhibit some properties that are very different from contour features, and some feature dimensions may be represented more extensively in either the dorsal or the ventral visual stream. Given such differences, we investigated feature binding across different feature dimensions and whether some feature dimensions might be more easily bound together than others. In Experiment 1, we looked at cross-dimension bindings for all combinations of color, orientation, and shape dimensions, while at the same time controlling for feature discriminability. Rates of correct binding, illusory conjunctions, and feature errors were equivalent in all cases. There was no bias so that some feature dimensions were easier to combine than others. In Experiment 2, we manipulated the difficulty of feature discrimination for the key, target-defining feature and the report feature. Rates of binding errors increased with difficulty of the key feature, but not with that of the report feature. The accuracy of feature discrimination could be dissociated from the accuracy of binding the feature to an object. Across both experiments, the accuracy of feature binding was independent of specific feature dimensions or perceptibility. These findings are discussed in relation to both feature integration and multiple-stage accounts of visual feature integration.

  8. Unconscious Evaluation of Faces on Social Dimensions

    ERIC Educational Resources Information Center

    Stewart, Lorna H.; Ajina, Sara; Getov, Spas; Bahrami, Bahador; Todorov, Alexander; Rees, Geraint

    2012-01-01

    It has been proposed that two major axes, dominance and trustworthiness, characterize the social dimensions of face evaluation. Whether evaluation of faces on these social dimensions is restricted to conscious appraisal or happens at a preconscious level is unknown. Here we provide behavioral evidence that such preconscious evaluations exist and…

  9. 49 CFR 178.360-3 - Dimensions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 3 2013-10-01 2013-10-01 false Dimensions. 178.360-3 Section 178.360-3 Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY... Packagings for Class 7 (Radioactive) Materials § 178.360-3 Dimensions. (a) The inside diameter of the vessel...

  10. [Penile dimensions in type 2 diabetes].

    PubMed

    Belousov, I I; Kogan, M I; Ibishev, H S; Vorobyev, S V; Khripun, I A; Gusova, Z R

    2015-12-01

    The current literature provides a wide range of publications on the anthropometry of the penis specifying the relationship between penile dimensions and sex hormones, weight, height and erectile function. But most of the studies involved healthy volunteers or young patients with erectile dysfunction. Our study was conducted in patients with type 2 diabetes. Penile measurements obtained in the present study were compared those of the average Russian man. The patients were divided into groups with preserved and impaired erectile function. Erectile function was also studied relative to the variability of penile dimensions. The effect of DM duration on erectile function was defined. Comparative analysis revealed the relationship between penile anatomical dimensions and erectile function. We studied the effect of type 2 diabetes on the anatomical dimensions and elasticity of the penis, established the relationship between penile dimensions and elasticity of the penis. The correlation between the severity of erectile dysfunction and serum testosterone levels on one side, and penile dimensions on the other was found. The effect of penile dimensions on erectile function in DM patients was also examined. Determining penile dimensions and their variability due to various pathological conditions or processes, may eventually lead to better result of ED management.

  11. 49 CFR 178.360-3 - Dimensions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 3 2012-10-01 2012-10-01 false Dimensions. 178.360-3 Section 178.360-3 Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY... Packagings for Class 7 (Radioactive) Materials § 178.360-3 Dimensions. (a) The inside diameter of the vessel...

  12. An Inventory of Listening Competency Dimensions

    ERIC Educational Resources Information Center

    Wolvin, Andrew D.; Cohen, Steven D.

    2012-01-01

    This article proposes the use of a one-page listening inventory sheet that helps students explore five dimensions of listening competency: cognitive, affective, behavioral, contextual, and ethical. After crafting their own responses, students will have the opportunity to engage in a class discussion about the impact of various dimensions of…

  13. Quality Dimensions of Internet Search Engines.

    ERIC Educational Resources Information Center

    Xie, M.; Wang, H.; Goh, T. N.

    1998-01-01

    Reviews commonly used search engines (AltaVista, Excite, infoseek, Lycos, HotBot, WebCrawler), focusing on existing comparative studies; considers quality dimensions from the customer's point of view based on a SERVQUAL framework; and groups these quality expectations in five dimensions: tangibles, reliability, responsiveness, assurance, and…

  14. Interlocked molecules: Moving into another dimension

    NASA Astrophysics Data System (ADS)

    Fournel-Marotte, Karine; Coutrot, Frédéric

    2016-12-01

    Molecular daisy-chain structures are typically made up of two interlocked components and can exhibit muscle-like contraction and extension in one dimension. Zinc-based multicomponent systems that can operate in two and three dimensions have now been designed and synthesized.

  15. Potential Dimension Yields From Direct Processing

    Treesearch

    Wenjie Lin; D. Earl Kline; Philip A. Araman

    1994-01-01

    As the price of timber increases and environmental leigslation limits harvestable log volumes, the process of converting logs directly into dimension parts needs further exploration. Direct processing converts logs directly into rough green dimension parts without the intermediate steps of lumber manufacturing, grading, trading, shipping and drying. A major attraction...

  16. Quantum Field Theory in (0 + 1) Dimensions

    ERIC Educational Resources Information Center

    Boozer, A. D.

    2007-01-01

    We show that many of the key ideas of quantum field theory can be illustrated simply and straightforwardly by using toy models in (0 + 1) dimensions. Because quantum field theory in (0 + 1) dimensions is equivalent to quantum mechanics, these models allow us to use techniques from quantum mechanics to gain insight into quantum field theory. In…

  17. Unconscious Evaluation of Faces on Social Dimensions

    ERIC Educational Resources Information Center

    Stewart, Lorna H.; Ajina, Sara; Getov, Spas; Bahrami, Bahador; Todorov, Alexander; Rees, Geraint

    2012-01-01

    It has been proposed that two major axes, dominance and trustworthiness, characterize the social dimensions of face evaluation. Whether evaluation of faces on these social dimensions is restricted to conscious appraisal or happens at a preconscious level is unknown. Here we provide behavioral evidence that such preconscious evaluations exist and…

  18. Understanding Dimensions of Organizational Evaluation Capacity

    ERIC Educational Resources Information Center

    Bourgeois, Isabelle; Cousins, J. Bradley

    2013-01-01

    Organizational evaluation capacity building has been a topic of increasing interest in recent years. However, the actual dimensions of evaluation capacity have not been clearly articulated through empirical research. This study sought to address this gap by identifying the key dimensions of evaluation capacity in Canadian federal government…

  19. Four Essential Dimensions of Workplace Learning

    ERIC Educational Resources Information Center

    Hopwood, Nick

    2014-01-01

    Purpose: This conceptual paper aims to argue that times, spaces, bodies and things constitute four essential dimensions of workplace learning. It examines how practices relate or hang together, taking Gherardi's texture of practices or connectedness in action as the foundation for making visible essential but often overlooked dimensions of…

  20. Quality Dimensions of Internet Search Engines.

    ERIC Educational Resources Information Center

    Xie, M.; Wang, H.; Goh, T. N.

    1998-01-01

    Reviews commonly used search engines (AltaVista, Excite, infoseek, Lycos, HotBot, WebCrawler), focusing on existing comparative studies; considers quality dimensions from the customer's point of view based on a SERVQUAL framework; and groups these quality expectations in five dimensions: tangibles, reliability, responsiveness, assurance, and…

  1. Determinant factors of Yemeni maxillary arch dimensions.

    PubMed

    Al-Zubair, Nabil Muhsen

    2015-01-01

    Information about maxillary arch and palatal dimensions in human populations is important for clinical orthodontics. This study was conducted to assess the determinants of maxillary arch dimensions in a sample of Yemeni individuals aged 18-25 years. The study sample comprised 214/765 adults (101 women, 113 men) who underwent clinical examination and fulfilled the study criteria. Study models were constructed and evaluated to measure maxillary arch and palatal dimensions. The majority of mean maxillary arch dimensions were significantly greater in men than in women, with inter-second molar distance showing the greatest difference and palatal depth showing the least difference. Measurements of palatal depth and relationships of the canines to one another and to other teeth thus had the widest ranges, implying that these dimensions are the strongest determinants of maxillary arch size.

  2. Positioner with long travel in two dimensions

    DOEpatents

    Trumper, David L.; Williams, Mark E.

    1997-12-23

    A precision positioning system is provided which provides long travel in two of the linear dimensions, while using non-contact bearings for both a first subassembly which provides long travel in one of the linear dimension and a second subassembly which provides long travel in the second linear dimension. The first or upper subassembly is preferably a magnetic subassembly which, in addition to providing long travel, also compensates or positions in three rotary dimensions and in the third linear dimension. The second subassembly is preferably either an air bearing or magnetic subassembly and is normally used only to provide long travel. Angled surfaces may be provided for magnetic bearings and capacitive or other gap sensing probes may be mounted to the stage and ground flush with the bearing actuators to provide more precise gap measurements.

  3. Measuring Five Dimensions of Religiosity across Adolescence.

    PubMed

    Pearce, Lisa D; Hayward, George M; Pearlman, Jessica A

    2017-09-01

    This paper theorizes and tests a latent variable model of adolescent religiosity in which five dimensions of religiosity are interrelated: religious beliefs, religious exclusivity, external religiosity, private practice, and religious salience. Research often theorizes overlapping and independent influences of single items or dimensions of religiosity on outcomes such as adolescent sexual behavior, but rarely operationalizes the dimensions in a measurement model accounting for their associations with each other and across time. We use longitudinal structural equation modeling (SEM) with latent variables to analyze data from two waves of the National Study of Youth and Religion. We test our hypothesized measurement model as compared to four alternate measurement models and find that our proposed model maintains superior fit. We then discuss the associations between the five dimensions of religiosity we measure and how these change over time. Our findings suggest how future research might better operationalize multiple dimensions of religiosity in studies of the influence of religion in adolescence.

  4. Measuring Five Dimensions of Religiosity across Adolescence

    PubMed Central

    Pearce, Lisa D.; Hayward, George M.; Pearlman, Jessica A.

    2017-01-01

    This paper theorizes and tests a latent variable model of adolescent religiosity in which five dimensions of religiosity are interrelated: religious beliefs, religious exclusivity, external religiosity, private practice, and religious salience. Research often theorizes overlapping and independent influences of single items or dimensions of religiosity on outcomes such as adolescent sexual behavior, but rarely operationalizes the dimensions in a measurement model accounting for their associations with each other and across time. We use longitudinal structural equation modeling (SEM) with latent variables to analyze data from two waves of the National Study of Youth and Religion. We test our hypothesized measurement model as compared to four alternate measurement models and find that our proposed model maintains superior fit. We then discuss the associations between the five dimensions of religiosity we measure and how these change over time. Our findings suggest how future research might better operationalize multiple dimensions of religiosity in studies of the influence of religion in adolescence. PMID:28931956

  5. Relationships between body dimensions, body weight, age, gender, breed and echocardiographic dimensions in young endurance horses.

    PubMed

    Trachsel, D S; Giraudet, A; Maso, D; Hervé, G; Hauri, D D; Barrey, E; Robert, C

    2016-10-10

    The heart's physiological adaptation to aerobic training leads to an increase in heart chamber size, and is referred to as the Athlete's heart. However, heart dimensions are also related to body weight (BWT), body size, growth and (in some species) breed. There are few published data on the relationships between heart dimensions and growth or aerobic training in Arabian and Arabian-related endurance horses. Therefore the objective of the present study was to describe the influence of body dimensions (body length (BL), thoracic circumference (TC), withers height (WH)), BWT, age, gender, breed (purebred Arabians, part-bred Arabians, Anglo-Arabians, and Others) and the initiation of endurance training on echocardiographic measurements in competition-fit endurance horses aged 4 to 6 years. Most left atrial (LA) and left ventricular (LV) dimensions increased with age, whereas LA and LV functional indices did not. Although there was no gender difference for LV dimensions, females had larger LA dimensions. In terms of breed, Anglo-Arabians had the largest LV dimensions. Regression models indicated that the included explanatory factors had a weak influence on heart dimensions. Age, body dimensions, breed and gender showed the most consistent influence on LA dimensions, whereas BWT, breed and kilometres covered in competition showed the most consistent influence on LV dimensions. The increase in echocardiographic dimensions with age indicates on-going growth in our population of 4 to 6 year-old horses. We also observed small changes associated with the initiation of endurance training. Morphometric dimensions had a greater influence on LA dimensions, whereas LV dimensions were also influenced (albeit weakly) by parameters associated with exercise intensity. These results may therefore reflect early adaptations linked to the initiation of endurance training.

  6. Earthquake spatial distribution: The correlation dimension

    NASA Astrophysics Data System (ADS)

    Kagan, Y. Y.

    2006-12-01

    We review methods for determining the fractal dimensions of earthquake epicenters and hypocenters, paying special attention to the problem of errors, biases and systematic effects. Among effects considered are earthquake location errors, boundary effects, inhomogeneity of depth distribution, and temporal dependence. In particular, the correlation dimension of earthquake spatial distribution is discussed, techniques for its evaluation presented, and results for several earthquake catalogs are analyzed. We show that practically any value for the correlation dimension can be obtained if many errors and inhomogeneities in observational data as well as deficiencies in data processing are not properly considered. It is likely that such technical difficulties are intensified when one attempts to evaluate multifractal measures of dimension. Taking into account possible errors and biases, we conclude that the fractal dimension for shallow seismicity asymptotically approaches 2.20 ± 0.05 for a catalog time span of decades and perhaps centuries. The value of the correlation dimension declines to 1.8-1.9 for intermediate events (depth interval 71-280 km) and to 1.5-1.6 for deeper ones. For plate tectonic deformation on the time scale of millions of years, it is possible that the correlation dimension for shallow earthquakes may increase to 2.6-2.7.

  7. Topological Hausdorff dimension and geodesic metric of critical percolation cluster in two dimensions

    NASA Astrophysics Data System (ADS)

    Balankin, Alexander S.; Mena, Baltasar; Martínez Cruz, M. A.

    2017-09-01

    In this work, we prove that the topological Hausdorff dimension of critical percolation cluster (CPC) in two dimensions is equal to DtH =Drb + 1 = 7 / 4, where Drb is the Hausdorff dimension of the set of red bonds. Hence, the CPC is infinitely ramified. We also argue that the mapping from the Euclidean metric to the geodesic metric on the CPC is governed by the Hausdorff dimension of the cluster skeleton Dsc =DH /dℓ >dmin, where DH, dℓ, and dmin are the Hausdorff and the connectivity (chemical) dimensions of the CPC and the fractal dimension of the minimum path, respectively. Then we introduce the notion of the topological connectivity dimension dtℓ. This allows us to establish the exact upper and lower bounds for the connectivity dimension dℓ of the CPC in d = 2. The upper and lower bounds for some other dimension numbers were established using the relations between dimension numbers. Narrow ranges defined by these bounds are much smaller than the error bars of numerical estimates reported in literature. Accordingly, the exact values of some dimension numbers are conjectured.

  8. Long-wavelength fluctuations and the glass transition in two dimensions and three dimensions

    NASA Astrophysics Data System (ADS)

    Vivek, Skanda; Kelleher, Colm P.; Chaikin, Paul M.; Weeks, Eric R.

    2017-02-01

    Phase transitions significantly differ between 2D and 3D systems, but the influence of dimensionality on the glass transition is unresolved. We use microscopy to study colloidal systems as they approach their glass transitions at high concentrations and find differences between two dimensions and three dimensions. We find that, in two dimensions, particles can undergo large displacements without changing their position relative to their neighbors, in contrast with three dimensions. This is related to Mermin-Wagner long-wavelength fluctuations that influence phase transitions in two dimensions. However, when measuring particle motion only relative to their neighbors, two dimensions and three dimensions have similar behavior as the glass transition is approached, showing that the long-wavelength fluctuations do not cause a fundamental distinction between 2D and 3D glass transitions.

  9. Long-wavelength fluctuations and the glass transition in two dimensions and three dimensions.

    PubMed

    Vivek, Skanda; Kelleher, Colm P; Chaikin, Paul M; Weeks, Eric R

    2017-02-21

    Phase transitions significantly differ between 2D and 3D systems, but the influence of dimensionality on the glass transition is unresolved. We use microscopy to study colloidal systems as they approach their glass transitions at high concentrations and find differences between two dimensions and three dimensions. We find that, in two dimensions, particles can undergo large displacements without changing their position relative to their neighbors, in contrast with three dimensions. This is related to Mermin-Wagner long-wavelength fluctuations that influence phase transitions in two dimensions. However, when measuring particle motion only relative to their neighbors, two dimensions and three dimensions have similar behavior as the glass transition is approached, showing that the long-wavelength fluctuations do not cause a fundamental distinction between 2D and 3D glass transitions.

  10. Faces of root polytopes in all dimensions.

    PubMed

    Szajewska, Marzena

    2016-07-01

    In this paper the root polytopes of all finite reflection groups W with a connected Coxeter-Dynkin diagram in {\\bb R}^n are identified, their faces of dimensions 0 ≤ d ≤ n - 1 are counted, and the construction of representatives of the appropriate W-conjugacy class is described. The method consists of recursive decoration of the appropriate Coxeter-Dynkin diagram [Champagne et al. (1995). Can. J. Phys. 73, 566-584]. Each recursion step provides the essentials of faces of a specific dimension and specific symmetry. The results can be applied to crystals of any dimension and any symmetry.

  11. Correspondence between Soft and Rapidity Anomalous Dimensions.

    PubMed

    Vladimirov, Alexey A

    2017-02-10

    We establish a correspondence between ultraviolet singularities of soft factors for multiparticle production and rapidity singularities of soft factors for multiparton scattering. This correspondence is a consequence of the conformal mapping between scattering geometries. The correspondence is valid to all orders of perturbation theory and in this way, provides one with a proof of rapidity renormalization procedure for multiparton scattering [including the transverse momentum dependent (TMD) factorization as a special case]. As a by-product, we obtain an exact relation between the rapidity anomalous dimension and the well-known soft anomalous dimension. The three-loop expressions for TMD and a general multiparton scattering rapidity anomalous dimension are derived.

  12. Three loop cusp anomalous dimension in QCD.

    PubMed

    Grozin, Andrey; Henn, Johannes M; Korchemsky, Gregory P; Marquard, Peter

    2015-02-13

    We present the full analytic result for the three loop angle-dependent cusp anomalous dimension in QCD. With this result, infrared divergences of planar scattering processes with massive particles can be predicted to that order. Moreover, we define a closely related quantity in terms of an effective coupling defined by the lightlike cusp anomalous dimension. We find evidence that this quantity is universal for any gauge theory and use this observation to predict the nonplanar n(f)-dependent terms of the four loop cusp anomalous dimension.

  13. Searching for extra-dimensions at CMS

    NASA Astrophysics Data System (ADS)

    Benucci, Leonardo

    2009-06-01

    A possible solution to the hierarchy problem is the presence of extra space dimensions beyond the three ones which are known from our everyday experience. The phenomenological ADD model of large extra-dimensions predicts a ETmiss +jet signature. Randall-Sundrum-type extra-dimensions predict di-lepton and di-jet resonances. This contribution addresses an overview of experimental issues and discovery potential for these new particles at the LHC, focusing on perspectives with the CMS detector during early data taking.

  14. Shape invariant potentials in higher dimensions

    SciTech Connect

    Sandhya, R.; Sree Ranjani, S.; Kapoor, A.K.

    2015-08-15

    In this paper we investigate the shape invariance property of a potential in one dimension. We show that a simple ansatz allows us to reconstruct all the known shape invariant potentials in one dimension. This ansatz can be easily extended to arrive at a large class of new shape invariant potentials in arbitrary dimensions. A reformulation of the shape invariance property and possible generalizations are proposed. These may lead to an important extension of the shape invariance property to Hamiltonians that are related to standard potential problems via space time transformations, which are found useful in path integral formulation of quantum mechanics.

  15. Effective dimension reduction for sparse functional data

    PubMed Central

    YAO, F.; LEI, E.; WU, Y.

    2015-01-01

    Summary We propose a method of effective dimension reduction for functional data, emphasizing the sparse design where one observes only a few noisy and irregular measurements for some or all of the subjects. The proposed method borrows strength across the entire sample and provides a way to characterize the effective dimension reduction space, via functional cumulative slicing. Our theoretical study reveals a bias-variance trade-off associated with the regularizing truncation and decaying structures of the predictor process and the effective dimension reduction space. A simulation study and an application illustrate the superior finite-sample performance of the method. PMID:26566293

  16. Le Higgs avec de grandes dimensions supplementaires

    NASA Astrophysics Data System (ADS)

    Benakli, Karim; Quirós, Mariano

    2003-04-01

    Transverse (submillimeter) and longitudinal (TeV) extra dimensions can help in dealing with the Higgs hierarchy problem. On the one hand large transverse dimensions can lower the fundamental scale of quantum gravity from the Planck scale to the TeV range. On the other hand longitudinal dimensions can provide genuine extra-dimensional symmetries (higher dimensional gauge symmetry and/or supersymmetry) to protect the Higgs mass against ultraviolet sensitivity. In this article we review recent developments along these directions. To cite this article: K. Benakli, M. Quirós, C. R. Physique 4 (2003).

  17. Correspondence between Soft and Rapidity Anomalous Dimensions

    NASA Astrophysics Data System (ADS)

    Vladimirov, Alexey A.

    2017-02-01

    We establish a correspondence between ultraviolet singularities of soft factors for multiparticle production and rapidity singularities of soft factors for multiparton scattering. This correspondence is a consequence of the conformal mapping between scattering geometries. The correspondence is valid to all orders of perturbation theory and in this way, provides one with a proof of rapidity renormalization procedure for multiparton scattering [including the transverse momentum dependent (TMD) factorization as a special case]. As a by-product, we obtain an exact relation between the rapidity anomalous dimension and the well-known soft anomalous dimension. The three-loop expressions for TMD and a general multiparton scattering rapidity anomalous dimension are derived.

  18. Phenomenology of Supersymmetric Large Extra Dimensions

    SciTech Connect

    Hewett, JoAnne L.

    2002-12-09

    We study the phenomenology of a supersymmetric bulk in the scenario of large extra dimensions. The virtual exchange of gravitino KK states in selectron pair production in polarized e{sup +}e{sup -} collisions is examined. The leading order operator for this exchange is dimension six, in contrast to that of graviton KK exchange which induces a dimension eight operator at lowest order. Some kinematic distributions for selectron production are presented. These processes yield an enormous sensitivity to the fundamental higher dimensional Planck scale.

  19. Effective dimension reduction for sparse functional data.

    PubMed

    Yao, F; Lei, E; Wu, Y

    2015-06-01

    We propose a method of effective dimension reduction for functional data, emphasizing the sparse design where one observes only a few noisy and irregular measurements for some or all of the subjects. The proposed method borrows strength across the entire sample and provides a way to characterize the effective dimension reduction space, via functional cumulative slicing. Our theoretical study reveals a bias-variance trade-off associated with the regularizing truncation and decaying structures of the predictor process and the effective dimension reduction space. A simulation study and an application illustrate the superior finite-sample performance of the method.

  20. Evolution Of The Concept Of Dimension

    SciTech Connect

    Journeau, Philippe F.

    2007-04-28

    Concepts of time elapsing 'in' a space measuring the real emerge over the centuries. But Kant refutes absolute time and defines it, with space, as forms reacting to Newtonian mechanics. Einstein and Minkowski open a 20th century where time is a dimension, a substratum of reality 'with' space rather than 'in' it. Kaluza-Klein and String theories then develop a trend of additional spatial dimensions while de Broglie and Bohm open the possiblity that form, to begin with wave, be a reality together 'with' a space-time particle. Other recent theories, such as spin networks, causal sets and twistor theory, even head to the idea of other 'systems of dimensions'. On the basis of such progresses and recent experiments the paper then considers a background independent fourfold time-form-action-space system of dimensions.