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Sample records for unique transcription mode

  1. A dynamic mode of mitotic bookmarking by transcription factors.

    Science.gov (United States)

    Teves, Sheila S; An, Luye; Hansen, Anders S; Xie, Liangqi; Darzacq, Xavier; Tjian, Robert

    2016-11-19

    During mitosis, transcription is shut off, chromatin condenses, and most transcription factors (TFs) are reported to be excluded from chromosomes. How do daughter cells re-establish the original transcription program? Recent discoveries that a select set of TFs remain bound on mitotic chromosomes suggest a potential mechanism for maintaining transcriptional programs through the cell cycle termed mitotic bookmarking. Here we report instead that many TFs remain associated with chromosomes in mouse embryonic stem cells, and that the exclusion previously described is largely a fixation artifact. In particular, most TFs we tested are significantly enriched on mitotic chromosomes. Studies with Sox2 reveal that this mitotic interaction is more dynamic than in interphase and is facilitated by both DNA binding and nuclear import. Furthermore, this dynamic mode results from lack of transcriptional activation rather than decreased accessibility of underlying DNA sequences in mitosis. The nature of the cross-linking artifact prompts careful re-examination of the role of TFs in mitotic bookmarking.

  2. Tempo and mode in evolution of transcriptional regulation.

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    Kacy L Gordon

    2012-01-01

    Full Text Available Perennial questions of evolutionary biology can be applied to gene regulatory systems using the abundance of experimental data addressing gene regulation in a comparative context. What is the tempo (frequency, rate and mode (way, mechanism of transcriptional regulatory evolution? Here we synthesize the results of 230 experiments performed on insects and nematodes in which regulatory DNA from one species was used to drive gene expression in another species. General principles of regulatory evolution emerge. Gene regulatory evolution is widespread and accumulates with genetic divergence in both insects and nematodes. Divergence in cis is more common than divergence in trans. Coevolution between cis and trans shows a particular increase over greater evolutionary timespans, especially in sex-specific gene regulation. Despite these generalities, the evolution of gene regulation is gene- and taxon-specific. The congruence of these conclusions with evidence from other types of experiments suggests that general principles are discoverable, and a unified view of the tempo and mode of regulatory evolution may be achievable.

  3. Transcript profiling of the ruminant liver indicates a unique program of transcriptional regulation of ketogenic enzymes during food restriction.

    Science.gov (United States)

    Doelman, John; Cao, Honghe; Purdie, Norman G; Kim, Julie J M; Swanson, Kendall C; Osborne, Vernon R; Tey, Jasper; Ali, Ayesha; Feng, Zeny; Karrow, Niel A; Cant, John P

    2012-09-01

    Ruminants absorb little glucose and rely on hepatic gluconeogenesis and ketogenesis in the fed state to convert short-chain fatty acids produced during digestion into glucose and ketone bodies, respectively. In contrast to the non-ruminant response, fluxes through gluconeogenic and ketogenic pathways decrease during food restriction. Transcriptional regulation responsible for these unique food restriction responses has not been established. To determine the hepatic transcriptional response of ruminants to an acute drop in dietary nutrient supply, 102 yearling heifers were assigned to either ad libitum feeding or 24 h of food withdrawal in a randomized block design. Liver biopsies were obtained for microarray and quantitative real-time PCR analyses of gene expression. Plasma concentrations of non-esterified fatty acids were higher in food restricted heifers, while levels of β-hydroxybutyrate, triacylglycerol, and glucose were decreased. Despite a decline in substrate supply and a lower hepatic production of glucose, expression of the key gluconeogenic enzymes pyruvate carboxylase, phosphoenolpyruvate carboxykinase and fructose-1,6-bisphosphatase was upregulated as in non-ruminants. Downregulation of cholesterolgenic genes and upregulation of fatty acid oxidative genes were consistent with SREBP-2 and PPARα control, respectively. Ketogenesis from short-chain fatty acids was downregulated, contrary to the non-ruminant response to food restriction. Short-chain fatty acids may exert transcriptional control in the ruminant liver similar to that demonstrated in the large intestine of non-ruminants. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Heat and water stress induce unique transcriptional signatures of heat-shock proteins and transcription factors in grapevine.

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    Rocheta, Margarida; Becker, Jörg D; Coito, João L; Carvalho, Luísa; Amâncio, Sara

    2014-03-01

    Grapevine is an extremely important crop worldwide.In southern Europe, post-flowering phases of the growth cycle can occur under high temperatures, excessive light, and drought conditions at soil and/or atmospheric level. In this study, we subjected greenhouse grown grapevine, variety Aragonez, to two individual abiotic stresses, water deficit stress(WDS), and heat stress (HS). The adaptation of plants to stress is a complex response triggered by cascades of molecular net works involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Approaches such as array-based transcript profiling allow assessing the expression of thousands of genes in control and stress tissues. Using microarrays, we analyzed the leaf transcriptomic profile of the grapevine plants. Photosynthesis measurements verified that the plants were significantly affected by the stresses applied. Leaf gene expression was obtained using a high-throughput transcriptomic grapevine array, the 23K custom-made Affymetrix Vitis GeneChip. We identified 1,594 genes as differentially expressed between control and treatments and grouped them into ten major functional categories using MapMan software. The transcriptome of Aragonez was more significantly affected by HS when compared with WDS. The number of genes coding for heat-shock proteins and transcription factors expressed solely in response to HS suggesting their expression as unique signatures of HS. However, across-talk between the response pathways to both stresses was observed at the level of AP2/ERF transcription factors.

  5. PRDM14 Is a Unique Epigenetic Regulator Stabilizing Transcriptional Networks for Pluripotency

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    Yoshiyuki Seki

    2018-02-01

    Full Text Available PR-domain containing protein 14 (PRDM14 is a site-specific DNA-binding protein and is required for establishment of pluripotency in embryonic stem cells (ESCs and primordial germ cells (PGCs in mice. DNA methylation status is regulated by the balance between de novo methylation and passive/active demethylation, and global DNA hypomethylation is closely associated with cellular pluripotency and totipotency. PRDM14 ensures hypomethylation in mouse ESCs and PGCs through two distinct layers, transcriptional repression of the DNA methyltransferases Dnmt3a/b/l and active demethylation by recruitment of TET proteins. However, the function of PRDM14 remains unclear in other species including humans. Hence, here we focus on the unique characteristics of mouse PRDM14 in the epigenetic regulation of pluripotent cells and primordial germ cells. In addition, we discuss the expression regulation and function of PRDM14 in other species compared with those in mice.

  6. Characterization of an insect heterodimeric voltage-gated sodium channel with unique alternative splicing mode.

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    Jiang, Xuan-Zhao; Pei, Yu-Xia; Lei, Wei; Wang, Ke-Yi; Shang, Feng; Jiang, Hong-Bo; Wang, Jin-Jun

    2017-01-01

    Recent discovery of the heterodimeric voltage-gated sodium channels (Na v ) in two aphid species, Acyrthosiphon pisum and Myzus persicae, aroused interest in exploring whether this kind of channel is conserved for aphids. Herewith, we aim to provide evidence for the conservation of heterodimeric Na v s in aphids and investigate whether they have unique splicing patterns. We found that the only identifiable Na v from Toxoptera citricida consisted of two subunits, forming a heterodimeric Na v , which carried an atypical "DENS" ion selectivity filter and a conventional "MFM" inactivation gate, confirming the heterodimeric Na v s' conservation within aphids. These unique heterodimeric channels may form a new Na v subfamily, specific to aphids. A more ancient member of four-domain Na v homolog was well preserved in T. citricida, carrying a typical "DEEA" and "MFL" motif. The presence of "DENS" in mammalian Na x s and "DEKT" in a fungus Na v suggested that the heterodimeric Na v s may still preserve Na + permeability. Sequencing 46 clones from nymphs and adults exposed unique splicing patterns for this heterodimeric Na v from T. citricida, revealing 7 alternatively spliced exons, evidencing that exon 5 was no longer unique to Bombyx mori, and exon k/l was semi-mutually exclusive. Two previously undescribed optional exons and a SNP site seemingly unique to aphids were identified. In conclusion, the dimeric Na v s might form a new aphids-specific heterodimeric N a v subfamily. This dimeric Na v from T. citricida was characterized with distinguishable alternative splicing modes, exemplified by the discovery of two novel alternative exons and unique usage patterns of alternative exons. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Unique transcriptional profile of sustained ligand-activated preconditioning in pre- and post-ischemic myocardium.

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    Kevin J Ashton

    Full Text Available BACKGROUND: Opioidergic SLP (sustained ligand-activated preconditioning induced by 3-5 days of opioid receptor (OR agonism induces persistent protection against ischemia-reperfusion (I-R injury in young and aged hearts, and is mechanistically distinct from conventional preconditioning responses. We thus applied unbiased gene-array interrogation to identify molecular effects of SLP in pre- and post-ischemic myocardium. METHODOLOGY/PRINCIPAL FINDINGS: Male C57Bl/6 mice were implanted with 75 mg morphine or placebo pellets for 5 days. Resultant SLP did not modify cardiac function, and markedly reduced dysfunction and injury in perfused hearts subjected to 25 min ischemia/45 min reperfusion. Microarray analysis identified 14 up- and 86 down-regulated genes in normoxic hearts from SLP mice (≥1.3-fold change, FDR≤5%. Induced genes encoded sarcomeric/contractile proteins (Myh7, Mybpc3,Myom2,Des, natriuretic peptides (Nppa,Nppb and stress-signaling elements (Csda,Ptgds. Highly repressed genes primarily encoded chemokines (Ccl2,Ccl4,Ccl7,Ccl9,Ccl13,Ccl3l3,Cxcl3, cytokines (Il1b,Il6,Tnf and other proteins involved in inflammation/immunity (C3,Cd74,Cd83, Cd86,Hla-dbq1,Hla-drb1,Saa1,Selp,Serpina3, together with endoplasmic stress proteins (known: Dnajb1,Herpud1,Socs3; putative: Il6, Gadd45g,Rcan1 and transcriptional controllers (Egr2,Egr3, Fos,Hmox1,Nfkbid. Biological themes modified thus related to inflammation/immunity, together with cellular/cardiovascular movement and development. SLP also modified the transcriptional response to I-R (46 genes uniquely altered post-ischemia, which may influence later infarction/remodeling. This included up-regulated determinants of cellular resistance to oxidant (Mgst3,Gstm1,Gstm2 and other forms of stress (Xirp1,Ankrd1,Clu, and repression of stress-response genes (Hspa1a,Hspd1,Hsp90aa,Hsph1,Serpinh1 and Txnip. CONCLUSIONS: Protection via SLP is associated with transcriptional repression of inflammation/immunity, up

  8. Reassessment of the unique mode of binding between angiotensin II type 1 receptor and their blockers.

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    Shin-Ichiro Miura

    Full Text Available While the molecular structures of angiotensin II (Ang II type 1 (AT1 receptor blockers (ARBs are very similar, they are also slightly different. Although each ARB has been shown to exhibit a unique mode of binding to AT1 receptor, different positions of the AT1 receptor have been analyzed and computational modeling has been performed using different crystal structures for the receptor as a template and different kinds of software. Therefore, we systematically analyzed the critical positions of the AT1 receptor, Tyr(113, Tyr(184, Lys(199, His(256 and Gln(257 using a mutagenesis study, and subsequently performed computational modeling of the binding of ARBs to AT1 receptor using CXCR4 receptor as a new template and a single version of software. The interactions between Tyr(113 in the AT1 receptor and the hydroxyl group of olmesartan, between Lys(199 and carboxyl or tetrazole groups, and between His(256 or Gln(257 and the tetrazole group were studied. The common structure, a tetrazole group, of most ARBs similarly bind to Lys(199, His(256 and Gln(257 of AT1 receptor. Lys(199 in the AT1 receptor binds to the carboxyl group of EXP3174, candesartan and azilsartan, whereas oxygen in the amidecarbonyl group of valsartan may bind to Lys(199. The benzimidazole portion of telmisartan may bind to a lipophilic pocket that includes Tyr(113. On the other hand, the n-butyl group of irbesartan may bind to Tyr(113. In conclusion, we confirmed that the slightly different structures of ARBs may be critical for binding to AT1 receptor and for the formation of unique modes of binding.

  9. A unique mode of tissue oxygenation and the adaptive radiation of teleost fishes.

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    Randall, D J; Rummer, J L; Wilson, J M; Wang, S; Brauner, C J

    2014-04-15

    Teleost fishes constitute 95% of extant aquatic vertebrates, and we suggest that this is related in part to their unique mode of tissue oxygenation. We propose the following sequence of events in the evolution of their oxygen delivery system. First, loss of plasma-accessible carbonic anhydrase (CA) in the gill and venous circulations slowed the Jacobs-Stewart cycle and the transfer of acid between the plasma and the red blood cells (RBCs). This ameliorated the effects of a generalised acidosis (associated with an increased capacity for burst swimming) on haemoglobin (Hb)-O2 binding. Because RBC pH was uncoupled from plasma pH, the importance of Hb as a buffer was reduced. The decrease in buffering was mediated by a reduction in the number of histidine residues on the Hb molecule and resulted in enhanced coupling of O2 and CO2 transfer through the RBCs. In the absence of plasma CA, nearly all plasma bicarbonate ultimately dehydrated to CO2 occurred via the RBCs, and chloride/bicarbonate exchange was the rate-limiting step in CO2 excretion. This pattern of CO2 excretion across the gills resulted in disequilibrium states for CO2 hydration/dehydration reactions and thus elevated arterial and venous plasma bicarbonate levels. Plasma-accessible CA embedded in arterial endothelia was retained, which eliminated the localized bicarbonate disequilibrium forming CO2 that then moved into the RBCs. Consequently, RBC pH decreased which, in conjunction with pH-sensitive Bohr/Root Hbs, elevated arterial oxygen tensions and thus enhanced tissue oxygenation. Counter-current arrangement of capillaries (retia) at the eye and later the swim bladder evolved along with the gas gland at the swim bladder. Both arrangements enhanced and magnified CO2 and acid production and, therefore, oxygen secretion to those specialised tissues. The evolution of β-adrenergically stimulated RBC Na(+)/H(+) exchange protected gill O2 uptake during stress and further augmented plasma disequilibrium states

  10. Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity.

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    Zhang, Peilan; Li, Kunhua; Yang, Guang; Xia, Changqing; Polston, Jane E; Li, Gengnan; Li, Shiwu; Lin, Zhao; Yang, Li-Jun; Bruner, Steven D; Ding, Yousong

    2017-08-22

    Glycans possess significant chemical diversity; glycan binding proteins (GBPs) recognize specific glycans to translate their structures to functions in various physiological and pathological processes. Therefore, the discovery and characterization of novel GBPs and characterization of glycan-GBP interactions are significant to provide potential targets for therapeutic intervention of many diseases. Here, we report the biochemical, functional, and structural characterization of a 130-amino-acid protein, Y3, from the mushroom Coprinus comatus Biochemical studies of recombinant Y3 from a yeast expression system demonstrated the protein is a unique GBP. Additionally, we show that Y3 exhibits selective and potent cytotoxicity toward human T-cell leukemia Jurkat cells compared with a panel of cancer cell lines via inducing caspase-dependent apoptosis. Screening of a glycan array demonstrated GalNAcβ1-4(Fucα1-3)GlcNAc (LDNF) as a specific Y3-binding ligand. To provide a structural basis for function, the crystal structure was solved to a resolution of 1.2 Å, revealing a single-domain αβα-sandwich motif. Two monomers were dimerized to form a large 10-stranded, antiparallel β-sheet flanked by α-helices on each side, representing a unique oligomerization mode among GBPs. A large glycan binding pocket extends into the dimeric interface, and docking of LDNF identified key residues for glycan interactions. Disruption of residues predicted to be involved in LDNF/Y3 interactions resulted in the significant loss of binding to Jurkat T-cells and severely impaired their cytotoxicity. Collectively, these results demonstrate Y3 to be a GBP with selective cytotoxicity toward human T-cell leukemia cells and indicate its potential use in cancer diagnosis and treatment.

  11. Unique method to determine the differential mode delay of specialty multimode fibers

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    Wittig, Marcus; Baselt, Tobias; Nelsen, Bryan L.; Hartmann, Peter

    2017-05-01

    We developed an experimental setup for the determination of the differential mode delay (DMD) in fibers. This unique method of measurement is the basis for the characterization of specialty fibers including properties such as the chromatic dispersion, the fiber geometry and the DMD. These fibers have their application in the nearinfrared and mid-infrared regime. Examples of uses of such fibers are supercontinuum light sources and high power lasers. Different modifications of these multimode fibers are applicable in extreme environments or for standard beam delivery over long distances. The exact knowledge of parameters such as the DMD is necessary to generate light sources with ether high energy, high intensity or high power or to analyze transmitted information when the fiber is used in a configuration for communication. For the most precise measurement of DMD, we investigated a new type of method. It is capable of measuring the modal dispersion in two different ways. The first way is the standard transversal measurement, where the launching condition is altered by moving the radial position of the injected pulse while maintaining a zero-angle launching condition. The second way involves changing the launching angle into the fiber. This is done to get the most precise value for the DMD. Also, using a supercontinuum light source for the injection pulse, it is possible to vary the wavelength to be able to measure near the zero dispersion wavelength in order to investigate the effects of the chromatic dispersion.

  12. Identification of a novel and unique transcription factor in the intraerythrocytic stage of Plasmodium falciparum.

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    Kanako Komaki-Yasuda

    Full Text Available The mechanisms of stage-specific gene regulation in the malaria parasite Plasmodium falciparum are largely unclear, with only a small number of specific regulatory transcription factors (AP2 family having been identified. In particular, the transcription factors that function in the intraerythrocytic stage remain to be elucidated. Previously, as a model case for stage-specific transcription in the P. falciparum intraerythrocytic stage, we analyzed the transcriptional regulation of pf1-cys-prx, a trophozoite/schizont-specific gene, and suggested that some nuclear factors bind specifically to the cis-element of pf1-cys-prx and enhance transcription. In the present study, we purified nuclear factors from parasite nuclear extract by 5 steps of chromatography, and identified a factor termed PREBP. PREBP is not included in the AP2 family, and is a novel protein with four K-homology (KH domains. The KH domain is known to be found in RNA-binding or single-stranded DNA-binding proteins. PREBP is well conserved in Plasmodium species and partially conserved in phylum Apicomplexa. To evaluate the effects of PREBP overexpression, we used a transient overexpression and luciferase assay combined approach. Overexpression of PREBP markedly enhanced luciferase expression under the control of the pf1-cys-prx cis-element. These results provide the first evidence of a novel transcription factor that activates the gene expression in the malaria parasite intraerythrocytic stage. These findings enhance our understanding of the evolution of specific transcription machinery in Plasmodium and other eukaryotes.

  13. A revisit of the mode of interaction of small transcription inhibitors ...

    Indian Academy of Sciences (India)

    A revisit of the mode of interaction of small transcription inhibitors with genomic DNA. Dipak Dasgupta Parijat ... the associated histone(s). Structural effects of the DNA-binding molecules upon chromatin in light of the above broad categories and the associated biological implications of the two types of binding are discussed.

  14. Identification of uniquely expressed transcription factors in highly purified B-cell lymphoma samples

    DEFF Research Database (Denmark)

    Andréasson, Ulrika; Edén, Patrik; Peterson, Carsten

    2010-01-01

    Transcription factors (TFs) are critical for B-cell differentiation, affecting gene expression both by repression and transcriptional activation. Still, this information is not used for classification of B-cell lymphomas (BCLs). Traditionally, BCLs are diagnosed based on a phenotypic resemblance...... to normal B-cells; assessed by immunohistochemistry or flow cytometry, by using a handful of phenotypic markers. In the last decade, diagnostic and prognostic evaluation has been facilitated by global gene expression profiling (GEP), providing a new powerful means for the classification, prediction...... of survival, and response to treatment of lymphomas. However, most GEP studies have typically been performed on whole tissue samples, containing varying degrees of tumor cell content, which results in uncertainties in data analysis. In this study, global GEP analyses were performed on highly purified, flow...

  15. Discovery of a Potent Class of PI3Kα Inhibitors with Unique Binding Mode via Encoded Library Technology (ELT).

    Science.gov (United States)

    Yang, Hongfang; Medeiros, Patricia F; Raha, Kaushik; Elkins, Patricia; Lind, Kenneth E; Lehr, Ruth; Adams, Nicholas D; Burgess, Joelle L; Schmidt, Stanley J; Knight, Steven D; Auger, Kurt R; Schaber, Michael D; Franklin, G Joseph; Ding, Yun; DeLorey, Jennifer L; Centrella, Paolo A; Mataruse, Sibongile; Skinner, Steven R; Clark, Matthew A; Cuozzo, John W; Evindar, Ghotas

    2015-05-14

    In the search of PI3K p110α wild type and H1047R mutant selective small molecule leads, an encoded library technology (ELT) campaign against the desired target proteins was performed which led to the discovery of a selective chemotype for PI3K isoforms from a three-cycle DNA encoded library. An X-ray crystal structure of a representative inhibitor from this chemotype demonstrated a unique binding mode in the p110α protein.

  16. Comparative assessment of chloroplast transcriptional responses highlights conserved and unique patterns across Triticeae members under salt stress.

    Science.gov (United States)

    Mirzaei, Saeid; Mansouri, Mehdi; Mohammadi-Nejad, Ghasem; Sablok, Gaurav

    2017-12-11

    Chloroplast functional genomics, in particular understanding the chloroplast transcriptional response is of immense importance mainly due to its role in oxygenic photosynthesis. As a photosynthetic unit, its efficiency and transcriptional activity is directly regulated by reactive oxygen species during abiotic and biotic stress and subsequently affects carbon assimilation, and plant biomass. In crops, understanding photosynthesis is crucial for crop domestication by identifying the traits that could be exploited for crop improvement. Transcriptionally and translationally active chloroplast plays a key role by regulating the PSI and PSII photo-reaction centres, which ubiquitously affects the light harvesting. Using a comparative transcriptomics mapping approach, we identified differential regulation of key chloroplast genes during salt stress across Triticeae members with potential genes involved in photosynthesis and electron transport system such as CytB6f. Apart from differentially regulated genes involved in PSI and PSII, we found widespread evidence of intron splicing events, specifically uniquely spliced petB and petD in Triticum aestivum and high proportion of RNA editing in ndh genes across the Triticeae members during salt stress. We also highlight the role and differential regulation of ATP synthase as member of CF0CF1 and also revealed the effect of salt stress on the water-splitting complex under salt stress. It is worthwhile to mention that the observed conserved down-regulation of psbJ across the Triticeae is limiting the assembly of water-splitting complexes and thus making the BEP clade Triticeae members more vulnerable to high light during the salt stress. Comparative understanding of the chloroplast transcriptional dynamics and photosynthetic regulation will improve the approaches for improved crop domestication.

  17. Gene expression analysis of early stage endometrial cancersreveals unique transcripts associated with grade and histologybut not depth of invasion

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    John eRisinger

    2013-06-01

    Full Text Available Endometrial cancer is the most common gynecologic malignancy in the United States but it remains poorly understood at the molecular level. This investigation was conducted to specifically assess whether gene expression changes underlie the clinical and pathologic factors traditionally used for determining treatment regimens in women with stage I endometrial cancer. These include the effect of tumor grade, depth of myometrial invasion and histotype. We utilized oligonucleotide microarrays to assess the transcript expression profile in epithelial glandular cells laser microdissected from 79 endometrioid and 12 serous stage I endometrial cancers with a heterogeneous distribution of grade and depth of myometrial invasion, along with 12 normal post-menopausal endometrial samples. Unsupervised multidimensional scaling analyses revealed that serous and endometrioid stage I cancers have similar transcript expression patterns when compared to normal controls where 900 transcripts were identified to be differentially expressed by at least 4-fold (univariate t-test, p <0.001 between the cancers and normal endometrium. This analysis also identified transcript expression differences between serous and endometrioid cancers and tumor grade, but no apparent differences were identified as a function of depth of myometrial invasion. Four genes were validated by quantitative PCR on an independent set of cancer and normal endometrium samples. These findings indicate that unique gene expression profiles are associated with histologic type and grade, but not myometrial invasion among early stage endometrial cancers. These data provide a comprehensive perspective on the molecular alterations associated with stage I endometrial cancer, particularly those subtypes that have the worst prognosis.

  18. Numerical analysis of a unique mode of locomotion: vertical climbing by Pacific lamprey.

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    Zhu, Q; Moser, M; Kemp, P

    2011-03-01

    Pacific lampreys are capable of climbing vertical wetted surfaces through a two-phase (bending and stretching) locomotion mode using the oral disc for adherence. We investigate the physical mechanism and performance of this process by using a continuous beam model. Two mechanisms, one akin to the jumping process and the other related to the fast stretching of the body, have been identified. This locomotion mode may inspire biomimetic designs of anguilliform swimming devices capable of overcoming steep obstacles. By using a genetic algorithm simulation we identify the combination of kinematic parameters corresponding to optimal efficiency (defined as the gravitational potential energy gained in each climbing step divided by the energy spent to activate the motion). These parameters are similar to laboratory observations of lamprey motion, suggesting that this type of locomotion has been optimized for maximum efficiency through evolution.

  19. Numerical analysis of a unique mode of locomotion: vertical climbing by Pacific lamprey

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Q [Department of Structural Engineering, University of California, San Diego, La Jolla, CA (United States); Moser, M [Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, WA (United States); Kemp, P, E-mail: qizhu@ucsd.edu [International Centre for Ecohydraulics Research, Faculty of Engineering and the Environment, University of Southampton, Southampton (United Kingdom)

    2011-03-15

    Pacific lampreys are capable of climbing vertical wetted surfaces through a two-phase (bending and stretching) locomotion mode using the oral disc for adherence. We investigate the physical mechanism and performance of this process by using a continuous beam model. Two mechanisms, one akin to the jumping process and the other related to the fast stretching of the body, have been identified. This locomotion mode may inspire biomimetic designs of anguilliform swimming devices capable of overcoming steep obstacles. By using a genetic algorithm simulation we identify the combination of kinematic parameters corresponding to optimal efficiency (defined as the gravitational potential energy gained in each climbing step divided by the energy spent to activate the motion). These parameters are similar to laboratory observations of lamprey motion, suggesting that this type of locomotion has been optimized for maximum efficiency through evolution.

  20. Unique aspects of transcriptional regulation in neurons – nuances in NFκB and Sp1-related factors

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    Chen Yuzhi

    2009-05-01

    Full Text Available Abstract The unique physiology and function of neurons create differences in their cellular physiology, including their regulation of gene expression. We began several years ago exploring the relationships between the NFκB transcription factor, neuronal survival, and glutamate receptor activation in telencephalic neurons. These studies led us to conclude that this population of cells is nearly incapable of activating the NFκB that is nonetheless expressed at reasonable levels. A subset of the κB cis elements are instead bound by members of the Sp1 family in neurons. Also surprising was our discovery that Sp1 itself, typically described as ubiquitous, is severely restricted in expression within forebrain neurons; Sp4 seems to be substituted during neuronal differentiation. These findings and their implications for neuronal differentiation – as well as potential dedifferentiation during degenerative processes – are discussed here.

  1. A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks

    DEFF Research Database (Denmark)

    Huang, Hongda; Strømme, Caroline B; Saredi, Giulia

    2015-01-01

    During DNA replication, chromatin is reassembled by recycling of modified old histones and deposition of new ones. How histone dynamics integrates with DNA replication to maintain genome and epigenome information remains unclear. Here, we reveal how human MCM2, part of the replicative helicase...... for MCM2-7 histone-chaperone function and normal cell proliferation. Further, we show that MCM2 can chaperone both new and old canonical histones H3-H4 as well as H3.3 and CENPA variants. The unique histone-binding mode of MCM2 thus endows the replicative helicase with ideal properties for recycling...... histones genome wide during DNA replication....

  2. Portraying the unique contribution of the default mode network to internally driven mnemonic processes.

    Science.gov (United States)

    Shapira-Lichter, Irit; Oren, Noga; Jacob, Yael; Gruberger, Michal; Hendler, Talma

    2013-03-26

    Numerous neuroimaging studies have implicated default mode network (DMN) involvement in both internally driven processes and memory. Nevertheless, it is unclear whether memory operations reflect a particular case of internally driven processing or alternatively involve the DMN in a distinct manner, possibly depending on memory type. This question is critical for refining neurocognitive memory theorem in the context of other endogenic processes and elucidating the functional significance of this key network. We used functional MRI to examine DMN activity and connectivity patterns while participants overtly generated words according to nonmnemonic (phonemic) or mnemonic (semantic or episodic) cues. Overall, mnemonic word fluency was found to elicit greater DMN activity and stronger within-network functional connectivity compared with nonmnemonic fluency. Furthermore, two levels of functional organization of memory retrieval were shown. First, across both mnemonic tasks, activity was greater mainly in the posterior cingulate cortex, implying selective contribution to generic aspects of memory beyond its general involvement in endogenous processes. Second, parts of the DMN showed distinct selectivity for each of the mnemonic conditions; greater recruitment of the anterior prefrontal cortex, retroesplenial cortex, and hippocampi and elevated connectivity between anterior and posterior medial DMN nodes characterized the semantic condition, whereas increased recruitment of posterior DMN components and elevated connectivity between them characterized the episodic condition. This finding emphasizes the involvement of DMN elements in discrete aspects of memory retrieval. Altogether, our results show a specific contribution of the DMN to memory processes, corresponding to the specific type of memory retrieval.

  3. A designed inhibitor of a CLC antiporter blocks function through a unique binding mode

    Science.gov (United States)

    Howery, Andrew E.; Elvington, Shelley; Abraham, Sherwin J.; Choi, Kee-Hyun; Phillips, Sabrina; Ryan, Christopher M.; Sanford, R. Lea; Simpson-Dworschak, Sierra; Almqvist, Jonas; Tran, Kevin; Chew, Thomas A.; Zachariae, Ulrich; Andersen, Olaf S.; Whitelegge, Julian; Matulef, Kimberly; Du Bois, Justin; Maduke, Merritt C.

    2012-01-01

    SUMMARY The lack of small-molecule inhibitors for anion-selective transporters and channels has impeded our understanding of the complex mechanisms that underlie ion passage. The ubiquitous CLC “Chloride Channel” family represents a unique target for biophysical and biochemical studies because its distinctive protein fold supports both passive chloride channels and secondary-active chloride-proton transporters. Here, we describe the synthesis and characterization of the first specific small-molecule inhibitor directed against a CLC antiporter (ClC-ec1). This compound, 4,4′-octanamidostilbene-2,2′-disulfonate (OADS), inhibits ClC-ec1 with low micromolar affinity and has no specific effect on a CLC channel (ClC-1). Inhibition of ClC-ec1 occurs by binding to two distinct intracellular sites. The location of these sites and the lipid-dependence of inhibition suggest potential mechanisms of action. The discovery of this compound will empower research to elucidate differences between antiporter and channel mechanisms and to develop treatments for CLC-mediated disorders. PMID:23177200

  4. A unique binding mode enables MCM2 to chaperone histones H3–H4 at replication forks

    Science.gov (United States)

    Huang, Hongda; Strømme, Caroline B; Saredi, Giulia; Hödl, Martina; Strandsby, Anne; González-Aguilera, Cristina; Chen, Shoudeng; Groth, Anja; Patel, Dinshaw J

    2015-01-01

    During DNA replication, chromatin is reassembled by recycling of modified old histones and deposition of new ones. How histone dynamics integrates with DNA replication to maintain genome and epigenome information remains unclear. Here, we reveal how human MCM2, part of the replicative helicase, chaperones histones H3–H4. Our first structure shows an H3–H4 tetramer bound by two MCM2 histone-binding domains (HBDs), which hijack interaction sites used by nucleosomal DNA. Our second structure reveals MCM2 and ASF1 cochaperoning an H3–H4 dimer. Mutational analyses show that the MCM2 HBD is required for MCM2–7 histone-chaperone function and normal cell proliferation. Further, we show that MCM2 can chaperone both new and old canonical histones H3–H4 as well as H3.3 and CENPA variants. The unique histone-binding mode of MCM2 thus endows the replicative helicase with ideal properties for recycling histones genome wide during DNA replication. PMID:26167883

  5. EXPRESSION PROFILING OF FIVE RAT STRAINS REVEAL TRANSCRIPTIONAL MODES IN THE ANTIGEN PROCESSING PATHWAY

    Science.gov (United States)

    Comparative gene expression profiling of rat strains with genetic predisposition to diverse cardiovascular diseases can help decode the transcriptional program that governs cellular behavior. We hypothesized that co-transcribed, intra-pathway, functionally coherent genes can be r...

  6. Transcriptional profiling of whole blood identifies a unique 5-gene signature for myelofibrosis and imminent myelofibrosis transformation.

    Directory of Open Access Journals (Sweden)

    Hans Carl Hasselbalch

    Full Text Available Identifying a distinct gene signature for myelofibrosis may yield novel information of the genes, which are responsible for progression of essential thrombocythemia and polycythemia vera towards myelofibrosis. We aimed at identifying a simple gene signature - composed of a few genes - which were selectively and highly deregulated in myelofibrosis patients. Gene expression microarray studies have been performed on whole blood from 69 patients with myeloproliferative neoplasms. Amongst the top-20 of the most upregulated genes in PMF compared to controls, we identified 5 genes (DEFA4, ELA2, OLFM4, CTSG, and AZU1, which were highly significantly deregulated in PMF only. None of these genes were significantly regulated in ET and PV patients. However, hierarchical cluster analysis showed that these genes were also highly expressed in a subset of patients with ET (n = 1 and PV (n = 4 transforming towards myelofibrosis and/or being featured by an aggressive phenotype. We have identified a simple 5-gene signature, which is uniquely and highly significantly deregulated in patients in transitional stages of ET and PV towards myelofibrosis and in patients with PMF only. Some of these genes are considered to be responsible for the derangement of bone marrow stroma in myelofibrosis. Accordingly, this gene-signature may reflect key processes in the pathogenesis and pathophysiology of myelofibrosis development.

  7. Near-isogenic lines of Triticum aestivum with distinct modes of resistance exhibit dissimilar transcriptional regulation during Diuraphis noxia feeding

    Directory of Open Access Journals (Sweden)

    Anna-Maria Botha

    2014-10-01

    Full Text Available Russian wheat aphid (Diuraphis noxia, Kurdjumov feeding on susceptible Triticum aestivum L. leads to leaf rolling, chlorosis and plant death – symptoms not present in resistant lines. Although the effects of several D. noxia (Dn resistance genes are known, none have been isolated or characterized. Wheat varieties expressing different Dn genes exhibit distinct modes of D. noxia resistance, such as antibiosis (Dn1, tolerance (Dn2, and antixenosis (Dn5. However, the mechanism whereby feeding aphids are perceived, and how subsequent transcriptional responses are partitioned into resistance categories, remains unclear. Here we report on downstream events in near-isogenic wheat lines containing different Dn genes after D. noxia biotype SA1 feeding. Transcripts involved in stress, signal transduction, photosynthesis, metabolism and gene regulation were differentially regulated during D. noxia feeding. Expression analyses using RT-qPCR and RNA hybridization, as well as enzyme activity profiling, provide evidence that the timing and intensity of pathways induced are critical in the development of particular modes of resistance. Pathways involved include the generation of kinase signalling cascades that lead to a sustained oxidative burst, and a hypersensitive response that is active during antibiosis. Tolerance is a passive resistance mechanism that acts through repair or de novo synthesis of photosystem proteins. Results further suggest that ethylene-mediated pathways are possibly involved in generating volatile compounds and cell wall fortification during the antixenosic response.

  8. Computational characterization of modes of transcriptional regulation of nuclear receptor genes.

    Science.gov (United States)

    Sharma, Yogita; Chilamakuri, Chandra Sekhar Reddy; Bakke, Marit; Lenhard, Boris

    2014-01-01

    Nuclear receptors are a large structural class of transcription factors that act with their co-regulators and repressors to maintain a variety of biological and physiological processes such as metabolism, development and reproduction. They are activated through the binding of small ligands, which can be replaced by drug molecules, making nuclear receptors promising drug targets. Transcriptional regulation of the genes that encode them is central to gaining a deeper understanding of the diversity of their biochemical and biophysical roles and their role in disease and therapy. Even though they share evolutionary history, nuclear receptor genes have fundamentally different expression patterns, ranging from ubiquitously expressed to tissue-specific and spatiotemporally complex. However, current understanding of regulation in nuclear receptor gene family is still nascent. In this study, we investigate the relationship between long-range regulation of nuclear receptor family and their known functionality. Towards this goal, we identify the nuclear receptor genes that are potential targets based on counts of highly conserved non-coding elements. We validate our results using publicly available expression (RNA-seq) and histone modification (ChIP-seq) data from the ENCODE project. We find that nuclear receptor genes involved in developmental roles show strong evidence of long-range mechanism of transcription regulation with distinct cis-regulatory content they feature clusters of highly conserved non-coding elements distributed in regions spanning several Megabases, long and multiple CpG islands, bivalent promoter marks and statistically significant higher enrichment of enhancer mark around their gene loci. On the other hand nuclear receptor genes that are involved in tissue-specific roles lack these features, having simple transcriptional controls and a greater variety of mechanisms for producing paralogs. We further examine the combinatorial patterns of histone maps

  9. Computational characterization of modes of transcriptional regulation of nuclear receptor genes.

    Directory of Open Access Journals (Sweden)

    Yogita Sharma

    Full Text Available Nuclear receptors are a large structural class of transcription factors that act with their co-regulators and repressors to maintain a variety of biological and physiological processes such as metabolism, development and reproduction. They are activated through the binding of small ligands, which can be replaced by drug molecules, making nuclear receptors promising drug targets. Transcriptional regulation of the genes that encode them is central to gaining a deeper understanding of the diversity of their biochemical and biophysical roles and their role in disease and therapy. Even though they share evolutionary history, nuclear receptor genes have fundamentally different expression patterns, ranging from ubiquitously expressed to tissue-specific and spatiotemporally complex. However, current understanding of regulation in nuclear receptor gene family is still nascent.In this study, we investigate the relationship between long-range regulation of nuclear receptor family and their known functionality. Towards this goal, we identify the nuclear receptor genes that are potential targets based on counts of highly conserved non-coding elements. We validate our results using publicly available expression (RNA-seq and histone modification (ChIP-seq data from the ENCODE project. We find that nuclear receptor genes involved in developmental roles show strong evidence of long-range mechanism of transcription regulation with distinct cis-regulatory content they feature clusters of highly conserved non-coding elements distributed in regions spanning several Megabases, long and multiple CpG islands, bivalent promoter marks and statistically significant higher enrichment of enhancer mark around their gene loci. On the other hand nuclear receptor genes that are involved in tissue-specific roles lack these features, having simple transcriptional controls and a greater variety of mechanisms for producing paralogs. We further examine the combinatorial patterns of

  10. A G-quadruplex-binding macrodomain within the "SARS-unique domain" is essential for the activity of the SARS-coronavirus replication-transcription complex.

    Science.gov (United States)

    Kusov, Yuri; Tan, Jinzhi; Alvarez, Enrique; Enjuanes, Luis; Hilgenfeld, Rolf

    2015-10-01

    The multi-domain non-structural protein 3 of SARS-coronavirus is a component of the viral replication/transcription complex (RTC). Among other domains, it contains three sequentially arranged macrodomains: the X domain and subdomains SUD-N as well as SUD-M within the "SARS-unique domain". The X domain was proposed to be an ADP-ribose-1"-phosphatase or a poly(ADP-ribose)-binding protein, whereas SUD-NM binds oligo(G)-nucleotides capable of forming G-quadruplexes. Here, we describe the application of a reverse genetic approach to assess the importance of these macrodomains for the activity of the SARS-CoV RTC. To this end, Renilla luciferase-encoding SARS-CoV replicons with selectively deleted macrodomains were constructed and their ability to modulate the RTC activity was examined. While the SUD-N and the X domains were found to be dispensable, the SUD-M domain was crucial for viral genome replication/transcription. Moreover, alanine replacement of charged amino-acid residues of the SUD-M domain, which are likely involved in G-quadruplex-binding, caused abrogation of RTC activity. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Transcriptional changes in canine distemper virus-induced demyelinating leukoencephalitis favor a biphasic mode of demyelination.

    Directory of Open Access Journals (Sweden)

    Reiner Ulrich

    Full Text Available Canine distemper virus (CDV-induced demyelinating leukoencephalitis in dogs (Canis familiaris is suggested to represent a naturally occurring translational model for subacute sclerosing panencephalitis and multiple sclerosis in humans. The aim of this study was a hypothesis-free microarray analysis of the transcriptional changes within cerebellar specimens of five cases of acute, six cases of subacute demyelinating, and three cases of chronic demyelinating and inflammatory CDV leukoencephalitis as compared to twelve non-infected control dogs. Frozen cerebellar specimens were used for analysis of histopathological changes including demyelination, transcriptional changes employing microarrays, and presence of CDV nucleoprotein RNA and protein using microarrays, RT-qPCR and immunohistochemistry. Microarray analysis revealed 780 differentially expressed probe sets. The dominating change was an up-regulation of genes related to the innate and the humoral immune response, and less distinct the cytotoxic T-cell-mediated immune response in all subtypes of CDV leukoencephalitis as compared to controls. Multiple myelin genes including myelin basic protein and proteolipid protein displayed a selective down-regulation in subacute CDV leukoencephalitis, suggestive of an oligodendrocyte dystrophy. In contrast, a marked up-regulation of multiple immunoglobulin-like expressed sequence tags and the delta polypeptide of the CD3 antigen was observed in chronic CDV leukoencephalitis, in agreement with the hypothesis of an immune-mediated demyelination in the late inflammatory phase of the disease. Analysis of pathways intimately linked to demyelination as determined by morphometry employing correlation-based Gene Set Enrichment Analysis highlighted the pathomechanistic importance of up-regulated genes comprised by the gene ontology terms "viral replication" and "humoral immune response" as well as down-regulated genes functionally related to "metabolite and energy

  12. Divergent mating patterns and a unique mode of external sperm transfer in Zoraptera: an enigmatic group of pterygote insects

    Science.gov (United States)

    Dallai, R.; Gottardo, M.; Mercati, D.; Machida, R.; Mashimo, Y.; Matsumura, Y.; Beutel, R. G.

    2013-06-01

    A remarkable external sperm transfer is described for the first time in a species of a group of winged insects (Pterygota), the enigmatic Zoraptera. Mating and sperm transfer of two species of the order were examined in detail, documented, and compared with each other and with patterns described for other species belonging to the order. The behavior differs strikingly in Zorotypus impolitus and Zorotypus magnicaudelli. A copula is performed by males and females of the latter, as it is also the case in other zorapteran species and generally in pterygote insects. In striking contrast to this, males of Z. impolitus do not copulate but deposit small (100 μm in diameter) spermatophores externally on the abdomen of the female. Each spermatophore contains only one giant spermatozoon (3 mm long and 3 μm wide), a unique feature in the entire Hexapoda. External sperm transfer in Pterygota is a highly unusual case of evolutionary reversal. The very small relict group Zoraptera displays a uniform general morphology but exhibits very different reproductive structures and patterns of mating behavior. This may be an extreme form of a more general situation in insects, with a specific form of selection resulting in an accelerated rate of evolution in the reproductive system.

  13. Multiple DNA-binding modes for the ETS family transcription factor PU.1.

    Science.gov (United States)

    Esaki, Shingo; Evich, Marina G; Erlitzki, Noa; Germann, Markus W; Poon, Gregory M K

    2017-09-29

    The eponymous DNA-binding domain of ETS ( E 26 t ransformation- s pecific) transcription factors binds a single sequence-specific site as a monomer over a single helical turn. Following our previous observation by titration calorimetry that the ETS member PU.1 dimerizes sequentially at a single sequence-specific DNA-binding site to form a 2:1 complex, we have carried out an extensive spectroscopic and biochemical characterization of site-specific PU.1 ETS complexes. Whereas 10 bp of DNA was sufficient to support PU.1 binding as a monomer, additional flanking bases were required to invoke sequential dimerization of the bound protein. NMR spectroscopy revealed a marked loss of signal intensity in the 2:1 complex, and mutational analysis implicated the distal surface away from the bound DNA as the dimerization interface. Hydroxyl radical DNA footprinting indicated that the site-specifically bound PU.1 dimers occupied an extended DNA interface downstream from the 5'-GGAA-3' core consensus relative to its 1:1 counterpart, thus explaining the apparent site size requirement for sequential dimerization. The site-specifically bound PU.1 dimer resisted competition from nonspecific DNA and showed affinities similar to other functionally significant PU.1 interactions. As sequential dimerization did not occur with the ETS domain of Ets-1, a close structural homolog of PU.1, 2:1 complex formation may represent an alternative autoinhibitory mechanism in the ETS family at the protein-DNA level. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Effects of transcription ability and transcription mode on translation: Evidence from written compositions, language bursts and pauses when students in grades 4 to 9, with and without persisting dyslexia or dysgraphia, compose by pen or by keyboard

    Directory of Open Access Journals (Sweden)

    Scott F. Beers

    2017-06-01

    Full Text Available This study explored the effects of transcription on translation products and processes of adolescent students in grades 4 to 9 with and without persisting specific language disabilities in written language (SLDs—WL. To operationalize transcription ability (handwriting and spelling and transcription mode (by pen on digital tablet or by standard US keyboard, diagnostic groups contrasting in patterns of transcription ability were compared while composing autobiographical (personal narratives by handwriting or by keyboarding: Typically developing students (n=15, students with dyslexia (impaired word reading and spelling, n=20, and students with dysgraphia (impaired handwriting, n=19. They were compared on seven outcomes: total words composed, total composing time, words per minute, percent of spelling errors, average length of pauses, average number of pauses per minute, and average length of language bursts. They were also compared on automaticity of transcription modes—writing the alphabet from memory by handwriting or keyboarding (they could look at keys. Mixed ANOVAs yielded main effects for diagnostic group on percent of spelling errors, words per minute, and length of language burst. Main effects for transcription modes were found for automaticity of writing modes, total words composed, words per minute, and length of language bursts; there were no significant interactions. Regardless of mode, the dyslexia group had more spelling errors, showed a slower rate of composing, and produced shorter language bursts than the typical group. The total number of words, total time composing, words composed per minute, and pauses per minute were greater for keyboarding than handwriting, but length of language bursts was greater for handwriting. Implications of these results for conceptual models of composing and educational assessment practices are discussed.

  15. A third mode of surface‐associated growth: immobilization of Salmonella enterica serovar Typhimurium modulates the RpoS‐directed transcriptional programme

    DEFF Research Database (Denmark)

    Knudsen, Gitte Maegaard; Nielsen, Maj‐Britt; Grassby, Terri

    2012-01-01

    environments in both food products and the GI tract. This immobilized mode of growth has not been widely studied. To develop our understanding of the effects of immobilization upon a food‐borne bacterial pathogen, we used the IFR Gel Cassette model. The transcriptional programme and metabolomic profile...

  16. Unique evolution of the UPR pathway with a novel bZIP transcription factor, Hxl1, for controlling pathogenicity of Cryptococcus neoformans.

    Directory of Open Access Journals (Sweden)

    Seon Ah Cheon

    2011-08-01

    Full Text Available In eukaryotic cells, the unfolded protein response (UPR pathway plays a crucial role in cellular homeostasis of the endoplasmic reticulum (ER during exposure to diverse environmental conditions that cause ER stress. Here we report that the human fungal pathogen Cryptococcus neoformans has evolved a unique UPR pathway composed of an evolutionarily conserved Ire1 protein kinase and a novel bZIP transcription factor encoded by HXL1 (HAC1 and XBP1-Like gene 1. C. neoformans HXL1 encodes a protein lacking sequence homology to any known fungal or mammalian Hac1/Xbp1 protein yet undergoes the UPR-induced unconventional splicing in an Ire1-dependent manner upon exposure to various stresses. The structural organization of HXL1 and its unconventional splicing is widely conserved in C. neoformans strains of divergent serotypes. Notably, both C. neoformans ire1 and hxl1 mutants exhibited extreme growth defects at 37°C and hypersensitivity to ER stress and cell wall destabilization. All of the growth defects of the ire1 mutant were suppressed by the spliced active form of Hxl1, supporting that HXL1 mRNA is a downstream target of Ire1. Interestingly, however, the ire1 and hxl1 mutants showed differences in thermosensitivity, expression patterns for a subset of genes, and capsule synthesis, indicating that Ire1 has both Hxl1-dependent and -independent functions in C. neoformans. Finally, Ire1 and Hxl1 were shown to be critical for virulence of C. neoformans, suggesting UPR signaling as a novel antifungal therapeutic target.

  17. The TetR-Type Transcriptional Repressor RolR from Corynebacterium glutamicum Regulates Resorcinol Catabolism by Binding to a Unique Operator, rolO

    OpenAIRE

    Li, Tang; Zhao, Kexin; Huang, Yan; Li, Defeng; Jiang, Cheng-Ying; Zhou, Nan; Fan, Zheng; Liu, Shuang-Jiang

    2012-01-01

    The rol (designated for resorcinol) gene cluster rolRHMD is involved in resorcinol catabolism in Corynebacterium glutamicum, and RolR is the TetR-type regulator. In this study, we investigated how RolR regulated the transcription of the rol genes in C. glutamicum. The transcription start sites and promoters of rolR and rolHMD were identified. Quantitative reverse transcription-PCR and promoter activity analysis indicated that RolR negatively regulated the transcription of rolHMD and of its ow...

  18. Intrahepatic bile ducts develop according to a new mode of tubulogenesis regulated by the transcription factor SOX9.

    Science.gov (United States)

    Antoniou, Aline; Raynaud, Peggy; Cordi, Sabine; Zong, Yiwei; Tronche, François; Stanger, Ben Z; Jacquemin, Patrick; Pierreux, Christophe E; Clotman, Frederic; Lemaigre, Frederic P

    2009-06-01

    A number of diseases are characterized by defective formation of the intrahepatic bile ducts. In the embryo, hepatoblasts differentiate to cholangiocytes, which give rise to the bile ducts. Here, we investigated duct development in mouse liver and characterized the role of the SRY-related HMG box transcription factor 9 (SOX9). We identified SOX9 as a new biliary marker and used it in immunostaining experiments to characterize bile duct morphogenesis. The expression of growth factors was determined by in situ hybridization and immunostaining, and their role was studied on cultured hepatoblasts. SOX9 function was investigated by phenotyping mice with a liver-specific inactivation of Sox9. Biliary tubulogenesis started with formation of asymmetrical ductal structures, lined on the portal side by cholangiocytes and on the parenchymal side by hepatoblasts. When the ducts grew from the hilum to the periphery, the hepatoblasts lining the asymmetrical structures differentiated to cholangiocytes, thereby allowing formation of symmetrical ducts lined only by cholangiocytes. We also provide evidence that transforming growth factor-beta promotes differentiation of the hepatoblasts lining the asymmetrical structures. In the absence of SOX9, the maturation of asymmetrical structures into symmetrical ducts was delayed. This was associated with abnormal expression of CCAAT/Enhancer Binding Protein alpha and Homolog of Hairy/Enhancer of Split-1, as well as of the transforming growth factor-beta receptor type II, which are regulators of biliary development. Our results suggest that biliary development proceeds according to a new mode of tubulogenesis characterized by transient asymmetry and whose timing is controlled by SOX9.

  19. The competence transcription factor of Bacillus subtilis recognizes short A/T-rich sequences arranged in a unique, flexible pattern along the DNA helix

    NARCIS (Netherlands)

    Hamoen, LW; Van Werkhoven, AF; Bijlsma, JJE; Dubnau, D; Venema, G

    1998-01-01

    The development of genetic competence in Bacillus subtilis is regulated by a complex signal transduction cascade, which leads to the synthesis of the competence transcription factor (CTF). Previous studies suggested that CTF is encoded by comK. ComK is required for the transcription of comK itself,

  20. Structure of the Human Angiotensin II Type 1 (AT1) Receptor Bound to Angiotensin II from Multiple Chemoselective Photoprobe Contacts Reveals a Unique Peptide Binding Mode*

    Science.gov (United States)

    Fillion, Dany; Cabana, Jérôme; Guillemette, Gaétan; Leduc, Richard; Lavigne, Pierre; Escher, Emanuel

    2013-01-01

    Breakthroughs in G protein-coupled receptor structure determination based on crystallography have been mainly obtained from receptors occupied in their transmembrane domain core by low molecular weight ligands, and we have only recently begun to elucidate how the extracellular surface of G protein-coupled receptors (GPCRs) allows for the binding of larger peptide molecules. In the present study, we used a unique chemoselective photoaffinity labeling strategy, the methionine proximity assay, to directly identify at physiological conditions a total of 38 discrete ligand/receptor contact residues that form the extracellular peptide-binding site of an activated GPCR, the angiotensin II type 1 receptor. This experimental data set was used in homology modeling to guide the positioning of the angiotensin II (AngII) peptide within several GPCR crystal structure templates. We found that the CXC chemokine receptor type 4 accommodated the results better than the other templates evaluated; ligand/receptor contact residues were spatially grouped into defined interaction clusters with AngII. In the resulting receptor structure, a β-hairpin fold in extracellular loop 2 in conjunction with two extracellular disulfide bridges appeared to open and shape the entrance of the ligand-binding site. The bound AngII adopted a somewhat vertical binding mode, allowing concomitant contacts across the extracellular surface and deep within the transmembrane domain core of the receptor. We propose that such a dualistic nature of GPCR interaction could be well suited for diffusible linear peptide ligands and a common feature of other peptidergic class A GPCRs. PMID:23386604

  1. Modelization, fabrication and evaluation avalanche photodiodes polarized in Geiger mode for the single photon in astrophysics applications; Modelisation, fabrication et evaluation des photodiodes a avalanche polarisees en mode Geiger pour la detection du photon unique dans les applications Astrophysiques

    Energy Technology Data Exchange (ETDEWEB)

    Pellion, D

    2008-12-15

    The genesis of the work presented in this this is in the field of very high energy astrophysics. One century ago, scientists identified a new type of messenger coming from space: cosmic rays. This radiation consists of particles (photons or other) of very high energy which bombard the Earth permanently. The passage of cosmic radiations in the Earth's atmosphere results in the creation of briefs luminous flashes (5 ns) of very low intensity (1 pW), a Cherenkov flash, and then becomes visible on the ground. In the current state of the art the best detector of light today is the Photomultiplier tube (PMT), thanks to its characteristics of sensitivity and speed. But there are some drawbacks: low quantum efficiency, cost, weight etc. We present in this thesis a new alternative technology: silicon photon counters, made of photodiodes polarized in Geiger mode. This operating mode makes it possible to obtain an effect of multiplication comparable to that of the PMT. A physical and electrical model was developed to reproduce the behaviour of this detector. We then present in this thesis work an original technological process allowing the realization of these devices in the Center of Technology of LAAS-CNRS, with the simulation of each operation of the process. We developed a scheme for the electric characterization of the device, from the static mode to the dynamic mode, in order to check conformity with SILVACO simulations and to the initial model. Results are already excellent, given this is only a first prototype step, and comparable with the results published in the literature. These silicon devices can intervene in all the applications where there is a photomultiplier and replace it. The applications are thus very numerous and the growth of the market of these detectors is very fast. We present a first astrophysical experiment installed at the 'Pic du Midi' site which has detected Cherenkov flashes from cosmic rays with this new semiconductor technology

  2. Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host.

    Science.gov (United States)

    Lang, Julien; Vigouroux, Armelle; Planamente, Sara; El Sahili, Abbas; Blin, Pauline; Aumont-Nicaise, Magali; Dessaux, Yves; Moréra, Solange; Faure, Denis

    2014-10-01

    By modifying the nuclear genome of its host, the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates. The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A. tumefaciens. In the pathogen-induced niche (the plant tumour), a selective advantage conferred by opine assimilation has been hypothesized, but not experimentally demonstrated. Here, using genetics and structural biology, we deciphered how the pathogen is able to bind opines and use them to efficiently compete in the plant tumour. We report high resolution X-ray structures of the periplasmic binding protein (PBP) NocT unliganded and liganded with the opine nopaline (a condensation product of arginine and α-ketoglurate) and its lactam derivative pyronopaline. NocT exhibited an affinity for pyronopaline (K(D) of 0.6 µM) greater than that for nopaline (KD of 3.7 µM). Although the binding-mode of the arginine part of nopaline/pyronopaline in NocT resembled that of arginine in other PBPs, affinity measurement by two different techniques showed that NocT did not bind arginine. In contrast, NocT presented specific residues such as M117 to stabilize the bound opines. NocT relatives that exhibit the nopaline/pyronopaline-binding mode were only found in genomes of the genus Agrobacterium. Transcriptomics and reverse genetics revealed that A. tumefaciens uses the same pathway for assimilating nopaline and pyronopaline. Fitness measurements showed that NocT is required for a competitive colonization of the plant tumour by A. tumefaciens. Moreover, even though the Ti-plasmid conjugal transfer was not regulated by nopaline, the competitive advantage gained by the nopaline-assimilating Ti-plasmid donors led to a preferential horizontal propagation of this Ti-plasmid amongst the agrobacteria colonizing the plant-tumour niche. This work provided structural and genetic evidences to support the niche

  3. Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host.

    Directory of Open Access Journals (Sweden)

    Julien Lang

    2014-10-01

    Full Text Available By modifying the nuclear genome of its host, the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates. The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A. tumefaciens. In the pathogen-induced niche (the plant tumour, a selective advantage conferred by opine assimilation has been hypothesized, but not experimentally demonstrated. Here, using genetics and structural biology, we deciphered how the pathogen is able to bind opines and use them to efficiently compete in the plant tumour. We report high resolution X-ray structures of the periplasmic binding protein (PBP NocT unliganded and liganded with the opine nopaline (a condensation product of arginine and α-ketoglurate and its lactam derivative pyronopaline. NocT exhibited an affinity for pyronopaline (K(D of 0.6 µM greater than that for nopaline (KD of 3.7 µM. Although the binding-mode of the arginine part of nopaline/pyronopaline in NocT resembled that of arginine in other PBPs, affinity measurement by two different techniques showed that NocT did not bind arginine. In contrast, NocT presented specific residues such as M117 to stabilize the bound opines. NocT relatives that exhibit the nopaline/pyronopaline-binding mode were only found in genomes of the genus Agrobacterium. Transcriptomics and reverse genetics revealed that A. tumefaciens uses the same pathway for assimilating nopaline and pyronopaline. Fitness measurements showed that NocT is required for a competitive colonization of the plant tumour by A. tumefaciens. Moreover, even though the Ti-plasmid conjugal transfer was not regulated by nopaline, the competitive advantage gained by the nopaline-assimilating Ti-plasmid donors led to a preferential horizontal propagation of this Ti-plasmid amongst the agrobacteria colonizing the plant-tumour niche. This work provided structural and genetic evidences to

  4. The Structure of the RAGE:S100A6 Complex Reveals a Unique Mode of Homodimerization for S100 Proteins.

    Science.gov (United States)

    Yatime, Laure; Betzer, Cristine; Jensen, Rasmus Kjeldsen; Mortensen, Sofia; Jensen, Poul Henning; Andersen, Gregers Rom

    2016-12-06

    S100 proteins are calcium-dependent regulators of homeostatic processes. Upon cellular response to stress, and notably during tumorigenesis, they relocalize to the extracellular environment where they induce pro-inflammatory signals by activating the receptor for advanced glycation end products (RAGE), thereby facilitating tumor growth and metastasis. Despite its importance in sustaining inflammation, the structural basis for RAGE-S100 crosstalk is still unknown. Here we report two crystal structures of the RAGE:S100A6 complex encompassing a full-length RAGE ectodomain. The structures, in combination with a comprehensive interaction analysis, suggest that the primary S100A6 binding site is formed by the RAGE C1 domain. Complex formation with S100A6 induces a unique dimeric conformation of RAGE that appears suited for signal transduction and intracellular effector recruitment. Intriguingly, S100A6 adopts a dimeric conformation radically different from all known S100 dimers. We discuss the physiological relevance of this non-canonical homodimeric form in vivo. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. The role of transcription factor FoxO1 in the pathogenesis of acne vulgaris and the mode of isotretinoin action.

    Science.gov (United States)

    Melnik, B C

    2010-10-01

    It is the purpose of this review to demonstrate that oral isotretinoin treatment restores all major pathogenetic factors of acne vulgaris by upregulation of the nuclear transcription factor FoxO1, which will be shown to be the major target of retinoid action. Nuclear FoxO1 deficiency is the result of increased growth factor signaling with activated phosphoinositol-3-kinase (PI3K) and Akt kinase during growth hormone signaling of puberty and increased insulin/IGF-1 signaling due to consumption of insulinotropic milk/dairy products as well as hyperglycemic carbohydrates of Western diet. Nuclear FoxO1 deficiency increases androgen receptor transactivation and modifies the activity of important nuclear receptors and key genes involved in pilosebaceous keratinocyte proliferation, sebaceous lipogenesis and expression of perifollicular inflammatory cytokines. Isotretinoin-induced upregulation of nuclear FoxO1 is proposed to be responsible for the mode of action of isotretinoin on all major pathogenetic factors in acne. Acne pathogenesis can be explained at the genomic level of transcriptional regulation. All major events in acne pathogenesis as well as all major effects of isotretinoin treatment appear to be related to modifications of the PI3K/Akt/FoxO1 signaling pathway, the well-known oncogenic pathway. These insights extend our understanding of FoxO1-mediated retinoid action in acne and other hyperproliferative skin diseases, cancer chemoprevention and cutaneous immune regulation. Understanding FoxO´s pivotal regulatory role in acne allows the development of novel treatment strategies and dietary interventions in acne which focus on the restoration of growth factor- and diet-induced imbalances of nuclear FoxO protein levels.

  6. Abortive intermediates in transcription by wheat-germ RNA polymerase II. Dynamic aspects of enzyme/template interactions in selection of the enzyme synthetic mode.

    Science.gov (United States)

    de Mercoyrol, L; Soulié, J M; Job, C; Job, D; Dussert, C; Palmari, J; Rasigni, M; Rasigni, G

    1990-08-01

    At constant enzyme concentration and with the full set of nucleotide substrates dictated by template sequence, the chain-length distribution of polymeric product varies with template concentration in reactions catalysed by wheat-germ RNA polymerase II. Under the same conditions, but in the presence of a single ribonucleoside triphosphate, the rate of condensation of the triphosphate substrate to a dinucleotide primer also exhibits a complex dependence with the template concentration. This effect is observed using poly[d(A-T)] as a template. For both reactions there are two extreme types of behaviour in each of which transcription appears to involve a single enzyme synthetic mode, characterized by either a high (at low template concentration) or a low (at high template concentration) probability of releasing the transcripts. A strong correlation is found between these two pathways, such that conditions favouring the abortive release of trinucleotide products in the single-step addition reaction are associated with the synthesis of short-length RNA species in productive elongation, and reciprocally. A model previously developed by Papanicolaou, Lecomte & Ninio [(1986) J. Mol. Biol. 189, 435-448] to account for the kinetics of polymerization/excision ratios with Escherichia coli DNA polymerase I, and by Job, Soulié, Job & Shire [(1988) J. Theor. Biol. 134, 273-289] for kinetics of RNA-chain elongation by wheat-germ RNA polymerase II provides an explanation for the observed behaviour with the plant transcriptase. The basic requirement of this model is a slow equilibrium between two states of the polymerization complex with distinct probabilities of releasing the product. In the presence of Mn2+, and under conditions allowing the synthesis of poly[r(A-U)], one of these states is involved in the formation of oligonucleotides shorter than 15 bases, whereas the other catalyses the polymerization of chains longer than 40 bases.

  7. Filovirus replication and transcription

    OpenAIRE

    Mühlberger, Elke

    2007-01-01

    The highly pathogenic filoviruses, Marburg and Ebola virus, belong to the nonsegmented negative-sense RNA viruses of the order Mononegavirales. The mode of replication and transcription is similar for these viruses. On one hand, the negative-sense RNA genome serves as a template for replication, to generate progeny genomes, and, on the other hand, for transcription, to produce mRNAs. Despite the similarities in the replication/transcription strategy, filoviruses have evolved structural and fu...

  8. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

    Science.gov (United States)

    Boyle, Alan P; Song, Lingyun; Lee, Bum-Kyu; London, Darin; Keefe, Damian; Birney, Ewan; Iyer, Vishwanath R; Crawford, Gregory E; Furey, Terrence S

    2011-03-01

    Regulation of gene transcription in diverse cell types is determined largely by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNase I hypersensitivity assay can delineate hundreds of thousands of base-pair resolution in vivo footprints in human cells that precisely mark individual transcription factor-DNA interactions. These annotations provide a unique resource for the investigation of cis-regulatory elements. We find that footprints for specific transcription factors correlate with ChIP-seq enrichment and can accurately identify functional versus nonfunctional transcription factor motifs. We also find that footprints reveal a unique evolutionary conservation pattern that differentiates functional footprinted bases from surrounding DNA. Finally, detailed analysis of CTCF footprints suggests multiple modes of binding and a novel DNA binding motif upstream of the primary binding site.

  9. Differential expression of brain-derived neurotrophic factor transcripts after pilocarpine-induced seizure-like activity is related to mode of Ca2+ entry

    DEFF Research Database (Denmark)

    Poulsen, F R; Lauterborn, J; Zimmer, J

    2004-01-01

    Activity-dependent brain-derived neurotrophic factor (BDNF) expression is Ca2+-dependent, yet little is known about the Ca2+ channel contributions that might direct selective expression of the multiple BDNF transcripts. Here, effects of pilocarpine-induced seizure activity on total BDNF expressio...

  10. Unique Identification Project Issues and Challenges Unique ...

    Indian Academy of Sciences (India)

    Unique Identification Project Issues and Challenges Unique Identification Authority of India (UIDAI) · Agenda · UIDAI will issue numbers, not cards · UIDAI will authenticate IDs online · Verifying ID is a common challenge · ID is the only focus of UIDAI · Who gets UID number? Inclusive potential of UID · UID ecosystem – A ...

  11. Nucleocytoplasmic shuttling of transcription factors

    DEFF Research Database (Denmark)

    Cartwright, P; Helin, K

    2000-01-01

    To elicit the transcriptional response following intra- or extracellular stimuli, the signals need to be transmitted to their site of action within the nucleus. The nucleocytoplasmic shuttling of transcription factors is a mechanism mediating this process. The activation and inactivation of the t......To elicit the transcriptional response following intra- or extracellular stimuli, the signals need to be transmitted to their site of action within the nucleus. The nucleocytoplasmic shuttling of transcription factors is a mechanism mediating this process. The activation and inactivation...... transcription factor families are regulated by similar mechanisms, there are several differences that allow for the specific activation of each transcription factor. This review discusses the general import and export pathways found to be common amongst many different transcription factors, and highlights...... a select group of transcription factors that demonstrate the diversity displayed in their mode of activation and inactivation....

  12. Unique Path Partitions

    DEFF Research Database (Denmark)

    Bessenrodt, Christine; Olsson, Jørn Børling; Sellers, James A.

    2013-01-01

    We give a complete classification of the unique path partitions and study congruence properties of the function which enumerates such partitions.......We give a complete classification of the unique path partitions and study congruence properties of the function which enumerates such partitions....

  13. Multiple modes of chromatin remodeling by Forkhead box proteins.

    Science.gov (United States)

    Lalmansingh, Avin S; Karmakar, Sudipan; Jin, Yetao; Nagaich, Akhilesh K

    2012-07-01

    Forkhead box (FOX) proteins represent a large family of transcriptional regulators unified by their DNA binding domain (DBD) known as a 'forkhead' or 'winged helix' domain. Over 40 FOX genes have been identified in the mammalian genome. FOX proteins share significant sequence similarities in the DBD which allow them to bind to a consensus DNA response element. However, their modes of action are quite diverse as they regulate gene expression by acting as pioneer factors, transcription factors, or both. This review focuses on the mechanisms of chromatin remodeling with an emphasis on three sub-classes-FOXA, FOXO, and FOXP members. FOXA proteins serve as pioneer factors to open up local chromatin structure and thereby increase accessibility of chromatin to factors regulating transcription. FOXP proteins, in contrast, function as classic transcription factors to recruit a variety of chromatin modifying enzymes to regulate gene expression. FOXO proteins represent a hybrid subclass having dual roles as pioneering factors and transcription factors. A subset of FOX proteins interacts with condensed mitotic chromatin and may function as 'bookmarking' agents to maintain transcriptional competence at specific genomic sites. The overall diversity in chromatin remodeling function by FOX proteins is related to unique structural motifs present within the DBD flanking regions that govern selective interactions with core histones and/or chromatin coregulatory proteins. This article is part of a Special Issue entitled: Chromatin in time and space. Published by Elsevier B.V.

  14. Regulation of Transcript Elongation

    Science.gov (United States)

    Belogurov, Georgiy A.; Artsimovitch, Irina

    2015-01-01

    Bacteria lack subcellular compartments and harbor a single RNA polymerase that synthesizes both structural and protein-coding RNAs, which are cotranscriptionally processed by distinct pathways. Nascent rRNAs fold into elaborate secondary structures and associate with ribosomal proteins, whereas nascent mRNAs are translated by ribosomes. During elongation, nucleic acid signals and regulatory proteins modulate concurrent RNA-processing events, instruct RNA polymerase where to pause and terminate transcription, or act as roadblocks to the moving enzyme. Communications among complexes that carry out transcription, translation, repair, and other cellular processes ensure timely execution of the gene expression program and survival under conditions of stress. This network is maintained by auxiliary proteins that act as bridges between RNA polymerase, ribosome, and repair enzymes, blurring boundaries between separate information-processing steps and making assignments of unique regulatory functions meaningless. Understanding the regulation of transcript elongation thus requires genome-wide approaches, which confirm known and reveal new regulatory connections. PMID:26132790

  15. Two independent transcription initiation codes overlap on vertebrate core promoters

    Science.gov (United States)

    Haberle, Vanja; Li, Nan; Hadzhiev, Yavor; Plessy, Charles; Previti, Christopher; Nepal, Chirag; Gehrig, Jochen; Dong, Xianjun; Akalin, Altuna; Suzuki, Ana Maria; van Ijcken, Wilfred F. J.; Armant, Olivier; Ferg, Marco; Strähle, Uwe; Carninci, Piero; Müller, Ferenc; Lenhard, Boris

    2014-03-01

    A core promoter is a stretch of DNA surrounding the transcription start site (TSS) that integrates regulatory inputs and recruits general transcription factors to initiate transcription. The nature and causative relationship of the DNA sequence and chromatin signals that govern the selection of most TSSs by RNA polymerase II remain unresolved. Maternal to zygotic transition represents the most marked change of the transcriptome repertoire in the vertebrate life cycle. Early embryonic development in zebrafish is characterized by a series of transcriptionally silent cell cycles regulated by inherited maternal gene products: zygotic genome activation commences at the tenth cell cycle, marking the mid-blastula transition. This transition provides a unique opportunity to study the rules of TSS selection and the hierarchy of events linking transcription initiation with key chromatin modifications. We analysed TSS usage during zebrafish early embryonic development at high resolution using cap analysis of gene expression, and determined the positions of H3K4me3-marked promoter-associated nucleosomes. Here we show that the transition from the maternal to zygotic transcriptome is characterized by a switch between two fundamentally different modes of defining transcription initiation, which drive the dynamic change of TSS usage and promoter shape. A maternal-specific TSS selection, which requires an A/T-rich (W-box) motif, is replaced with a zygotic TSS selection grammar characterized by broader patterns of dinucleotide enrichments, precisely aligned with the first downstream (+1) nucleosome. The developmental dynamics of the H3K4me3-marked nucleosomes reveal their DNA-sequence-associated positioning at promoters before zygotic transcription and subsequent transcription-independent adjustment to the final position downstream of the zygotic TSS. The two TSS-defining grammars coexist, often physically overlapping, in core promoters of constitutively expressed genes to enable

  16. Promoter-mediated transcriptional dynamics.

    Science.gov (United States)

    Zhang, Jiajun; Zhou, Tianshou

    2014-01-21

    Genes in eukaryotic cells are typically regulated by complex promoters containing multiple binding sites for a variety of transcription factors, but how promoter dynamics affect transcriptional dynamics has remained poorly understood. In this study, we analyze gene models at the transcriptional regulation level, which incorporate the complexity of promoter structure (PS) defined as transcriptional exits (i.e., ON states of the promoter) and the transition pattern (described by a matrix consisting of transition rates among promoter activity states). We show that multiple exits of transcription are the essential origin of generating multimodal distributions of mRNA, but promoters with the same transition pattern can lead to multimodality of different modes, depending on the regulation of transcriptional factors. In turn, for similar mRNA distributions in the models, the mean ON or OFF time distributions may exhibit different characteristics, thus providing the supplemental information on PS. In addition, we demonstrate that the transcriptional noise can be characterized by a nonlinear function of mean ON and OFF times. These results not only reveal essential characteristics of promoter-mediated transcriptional dynamics but also provide signatures useful for inferring PS based on characteristics of transcriptional outputs. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. NASA's unique networking environment

    Science.gov (United States)

    Johnson, Marjory J.

    1988-01-01

    Networking is an infrastructure technology; it is a tool for NASA to support its space and aeronautics missions. Some of NASA's networking problems are shared by the commercial and/or military communities, and can be solved by working with these communities. However, some of NASA's networking problems are unique and will not be addressed by these other communities. Individual characteristics of NASA's space-mission networking enviroment are examined, the combination of all these characteristics that distinguish NASA's networking systems from either commercial or military systems is explained, and some research areas that are important for NASA to pursue are outlined.

  18. Is Life Unique?

    Science.gov (United States)

    Abel, David L.

    2011-01-01

    Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity—heat agitation and the cause-and-effect determinism of nature’s orderliness—cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical. PMID:25382119

  19. Identification of sumoylation sites in CCDC6, the first identified RET partner gene in papillary thyroid carcinoma, uncovers a mode of regulating CCDC6 function on CREB1 transcriptional activity.

    Directory of Open Access Journals (Sweden)

    Chiara Luise

    Full Text Available CCDC6 was originally identified in chimeric genes as caused by chromosomal translocation involving the RET protooncogene in some thyroid tumors. Recognised as a 65 kDa pro-apoptotic phosphoprotein, CCDC6 has been enrolled as an ATM substrate that contribute to protect genome integrity by modulating PP4c activity in response to genotoxic stress. Recently, CCDC6 has been identified as a repressor of CREB1-dependent transcription. Sumoylation has emerged as an important mechanism in transcriptional control. Here, we report the identification and characterization of three sites of sumoylation in CCDC6 (K74, K266 and K424 which are highly conserved in vertebrates. We demonstrate that the post-translational modifications by SUMO2 constrain most of the CCDC6 protein in the cytosol and affect its functional interaction with CREB1 with a decrease of CCDC6 repressive function on CREB1 transcriptional activity. Indeed, the impairment of functional outcome of sumoylated CCDC6 is obtained knocking down all three the sumoylation sites. Interestingly, in thyroid cells the SUMO2-mediated CCDC6 post-translational modifications are induced by Forskolin, a cAMP analog. Signal transduction via the cAMP pathway is known to be ubiquitous and represents a major line of communication between many organisms and their environment. We believe that CCDC6 could be an important player in the dynamics of cAMP signaling by fine regulating CREB1 transcriptional activity in normal and transformed thyroid cells.

  20. Monolithic mode-selective few-mode multicore fiber multiplexers.

    Science.gov (United States)

    Riesen, Nicolas; Gross, Simon; Love, John D; Sasaki, Yusuke; Withford, Michael J

    2017-08-01

    With the capacity limits of standard single-mode optical fiber fast approaching, new technologies such as space-division multiplexing are required to avoid an Internet capacity crunch. Few-mode multicore fiber (FM-MCF) could allow for a two orders of magnitude increase in capacity by using the individual spatial modes in the different cores as unique data channels. We report the realization of a monolithic mode-selective few-mode multicore fiber multiplexer capable of addressing the individual modes of such a fiber. These compact multiplexers operate across the S + C + L telecommunications bands and were inscribed into a photonic chip using ultrafast laser inscription. They allow for the simultaneous multiplexing of the LP 01 , LP 11a and LP 11b modes of all cores in a 3-mode, 4-core fiber with excellent mode extinction ratios and low insertion losses. The devices are scalable to more modes and cores and therefore could represent an enabling technology for practical ultra-high capacity dense space-division multiplexing.

  1. Nonlinear oscillations of TM-mode gyrotrons

    Science.gov (United States)

    Chang, Tsun-Hsu; Yao, Hsin-Yu; Su, Bo-Yuan; Huang, Wei-Chen; Wei, Bo-Yuan

    2017-12-01

    This study investigates the interaction between the relativistic electrons and the waves in cavities with fixed field profiles. Both the transverse electric (TE) and the transverse magnetic (TM) cavity modes are examined, including three first-axial modes, TE011, TM011, and TM111, and two zero-axial modes, TM010 and TM110. The first-axial modes have the same resonant frequency, so a direct comparison can be made. By sweeping the electron pitch factor (α) and the electron transit angle (Θ), the optimal converting efficiency of TM modes occurs at α = 1.5 and Θ = 1.5π, unlike the TE mode of α = 2.0 and Θ = 1.0π. The converting efficiencies of both the first-axial TM modes are much lower than that of TE011 mode. The starting currents of TM011 and TM111 modes are four times higher than that of TE011 mode, indicating that these two TM modes are very difficult to oscillate. This evidences that under the traditional operating conditions, the TM-mode gyrotrons are insignificant. However, the two unique, zero-axial TM modes have relatively high converting efficiency. The highest converting efficiency of TM110 is 27.4%, the same value as that of TE011 mode. The starting currents of TM110 mode and TE011 mode are at the same level. The results suggest that some TM-mode gyrotron oscillators are feasible and deserve further theoretical and experimental studies.

  2. Failure Modes

    DEFF Research Database (Denmark)

    Jakobsen, K. P.; Burcharth, H. F.; Ibsen, Lars Bo

    1999-01-01

    The present appendix contains the derivation of ten different limit state equations divided on three different failure modes. Five of the limit state equations can be used independently of the characteristics of the subsoil, whereas the remaining five can be used for either drained or undrained s...

  3. Mode Combinations and International Operations

    DEFF Research Database (Denmark)

    Benito, Gabriel R. G.; Petersen, Bent; Welch, Lawrence S.

    2011-01-01

    An enduring characteristic of extant literature on foreign operation modes is its discrete choice approach, where companies are assumed to choose one among a small number of distinctive alternatives. In this paper we use detailed information about the operations of six Norwegian companies in three...... key markets (China, UK and USA) as the basis for an exploration of the extent to which, and how and why, companies combine clearly different foreign operation modes. We examine their use of foreign operation mode combinations within given value activities as well as within given countries. The study...... reveals that companies tend to combine modes of operation; thereby producing unique foreign operation mode “packages” for given activities and/or countries, and that the packages are liable to be modified over time – providing a potentially important optional path for international expansion. Our data...

  4. Mode Combinations and International Operations

    DEFF Research Database (Denmark)

    Benito, Gabriel R. G.; Petersen, Bent; Welch, Lawrence S.

    2011-01-01

    An enduring characteristic of extant literature on foreign operation modes is its discrete choice approach, where companies are assumed to choose one among a small number of distinctive alternatives. In this paper, detailed information about the operations of six Norwegian companies in three key...... markets (China, UK and USA) is used as the basis for an exploration of the extent to which, and how and why, companies combine clearly different foreign operation modes. We examine their use of foreign operation mode combinations within given value activities as well as within given countries. The study...... reveals that companies tend to combine modes of operation; thereby producing unique foreign operation mode “packages” for given activities and/or countries, and that the packages are liable to be modified over time—providing a potentially important optional path for international expansion. The data show...

  5. Unique Factors Affecting Canadian Education.

    Science.gov (United States)

    Farquhar, Robin H.

    In a background statement identifying what is unique about Canada and the issues it currently faces, this paper begins by discussing the concurrent movements toward Canadian nationalism and Quebec nationalism as an illustration of the problems caused by large size and great diversity. It then focuses on unique aspects of Canadian education,…

  6. Imposing Uniqueness to Achieve Sparsity.

    Science.gov (United States)

    Dillon, Keith; Wang, Yu-Ping

    2016-06-01

    In this paper we take a novel approach to the regularization of underdetermined linear systems. Typically, a prior distribution is imposed on the unknown to hopefully force a sparse solution, which often relies on uniqueness of the regularized solution (something which is typically beyond our control) to work as desired. But here we take a direct approach, by imposing the requirement that the system takes on a unique solution. Then we seek a minimal residual for which this uniqueness requirement holds. When applied to systems with non-negativity constraints or forms of regularization for which sufficient sparsity is a requirement for uniqueness, this approach necessarily gives a sparse result. The approach is based on defining a metric of distance to uniqueness for the system, and optimizing an adjustment that drives this distance to zero. We demonstrate the performance of the approach with numerical experiments.

  7. Copies of Unique Comment Letters

    OpenAIRE

    Mark Belles; Bureau of Reclamation

    2005-01-01

    Unique letters and messages regarding the "Notice to solicit comments and hold public meetings on the development of management strategies for Lake Powell and Lake Mead, including Lower Basin shortage guidelines, under low reservoir conditions."

  8. Is life on Earth unique?

    Science.gov (United States)

    Jayawardhana, Ray

    2013-10-01

    From finding unusual creatures on Earth to spying life's building blocks beyond our solar system, Ray Jayawardhana examines what we know about the nature of life's uniqueness, and the possibility of its existence in faraway realms such as extrasolar planets.

  9. Stroke: Unique to Older Adults

    Science.gov (United States)

    ... Problems Osteoporosis Urinary Incontinence Join our e-newsletter! Aging & Health A to Z Stroke Unique to Older ... it is often a sign of worse mental consequences, longer hospitalization, and a higher risk of death. ...

  10. Nutrition: Unique to Older Adults

    Science.gov (United States)

    ... Monday, March 23, 2015 Join our e-newsletter! Aging & Health A to Z Nutrition Unique to Older ... lack of B vitamins can lead to serious consequences for older adults. B vitamins include B6, B12, ...

  11. COPD: Unique to Older Adults

    Science.gov (United States)

    ... our e-newsletter! Aging & Health A to Z COPD Unique to Older Adults This section provides information ... care and improve or maintain quality of life. COPD and Other Medical Conditions Depression and COPD When ...

  12. Diabetes: Unique to Older Adults

    Science.gov (United States)

    ... Stroke Urinary Incontinence Related Documents PDF Choosing Wisely: Diabetes Tests and Treatments Download Related Video Join our e-newsletter! Aging & Health A to Z Diabetes Unique to Older Adults This section provides information ...

  13. Uniqueness property for quasiharmonic functions

    Directory of Open Access Journals (Sweden)

    Sevdiyor A. Imomkulov

    2014-10-01

    Full Text Available In this paper we consider a class of continuous functions, called quasiaharmonic functions, admitting best approximations by harmonic polynomials. In this class we prove a uniqueness theorem by analogy with the analytic functions.

  14. Unique Fock quantization of scalar cosmological perturbations

    Science.gov (United States)

    Fernández-Méndez, Mikel; Mena Marugán, Guillermo A.; Olmedo, Javier; Velhinho, José M.

    2012-05-01

    We investigate the ambiguities in the Fock quantization of the scalar perturbations of a Friedmann-Lemaître-Robertson-Walker model with a massive scalar field as matter content. We consider the case of compact spatial sections (thus avoiding infrared divergences), with the topology of a three-sphere. After expanding the perturbations in series of eigenfunctions of the Laplace-Beltrami operator, the Hamiltonian of the system is written up to quadratic order in them. We fix the gauge of the local degrees of freedom in two different ways, reaching in both cases the same qualitative results. A canonical transformation, which includes the scaling of the matter-field perturbations by the scale factor of the geometry, is performed in order to arrive at a convenient formulation of the system. We then study the quantization of these perturbations in the classical background determined by the homogeneous variables. Based on previous work, we introduce a Fock representation for the perturbations in which: (a) the complex structure is invariant under the isometries of the spatial sections and (b) the field dynamics is implemented as a unitary operator. These two properties select not only a unique unitary equivalence class of representations, but also a preferred field description, picking up a canonical pair of field variables among all those that can be obtained by means of a time-dependent scaling of the matter field (completed into a linear canonical transformation). Finally, we present an equivalent quantization constructed in terms of gauge-invariant quantities. We prove that this quantization can be attained by a mode-by-mode time-dependent linear canonical transformation which admits a unitary implementation, so that it is also uniquely determined.

  15. Urticarial vasculitis: a unique presentation.

    Science.gov (United States)

    Stigall, Landon E; Sigmon, Justin R; Leicht, Stuart S

    2009-05-01

    Urticarial vasculitis is a relatively rare diagnosis in a patient presenting with urticaria. The process is classically described as a generalized eruption, painful more so than pruritic, lasting longer than 24 hours. Two forms of urticarial vasculitis have been described: ahypocomplementemic form more commonly associated with systemic disease, and a normocomplementemic form that is generally limited to the skin. We report on a uniquely distributed vasculitic eruption restricted mainly to the anterior belt line area in a patient presenting with urticaria and intense pruritus. Urticarial vasculitis as a unique entity is reviewed along with its clinical and histopathologic presentation and the pharmacologic agents used for treatment.

  16. Analysis of unique beta transitions

    DEFF Research Database (Denmark)

    Eman, B.; Krmpotic, F.; Tadic, D

    1967-01-01

    The Heidelberg group measurements [For abstr. see Phys. Rev. Nucl. Sci. Vol. 15 (1965)] of unique forbidden transitions have been analysed. It has been found that experimental shape factors can be reproduced only with the induced pseudoscalar form factor d <0, and/or with the induced G-non-conser...

  17. Kosovo case: A unique arbitrariness

    Directory of Open Access Journals (Sweden)

    Nakarada Radmila

    2007-01-01

    Full Text Available The end of Cold war, contrary to expectations has brought new conflicts and forms of violence, new divisions and new relativizations of the international legal order. Taking as an example the endeavors to resolve the Kosovo conflict, the author attempts to indicate the broader implications of the international efforts to constitute an independent state on part of the territory of an existing sovereign state. The arguments used to justify the redefinition of the borders of the Serbian state without its consent, the moral, democratic, peace arguments, are reviewed. Particular attention is paid to the argument that Kosovo is a unique case and therefore unique rules should be applied. The author seeks to understand the deeper significance of these efforts, concluding that dismantling the present international legal order is not only a potential danger but a possible aim.

  18. Uniqueness theorems in linear elasticity

    CERN Document Server

    Knops, Robin John

    1971-01-01

    The classical result for uniqueness in elasticity theory is due to Kirchhoff. It states that the standard mixed boundary value problem for a homogeneous isotropic linear elastic material in equilibrium and occupying a bounded three-dimensional region of space possesses at most one solution in the classical sense, provided the Lame and shear moduli, A and J1 respectively, obey the inequalities (3 A + 2 J1) > 0 and J1>O. In linear elastodynamics the analogous result, due to Neumann, is that the initial-mixed boundary value problem possesses at most one solution provided the elastic moduli satisfy the same set of inequalities as in Kirchhoffs theorem. Most standard textbooks on the linear theory of elasticity mention only these two classical criteria for uniqueness and neglect altogether the abundant literature which has appeared since the original publications of Kirchhoff. To remedy this deficiency it seems appropriate to attempt a coherent description ofthe various contributions made to the study of uniquenes...

  19. Uniqueness of large positive solutions

    Science.gov (United States)

    López-Gómez, Julián; Maire, Luis

    2017-08-01

    We establish the uniqueness of the positive solution of the singular problem (1.1) through some standard comparison techniques involving the maximum principle. Our proofs do not invoke to the blow-up rates of the solutions, as in most of the specialized literature. We give two different types of results according to the geometrical properties of Ω and the regularity of partial Ω . Even in the autonomous case, our theorems are extremely sharp extensions of all existing results. Precisely, when a(x)≡ 1, it is shown that the monotonicity and superadditivity of f( u) with constant C≥ 0 entail the uniqueness; f is said to be superadditive with constant C≥ 0 if f(a+b) ≥ f(a) + f(b) - C \\quad for all a, b ≥ 0. This condition, introduced by Marcus and Véron (J Evol Equ 3:637-652, 2004), weakens all previous sufficient conditions for uniqueness, as it will become apparent in this paper.

  20. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

    Directory of Open Access Journals (Sweden)

    Putta Srikrishna

    2010-06-01

    Full Text Available Abstract Background The Mexican axolotl (Ambystoma mexicanum is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum that typically undergo a metamorphosis. Results Transcript abundances from whole brain and pituitary were estimated via microarray analysis on four different days post hatching (42, 56, 70, 84 dph and regression modeling was used to independently identify genes that were differentially expressed as a function of time in both species. Collectively, more differentially expressed genes (DEGs were identified as unique to the axolotl (n = 76 and tiger salamander (n = 292 than were identified as shared (n = 108. All but two of the shared DEGs exhibited the same temporal pattern of expression and the unique genes tended to show greater changes later in the larval period when tiger salamander larvae were undergoing anatomical metamorphosis. A second, complementary analysis that directly compared the expression of 1320 genes between the species identified 409 genes that differed as a function of species or the interaction between time and species. Of these 409 DEGs, 84% exhibited higher abundances in tiger salamander larvae at all sampling times. Conclusions Many of the unique tiger salamander transcriptional responses are probably associated with metamorphic biological processes. However, the axolotl also showed unique patterns of transcription early in development. In particular, the axolotl showed a genome

  1. WRKY transcription factors.

    Science.gov (United States)

    Rushton, Paul J; Somssich, Imre E; Ringler, Patricia; Shen, Qingxi J

    2010-05-01

    WRKY transcription factors are one of the largest families of transcriptional regulators in plants and form integral parts of signalling webs that modulate many plant processes. Here, we review recent significant progress in WRKY transcription factor research. New findings illustrate that WRKY proteins often act as repressors as well as activators, and that members of the family play roles in both the repression and de-repression of important plant processes. Furthermore, it is becoming clear that a single WRKY transcription factor might be involved in regulating several seemingly disparate processes. Mechanisms of signalling and transcriptional regulation are being dissected, uncovering WRKY protein functions via interactions with a diverse array of protein partners, including MAP kinases, MAP kinase kinases, 14-3-3 proteins, calmodulin, histone deacetylases, resistance proteins and other WRKY transcription factors. WRKY genes exhibit extensive autoregulation and cross-regulation that facilitates transcriptional reprogramming in a dynamic web with built-in redundancy. 2010 Elsevier Ltd. All rights reserved.

  2. Viscoelastic pulsational mode

    Science.gov (United States)

    Dutta, Pranamika; Karmakar, Pralay Kumar

    2017-08-01

    We present a theoretical model analysis to study the linear pulsational mode dynamics in viscoelastic complex self-gravitating infinitely extended clouds in the presence of active frictional coupling and dust-charge fluctuations. The complex cloud consists of uniformly distributed lighter hot mutually thermalized electrons and ions, and heavier cold dust grains amid partial ionization in a homogeneous, quasi-neutral, hydrostatic equilibrium configuration. A normal mode analysis over the closed set of slightly perturbed cloud governing equations is employed to obtain a generalized dispersion relation (septic) of unique analytic construct on the plasma parameters. Two extreme cases of physical interest depending on the perturbation scaling, hydrodynamic limits and kinetic limits are considered. It is shown that the grain mass and viscoelastic relaxation time associated with the charged dust fluid play stabilizing roles to the fluctuations in the hydrodynamic regime. In contrast, however in the kinetic regime, the stabilizing effects are introduced by the dust mass, dust equilibrium density and equilibrium ionic population distribution. Besides, the oscillatory and propagatory features are illustrated numerically and interpreted in detail. The results are in good agreement with the previously reported findings as special corollaries in like situations. Finally, a focalized indication to new implications and applications of the outcomes in the astronomical context is foregrounded.

  3. Oligo-dT selected spermatozoal transcript profiles differ among higher and lower fertility dairy sires.

    Science.gov (United States)

    Card, C J; Krieger, K E; Kaproth, M; Sartini, B L

    2017-02-01

    Spermatozoal messenger RNA (mRNA) has the potential as a molecular marker for sire fertility because this population can reflect gene expression that occurred during spermatogenesis and may have a functional role in early embryonic development. The goal of this study was to compare the oligo-dT selected spermatozoal transcript profiles of higher fertility (Conception Rate (CR) 1.8-3.5) and lower fertility (CR -2.9 to -0.4) sires using Ribonucleic Acid Sequencing (RNA-Seq). A total of 3227 transcripts and 5366 transcripts were identified in the higher and lower fertility populations, respectively. While common transcripts between the two populations were identified (2422 transcripts), several transcripts were also unique to the fertility populations including 805 transcripts that were unique to the higher fertility population and 2944 transcripts that were unique to the lower fertility population. From gene ontological analysis, the transcripts unique to each fertility population differed in Biological Processes (BP), including enrichment of regulatory transcripts for growth and protein kinase activity in the higher fertility bulls. Biological variation in transcript presence among individual sires was also found. Of the candidate fertility spermatozoal transcripts chosen from the RNA-Seq population analysis reported here and previous publications, COX7C was negatively correlated with sire fertility. Using high-throughput sequencing, candidate spermatozoal transcripts were identified for further study as potential markers for sire fertility. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. The impact of transcription on posttranscriptional processes in yeast.

    Science.gov (United States)

    Turowski, Tomasz W

    2013-08-15

    In eukaryotes, three RNA polymerases are responsible for transcription. These complex enzymes show many similarities with one another, such as several common or highly homologue subunits, while some other features, such as transcript length, diversity, processing, and transcription regulation, are unique to each polymerase. The present article reviews recent publications focusing on the impact of transcription of various RNA species in yeast on posttranscriptional steps such as pre-RNA processing, transport and decay. Two major conclusions emerge from a critical analysis of the current knowledge. (1) The kinetics of transcription elongation affects cotranscriptional pre-RNA processing. (2) The efficiency of transcription, by saturating the proteins interacting with RNA, indirectly affects the processing, export and decay of transcripts. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Transcription regulatory elements are punctuation marks for DNA replication

    Science.gov (United States)

    Mirkin, Ekaterina V.; Castro Roa, Daniel; Nudler, Evgeny; Mirkin, Sergei M.

    2006-01-01

    Collisions between DNA replication and transcription significantly affect genome organization, regulation, and stability. Previous studies have described collisions between replication forks and elongating RNA polymerases. Although replication collisions with the transcription-initiation or -termination complexes are potentially even more important because most genes are not actively transcribed during DNA replication, their existence and mechanisms remained unproven. To address this matter, we have designed a bacterial promoter that binds RNA polymerase and maintains it in the initiating mode by precluding the transition into the elongation mode. By using electrophoretic analysis of replication intermediates, we have found that this steadfast transcription-initiation complex inhibits replication fork progression in an orientation-dependent manner during head-on collisions. Transcription terminators also appeared to attenuate DNA replication, but in the opposite, codirectional orientation. Thus, transcription regulatory signals may serve as “punctuation marks” for DNA replication in vivo. PMID:16670199

  6. Detecting novel low-abundant transcripts in Drosophila

    DEFF Research Database (Denmark)

    Lee, Sanggyu; Bao, Jingyue; Zhou, Guolin

    2005-01-01

    Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244......,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts......, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons...

  7. WRKY transcription factors

    Science.gov (United States)

    Bakshi, Madhunita; Oelmüller, Ralf

    2014-01-01

    WRKY transcription factors are one of the largest families of transcriptional regulators found exclusively in plants. They have diverse biological functions in plant disease resistance, abiotic stress responses, nutrient deprivation, senescence, seed and trichome development, embryogenesis, as well as additional developmental and hormone-controlled processes. WRKYs can act as transcriptional activators or repressors, in various homo- and heterodimer combinations. Here we review recent progress on the function of WRKY transcription factors in Arabidopsis and other plant species such as rice, potato, and parsley, with a special focus on abiotic, developmental, and hormone-regulated processes. PMID:24492469

  8. The Evolution of Human Uniqueness.

    Science.gov (United States)

    Boyd, Robert

    2017-01-09

    The human species is an outlier in the natural world. Two million years ago our ancestors were a slightly odd apes. Now we occupy the largest ecological and geographical range of any species, have larger biomass, and process more energy. Usually, this transformation is explained in terms of cognitive ability-people are just smarter than all the rest. In this paper I argue that culture, our ability to learn from each other, and cooperation, our ability to make common cause with large groups of unrelated individuals are the real roots of human uniqueness, and sketch an evolutionary account of how these crucial abilities co-evolved with each other and with other features of our life histories.

  9. ORRM5, an RNA recognition motif-containing protein, has a unique effect on mitochondrial RNA editing.

    Science.gov (United States)

    Shi, Xiaowen; Castandet, Benoit; Germain, Arnaud; Hanson, Maureen R; Bentolila, Stéphane

    2017-05-17

    Plants have an RNA editing mechanism that prevents deleterious organelle mutations from resulting in impaired proteins. A typical flowering plant modifies about 40 cytidines in chloroplast transcripts and many hundreds of cytidines in mitochondrial transcripts. The plant editosome, the molecular machinery responsible for this process, contains members of several protein families, including the organelle RNA recognition motif (ORRM)-containing family. ORRM1 and ORRM6 are chloroplast editing factors, while ORRM2, ORRM3, and ORRM4 are mitochondrial editing factors. Here we report the identification of organelle RRM protein 5 (ORRM5) as a mitochondrial editing factor with a unique mode of action. Unlike other ORRM editing factors, the absence of ORRM5 in orrm5 mutant plants results in an increase of the editing extent in 14% of the mitochondrial sites surveyed. The orrm5 mutant also exhibits a reduced splicing efficiency of the first nad5 intron and slower growth and delayed flowering time. ORRM5 contains an RNA recognition motif (RRM) and a glycine-rich domain at the C terminus. The RRM provides the editing activity of ORRM5 and is able to complement the splicing but not the morphological defects. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  10. Quantitative characterization of the interactions among c-myc transcriptional regulators FUSE, FBP, and FIR.

    Science.gov (United States)

    Hsiao, Hsin-Hao; Nath, Abhinav; Lin, Chi-Yen; Folta-Stogniew, Ewa J; Rhoades, Elizabeth; Braddock, Demetrios T

    2010-06-08

    Human c-myc is critical for cell homeostasis and growth but is a potent oncogenic factor if improperly regulated. The c-myc far-upstream element (FUSE) melts into single-stranded DNA upon active transcription, and the noncoding strand FUSE recruits an activator [the FUSE-binding protein (FBP)] and a repressor [the FBP-interacting repressor (FIR)] to fine-tune c-myc transcription in a real-time manner. Despite detailed biological experiments describing this unique mode of transcriptional regulation, quantitative measurements of the physical constants regulating the protein-DNA interactions remain lacking. Here, we first demonstrate that the two FUSE strands adopt different conformations upon melting, with the noncoding strand DNA in an extended, linear form. FBP binds to the linear noncoding FUSE with a dissociation constant in the nanomolar range. FIR binds to FUSE more weakly, having its modest dissociation constants in the low micromolar range. FIR is monomeric under near-physiological conditions but upon binding of FUSE dimerizes into a 2:1 FIR(2)-FUSE complex mediated by the RRMs. In the tripartite interaction, our analysis suggests a stepwise addition of FIR onto an activating FBP-FUSE complex to form a quaternary FIR(2)-FBP-FUSE inhibitory complex. Our quantitative characterization enhances understanding of DNA strand preference and the mechanism of the stepwise complex formation in the FUSE-FBP-FIR regulatory system.

  11. Challenge to unique researches; Unique na kenkyu eno challenge

    Energy Technology Data Exchange (ETDEWEB)

    Kato, M. [Central Research Inst. of Electric Power Industry, Tokyo (Japan)

    2000-05-10

    Mr. Takashi Tachibana, a critic, enumerates two reasons for why the U.S.A. is maintaining the high research level. One is the U.S. research institution in which foreigners can perform their actions freely. Another is the American frontier spirit that evaluates highly the challenge to new things. In the fields where the Central Research Institute of Electric Power Industry of Japan has achieved world-wide excellent accomplishments, many are the cases in which foreign researchers participate and work actively as the visiting researchers or the Science and Technology Agency (STA) fellows. In the latter case, the Central Research Institute of Electric Power Industry has introduced since a few years ago a system in which challenges can be made on unique researches that the researchers can draw their inspirations by themselves. Results are beginning to appear in several subjects, including the environmental hormone measuring method utilizing biotechnology. The 21st century requires solution of different problems in the electric power business, such as energy and environment issues. It would become increasingly important to work positively on creative and advanced researches and further strengthen the research power as the base for problem solution under the internationally opened research institution where first-class researchers inside and outside the country will get together. (NEDO)

  12. The Transcription Factor Encyclopedia

    DEFF Research Database (Denmark)

    Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I

    2012-01-01

    ABSTRACT: Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130...

  13. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and that there is substantial overlap of transcripts derived from the two strands of DNA. In protein codi...

  14. Mechanical Properties of Transcription.

    Science.gov (United States)

    Sevier, Stuart A; Levine, Herbert

    2017-06-30

    The mechanical properties of transcription have recently been shown to play a central role in gene expression. However, a full physical characterization of this central biological process is lacking. In this Letter, we introduce a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase rotation, and DNA supercoiling are coupled. The resulting framework describes the relative amount of RNA polymerase rotation and DNA supercoiling that occurs during RNA elongation. Asymptotic behavior is derived and can be used to experimentally extract unknown mechanical parameters of transcription. Mechanical limits to transcription are incorporated through the addition of a DNA supercoiling-dependent RNA polymerase velocity. This addition can lead to transcriptional stalling and resulting implications for gene expression, chromatin structure and genome organization are discussed.

  15. Negotiating Transcription as a Relative Insider: Implications for Rigor

    Directory of Open Access Journals (Sweden)

    Chad S. G. Witcher MA

    2010-06-01

    Full Text Available Despite the prevalence of the transcription of language data in qualitative research, few published studies provide insight into how the transcription process is negotiated. The purpose of this article is to describe unique challenges to quality transcription faced by a “relative insider” by reflexively exploring the research process (in particular the researcher's position and to explicate the implications for transcription quality and research rigor/trustworthiness. Inaccuracies within transcripts created by discrepancies between participants' intended meaning and the researcher's/transcriptionist's interpretation can compromise the rigor of one's findings. Therefore, when conducting research among speakers of regional dialects, researchers/transcriptionists should plan how issues related to interviewing and particularly to transcription will be negotiated.

  16. Symbols are not uniquely human.

    Science.gov (United States)

    Ribeiro, Sidarta; Loula, Angelo; de Araújo, Ivan; Gudwin, Ricardo; Queiroz, João

    2007-01-01

    Modern semiotics is a branch of logics that formally defines symbol-based communication. In recent years, the semiotic classification of signs has been invoked to support the notion that symbols are uniquely human. Here we show that alarm-calls such as those used by African vervet monkeys (Cercopithecus aethiops), logically satisfy the semiotic definition of symbol. We also show that the acquisition of vocal symbols in vervet monkeys can be successfully simulated by a computer program based on minimal semiotic and neurobiological constraints. The simulations indicate that learning depends on the tutor-predator ratio, and that apprentice-generated auditory mistakes in vocal symbol interpretation have little effect on the learning rates of apprentices (up to 80% of mistakes are tolerated). In contrast, just 10% of apprentice-generated visual mistakes in predator identification will prevent any vocal symbol to be correctly associated with a predator call in a stable manner. Tutor unreliability was also deleterious to vocal symbol learning: a mere 5% of "lying" tutors were able to completely disrupt symbol learning, invariably leading to the acquisition of incorrect associations by apprentices. Our investigation corroborates the existence of vocal symbols in a non-human species, and indicates that symbolic competence emerges spontaneously from classical associative learning mechanisms when the conditioned stimuli are self-generated, arbitrary and socially efficacious. We propose that more exclusive properties of human language, such as syntax, may derive from the evolution of higher-order domains for neural association, more removed from both the sensory input and the motor output, able to support the gradual complexification of grammatical categories into syntax.

  17. Eukaryotic transcription factors

    DEFF Research Database (Denmark)

    Staby, Lasse; O'Shea, Charlotte; Willemoës, Martin

    2017-01-01

    Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains...

  18. Transcriptional features of genomic regulatory blocks.

    Science.gov (United States)

    Akalin, Altuna; Fredman, David; Arner, Erik; Dong, Xianjun; Bryne, Jan Christian; Suzuki, Harukazu; Daub, Carsten O; Hayashizaki, Yoshihide; Lenhard, Boris

    2009-01-01

    Genomic regulatory blocks (GRBs) are chromosomal regions spanned by highly conserved non-coding elements (HCNEs), most of which serve as regulatory inputs of one target gene in the region. The target genes are most often transcription factors involved in embryonic development and differentiation. GRBs often contain extensive gene deserts, as well as additional 'bystander' genes intertwined with HCNEs but whose expression and function are unrelated to those of the target gene. The tight regulation of target genes, complex arrangement of regulatory inputs, and the differential responsiveness of genes in the region call for the examination of fundamental rules governing transcriptional activity in GRBs. Here we use extensive CAGE tag mapping of transcription start sites across different human tissues and differentiation stages combined with expression data and a number of sequence and epigenetic features to discover these rules and patterns. We show evidence that GRB target genes have properties that set them apart from their bystanders as well as other genes in the genome: longer CpG islands, a higher number and wider spacing of alternative transcription start sites, and a distinct composition of transcription factor binding sites in their core/proximal promoters. Target gene expression correlates with the acetylation state of HCNEs in the region. Additionally, target gene promoters have a distinct combination of activating and repressing histone modifications in mouse embryonic stem cell lines. GRB targets are genes with a number of unique features that are the likely cause of their ability to respond to regulatory inputs from very long distances.

  19. Squint mode SAR processing algorithms

    Science.gov (United States)

    Chang, C. Y.; Jin, M.; Curlander, J. C.

    1989-01-01

    The unique characteristics of a spaceborne SAR (synthetic aperture radar) operating in a squint mode include large range walk and large variation in the Doppler centroid as a function of range. A pointing control technique to reduce the Doppler drift and a new processing algorithm to accommodate large range walk are presented. Simulations of the new algorithm for squint angles up to 20 deg and look angles up to 44 deg for the Earth Observing System (Eos) L-band SAR configuration demonstrate that it is capable of maintaining the resolution broadening within 20 percent and the ISLR within a fraction of a decibel of the theoretical value.

  20. Transcriptional regulation of metabolism.

    Science.gov (United States)

    Desvergne, Béatrice; Michalik, Liliane; Wahli, Walter

    2006-04-01

    Our understanding of metabolism is undergoing a dramatic shift. Indeed, the efforts made towards elucidating the mechanisms controlling the major regulatory pathways are now being rewarded. At the molecular level, the crucial role of transcription factors is particularly well-illustrated by the link between alterations of their functions and the occurrence of major metabolic diseases. In addition, the possibility of manipulating the ligand-dependent activity of some of these transcription factors makes them attractive as therapeutic targets. The aim of this review is to summarize recent knowledge on the transcriptional control of metabolic homeostasis. We first review data on the transcriptional regulation of the intermediary metabolism, i.e., glucose, amino acid, lipid, and cholesterol metabolism. Then, we analyze how transcription factors integrate signals from various pathways to ensure homeostasis. One example of this coordination is the daily adaptation to the circadian fasting and feeding rhythm. This section also discusses the dysregulations causing the metabolic syndrome, which reveals the intricate nature of glucose and lipid metabolism and the role of the transcription factor PPARgamma in orchestrating this association. Finally, we discuss the molecular mechanisms underlying metabolic regulations, which provide new opportunities for treating complex metabolic disorders.

  1. Broadband high-order mode pass filter based on mode conversion.

    Science.gov (United States)

    Ahmmed, Kazi Tanvir; Chan, Hau Ping; Li, Binghui

    2017-09-15

    We report a unique concept to implement a high-order mode pass filter using mode converters. Our proposed design method implements a high-order mode pass filter of any order, uses different mode converters available, and applies to a variety of planar lightwave circuit material platforms. We fabricate a broadband fundamental mode filter device using a Mach-Zehnder interferometer and Y-junctions to demonstrate our idea. The performance of the fabricated device is demonstrated experimentally in the wavelength range of 1.530-1.565 μm (C-band). This filter exhibits a simulated extinction ratio of 37 dB with an excess loss of 0.52 dB for the first-order mode transmission.

  2. Genome organization and transcriptional regulation of respiratory syncytial virus

    Energy Technology Data Exchange (ETDEWEB)

    Dickens, L.E.

    1987-01-01

    The goal of this work was to analyze the RS virus order of transcription, gene organization and transcriptional regulation to determine other unique RS virus features and better compare RS virus to other paramyxoviruses. The number of viral promoters and the order of transcription was determined using UV inactivation experiments. RNA transcribed from UV damaged genomes was analyzed by gel electrophoresis and dot blot hybridization. These experiments revealed that RS virus has a single transcriptional promoter, as has been shown for other paramyxoviruses. Also like other paramyxoviruses, the gene encoding the major nucleocapsid protein (N) lies close to the promoter site at the 3' end of the genome while the gene presumed to encode the viral polymerase is found at the 5' end of the genome. However, unlike other paramyxoviruses, two genes coding for small, unique nonstructural proteins lie before the N gene at the 3' end of the genome.

  3. A PC based seismic data transcription system

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Sang Yong; Chung, Bu Heung; Jang, Seong Hyung [Korea Institute of Geology Mining and Materials, Taejon (Korea, Republic of)

    1997-12-01

    Old seismic data recorded on magnetic tapes is often difficult to read because of the tape sticking problem known as the `sticky syndrome`. It has to be transcribed to other suitable media using dedicated multiple systems during the whole project years. The first system requirement is the capability of reading gapless magnetic tape, which is peculiar to the old seismic data tapes. The second requirement would be the availability of storage devices with compact and huge capacity. The system must be cheap enough compared to the total cost of the data being transcribed. We introduce a PC based seismic data transcribing system. The system is equipped with an tape drive which can handle 800, 1600, 3200, and 6250 BPI densities. Well known storage devices such as 8mm Exabyte, 4mm DDS-2, and the SCSI CD recorder, are selected for the output devices. These output media should provide more durability, compactness, and portability than the original. Linux is chosen for the operating system. Unfortunately, the Linux, like other Unix systems, is subject to the limit in maximum i/o block size. The maximum block size of the SCSI tape driver is fixed to 32 KB, which is far less than the requirements in SEG-A, B, and C seismic tapes. A kernel patch is written to extend such a limit up to 2048 KB. Input and output programs are written to handle the tape data in variable block mode. A unique disk file format is designed to preserve the IBG(inter-block gap) within the disk copy. A utility program is also provided to manipulate the disk copy and to convert to SU(Seismic Unix) compatible SEG-Y file. Of the total two months of the transcription period, we spend most of the time in reading the sticky magnetic tapes. The seismic tapes had to be `baked` to dry out the moisture before reading. It took nine days to burn the all 85 diskettes. Writing two sets of 8mm Exabytes took only one day. It is considered that 8mm Exabyte can be the optimum output media for the main seismic data storage

  4. 21 CFR 12.98 - Official transcript.

    Science.gov (United States)

    2010-04-01

    ... a verbatim stenographic transcript of oral testimony and for necessary copies of the transcript. (b... the transcript of oral testimony. Corrections are permitted only for transcription errors. The...

  5. Acausality and Non-Unique Evolution in Generalized Teleparallel Gravity

    CERN Document Server

    Izumi, Keisuke; Ong, Yen Chin

    2013-01-01

    We show the existence of physical superluminal modes and acausality in the Brans-Dicke type extension of teleparallel gravity that includes F(T) gravity and teleparallel dark energy as special cases. We derive the characteristic hypersurface for the extra degrees of freedom in the theory, thereby showing that the time evolution is not unique and closed causal curves can appear. Furthermore, we present a concrete disastrous solution in Bianchi type-I spacetime, in which the anisotropy in expansion can be any function of time and thus anisotropy can emerge suddenly, a simple demonstration that the theory is physically problematic.

  6. The pluripotency transcription factor network at work in reprogramming.

    Science.gov (United States)

    Niwa, Hitoshi

    2014-10-01

    Pluripotency-associated transcription factors possess a pivotal role to maintain pluripotency in pluripotent stem cells as well as to induce pluripotency in somatic cells. They direct specific pattern of gene expression from the genome by co-operating with the genetic and epigenetic mechanisms. Recent findings revealed that these mechanisms possess unique features in pluripotent stem cells, which is different from that in somatic cells either qualitatively and quantitatively. To reprogram somatic cells, pluripotency-associated transcription factors should modulate the co-operating machineries to establish the optimal environment for their function to maintain pluripotency-associated transcription factor network. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. SNV's modes of ordering

    NARCIS (Netherlands)

    Hummel, John; Duim, van der Rene

    2016-01-01

    This article adopts an aidnographic approach to examine how internal organizational modes of ordering have influenced tourism development practices of SNV Netherlands Development Organisation (SNV). Our research revealed six modes of ordering: administration, project management, enterprising,

  8. Deciphering Transcriptional Regulation

    DEFF Research Database (Denmark)

    Valen, Eivind

    control spanning the range from completely muted to cranked up to maximum. The volume, in this case, is the production rate of proteins. This production is the result of a two step procedure: i) transcription, in which a small part of DNA from the genome (a gene) is transcribed into an RNA molecule (an mRNA...... prediction and provide tools that help investigators use these. In addition, a de novo motif discovery tool was developed that locates these patterns in DNA sequences. This compared favorably to many contemporary methods. A novel experimental method, cap-analysis of gene expression (CAGE), was recently......); and ii) translation, in which the mRNA is translated into a protein. This thesis focus on the ¿rst of these steps, transcription, and speci¿cally the initiation of this. Simpli¿ed, initiation is preceded by the binding of several proteins, known as transcription factors (TFs), to DNA. This takes place...

  9. Identification of uniquely expressed transcription factors in highly purified B-cell lymphoma samples

    DEFF Research Database (Denmark)

    Andréasson, Ulrika; Edén, Patrik; Peterson, Carsten

    2010-01-01

    to normal B-cells; assessed by immunohistochemistry or flow cytometry, by using a handful of phenotypic markers. In the last decade, diagnostic and prognostic evaluation has been facilitated by global gene expression profiling (GEP), providing a new powerful means for the classification, prediction...... of survival, and response to treatment of lymphomas. However, most GEP studies have typically been performed on whole tissue samples, containing varying degrees of tumor cell content, which results in uncertainties in data analysis. In this study, global GEP analyses were performed on highly purified, flow-cytometry...

  10. Mode and Context Effects of Measuring Household Assets

    NARCIS (Netherlands)

    van Soest, A.H.O.; Kapteyn, A.

    2009-01-01

    Differences in answers in Internet and traditional surveys can be due to selection, mode, or context effects. We exploit unique experimental data to analyze mode and context effects controlling for arbitrary selection. The Health and Retirement Study (HRS) surveys a random sample of the US 50+

  11. Applications of sliding mode control in science and engineering

    CERN Document Server

    Lien, Chang-Hua

    2017-01-01

    Gathering 20 chapters contributed by respected experts, this book reports on the latest advances in and applications of sliding mode control in science and engineering. The respective chapters address applications of sliding mode control in the broad areas of chaos theory, robotics, electrical engineering, physics, chemical engineering, memristors, mechanical engineering, environmental engineering, finance, and biology. Special emphasis has been given to papers that offer practical solutions, and which examine design and modeling involving new types of sliding mode control such as higher order sliding mode control, terminal sliding mode control, super-twisting sliding mode control, and integral sliding mode control. This book serves as a unique reference guide to sliding mode control and its recent applications for graduate students and researchers with a basic knowledge of electrical and control systems engineering.

  12. Modes of log gravity

    NARCIS (Netherlands)

    Bergshoeff, Eric A.; Hohm, Olaf; Rosseel, Jan; Townsend, Paul K.

    2011-01-01

    The physical modes of a recently proposed D-dimensional "critical gravity'', linearized about its anti-de Sitter vacuum, are investigated. All "log mode'' solutions, which we categorize as "spin-2'' or "Proca'', arise as limits of the massive spin-2 modes of the noncritical theory. The linearized

  13. The ubiquitous transcription factor CTCF promotes lineage-specific epigenomic remodeling and establishment of transcriptional networks driving cell differentiation.

    Science.gov (United States)

    Dubois-Chevalier, Julie; Staels, Bart; Lefebvre, Philippe; Eeckhoute, Jérôme

    2015-01-01

    Cell differentiation relies on tissue-specific transcription factors (TFs) that cooperate to establish unique transcriptomes and phenotypes. However, the role of ubiquitous TFs in these processes remains poorly defined. Recently, we have shown that the CCCTC-binding factor (CTCF) is required for adipocyte differentiation through epigenomic remodelling of adipose tissue-specific enhancers and transcriptional activation of Peroxisome proliferator-activated receptor gamma (PPARG), the main driver of the adipogenic program (PPARG), and its target genes. Here, we discuss how these findings, together with the recent literature, illuminate a functional role for ubiquitous TFs in lineage-determining transcriptional networks.

  14. TCP transcription factors: architectures of plant form.

    Science.gov (United States)

    Manassero, Nora G Uberti; Viola, Ivana L; Welchen, Elina; Gonzalez, Daniel H

    2013-04-01

    After its initial definition in 1999, the TCP family of transcription factors has become the focus of a multiplicity of studies related with plant development at the cellular, organ, and tissue levels. Evidence has accumulated indicating that TCP transcription factors are the main regulators of plant form and architecture and constitute a tool through which evolution shapes plant diversity. The TCP transcription factors act in a multiplicity of pathways related with cell proliferation and hormone responses. In recent years, the molecular pathways of TCP protein action and biochemical studies on their mode of interaction with DNA have begun to shed light on their mechanism of action. However, the available information is fragmented and a unifying view of TCP protein action is lacking, as well as detailed structural studies of the TCP-DNA complex. Also important, the possible role of TCP proteins as integrators of plant developmental responses to the environment has deserved little attention. In this review, we summarize the current knowledge about the structure and functions of TCP transcription factors and analyze future perspectives for the study of the role of these proteins and their use to modify plant development.

  15. Unique Physician Identification Number (UPIN) Directory

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Unique Physician Identification Number (UPIN) Directory contains selected information on physicians, doctors of Osteopathy, limited licensed practitioners and...

  16. Rhythm quantization for transcription

    NARCIS (Netherlands)

    Cemgil, A.T.; Desain, P.W.M.; Kappen, H.J.

    1999-01-01

    Automatic Music Transcription is the extraction of an acceptable notation from performed music. One important task in this problem is rhythm quantization which refers to categorization of note durations. Although quantization of a pure mechanical performance is rather straightforward, the task

  17. Actinomycin and DNA transcription.

    OpenAIRE

    Sobell, H M

    1985-01-01

    Recent advances in understanding how actinomycin binds to DNA have suggested its mechanism of action. Actinomycin binds to a premelted DNA conformation present within the transcriptional complex. This immobilizes the complex, interfering with the elongation of growing RNA chains. The model has a number of implications for understanding RNA synthesis.

  18. Actinomycin and DNA transcription.

    Science.gov (United States)

    Sobell, H M

    1985-01-01

    Recent advances in understanding how actinomycin binds to DNA have suggested its mechanism of action. Actinomycin binds to a premelted DNA conformation present within the transcriptional complex. This immobilizes the complex, interfering with the elongation of growing RNA chains. The model has a number of implications for understanding RNA synthesis. Images PMID:2410919

  19. transcriptional regulatory element

    African Journals Online (AJOL)

    ARL

    2012-06-12

    Jun 12, 2012 ... Further test of the effect of WPRE on plasmid-mediated gene expression with two therapeutic proteins showed substantial ... promoter-independent, and provide valuable information to improve vectors for efficient and stable gene expression in ... transcriptional events concerning the recombinant. mRNA.

  20. Bayesian Music Transcription

    NARCIS (Netherlands)

    Cemgil, A.T.

    2004-01-01

    Music transcription refers to extraction of a human readable and interpretable description from a recording of a music performance. The final goal is to implement a program that can automatically infer a musical notation that lists the pitch levels of notes and corresponding score positions in any

  1. Actinomycin and DNA transcription

    Energy Technology Data Exchange (ETDEWEB)

    Sobell, H.M.

    1985-08-01

    Recent advances in understanding how actinomycin binds to DNA have suggested its mechanism of action. Actinomycin binds to a premelted DNA conformation present within the transcriptional complex. This immobilizes the complex, interfering with the elongation of growing RNA chains. The model has a number of implications for understanding RNA synthesis.

  2. GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

    Science.gov (United States)

    Gubelmann, Carine; Gattiker, Alexandre; Massouras, Andreas; Hens, Korneel; David, Fabrice; Decouttere, Frederik; Rougemont, Jacques; Deplancke, Bart

    2011-01-01

    The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch. PMID:21917859

  3. Streaming tearing mode

    Science.gov (United States)

    Shigeta, M.; Sato, T.; Dasgupta, B.

    1985-01-01

    The magnetohydrodynamic stability of streaming tearing mode is investigated numerically. A bulk plasma flow parallel to the antiparallel magnetic field lines and localized in the neutral sheet excites a streaming tearing mode more strongly than the usual tearing mode, particularly for the wavelength of the order of the neutral sheet width (or smaller), which is stable for the usual tearing mode. Interestingly, examination of the eigenfunctions of the velocity perturbation and the magnetic field perturbation indicates that the streaming tearing mode carries more energy in terms of the kinetic energy rather than the magnetic energy. This suggests that the streaming tearing mode instability can be a more feasible mechanism of plasma acceleration than the usual tearing mode instability.

  4. Mode selection laser

    DEFF Research Database (Denmark)

    2014-01-01

    The invention relates to a semiconductor mode selection laser, particularly to a VCSEL laser (200) having mode selection properties. The mode selection capability of the laser is achieved by configuring one of the reflectors (15,51) in the resonance cavity so that a reflectivity of the reflector...... (15) varies spatially in one dimension or two dimensions. Accordingly, the reflector (15) with spatially varying reflectivity is part both of the resonance cavity and the mode selection functionality of the laser. A plurality of the lasers configured with different mode selectors, i.e. different...... spatial reflector variations, may be combined to generate a laser beam containing a plurality of orthogonal modes. The laser beam may be injected into a few- mode optical fiber, e.g. for the purpose of optical communication. The VCSEL may have intra-cavity contacts (31,37) and a Tunnel junction (33...

  5. Metric spaces with unique pretangent spaces

    OpenAIRE

    Dovgoshey, Oleksiy; Abdullayev, Fahreddin; Kuchukaslan, Mehmet

    2009-01-01

    We find necessary and sufficient conditions under which an arbitrary metric space $X$ has a unique pretangent space at the marked point $a\\in X$. Key words: Metric spaces; Tangent spaces to metric spaces; Uniqueness of tangent metric spaces; Tangent space to the Cantor set.

  6. Uniqueness of time-independent electromagnetic fields

    DEFF Research Database (Denmark)

    Karlsson, Per W.

    1974-01-01

    As a comment on a recent paper by Steele, a more general uniqueness theorem for time-independent fields is mentioned. ©1974 American Institute of Physics......As a comment on a recent paper by Steele, a more general uniqueness theorem for time-independent fields is mentioned. ©1974 American Institute of Physics...

  7. A note on uniquely (nil clean ring

    Directory of Open Access Journals (Sweden)

    Shervin Sahebi

    2014-05-01

    Full Text Available A ring $R$ is uniquely (nil clean in case for any $a\\in R$‎ ‎there exists a uniquely idempotent $e\\in R$ such that $a-e$ is‎ ‎invertible (nilpotent‎. ‎Let‎ ‎$C=\\small\\left(‎‎\\begin{array}{cc}‎‎A & V \\\\‎ ‎W & B‎‎\\end{array}‎‎\\right$‎ ‎be the Morita Context ring‎. ‎We determine conditions under which the rings $A‎, ‎B$‎ ‎are uniquely (nil clean‎. ‎Moreover we show that the center of a uniquely (nil‎‎clean ring is uniquely (nil clean.

  8. Surface Modes of Coherent Spinodal Decomposition

    Science.gov (United States)

    Tang, Ming; Karma, Alain

    2012-06-01

    We use linear stability theory and numerical simulations to show that spontaneous phase separation in elastically coherent solids is fundamentally altered by the presence of free surfaces. Because of misfit stress relaxation near surfaces, phase separation is mediated by unique surface modes of spinodal decomposition that have faster kinetics than bulk modes and are unstable even when spinodal decomposition is suppressed in the bulk. Consequently, in the presence of free surfaces, the limit of metastability of supersaturated solid solutions of crystalline materials is shifted from the coherent to chemical spinodal.

  9. Genome-wide transcription analyses in rice using tiling microarrays

    DEFF Research Database (Denmark)

    Li, Lei; Wang, Xiangfeng; Stolc, Viktor

    2006-01-01

    . We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions...

  10. DNA Topoisomerases in Transcription

    DEFF Research Database (Denmark)

    Rødgaard, Morten Terpager

    2015-01-01

    This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most of the ex......This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most...... topoisomerase-DNA cleavage complex. The second study is an investigation of how topoisomerases influence gene regulation by keeping the genome in an optimal topological state....

  11. Spanish dialects: phonetic transcription

    OpenAIRE

    Moreno Bilbao, M. Asunción; Mariño Acebal, José Bernardo

    1998-01-01

    It is well known that canonical Spanish, the dialectal variant `central' of Spain, so called Castilian, can be transcribed by rules. This paper deals with the automatic grapheme to phoneme transcription rules in several Spanish dialects from Latin America. Spanish is a language spoken by more than 300 million people, has an important geographical dispersion compared among other languages and has been historically influenced by many native languages. In this paper authors expand the Castilian ...

  12. Tiny individuals attached to a new Silurian arthropod suggest a unique mode of brood care

    Science.gov (United States)

    Briggs, Derek E. G.; Siveter, Derek J.; Siveter, David J.; Sutton, Mark D.

    2016-04-01

    The ˜430-My-old Herefordshire, United Kingdom, Lagerstätte has yielded a diversity of remarkably preserved invertebrates, many of which provide fundamental insights into the evolutionary history and ecology of particular taxa. Here we report a new arthropod with 10 tiny arthropods tethered to its tergites by long individual threads. The head of the host, which is covered by a shield that projects anteriorly, bears a long stout uniramous antenna and a chelate limb followed by two biramous appendages. The trunk comprises 11 segments, all bearing limbs and covered by tergites with long slender lateral spines. A short telson bears long parallel cerci. Our phylogenetic analysis resolves the new arthropod as a stem-group mandibulate. The evidence suggests that the tethered individuals are juveniles and the association represents a complex brooding behavior. Alternative possibilities—that the tethered individuals represent a different epizoic or parasitic arthropod—appear less likely.

  13. MtrA of the sodium ion pumping methyltransferase binds cobalamin in a unique mode.

    Science.gov (United States)

    Wagner, Tristan; Ermler, Ulrich; Shima, Seigo

    2016-06-21

    In the three domains of life, vitamin B12 (cobalamin) is primarily used in methyltransferase and isomerase reactions. The methyltransferase complex MtrA-H of methanogenic archaea has a key function in energy conservation by catalysing the methyl transfer from methyl-tetrahydromethanopterin to coenzyme M and its coupling with sodium-ion translocation. The cobalamin-binding subunit MtrA is not homologous to any known B12-binding proteins and is proposed as the motor of the sodium-ion pump. Here, we present crystal structures of the soluble domain of the membrane-associated MtrA from Methanocaldococcus jannaschii and the cytoplasmic MtrA homologue/cobalamin complex from Methanothermus fervidus. The MtrA fold corresponds to the Rossmann-type α/β fold, which is also found in many cobalamin-containing proteins. Surprisingly, the cobalamin-binding site of MtrA differed greatly from all the other cobalamin-binding sites. Nevertheless, the hydrogen-bond linkage at the lower axial-ligand site of cobalt was equivalently constructed to that found in other methyltransferases and mutases. A distinct polypeptide segment fixed through the hydrogen-bond linkage in the relaxed Co(III) state might be involved in propagating the energy released upon corrinoid demethylation to the sodium-translocation site by a conformational change.

  14. Dual-Mode Combustor

    Science.gov (United States)

    Trefny, Charles J (Inventor); Dippold, Vance F (Inventor)

    2013-01-01

    A new dual-mode ramjet combustor used for operation over a wide flight Mach number range is described. Subsonic combustion mode is usable to lower flight Mach numbers than current dual-mode scramjets. High speed mode is characterized by supersonic combustion in a free-jet that traverses the subsonic combustion chamber to a variable nozzle throat. Although a variable combustor exit aperture is required, the need for fuel staging to accommodate the combustion process is eliminated. Local heating from shock-boundary-layer interactions on combustor walls is also eliminated.

  15. Mechanochemical ATPases and transcriptional activation

    National Research Council Canada - National Science Library

    Zhang, X; Chaney, M; Wigneshweraraj, Siva R; Schumacher, J; Bordes, P; Cannon, W; Buck, M

    2002-01-01

    ... transcription from other ATP‐independent activation mechanisms that rely on the recruitment of RNAP by transcription factors. As described below, productive interactions between σ 54 and its a...

  16. The Uniqueness of -Matrix Graph Invariants

    Science.gov (United States)

    Dehmer, Matthias; Shi, Yongtang

    2014-01-01

    In this paper, we examine the uniqueness (discrimination power) of a newly proposed graph invariant based on the matrix defined by Randić et al. In order to do so, we use exhaustively generated graphs instead of special graph classes such as trees only. Using these graph classes allow us to generalize the findings towards complex networks as they usually do not possess any structural constraints. We obtain that the uniqueness of this newly proposed graph invariant is approximately as low as the uniqueness of the Balaban index on exhaustively generated (general) graphs. PMID:24392099

  17. Transcriptional networks controlling adipocyte differentiation

    DEFF Research Database (Denmark)

    Siersbæk, R; Mandrup, Susanne

    2011-01-01

    Adipocyte differentiation is regulated by a complex cascade of signals that drive the transcriptional reprogramming of the fibroblastic precursors. Genome-wide analyses of chromatin accessibility and binding of adipogenic transcription factors make it possible to generate "snapshots" of the trans......Adipocyte differentiation is regulated by a complex cascade of signals that drive the transcriptional reprogramming of the fibroblastic precursors. Genome-wide analyses of chromatin accessibility and binding of adipogenic transcription factors make it possible to generate "snapshots...

  18. Transcription and processing of mitochondrial RNA in the human pathogen Acanthamoeba castellanii.

    Science.gov (United States)

    Accari, Jessica; Barth, Christian

    2015-07-01

    The size, structure, gene content and organisation of mitochondrial genomes can be highly diverse especially amongst the protists. We investigated the transcription and processing of the mitochondrial genome of the opportunistic pathogen Acanthamoeba castellanii and here we present a detailed transcription map of the 41.6 kb genome that encodes 33 proteins, 16 tRNAs and 2 rRNAs. Northern hybridisation studies identified six major polycistronic transcripts, most of which are co-transcriptionally processed into smaller mono-, di- and tricistronic RNAs. The maturation of the polycistronic transcripts is likely to involve endonucleolytic cleavage where tRNAs serve as processing signals. Reverse transcription polymerase chain reactions across the intervening regions between the six major polycistronic transcripts suggest that these transcripts were once part of an even larger transcript. Our findings indicate that the mitochondrial genome of A. castellanii is transcribed from only one or two promoters, very similar to the mode of transcription in the mitochondria of its close relative Dictyostelium discoideum, where transcription is known to occur from only a single transcription initiation site. Transcription initiation from a minimal number of promoters despite a large genome size may be an emerging trend in the mitochondria of protists. Copyright © 2015. Published by Elsevier B.V.

  19. Unique Ethical Dilemmas in Counselor Training.

    Science.gov (United States)

    Patrick, Kathy D.

    1989-01-01

    Proposes that when counselor candidates are allowed to participate as clients in counselor-training laboratories, an indirect dual relationship is established, which may create unique ethical conflicts. Recommends informed consent as a possible solution. (Author/TE)

  20. Heart Failure: Unique to Older Adults

    Science.gov (United States)

    ... our e-newsletter! Aging & Health A to Z Heart Failure Unique to Older Adults This section provides information ... or maintain quality of life. Urinary Incontinence and Heart Failure If you have heart failure, you may experience ...

  1. A unique transformation from ordinary differential equations to reaction networks.

    Directory of Open Access Journals (Sweden)

    Sylvain Soliman

    Full Text Available Many models in Systems Biology are described as a system of Ordinary Differential Equations, which allows for transient, steady-state or bifurcation analysis when kinetic information is available. Complementary structure-related qualitative analysis techniques have become increasingly popular in recent years, like qualitative model checking or pathway analysis (elementary modes, invariants, flux balance analysis, graph-based analyses, chemical organization theory, etc.. They do not rely on kinetic information but require a well-defined structure as stochastic analysis techniques equally do. In this article, we look into the structure inference problem for a model described by a system of Ordinary Differential Equations and provide conditions for the uniqueness of its solution. We describe a method to extract a structured reaction network model, represented as a bipartite multigraph, for example, a continuous Petri net (CPN, from a system of Ordinary Differential Equations (ODEs. A CPN uniquely defines an ODE, and each ODE can be transformed into a CPN. However, it is not obvious under which conditions the transformation of an ODE into a CPN is unique, that is, when a given ODE defines exactly one CPN. We provide biochemically relevant sufficient conditions under which the derived structure is unique and counterexamples showing the necessity of each condition. Our method is implemented and available; we illustrate it on some signal transduction models from the BioModels database. A prototype implementation of the method is made available to modellers at http://contraintes.inria.fr/~soliman/ode2pn.html, and the data mentioned in the "Results" section at http://contraintes.inria.fr/~soliman/ode2pn_data/. Our results yield a new recommendation for the import/export feature of tools supporting the SBML exchange format.

  2. Modularity, comparative cognition and human uniqueness

    Science.gov (United States)

    Shettleworth, Sara J.

    2012-01-01

    Darwin's claim ‘that the difference in mind between man and the higher animals … is certainly one of degree and not of kind’ is at the core of the comparative study of cognition. Recent research provides unprecedented support for Darwin's claim as well as new reasons to question it, stimulating new theories of human cognitive uniqueness. This article compares and evaluates approaches to such theories. Some prominent theories propose sweeping domain-general characterizations of the difference in cognitive capabilities and/or mechanisms between adult humans and other animals. Dual-process theories for some cognitive domains propose that adult human cognition shares simple basic processes with that of other animals while additionally including slower-developing and more explicit uniquely human processes. These theories are consistent with a modular account of cognition and the ‘core knowledge’ account of children's cognitive development. A complementary proposal is that human infants have unique social and/or cognitive adaptations for uniquely human learning. A view of human cognitive architecture as a mosaic of unique and species-general modular and domain-general processes together with a focus on uniquely human developmental mechanisms is consistent with modern evolutionary-developmental biology and suggests new questions for comparative research. PMID:22927578

  3. An empirical test of schema mode conceptualizations in personality disorders.

    Science.gov (United States)

    Lobbestael, Jill; Van Vreeswijk, Michiel F; Arntz, Arnoud

    2008-07-01

    Although the use of schema modes in schema-focused therapy (SFT) has been very popular since its introduction, Young's schema mode concept remained largely empirically untested. In order to provide insight into the mode conceptualization of personality disorders (PDs), the current study assessed the relationships between 14 schema modes and all PDs. Relationships between dimensional PD scores and self-reported mode scores were tested in a mixed study group of 489 participants, consisting of axis I and axis II patients, and non-patients. Psychopathology was assessed by means of the Structured Clinical Interview for DSM-IV axis I and axis II disorders (SCID I and SCID II) or the Structural Interview for DSM-IV Personality Disorders (SIDP-IV), and modes were assessed by the Schema Mode Inventory. Kendall's partial tau coefficients, controlling each PD-mode correlation for all other PD scores, indicated unique mode profiles for all PDs and corroborated most of the hypothesized PD-mode correlations, supporting the construct validity of the mode model. Nevertheless, the high number of correlations found for some PDs raises concerns about the specificity of the mode model. Implications for both research and therapy are discussed.

  4. Microbubble Surface Modes

    NARCIS (Netherlands)

    Versluis, Michel; Palanchon, P.; Goertz, D.; van der Meer, S.M.; Chin, C.T.; Lohse, Detlef; de Jong, N.

    2004-01-01

    We have investigated surface vibrations generated by ultrasound excitation of individual unencapsulated micron-sized bubbles. In addition, we present surface modes (n=2 and 3) observed for phospholipid-coated ultrasound contrast agents excited through excitation of radial modes at frequencies

  5. Mode decomposition evolution equations.

    Science.gov (United States)

    Wang, Yang; Wei, Guo-Wei; Yang, Siyang

    2012-03-01

    Partial differential equation (PDE) based methods have become some of the most powerful tools for exploring the fundamental problems in signal processing, image processing, computer vision, machine vision and artificial intelligence in the past two decades. The advantages of PDE based approaches are that they can be made fully automatic, robust for the analysis of images, videos and high dimensional data. A fundamental question is whether one can use PDEs to perform all the basic tasks in the image processing. If one can devise PDEs to perform full-scale mode decomposition for signals and images, the modes thus generated would be very useful for secondary processing to meet the needs in various types of signal and image processing. Despite of great progress in PDE based image analysis in the past two decades, the basic roles of PDEs in image/signal analysis are only limited to PDE based low-pass filters, and their applications to noise removal, edge detection, segmentation, etc. At present, it is not clear how to construct PDE based methods for full-scale mode decomposition. The above-mentioned limitation of most current PDE based image/signal processing methods is addressed in the proposed work, in which we introduce a family of mode decomposition evolution equations (MoDEEs) for a vast variety of applications. The MoDEEs are constructed as an extension of a PDE based high-pass filter (Europhys. Lett., 59(6): 814, 2002) by using arbitrarily high order PDE based low-pass filters introduced by Wei (IEEE Signal Process. Lett., 6(7): 165, 1999). The use of arbitrarily high order PDEs is essential to the frequency localization in the mode decomposition. Similar to the wavelet transform, the present MoDEEs have a controllable time-frequency localization and allow a perfect reconstruction of the original function. Therefore, the MoDEE operation is also called a PDE transform. However, modes generated from the present approach are in the spatial or time domain and can be

  6. Shaft mode shape demonstration

    Science.gov (United States)

    Grissom, R.

    1985-01-01

    The dynamic response of a rotating machine is directly influenced by its geometric configuration and all aspects of the rotor construction. These determine two significant parameters, mass distribution and stiffness, which yield a spectrum of natural frequencies and mode shapes. The mode shapes can be presented as snapshots of the characteristic amplitude/phase reponse patterns of the shaft, due to the major forcing function of unbalance, at different rotative speeds. To demonstrate the three shaft mode shapes of the rotor rig using the Shaft Mode Demonstrator and oscilloscopes. The synchronous (1X) amplitude and phase of the rotor vibration in the vertical direction from several points along the shaft is displayed on corresponding points of the demonstrator. Unfiltered vibration from vertical and horizontal probe pairs is displayed on the oscilloscopes in orbit format for a dynamic presentation of the mode shape.

  7. Higher Order Mode Fibers

    DEFF Research Database (Denmark)

    Israelsen, Stine Møller

    This PhD thesis considers higher order modes (HOMs) in optical fibers. That includes their excitation and characteristics. Within the last decades, HOMs have been applied both for space multiplexing in optical communications, group velocity dispersion management and sensing among others....... The research presented in this thesis falls in three parts. In the first part, a first time demonstration of the break of the azimuthal symmetry of the Bessel-like LP0X modes is presented. This effect, known as the bowtie effect, causes the mode to have an azimuthal dependence as well as a quasi......-radial polarization as opposed to the linear polarization of the LP0X modes. The effect is investigated numerically in a double cladding fiber with an outer aircladding using a full vectorial modesolver. Experimentally, the bowtie modes are excited using a long period grating and their free space characteristics...

  8. Mode demultiplexer using angularly multiplexed volume holograms.

    Science.gov (United States)

    Wakayama, Yuta; Okamoto, Atsushi; Kawabata, Kento; Tomita, Akihisa; Sato, Kunihiro

    2013-05-20

    This study proposes a volume holographic demultiplexer (VHDM) for extracting the spatial modes excited in a multimode fiber. A unique feature of the demultiplexer is that it can separate a number of multiplexed modes output from a fiber in different directions by using multi-recorded holograms without beam splitters, which results in a simple configuration as compared with that using phase plates instead of holograms. In this study, an experiment is conducted to demonstrate the basic operations for three LP mode groups to confirm the performance of the proposed VHDM and to estimate the signal-to-crosstalk noise ratio (SNR). As a result, an SNR of greater than 20 dB is obtained.

  9. Accumulation of Transcripts Abundance after Barley Inoculation with Cochliobolus sativus

    Directory of Open Access Journals (Sweden)

    Mohammad Imad Eddin Arabi

    2015-03-01

    Full Text Available Spot blotch caused by the hemibiotrophic pathogen Cochliobolus sativus has been the major yield-reducing factor for barley production during the last decade. Monitoring transcriptional reorganization triggered in response to this fungus is an essential first step for the functional analysis of genes involved in the process. To characterize the defense responses initiated by barley resistant and susceptible cultivars, a survey of transcript abundance at early time points of C. sativus inoculation was conducted. A notable number of transcripts exhibiting significant differential accumulations in the resistant and susceptible cultivars were detected compared to the non-inoculated controls. At the p-value of 0.0001, transcripts were divided into three general categories; defense, regulatory and unknown function, and the resistant cultivar had the greatest number of common transcripts at different time points. Quantities of differentially accumulated gene transcripts in both cultivars were identified at 24 h post infection, the approximate time when the pathogen changes trophic lifestyles. The unique and common accumulated transcripts might be of considerable interest for enhancing effective resistance to C. sativus.

  10. Child writers’ construction and reconstruction of single sentences and construction of multi-sentence texts: contributions of syntax and transcription to translation

    Science.gov (United States)

    Berninger, Virginia W.; Nagy, William; Beers, Scott

    2011-01-01

    Children in grades one to four completed two sentence construction tasks: (a) Write one complete sentence about a topic prompt (sentence integrity, Study 1); and (b) Integrate two sentences into one complete sentence without changing meaning (sentence combining, Study 2). Most, but not all, children in first through fourth grade could write just one sentence. The sentence integrity task was not correlated with sentence combining until fourth grade, when in multiple regression, sentence integrity explained unique variance in sentence combining, along with spelling. Word-level skills (morphology in first and spelling in second through fourth grade) consistently explained unique variance in sentence combining. Thus, many beginning writers have syntactic knowledge of what constitutes a complete sentence, but not until fourth grade do both syntax and transcription contribute uniquely to flexible translation of ideas into the syntax of a written sentence. In Study 3, eleven syntactic categories were identified in single- and multi- sentence composing from second to fifth grade. Complex clauses (independent plus subordinate) occurred more often on single-sentence composing, but single independent clauses occurred more often on multi-sentence composing. For multi-sentence text, more single, independent clauses were produced by pen than keyboard in grades 3 to 7. The most frequent category of complex clauses in multi-sentence texts varied with genre (relative for essays and subordinate for narratives). Thus, in addition to syntax-level sentence construction and word-level transcription, amount of translation (number of sentences), mode of transcription, and genre for multiple sentence text also influence translation of ideas into written language of child writers. Results of these studies employing descriptive linguistic analyses are discussed in reference to cognitive theory of writing development. PMID:21383865

  11. Child writers' construction and reconstruction of single sentences and construction of multi-sentence texts: contributions of syntax and transcription to translation.

    Science.gov (United States)

    Berninger, Virginia W; Nagy, William; Beers, Scott

    2011-02-01

    Children in grades one to four completed two sentence construction tasks: (a) Write one complete sentence about a topic prompt (sentence integrity, Study 1); and (b) Integrate two sentences into one complete sentence without changing meaning (sentence combining, Study 2). Most, but not all, children in first through fourth grade could write just one sentence. The sentence integrity task was not correlated with sentence combining until fourth grade, when in multiple regression, sentence integrity explained unique variance in sentence combining, along with spelling. Word-level skills (morphology in first and spelling in second through fourth grade) consistently explained unique variance in sentence combining. Thus, many beginning writers have syntactic knowledge of what constitutes a complete sentence, but not until fourth grade do both syntax and transcription contribute uniquely to flexible translation of ideas into the syntax of a written sentence. In Study 3, eleven syntactic categories were identified in single- and multi- sentence composing from second to fifth grade. Complex clauses (independent plus subordinate) occurred more often on single-sentence composing, but single independent clauses occurred more often on multi-sentence composing. For multi-sentence text, more single, independent clauses were produced by pen than keyboard in grades 3 to 7. The most frequent category of complex clauses in multi-sentence texts varied with genre (relative for essays and subordinate for narratives). Thus, in addition to syntax-level sentence construction and word-level transcription, amount of translation (number of sentences), mode of transcription, and genre for multiple sentence text also influence translation of ideas into written language of child writers. Results of these studies employing descriptive linguistic analyses are discussed in reference to cognitive theory of writing development.

  12. Mode choice model parameters estimation

    OpenAIRE

    Strnad, Irena

    2010-01-01

    The present work focuses on parameter estimation of two mode choice models: multinomial logit and EVA 2 model, where four different modes and five different trip purposes are taken into account. Mode choice model discusses the behavioral aspect of mode choice making and enables its application to a traffic model. Mode choice model includes mode choice affecting trip factors by using each mode and their relative importance to choice made. When trip factor values are known, it...

  13. Surface modes in physics

    CERN Document Server

    Sernelius, Bo E

    2011-01-01

    Electromagnetic surface modes are present at all surfaces and interfaces between material of different dielectric properties. These modes have very important effects on numerous physical quantities: adhesion, capillary force, step formation and crystal growth, the Casimir effect etc. They cause surface tension and wetting and they give rise to forces which are important e.g. for the stability of colloids.This book is a useful and elegant approach to the topic, showing how the concept of electromagnetic modes can be developed as a unifying theme for a range of condensed matter physics. The

  14. Novel modes of RNA editing in mitochondria.

    Science.gov (United States)

    Moreira, Sandrine; Valach, Matus; Aoulad-Aissa, Mohamed; Otto, Christian; Burger, Gertraud

    2016-06-02

    Gene structure and expression in diplonemid mitochondria are unparalleled. Genes are fragmented in pieces (modules) that are separately transcribed, followed by the joining of module transcripts to contiguous RNAs. Some instances of unique uridine insertion RNA editing at module boundaries were noted, but the extent and potential occurrence of other editing types remained unknown. Comparative analysis of deep transcriptome and genome data from Diplonema papillatum mitochondria reveals ∼220 post-transcriptional insertions of uridines, but no insertions of other nucleotides nor deletions. In addition, we detect in total 114 substitutions of cytosine by uridine and adenosine by inosine, amassed into unusually compact clusters. Inosines in transcripts were confirmed experimentally. This is the first report of adenosine-to-inosine editing of mRNAs and ribosomal RNAs in mitochondria. In mRNAs, editing causes mostly amino-acid additions and non-synonymous substitutions; in ribosomal RNAs, it permits formation of canonical secondary structures. Two extensively edited transcripts were compared across four diplonemids. The pattern of uridine-insertion editing is strictly conserved, whereas substitution editing has diverged dramatically, but still rendering diplonemid proteins more similar to other eukaryotic orthologs. We posit that RNA editing not only compensates but also sustains, or even accelerates, ultra-rapid evolution of genome structure and sequence in diplonemid mitochondria. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Is there a unique nursing ethic?

    Science.gov (United States)

    Volker, Deborah Lowe

    2003-07-01

    There is no agreement in the nursing literature as to the meaning of the term, nursing ethics. Proposed definitions refer to nurses' moral decision-making and behaviors, ethical conflicts, and analysis of ethical issues that arise within nurses' practice. Presumably, a distinct nursing ethic should address unique theories, standards, and inquiry into what comprises nurses' ethical behavior and study of how nurses actually behave and reason about ethical issues. The purpose of this column is to synthesize the dialogue regarding the potential existence of a unique nursing ethic, and to propose that such an ethic has yet to emerge.

  16. Pulsations Beneath the Winds: Unique Precise Photometry from MOST

    Science.gov (United States)

    Moffat, A. F. J.; Marchenko, S. V.; Lefèvre, L.; Chené, A.-N.; St-Louis, N.; Zhilyaev, B. E.; Aerts, C.; Saio, H.; Walker, G. A. H.; Matthews, J. M.; Kuschnig, R.; Cameron, C.; Rowe, J. F.; Guenther, D. B.; Rucinski, S. M.; Sasselov, D.; Weiss, W. W.

    2008-06-01

    It has now been three years since the first Canadian space telescope MOST (Microvariability and Oscillations of STars) continues to make its unique mark in stellar asteroseismology, exoplanetology and other studies of high-precision photometric variability. Among massive stars, three OB, three later-type B stars and two Wolf-Rayet stars have been studied so far with unprecedented precision and time coverage in samples with of order 100 000 data points collected without a break over several weeks. Of particular interest are: a first clear pulsation period of P = 9.8h has been found in a WR star (WR123, WN8); no short periods between a minute and an hour have been seen in either of the two WR stars observed (WR123; WR103, WC9d) to the 0.2 mmag level, although these stars both exhibit numerous short-lived oscillations mostly with periods longer than a day, which must be related to stellar pulsations; g-mode pulsations were detected in a blue supergiant; non-radial g-mode pulsations may be excited in all classical Be stars and thus may play a pivotal rôle in the Be-star mass-ejection process. A review of all the massive-star results to date from MOST and their implications are presented.

  17. Mode Gaussian beam tracing

    Science.gov (United States)

    Trofimov, M. Yu.; Zakharenko, A. D.; Kozitskiy, S. B.

    2016-10-01

    A mode parabolic equation in the ray centered coordinates for 3D underwater sound propagation is developed. The Gaussian beam tracing in this case is constructed. The test calculations are carried out for the ASA wedge benchmark and proved an excellent agreement with the source images method in the case of cross-slope propagation. But in the cases of wave propagation at some angles to the cross-slope direction an account of mode interaction becomes necessary.

  18. Transcriptional Regulation in Haematopoiesis:

    DEFF Research Database (Denmark)

    Lauridsen, Felicia K B

    in transplantation studies. Consistent with this, transcriptome profiling revealed very low expression of cell cycle genes in these reporter-dim HSCs. Sequencing of >1200 single HSCs confirmed that the main source of transcriptional heterogeneity was the cell cycle. It also revealed a low-level expression...... of distinct lineage affiliated genes in the otherwise highly purified HSCs. Taken together, these studies demonstrate the use of our model as a tool for isolating superior HSCs, and show that low-level expression of mature lineage markers is inherent in the highly purified stem cell compartment. In the second...... study we profiled the global DNA binding sites of two major players in myeloid differentiation – PU.1 and C/EBPα - together with histone modifications in four successive stages of myeloid differentiation (LSK, preGM, GMP and mature granulocytes). Consistent with their haematopoietic expression patterns...

  19. Euglena Transcript Processing.

    Science.gov (United States)

    McWatters, David C; Russell, Anthony G

    2017-01-01

    RNA transcript processing is an important stage in the gene expression pathway of all organisms and is subject to various mechanisms of control that influence the final levels of gene products. RNA processing involves events such as nuclease-mediated cleavage, removal of intervening sequences referred to as introns and modifications to RNA structure (nucleoside modification and editing). In Euglena, RNA transcript processing was initially examined in chloroplasts because of historical interest in the secondary endosymbiotic origin of this organelle in this organism. More recent efforts to examine mitochondrial genome structure and RNA maturation have been stimulated by the discovery of unusual processing pathways in other Euglenozoans such as kinetoplastids and diplonemids. Eukaryotes containing large genomes are now known to typically contain large collections of introns and regulatory RNAs involved in RNA processing events, and Euglena gracilis in particular has a relatively large genome for a protist. Studies examining the structure of nuclear genes and the mechanisms involved in nuclear RNA processing have revealed that indeed Euglena contains large numbers of introns in the limited set of genes so far examined and also possesses large numbers of specific classes of regulatory and processing RNAs, such as small nucleolar RNAs (snoRNAs). Most interestingly, these studies have also revealed that Euglena possesses novel processing pathways generating highly fragmented cytosolic ribosomal RNAs and subunits and non-conventional intron classes removed by unknown splicing mechanisms. This unexpected diversity in RNA processing pathways emphasizes the importance of identifying the components involved in these processing mechanisms and their evolutionary emergence in Euglena species.

  20. Unique Juxtaposition of Onchocerca Nodule and Tumoural ...

    African Journals Online (AJOL)

    A 45-year-old Igbo man presented with a subcutaneous nodule in the lateral aspect of his left thigh. Following its excision, the lesion turned out on microscopy to be due to the unique juxtaposition of onchocerca nodule and tumoural calcinosis. Such selectivity in disease localization is deemed to be worthy of documentation ...

  1. Esperanto: A Unique Model for General Linguistics.

    Science.gov (United States)

    Dulichenko, Aleksandr D.

    1988-01-01

    Esperanto presents a unique model for linguistic research by allowing the study of language development from project to fully functioning language. Esperanto provides insight into the growth of polysemy and redundancy, as well as into language universals and the phenomenon of social control. (Author/CB)

  2. LCA – Unique and Controversial Case Studies

    Science.gov (United States)

    This session will focus on case studies and applications that have a unique or controversial aspect. Some of the most recent topics that seem to have significant interest include: LCA-based product declarations, LCA-based standards, LCA-based labels, alternative energy, agricul...

  3. Asima Chatterjee: A Unique Natural Products Chemist

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 1. Asima Chatterjee: A Unique Natural Products Chemist. Asish De. General Article Volume 20 Issue 1 January 2015 pp 6-22. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/020/01/0006-0022 ...

  4. The Unique School Environment of Rural Children.

    Science.gov (United States)

    Dodendorf, Diane M.

    Recorded observations, camera work, conversations with 19 children in grades K-4 in a Nebraska 2-room school house, and interviews with the teacher were techniques used to assess the advantages and disadvantages of the small rural school environment and its impact on children. Five attributes were found to be significant and unique small school…

  5. Unique characteristics of Geneva apple rootstocks

    Science.gov (United States)

    The Geneva® apple rootstock breeding program has been operating since the early 1970’s. It is a unique program in that it had access to important germplasm resources that later became the USDA ARS apple collection in Geneva, NY. This genetic diversity allowed for the achievement of one of the proj...

  6. Unraveling the evolution of uniquely human cognition.

    Science.gov (United States)

    MacLean, Evan L

    2016-06-07

    A satisfactory account of human cognitive evolution will explain not only the psychological mechanisms that make our species unique, but also how, when, and why these traits evolved. To date, researchers have made substantial progress toward defining uniquely human aspects of cognition, but considerably less effort has been devoted to questions about the evolutionary processes through which these traits have arisen. In this article, I aim to link these complementary aims by synthesizing recent advances in our understanding of what makes human cognition unique, with theory and data regarding the processes of cognitive evolution. I review evidence that uniquely human cognition depends on synergism between both representational and motivational factors and is unlikely to be accounted for by changes to any singular cognitive system. I argue that, whereas no nonhuman animal possesses the full constellation of traits that define the human mind, homologies and analogies of critical aspects of human psychology can be found in diverse nonhuman taxa. I suggest that phylogenetic approaches to the study of animal cognition-which can address questions about the selective pressures and proximate mechanisms driving cognitive change-have the potential to yield important insights regarding the processes through which the human cognitive phenotype evolved.

  7. Weeping dragon, a unique ornamenal citrus

    Science.gov (United States)

    ‘Weeping Dragon’ is a new ornamental citrus cultivar developed by intercrossing of two unusual and unique citrus types, Poncirus trifoliata cultivated variety (cv.) Flying Dragon, and Citrus sinensis cv. ‘Cipo’. This new hybrid cultivar combines strongly contorted and weeping growth traits in a smal...

  8. The symbolic uniqueness of wilderness participation | Greffrath ...

    African Journals Online (AJOL)

    Through restoration, physical self, primitiveness, humility, timelessness, solitude, privacy, freedom of choice, personal self and spiritual upliftment, this study aims at determining whether wilderness can be experienced as symbolically unique and whether this natural world can be considered a necessity for achieving ...

  9. Is There a Unique Black Personality?

    Science.gov (United States)

    Mosby, Doris P.

    This article reviews research from the 1940's, 1950's and 1960's on the effects of discrimination on blacks. Data from these studies indicate that adverse cultural restrictions have fostered a unique and distinctive black personality. Among traits identified are: a negative or inferior self-image, pessimism about the future, attachment to the…

  10. In a unique position or squeezed out?

    DEFF Research Database (Denmark)

    Hølge-Hazelton, Bibi; Christensen, Inge

    2009-01-01

    language, they experience that their patients disappear, they are seldom involved, and they lack knowledge. CONCLUSIONS: GPs have few experiences with YA cancer patients, but they have a potentially unique role in general primary cancer care if they develop their vocational vocabulary, relate more...

  11. Marketing the Uniqueness of Small Towns. Revised.

    Science.gov (United States)

    Dunn, Douglas; Hogg, David H.

    The key to marketing a town is determining and promoting the town's "differential advantage" or uniqueness that would make people want to visit or live there. Exercises to help communities gain important insights into the town's competitive edge include a brainstorming session with knowledgeable community members, a visitor…

  12. The Escherichia coli modE gene: effect of modE mutations on molybdate dependent modA expression.

    Science.gov (United States)

    McNicholas, P M; Chiang, R C; Gunsalus, R P

    1996-11-15

    The Escherichia coli modABCD operon, which encodes a high-affinity molybdate uptake system, is transcriptionally regulated in response to molybdate availability by ModE. Here we describe a highly effective enrichment protocol, applicable to any gene with a repressor role, and establish its application in the isolation of transposon mutations in modE. In addition we show that disruption of the ModE C-terminus abolishes derepression in the absence of molybdate, implying this region of ModE controls the repressor activity. Finally, a mutational analysis of a proposed molybdate binding motif indicates that this motif does not function in regulating the repressor activity of ModE.

  13. Transcriptional regulation of the uncoupling protein-1 gene.

    Science.gov (United States)

    Villarroya, Francesc; Peyrou, Marion; Giralt, Marta

    2017-03-01

    Regulated transcription of the uncoupling protein-1 (UCP1) gene, and subsequent UCP1 protein synthesis, is a hallmark of the acquisition of the differentiated, thermogenically competent status of brown and beige/brite adipocytes, as well as of the responsiveness of brown and beige/brite adipocytes to adaptive regulation of thermogenic activity. The 5' non-coding region of the UCP1 gene contains regulatory elements that confer tissue specificity, differentiation dependence, and neuro-hormonal regulation to UCP1 gene transcription. Two main regions-a distal enhancer and a proximal promoter region-mediate transcriptional regulation through interactions with a plethora of transcription factors, including nuclear hormone receptors and cAMP-responsive transcription factors. Co-regulators, such as PGC-1α, play a pivotal role in the concerted regulation of UCP1 gene transcription. Multiple interactions of transcription factors and co-regulators at the promoter region of the UCP1 gene result in local chromatin remodeling, leading to activation and increased accessibility of RNA polymerase II and subsequent gene transcription. Moreover, a commonly occurring A-to-G polymorphism in close proximity to the UCP1 gene enhancer influences the extent of UCP1 gene transcription. Notably, it has been reported that specific aspects of obesity and associated metabolic diseases are associated with human population variability at this site. On another front, the unique properties of the UCP1 promoter region have been exploited to develop brown adipose tissue-specific gene delivery tools for experimental purposes. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  14. Transcriptional regulation in Drosophila: the post-genome challenge.

    Science.gov (United States)

    Biggin, M D; Tjian, R

    2001-03-01

    Drosophila melanogaster has long been at the forefront of studies of transcriptional regulation in animals. Many fundamental ideas--such as cis control elements that act over long distances, the regulation of development by hierarchical cascades of transcription factors, dosage compensation, and position effect variegation--originated from studies of the fruit fly. The recent completion of the euchromatic DNA sequence of Drosophila is another breakthrough. The sequence data highlight important unanswered questions. For example, only one-fifth of the 124 Mb of Drosophila euchromatic DNA codes for protein. The function of the remaining 100 Mb of mostly unique DNA is largely unknown. Some proportion of this non-reading frame DNA must encode the functional recognition sites targeted by the approximately 700 sequence-specific DNA binding proteins that regulate transcription in Drosophila, but what proportion? Most or very little? Promoter sequences by definition contain all of the cis information that specifies how gene transcription is regulated. However, it has been difficult to decipher this information and predict the patterns of RNA expression. How do we break this "transcriptional code"? Mechanistic studies, using simple model promoters, indicate that transcription is controlled by the coordinate action of sequence-specific DNA binding proteins interacting with the general transcriptional machinery via intermediary adapters and chromatin remodeling activities. How can we integrate this biochemical information with data from genome-wide studies to describe the generation of highly complex patterns of transcription? Here, we discuss recent studies that may point the way ahead. We also highlight difficulties that the field faces in dissecting transcriptional control in the post-genome era.

  15. Initiation of HIV Reverse Transcription

    Directory of Open Access Journals (Sweden)

    Roland Marquet

    2010-01-01

    Full Text Available Reverse transcription of retroviral genomes into double stranded DNA is a key event for viral replication. The very first stage of HIV reverse transcription, the initiation step, involves viral and cellular partners that are selectively packaged into the viral particle, leading to an RNA/protein complex with very specific structural and functional features, some of which being, in the case of HIV-1, linked to particular isolates. Recent understanding of the tight spatio-temporal regulation of reverse transcription and its importance for viral infectivity further points toward reverse transcription and potentially its initiation step as an important drug target.

  16. The post-transcriptional operon

    DEFF Research Database (Denmark)

    2011-01-01

    A post-transcriptional operon is a set of monocistronic mRNAs encoding functionally related proteins that are co-regulated by a group of RNA-binding proteins and/or small non-coding RNAs so that protein expression is coordinated at the post-transcriptional level. The post-transcriptional operon...... model (PTO) is used to describe data from an assortment of methods (e.g. RIP-Chip, CLIP-Chip, miRNA profiling, ribosome profiling) that globally address the functionality of mRNA. Several examples of post-transcriptional operons have been documented in the literature and demonstrate the usefulness...

  17. Herschel SPIRE fourier transform spectrometer: calibration of its bright-source mode

    Science.gov (United States)

    Lu, Nanyao; Polehampton, Edward T.; Swinyard, Bruce M.; Benielli, Dominique; Fulton, Trevor; Hopwood, Rosalind; Imhof, Peter; Lim, Tanya; Marchili, Nicola; Naylor, David A.; Schulz, Bernhard; Sidher, Sunil; Valtchanov, Ivan

    2014-07-01

    The Fourier Transform Spectrometer (FTS) of the Spectral and Photometric Imaging REceiver (SPIRE) on board the ESA Herschel Space Observatory has two detector setting modes: (a) a nominal mode, which is optimized for observing moderately bright to faint astronomical targets, and (b) a bright-source mode recommended for sources significantly brighter than 500 Jy, within the SPIRE FTS bandwidth of 446.7-1544 GHz (or 194-671 microns in wavelength), which employs a reduced detector responsivity and out-of-phase analog signal amplifier/demodulator. We address in detail the calibration issues unique to the bright-source mode, describe the integration of the bright-mode data processing into the existing pipeline for the nominal mode, and show that the flux calibration accuracy of the bright-source mode is generally within 2 % of that of the nominal mode, and that the bright-source mode is 3 to 4 times less sensitive than the nominal mode.

  18. Putting the brakes on snake venom evolution: the unique molecular evolutionary patterns of Aipysurus eydouxii (Marbled sea snake) phospholipase A2 toxins.

    Science.gov (United States)

    Li, Min; Fry, Bryan G; Kini, R Manjunatha

    2005-04-01

    Accelerated evolution of toxins is a unique feature of venoms, with the toxins evolving via the birth-and-death mode of molecular evolution. The venoms of sea snakes, however, are remarkably simple in comparison to those of land snakes, which contain highly complex venoms. Aipysurus eydouxii (Marbled sea snake) is a particularly unique sea snake, feeding exclusively upon fish eggs. Secondary to this ecological change, the fangs have been lost and the venom glands greatly atrophied. We recently showed that the only neurotoxin (a three-finger toxin) gene found in the sea snake A. eydouxii has a dinucleotide deletion, resulting in the loss of neurotoxic activity. During these studies, we isolated and identified a number of cDNA clones encoding isozymes of phospholipase A(2) (PLA(2)) toxins from its venom gland. Sixteen unique PLA(2) clones were sequenced from the cDNA library and TA cloning of reverse transcription-polymerase chain reaction products. Phylogenetic analysis of these clones revealed that less diversification of the PLA(2) toxins has occurred in the A. eydouxii venom gland in comparison to equivalent terrestrial and other marine snakes. As there is no longer a positive selection pressure acting upon the venom, mutations have accumulated in the toxin-coding regions that would have otherwise had a deleterious effect upon the ability to use the venom for prey capture. Such mutations include substitutions of highly conserved residues; in one clone, the active site His(48) is replaced by Arg, and in two other clones, highly conserved cysteine residues are replaced. These mutations significantly affect the functional and structural properties of these PLA(2) enzymes, respectively. Thus, in A. eydouxii, the loss of the main neurotoxin is accompanied by a much slower rate of molecular evolution of the PLA(2) toxins as a consequence of the snake's shift in ecological niche. This is the first case of decelerated evolution of toxins in snake venom.

  19. Synthetic transcription elongation factors license transcription across repressive chromatin.

    Science.gov (United States)

    Erwin, Graham S; Grieshop, Matthew P; Ali, Asfa; Qi, Jun; Lawlor, Matthew; Kumar, Deepak; Ahmad, Istaq; McNally, Anna; Teider, Natalia; Worringer, Katie; Sivasankaran, Rajeev; Syed, Deeba N; Eguchi, Asuka; Ashraf, Md; Jeffery, Justin; Xu, Mousheng; Park, Paul M C; Mukhtar, Hasan; Srivastava, Achal K; Faruq, Mohammed; Bradner, James E; Ansari, Aseem Z

    2017-11-30

    Releasing a paused RNA polymerase II into productive elongation is tightly-regulated, especially at genes that impact human development and disease. To exert control over this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that engages the transcription elongation machinery. By limiting activity to targeted loci, Syn-TEFs convert constituent modules from broad-spectrum inhibitors of transcription into gene-specific stimulators. We present Syn-TEF1, a molecule that actively enables transcription across repressive GAA repeats that silence frataxin expression in Friedreich's ataxia, a terminal neurodegenerative disease with no effective therapy. Furthermore, the modular design of Syn-TEF1 defines a general framework for developing a class of molecules that license transcription elongation at targeted genomic loci. Copyright © 2017, American Association for the Advancement of Science.

  20. The Natural Product Resveratrol Inhibits Yeast Cell Separation by Extensively Modulating the Transcriptional Landscape and Reprogramming the Intracellular Metabolome.

    Directory of Open Access Journals (Sweden)

    Zhe Wang

    Full Text Available An increasing number of studies have shown that the promising compound resveratrol treats multiple diseases, such as cancer and aging; however, the resveratrol mode-of-action (MoA remains largely unknown. Here, by virtue of multiple omics approaches, we adopted fission yeast as a model system with the goal of dissecting the common MoA of the anti-proliferative activity of resveratrol. We found that the anti-proliferative activity of resveratrol is mainly due to its unique role of inhibiting the separation of sister cells, similar phenotype with the C2H2 zinc finger transcription factor Ace2 knock-out strain. Microarray analysis shown that resveratrol has extensive impact on the fission yeast transcription levels. Among the changed gene's list, 40% of up-regulated genes are Core Environmental Stress Responses genes, and 57% of the down-regulated genes are periodically expressed. Moreover, resveratrol leverages the metabolome, which unbalances the intracellular pool sizes of several classes of amino acids, nucleosides, sugars and lipids, thus reflecting the remodulated metabolic networks. The complexity of the resveratrol MoA displayed in previous reports and our work demonstrates that multiple omics approaches must be applied together to obtain a complete picture of resveratrol's anti-proliferative function.

  1. Unique mechanical properties of nanostructured metals.

    Science.gov (United States)

    Tsuji, Nobuhiro

    2007-11-01

    Recently, it becomes possible to fabricate bulk metals having ultrafine grained or nanocrystalline structures of which grain size is in nano-meter dimensions. One of the promising ways to realize bulk nanostructured metals is severe plastic deformation (SPD) above logarithmic equivalent strain of 4. We have developed an original SPD process, named Accumulative Roll Bonding (ARB) using rolling deformation in principle, and have succeeded in fabricating bulk nanostructured sheets of various kinds of metals and alloys. The ARB process and the nanostructured metals fabricated by the ARB are introduced in this paper. The nanostructured metals sometimes perform quite unique mechanical properties, that is rather surprising compared with conventionally coarse grained materials. The unique properties seem to be attributed to the characteristic structures of the nano-metals full of grain boundaries.

  2. Unique stoichiometric representation for computational thermochemistry.

    Science.gov (United States)

    Fishtik, Ilie

    2012-02-23

    Evaluation of the enthalpy of formation of species via quantum chemical methods, as well as the evaluation of their performance, is mainly based on single reaction schemes, i.e., reaction schemes that involve a minimal number of reference species where minimal means that, if a reference species is omitted, there is no way to write a balanced reaction scheme involving the remaining species. When the number of reference species exceeds the minimal number, the main problem of computational thermochemistry is inevitably becoming an optimization problem. In this communication we present an exact and unique solution of the optimization problem in computational thermochemistry along with a stoichiometric interpretation of the solution. Namely, we prove that the optimization problem may be identically solved by enumerating a finite and unique set of reactions referred to as group additivity (GA) response reactions (RERs). © 2012 American Chemical Society

  3. Unique removal of a kinked nasogastric tube

    Directory of Open Access Journals (Sweden)

    Kumar Shwetanshu Narayan

    2017-01-01

    Full Text Available Nasogastric (NG tube insertion is a common clinical procedure used for both diagnostic and therapeutic purposes. As the importance of enteral nutrition is being increasingly recognized; the use of NG tube insertion has steadily increased. Here, we present an interesting case in which a kinked NG tube was removed in a unique manner with “push and pull” technique without untoward trauma.

  4. Modularity, comparative cognition and human uniqueness

    OpenAIRE

    Shettleworth, Sara J.

    2012-01-01

    Darwin's claim ‘that the difference in mind between man and the higher animals … is certainly one of degree and not of kind’ is at the core of the comparative study of cognition. Recent research provides unprecedented support for Darwin's claim as well as new reasons to question it, stimulating new theories of human cognitive uniqueness. This article compares and evaluates approaches to such theories. Some prominent theories propose sweeping domain-general characterizations of the difference ...

  5. Brain metastasis: Unique challenges and open opportunities.

    Science.gov (United States)

    Lowery, Frank J; Yu, Dihua

    2017-01-01

    The metastasis of cancer to the central nervous system (CNS) remains a devastating clinical reality, carrying an estimated survival time of less than one year in spite of recent therapeutic breakthroughs for other disease contexts. Advances in brain metastasis research are hindered by a number of factors, including its complicated nature and the difficulty of modeling metastatic cancer growth in the unique brain microenvironment. In this review, we will discuss the clinical challenge, and compare the merits and limitations of the available models for brain metastasis research. Additionally, we will specifically address current knowledge on how brain metastases take advantage of the unique brain environment to benefit their own growth. Finally, we will explore the distinctive metabolic and chemical characteristics of the brain and how these paradoxically represent barriers to establishment of brain metastasis, but also provide ample supplies for metastatic cells' growth in the brain. We envision that multi-disciplinary innovative approaches will open opportunities for the field to make breakthroughs in tackling unique challenges of brain metastasis. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Unique characteristics of informal hospice cancer caregiving

    Science.gov (United States)

    Washington, Karla T.; Pike, Kenneth C.; Demiris, George; Oliver, Debra Parker

    2015-01-01

    Purpose The purpose of this study was to describe the unique characteristics of informal hospice cancer caregiving. Methods Researchers conducted a secondary analysis of data drawn from a randomized clinical trial of an informal hospice caregiving intervention (N=348). Demographic characteristics and measures of the informal caregiving experience of hospice patients and their informal caregivers were compared based on the patient’s diagnosis using chi-square tests for association of categorical variables and t tests for continuous variables. Results Informal caregivers of cancer patients differed from their non-cancer counterparts in a number of respects including patient age, caregiver age, patient residence, relationship between patient and caregiver, amount and duration of care provided, likelihood to incur out-of-pocket expenses related to patient care, caregiver problem-solving style, and impact on caregiver daily schedule. There were no statistically significant differences between cancer and non-cancer caregivers in terms of gender, race, employment status, anxiety, and quality of life. Conclusions While cancer and non-cancer caregivers are similar in many respects, a number of unique features characterize the informal hospice cancer caregiving experience. Attention to these unique features will allow hospice providers to tailor supportive care interventions to better address cancer caregivers’ needs. PMID:25547480

  7. Common and Unique Network Dynamics in Football Games

    Science.gov (United States)

    Yamamoto, Yuji; Yokoyama, Keiko

    2011-01-01

    The sport of football is played between two teams of eleven players each using a spherical ball. Each team strives to score by driving the ball into the opposing goal as the result of skillful interactions among players. Football can be regarded from the network perspective as a competitive relationship between two cooperative networks with a dynamic network topology and dynamic network node. Many complex large-scale networks have been shown to have topological properties in common, based on a small-world network and scale-free network models. However, the human dynamic movement pattern of this network has never been investigated in a real-world setting. Here, we show that the power law in degree distribution emerged in the passing behavior in the 2006 FIFA World Cup Final and an international “A” match in Japan, by describing players as vertices connected by links representing passes. The exponent values are similar to the typical values that occur in many real-world networks, which are in the range of , and are larger than that of a gene transcription network, . Furthermore, we reveal the stochastically switched dynamics of the hub player throughout the game as a unique feature in football games. It suggests that this feature could result not only in securing vulnerability against intentional attack, but also in a power law for self-organization. Our results suggest common and unique network dynamics of two competitive networks, compared with the large-scale networks that have previously been investigated in numerous works. Our findings may lead to improved resilience and survivability not only in biological networks, but also in communication networks. PMID:22216336

  8. Adaptation with transcriptional regulation

    Science.gov (United States)

    Shi, Wenjia; Ma, Wenzhe; Xiong, Liyang; Zhang, Mingyue; Tang, Chao

    2017-02-01

    Biochemical adaptation is one of the basic functions that are widely implemented in biological systems for a variety of purposes such as signal sensing, stress response and homeostasis. The adaptation time scales span from milliseconds to days, involving different regulatory machineries in different processes. The adaptive networks with enzymatic regulation (ERNs) have been investigated in detail. But it remains unclear if and how other forms of regulation will impact the network topology and other features of the function. Here, we systematically studied three-node transcriptional regulatory networks (TRNs), with three different types of gene regulation logics. We found that the topologies of adaptive gene regulatory networks can still be grouped into two general classes: negative feedback loop (NFBL) and incoherent feed-forward loop (IFFL), but with some distinct topological features comparing to the enzymatic networks. Specifically, an auto-activation loop on the buffer node is necessary for the NFBL class. For IFFL class, the control node can be either a proportional node or an inversely-proportional node. Furthermore, the tunability of adaptive behavior differs between TRNs and ERNs. Our findings highlight the role of regulation forms in network topology, implementation and dynamics.

  9. Sliding mode control and observation

    CERN Document Server

    Shtessel, Yuri; Fridman, Leonid; Levant, Arie

    2014-01-01

    The sliding mode control methodology has proven effective in dealing with complex dynamical systems affected by disturbances, uncertainties and unmodeled dynamics. Robust control technology based on this methodology has been applied to many real-world problems, especially in the areas of aerospace control, electric power systems, electromechanical systems, and robotics. Sliding Mode Control and Observation represents the first textbook that starts with classical sliding mode control techniques and progresses toward newly developed higher-order sliding mode control and observation algorithms and their applications. The present volume addresses a range of sliding mode control issues, including: *Conventional sliding mode controller and observer design *Second-order sliding mode controllers and differentiators *Frequency domain analysis of conventional and second-order sliding mode controllers *Higher-order sliding mode controllers and differentiators *Higher-order sliding mode observers *Sliding mode disturbanc...

  10. Free boundary ballooning mode representation

    Science.gov (United States)

    Zheng, Linjin

    2012-03-01

    Considerable efforts have been made in this field to develop a free boundary ballooning mode representation, which can incorporate the peeling mode stability criterion. Those efforts have not succeeded, simply because the so-called ballooning mode invariance is broken toward plasma edge. This makes 1D description of high n modes at plasma edge become impossible, where n is toroidal mode number. Nevertheless, we prove that the existence of ``half" ballooning mode invariance toward plasma core enables an 1.δ-dimentional representation of the modes, where δ˜O(1/n). This considerably reduces the complicity in investigating high n modes at plasma edge and can be used to study peeling-ballooning modes. This technique can also be useful to extend the 1D calculation of fixed boundary ballooning modes for free boundary ballooning modes. Numerical example will also be presented together with the topological symmetry analysis.

  11. Real-Time Transportation Mode Identification Using Artificial Neural Networks Enhanced with Mode Availability Layers: A Case Study in Dubai

    Directory of Open Access Journals (Sweden)

    Young-Ji Byon

    2017-09-01

    Full Text Available Traditionally, departments of transportation (DOTs have dispatched probe vehicles with dedicated vehicles and drivers for monitoring traffic conditions. Emerging assisted GPS (AGPS and accelerometer-equipped smartphones offer new sources of raw data that arise from voluntarily-traveling smartphone users provided that their modes of transportation can correctly be identified. By introducing additional raster map layers that indicate the availability of each mode, it is possible to enhance the accuracy of mode detection results. Even in its simplest form, an artificial neural network (ANN excels at pattern recognition with a relatively short processing timeframe once it is properly trained, which is suitable for real-time mode identification purposes. Dubai is one of the major cities in the Middle East and offers unique environments, such as a high density of extremely high-rise buildings that may introduce multi-path errors with GPS signals. This paper develops real-time mode identification ANNs enhanced with proposed mode availability geographic information system (GIS layers, firstly for a universal mode detection and, secondly for an auto mode detection for the particular intelligent transportation system (ITS application of traffic monitoring, and compares the results with existing approaches. It is found that ANN-based real-time mode identification, enhanced by mode availability GIS layers, significantly outperforms the existing methods.

  12. Mitotic bookmarking by transcription factors.

    Science.gov (United States)

    Kadauke, Stephan; Blobel, Gerd A

    2013-04-02

    Mitosis is accompanied by dramatic changes in chromatin organization and nuclear architecture. Transcription halts globally and most sequence-specific transcription factors and co-factors are ejected from mitotic chromatin. How then does the cell maintain its transcriptional identity throughout the cell division cycle? It has become clear that not all traces of active transcription and gene repression are erased within mitotic chromatin. Many histone modifications are stable or only partially diminished throughout mitosis. In addition, some sequence-specific DNA binding factors have emerged that remain bound to select sites within mitotic chromatin, raising the possibility that they function to transmit regulatory information through the transcriptionally silent mitotic phase, a concept that has been termed "mitotic bookmarking." Here we review recent approaches to studying potential bookmarking factors with regards to their mitotic partitioning, and summarize emerging ideas concerning the in vivo functions of mitotically bound nuclear factors.

  13. Modeli diskretne izbire

    Directory of Open Access Journals (Sweden)

    Boštjan Kerbler – Kefo

    2006-01-01

    Full Text Available V članku je sistematično predstavljena posebna oblika regresijskih metod – modelov diskretne izbire –, imenovanih tudi verjetnostni modeli. Poleg njihovega pomena so opisane še metodološke značilnosti pri njihovi izvedbi, natančneje pa so predstavljeni modeli binarne izbire in tisti z omejeno odvisno spremenljivko, logistični model ter modela probit in tobit kot izhodiščni metodološki pristopi k izvedbi modelov.

  14. Mode og mozzarella

    DEFF Research Database (Denmark)

    Nielsen, Jakob Isak

    2013-01-01

    Under en samtale i Paolo Sorrentinos La grande bellezza/da. Den store skønhed (2013) anføres det, at Italiens primære eksportvarer er mode og mozzarella. Selve filmen vidner om, at Italien har andet at byde på – heriblandt filmkunst og Roms righoldige kulturhistorie.......Under en samtale i Paolo Sorrentinos La grande bellezza/da. Den store skønhed (2013) anføres det, at Italiens primære eksportvarer er mode og mozzarella. Selve filmen vidner om, at Italien har andet at byde på – heriblandt filmkunst og Roms righoldige kulturhistorie....

  15. Nonclassicality in two-mode BEC

    OpenAIRE

    Giri, Sandip Kumar; Sen, Biswajit; Ooi, C H Raymond; Pathak, Anirban

    2013-01-01

    The operator solution of a completely quantum mechanical Hamiltonian of the Raman processes is used here to investigate the possibility of obtaining intermodal entanglement between different modes involved in the Raman processes (e.g. pump mode, Stokes mode, vibration (phonon) mode and anti-Stokes mode). Intermodal entanglement is reported between a) pump mode and anti-Stokes mode, b) pump mode and vibration (phonon) mode c) Stokes mode and vibration phonon mode, d) Stokes mode and anti-stoke...

  16. Failure Modes and Effects Analysis (FMEA) Assistant Tool Feasibility Study

    Science.gov (United States)

    Flores, Melissa D.; Malin, Jane T.; Fleming, Land D.

    2013-09-01

    An effort to determine the feasibility of a software tool to assist in Failure Modes and Effects Analysis (FMEA) has been completed. This new and unique approach to FMEA uses model based systems engineering concepts to recommend failure modes, causes, and effects to the user after they have made several selections from pick lists about a component's functions and inputs/outputs. Recommendations are made based on a library using common failure modes identified over the course of several major human spaceflight programs. However, the tool could be adapted for use in a wide range of applications from NASA to the energy industry.

  17. Novel fusion genes and chimeric transcripts in ependymal tumors

    DEFF Research Database (Denmark)

    Olsen, Thale Kristin; Panagopoulos, Ioannis; Gorunova, Ludmila

    2016-01-01

    with subsequent Sanger sequencing was used to validate the potential fusions. Fluorescent in situ hybridization (FISH) using locus-specific probes was also performed. A total of 841 candidate chimeric transcripts were identified in the 12 tumors, with an average of 49 unique candidate fusions per tumor. After......We have previously identified two ALK rearrangements in a subset of ependymal tumors using a combination of cytogenetic data and RNA sequencing. The aim of this study was to perform an unbiased search for fusion transcripts in our entire series of ependymal tumors. Fusion analysis was performed...... using the FusionCatcher algorithm on 12 RNA-sequenced ependymal tumors. Candidate transcripts were prioritized based on the software's filtering and manual visualization using the BLAST (Basic Local Alignment Search Tool) and BLAT (BLAST-like alignment tool) tools. Genomic and reverse transcriptase PCR...

  18. Transcriptome pathways unique to dehydration tolerant relatives of modern wheat.

    Science.gov (United States)

    Ergen, Neslihan Z; Thimmapuram, Jyothi; Bohnert, Hans J; Budak, Hikmet

    2009-08-01

    Among abiotic stressors, drought is a major factor responsible for dramatic yield loss in agriculture. In order to reveal differences in global expression profiles of drought tolerant and sensitive wild emmer wheat genotypes, a previously deployed shock-like dehydration process was utilized to compare transcriptomes at two time points in root and leaf tissues using the Affymetrix GeneChip(R) Wheat Genome Array hybridization. The comparison of transcriptomes reveal several unique genes or expression patterns such as differential usage of IP(3)-dependent signal transduction pathways, ethylene- and abscisic acid (ABA)-dependent signaling, and preferential or faster induction of ABA-dependent transcription factors by the tolerant genotype that distinguish contrasting genotypes indicative of distinctive stress response pathways. The data also show that wild emmer wheat is capable of engaging known drought stress responsive mechanisms. The global comparison of transcriptomes in the absence of and after dehydration underlined the gene networks especially in root tissues that may have been lost in the selection processes generating modern bread wheats.

  19. Adult spinal cord radial glia display a unique progenitor phenotype.

    Directory of Open Access Journals (Sweden)

    Audrey Petit

    Full Text Available Radial glia (RG are primarily embryonic neuroglial progenitors that express Brain Lipid Binding Protein (Blbp a.k.a. Fabp7 and Glial Fibrillary Acidic Protein (Gfap. We used these transcripts to demarcate the distribution of spinal cord radial glia (SCRG and screen for SCRG gene expression in the Allen Spinal Cord Atlas (ASCA. We reveal that neonatal and adult SCRG are anchored in a non-ventricular niche at the spinal cord (SC pial boundary, and express a "signature" subset of 122 genes, many of which are shared with "classic" neural stem cells (NSCs of the subventricular zone (SVZ and SC central canal (CC. A core expressed gene set shared between SCRG and progenitors of the SVZ and CC is particularly enriched in genes associated with human disease. Visualizing SCRG in a Fabp7-EGFP reporter mouse reveals an extensive population of SCRG that extend processes around the SC boundary and inwardly (through the SC white matter (WM, whose abundance increases in a gradient from cervical to lumbar SC. Confocal analysis of multiple NSC-enriched proteins reveals that postnatal SCRG are a discrete and heterogeneous potential progenitor population that become activated by multiple SC lesions, and that CC progenitors are also more heterogeneous than previously appreciated. Gene ontology analysis highlights potentially unique regulatory pathways that may be further manipulated in SCRG to enhance repair in the context of injury and SC disease.

  20. Vibrational modes of nanolines

    Science.gov (United States)

    Heyliger, Paul R.; Flannery, Colm M.; Johnson, Ward L.

    2008-04-01

    Brillouin-light-scattering spectra previously have been shown to provide information on acoustic modes of polymeric lines fabricated by nanoimprint lithography. Finite-element methods for modeling such modes are presented here. These methods provide a theoretical framework for determining elastic constants and dimensions of nanolines from measured spectra in the low gigahertz range. To make the calculations feasible for future incorporation in inversion algorithms, two approximations of the boundary conditions are employed in the calculations: the rigidity of the nanoline/substrate interface and sinusoidal variation of displacements along the nanoline length. The accuracy of these approximations is evaluated as a function of wavenumber and frequency. The great advantage of finite-element methods over other methods previously employed for nanolines is the ability to model any cross-sectional geometry. Dispersion curves and displacement patterns are calculated for modes of polymethyl methacrylate nanolines with cross-sectional dimensions of 65 nm × 140 nm and rectangular or semicircular tops. The vibrational displacements and dispersion curves are qualitatively similar for the two geometries and include a series of flexural, Rayleigh-like, and Sezawa-like modes. This paper is a contribution of the National Institute of Standards and Technology and is not subject to copyright in the United States.

  1. Mode Gaussian beam tracing

    CERN Document Server

    Trofimov, M Yu; Kozitskiy, S B

    2015-01-01

    An adiabatic mode Helmholtz equation for 3D underwater sound propagation is developed. The Gaussian beam tracing in this case is constructed. The test calculations are carried out for the crosswedge benchmark and proved an excellent agreement with the source images method.

  2. New Modes of Citizenship

    DEFF Research Database (Denmark)

    Nickelsen, Niels Christian Mossfeldt

    2017-01-01

    in common that they involve important elements of autonomy and self-care and are part of an international movement toward empowering citizens and patients. This chapter discusses the relation between care innovation and new modes of citizenship in terms of the ‘active’ citizen. By way of an ethnographic...

  3. Thermodynamics of Radiation Modes

    Science.gov (United States)

    Pina, Eduardo; de la Selva, Sara Maria Teresa

    2010-01-01

    We study the equilibrium thermodynamics of the electromagnetic radiation in a cavity of a given volume and temperature. We found three levels of description, the thermodynamics of one mode, the thermodynamics of the distribution of frequencies in a band by summing over the frequencies in it and the global thermodynamics by summing over all the…

  4. Theories and Modes

    Science.gov (United States)

    Apsche, Jack A.

    2005-01-01

    In his work on the Theory of Modes, Beck (1996) suggested that there were flaws with his cognitive theory. He suggested that though there are shortcomings to his cognitive theory, there were not similar shortcomings to the practice of Cognitive Therapy. The author suggests that if there are shortcomings to cognitive theory the same shortcomings…

  5. Signature of nonadiabatic coupling in excited-state vibrational modes.

    Science.gov (United States)

    Soler, Miguel A; Nelson, Tammie; Roitberg, Adrian E; Tretiak, Sergei; Fernandez-Alberti, Sebastian

    2014-11-13

    Using analytical excited-state gradients, vibrational normal modes have been calculated at the minimum of the electronic excited-state potential energy surfaces for a set of extended conjugated molecules with different coupling between them. Molecular model systems composed of units of polyphenylene ethynylene (PPE), polyphenylenevinylene (PPV), and naphthacene/pentacene (NP) have been considered. In all cases except the NP model, the influence of the nonadiabatic coupling on the excited-state equilibrium normal modes is revealed as a unique highest frequency adiabatic vibrational mode that overlaps with the coupling vector. This feature is removed by using a locally diabatic representation in which the effect of NA interaction is removed. Comparison of the original adiabatic modes with a set of vibrational modes computed in the locally diabatic representation demonstrates that the effect of nonadiabaticity is confined to only a few modes. This suggests that the nonadiabatic character of a molecular system may be detected spectroscopically by identifying these unique state-specific high frequency vibrational modes.

  6. Synergistic modes of vocal tract articulation for American English vowels.

    Science.gov (United States)

    Story, Brad H

    2005-12-01

    The purpose of this study was to investigate the spatial similarity of vocal tract shaping patterns across speakers and the similarity of their acoustic effects. Vocal tract area functions for 11 American English vowels were obtained from six speakers, three female and three male, using magnetic resonance imaging (MRI). Each speaker's set of area functions was then decomposed into mean area vectors and representative modes (eigenvectors) using principal components analysis (PCA). Three modes accounted for more than 90% of the variance in the original data sets for each speaker. The general shapes of the first two modes were found to be highly correlated across all six speakers. To demonstrate the acoustic effects of each mode, both in isolation and combined, a mapping between the mode scaling coefficients and [F1, F2] pairs was generated for each speaker. The mappings were unique for all six speakers in terms of the exact shape of the [F1, F2] vowel space, but the general effect of the modes was the same in each case. The results support the idea that the modes provide a common system for perturbing a unique underlying neutral vocal tract shape.

  7. An assessment of spacecraft target mode selection methods

    Science.gov (United States)

    Mercer, J. F.; Aglietti, G. S.; Remedia, M.; Kiley, A.

    2017-11-01

    Coupled Loads Analyses (CLAs), using finite element models (FEMs) of the spacecraft and launch vehicle to simulate critical flight events, are performed in order to determine the dynamic loadings that will be experienced by spacecraft during launch. A validation process is carried out on the spacecraft FEM beforehand to ensure that the dynamics of the analytical model sufficiently represent the behavior of the physical hardware. One aspect of concern is the containment of the FEM correlation and update effort to focus on the vibration modes which are most likely to be excited under test and CLA conditions. This study therefore provides new insight into the prioritization of spacecraft FEM modes for correlation to base-shake vibration test data. The work involved example application to large, unique, scientific spacecraft, with modern FEMs comprising over a million degrees of freedom. This comprehensive investigation explores: the modes inherently important to the spacecraft structures, irrespective of excitation; the particular 'critical modes' which produce peak responses to CLA level excitation; an assessment of several traditional target mode selection methods in terms of ability to predict these 'critical modes'; and an indication of the level of correlation these FEM modes achieve compared to corresponding test data. Findings indicate that, although the traditional methods of target mode selection have merit and are able to identify many of the modes of significance to the spacecraft, there are 'critical modes' which may be missed by conventional application of these methods. The use of different thresholds to select potential target modes from these parameters would enable identification of many of these missed modes. Ultimately, some consideration of the expected excitations is required to predict all modes likely to contribute to the response of the spacecraft in operation.

  8. Sliding mode control the delta-sigma modulation approach

    CERN Document Server

    Sira-Ramírez, Hebertt

    2015-01-01

    This monograph presents a novel method of sliding mode control for switch-regulated nonlinear systems. The Delta Sigma modulation approach allows one to implement a continuous control scheme using one or multiple, independent switches, thus effectively merging the available linear and nonlinear controller design techniques with sliding mode control.   Sliding Mode Control: The Delta-Sigma Modulation Approach, combines rigorous mathematical derivation of the unique features of Sliding Mode Control and Delta-Sigma modulation with numerous illustrative examples from diverse areas of engineering. In addition, engineering case studies demonstrate the applicability of the technique and the ease with which one can implement the exposed results. This book will appeal to researchers in control engineering and can be used as graduate-level textbook for a first course on sliding mode control.

  9. Stress-induced Oryza sativa BAT1 dual helicase exhibits unique bipolar translocation.

    Science.gov (United States)

    Tuteja, Narendra; Tarique, Mohammed; Trivedi, Dipesh Kumar; Sahoo, Ranjan Kumar; Tuteja, Renu

    2015-11-01

    HLA-B associated transcript 1 (BAT1) protein, also named as spliceosome RNA helicase UAP56, is a member of the DExD/H-box family of helicases. However, regulation under stress, biochemical properties, and functions of plant homologue of BAT1 are poorly understood. Here, we report the purification and detailed biochemical characterization of the Oryza sativa homologue of BAT1 (OsBAT1/UAP56) protein (52 kDa) and regulation of its transcript under abiotic stress. OsBAT1 transcript levels are enhanced in rice seedlings in response to abiotic stress including salt stress and abscisic acid. Purified OsBAT1 protein exhibits the DNA- and RNA-dependent ATPase, RNA helicase, and DNA- and RNA-binding activities. Interestingly OsBAT1 also exhibits unique DNA helicase activity, which has not been reported so far in any BAT1 homologue. Moreover, OsBAT1 translocates in both the 3' to 5' and 5' to 3' directions, which is also a unique property. The K m value for OsBAT1 DNA helicase is 0.9753 nM and for RNA helicase is 1.7536 nM, respectively. This study demonstrates several unique characteristics of OsBAT1 especially its ability to unwind both DNA and RNA duplexes; bipolar translocation and its transcript upregulation under abiotic stresses indicate that it is a multifunctional protein. Overall, this study represents significant contribution in advancing our knowledge regarding functions of OsBAT1 in RNA and DNA metabolism and its putative role in abiotic stress signaling in plants.

  10. 7 CFR 614.12 - Transcripts.

    Science.gov (United States)

    2010-01-01

    ... verbatim transcript must pay for the transcription service and provide a copy of the transcript to NRCS at... participant may obtain a verbatim transcript as provided in paragraph (b) of this section. (b) Any party to an informal hearing appeal under § 614.9 may request that a verbatim transcript is made of the hearing...

  11. Unique properties of Drosophila spermatocyte primary cilia

    Directory of Open Access Journals (Sweden)

    Maria Giovanna Riparbelli

    2013-09-01

    The primary cilium is an essential organelle required for animal development and adult homeostasis that is found on most animal cells. The primary cilium contains a microtubule-based axoneme cytoskeleton that typically grows from the mother centriole in G0/G1 phase of the cell cycle as a membrane-bound compartment that protrudes from the cell surface. A unique system of bidirectional transport, intraflagellar transport (IFT, maintains the structure and function of cilia. While the axoneme is dynamic, growing and shrinking at its tip, at the same time it is very stable to the effects of microtubule-targeting drugs. The primary cilia found on Drosophila spermatocytes diverge from the general rules of primary cilium biology in several respects. Among these unique attributes, spermatocyte cilia assemble from all four centrioles in an IFT-independent manner in G2 phase, and persist continuously through two cell divisions. Here, we show that Drosophila spermatocyte primary cilia are extremely sensitive to microtubule-targeting drugs, unlike their mammalian counterparts. Spermatocyte cilia and their axonemes fail to assemble or be maintained upon nocodazole treatment, while centriole replication appears unperturbed. On the other hand, paclitaxel (Taxol, a microtubule-stabilizing drug, disrupted transition zone assembly and anchoring to the plasma membrane while causing spermatocyte primary cilia to grow extensively long during the assembly/elongation phase, but did not overtly affect the centrioles. However, once assembled to their mature length, spermatocyte cilia appeared unaffected by Taxol. The effects of these drugs on axoneme dynamics further demonstrate that spermatocyte primary cilia are endowed with unique assembly properties.

  12. Stationary Black Holes: Uniqueness and Beyond

    Directory of Open Access Journals (Sweden)

    Piotr T. Chruściel

    2012-05-01

    Full Text Available The spectrum of known black-hole solutions to the stationary Einstein equations has been steadily increasing, sometimes in unexpected ways. In particular, it has turned out that not all black-hole-equilibrium configurations are characterized by their mass, angular momentum and global charges. Moreover, the high degree of symmetry displayed by vacuum and electro vacuum black-hole spacetimes ceases to exist in self-gravitating non-linear field theories. This text aims to review some developments in the subject and to discuss them in light of the uniqueness theorem for the Einstein-Maxwell system.

  13. Stationary Black Holes: Uniqueness and Beyond

    Directory of Open Access Journals (Sweden)

    Heusler Markus

    1998-01-01

    Full Text Available The spectrum of known black hole solutions to the stationary Einstein equations has increased in an unexpected way during the last decade. In particular, it has turned out that not all black hole equilibrium configurations are characterized by their mass, angular momentum and global charges. Moreover, the high degree of symmetry displayed by vacuum and electro-vacuum black hole space-times ceases to exist in self-gravitating non-linear field theories. This text aims to review some of the recent developments and to discuss them in the light of the uniqueness theorem for the Einstein-Maxwell system.

  14. Unique roles for lipids in Schistosoma mansoni.

    Science.gov (United States)

    Furlong, S T

    1991-02-01

    The dynamic interplay among lipids has been exploited by S. mansoni to evolve some unique processes that are vital for its long-term survival within the mammalian host. Lipids are required by the parasite not only to maintain its surface integrity and structural requirements but also for egg production and cell-cell signalling. However, S. mansoni is incapable of synthesizing essential lipids and must obtain these from its host. In this review, Stephen Furlong describes the roles and routes of acquisition o f lipids by this parasite.

  15. Unique double recurrence of cerebral arteriovenous malformation.

    Science.gov (United States)

    Nagm, Alhusain; Horiuchi, Tetsuyoshi; Ichinose, Shunsuke; Hongo, Kazuhiro

    2015-09-01

    Surgically treated patients with arteriovenous malformations (AVMs) are considered cured when the postoperative angiogram proves complete resection. However, despite no residual nidus or early draining vein on postoperative angiogram, rare instances of AVM recurrence have been reported in adults. In this paper, the authors present a case of a 24-year-old woman with asymptomatic double recurrence of her cerebral AVM after angiographically proven complete resection. To the authors' knowledge, this patient represents the first case with double de novo asymptomatic recurrence of Spetzler-Martin grade I AVM. Also, she represents the first case with unique AVM criteria in each recurrence.

  16. The end of the unique myocardial band

    DEFF Research Database (Denmark)

    MacIver, David H; Partridge, John B; Agger, Peter

    2018-01-01

    Two of the leading concepts of mural ventricular architecture are the unique myocardial band and the myocardial mesh model. We have described, in an accompanying article published in this journal, how the anatomical, histological and high-resolution computed tomographic studies strongly favour...... the latter concept. We now extend the argument to describe the linkage between mural architecture and ventricular function in both health and disease. We show that clinical imaging by echocardiography and magnetic resonance imaging, and electrophysiological studies, all support the myocardial mesh model. We...

  17. Modes of perceiving and imagining

    OpenAIRE

    Nudds, Matthew

    2000-01-01

    We enjoy modes of sensory imagining corresponding to our five modes of perception - seeing, touching, hearing, smelling and tasting. An account of what constitutes these different modes of perseption needs also to explain what constitutes the corresponding modes of sensory perception. In this paper I argue that we can explain what distinguishes the different modes of sensory imagination in terms of their characteristic experiences without supposing that we must distinguish the senses in terms...

  18. Fatigue mixed-mode delamination testing

    Science.gov (United States)

    Khourchid, Y. A.

    1993-01-01

    The separation of adjacent plies in a composite laminate (delamination) has been identified as the dominant failure mechanism in which most advanced composite materials fail. The resistance of a material to delamination is quantified in terms of the delamination fracture toughness, G(c), which is also known to change with the ratio of mode mix. The recently developed mixed mode bending (MMB) testing method is unique in that it allows the measurement of G(c) under any combination of mixed Mode I and Mode II loading. This makes it an ideal tool for mapping the interlaminar fracture behavior of the various material systems. The present work is concerned with the use of the MMB apparatus for fatigue testing, from which G(c) Vs N plots are obtained. These allowed the identification of the threshold value G(threshold). Preliminary static and fatigue results are presented for two aerospace type materials, IM7/8320 graphite/thermoplastic and IM7/5260 graphite/bismaleimide specimens, under various GI/GII ratios.

  19. Harnessing optical loss for unique microlaser functionality (Conference Presentation)

    Science.gov (United States)

    Feng, Liang

    2017-05-01

    Lasers, as the key driving force in the field of optics and photonics over other photonic components, are now being significantly benefited from the studies of nanophotonics and metamaterials, broadening laser physics and device applications. The properties of light are much more beyond its simple intensity and temporal characteristics. The fruitful nature of light provides a great variety of freedoms in manipulating light for modern photonic applications, including spin (polarization), chirality, angular momentum, and spin-orbit coupling. Unfortunately, all these fundamental properties and functionalities of light have not been fully exploited in micro/nano-laser systems because the conventional principles of laser design in bulk optics cannot be easily scaled down to the micro/nano scale. The capability of creating microlasers with controlled spin/orbital information and chirality in their radiations is expected to revolutionize next generation of photonic systems for computing and communication. In this talk, I will focus on our recent effort in harnessing optical losses for unique microlaser functionalities, in particular, an orbital angular momentum (OAM) microlaser that structure and twist the lasing radiation at the microscale. The effective generation of OAM lasing, especially at a micro/nano-scale, could address the growing demand for information capacity. By exploiting the emerging non-Hermitian photonics design at an exceptional point, we demonstrate a microring laser producing a single-mode OAM vortex lasing with the ability to precisely define the topological charge of the OAM mode and its polarization state. Our OAM microlaser could find applications in the next generation of integrated optoelectronic devices for optical communications.

  20. Cockayne syndrome--a primary defect in DNA repair, transcription, both or neither?

    Science.gov (United States)

    Friedberg, E C

    1996-09-01

    Cockayne syndrome is a rare autosomal recessive disease characterized by a complex clinical phenotype. Most Cockayne syndrome cells are hypersensitive to killing by ultraviolet radiation. This observation has prompted a wealth of studies on the DNA repair capacity of Cockayne syndrome cells in vitro. Many studies support the notion that such cells are defective in a DNA repair mode(s) that is transcription-dependent. However, it remains to be established that this is a primary molecular defect in Cockayne syndrome cells and that it explains the complex clinical phenotype associated with the disease. An alternative hypothesis is that Cockayne syndrome cells have a defect in transcription affecting the expression of certain genes, which is compatible with embryogenesis but not with normal post-natal development. Defective transcription may impair the normal processing of DNA damage during transcription-dependent repair.

  1. Unmanned Aerial Vehicles unique cost estimating requirements

    Science.gov (United States)

    Malone, P.; Apgar, H.; Stukes, S.; Sterk, S.

    Unmanned Aerial Vehicles (UAVs), also referred to as drones, are aerial platforms that fly without a human pilot onboard. UAVs are controlled autonomously by a computer in the vehicle or under the remote control of a pilot stationed at a fixed ground location. There are a wide variety of drone shapes, sizes, configurations, complexities, and characteristics. Use of these devices by the Department of Defense (DoD), NASA, civil and commercial organizations continues to grow. UAVs are commonly used for intelligence, surveillance, reconnaissance (ISR). They are also use for combat operations, and civil applications, such as firefighting, non-military security work, surveillance of infrastructure (e.g. pipelines, power lines and country borders). UAVs are often preferred for missions that require sustained persistence (over 4 hours in duration), or are “ too dangerous, dull or dirty” for manned aircraft. Moreover, they can offer significant acquisition and operations cost savings over traditional manned aircraft. Because of these unique characteristics and missions, UAV estimates require some unique estimating methods. This paper describes a framework for estimating UAV systems total ownership cost including hardware components, software design, and operations. The challenge of collecting data, testing the sensitivities of cost drivers, and creating cost estimating relationships (CERs) for each key work breakdown structure (WBS) element is discussed. The autonomous operation of UAVs is especially challenging from a software perspective.

  2. ENDF Cross Sections are not Uniquely Defined

    Energy Technology Data Exchange (ETDEWEB)

    Cullen, D. E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2010-06-11

    Most evaluated data that is coded into the ENDF format [1] does not uniquely define cross sections, because the evaluator defined total is not equal to the sum of evaluator defined partial cross sections, i.e., the total is not equal to elastic plus capture, etc. So we have always had the question: What is the correct total cross section? This is not a new problem; it has existed since the very beginning of ENDF over forty years ago. It is a problem that is periodically discussed and apparently handled, only to have it pop up again every ten years or so, as we have the next generation of ENDF format users who are not aware of the problem. See the Appendices for a summary of the differences that exist today for the ENDF/B-VII.0 (Appendix C), JEFF- 3.1(Appendix D), JENDL-3.3 (Appendix E), and CENDL-3.1 (Appendix F) data libraries. For use in our application we need consistent, unique data. To accomplish this for decades we [2, 3] have been ignoring the evaluator defined total, and re-defining it as equal to the sum of its evaluator defined parts. This has never been completely satisfactory to us, because we have been doing this without consulting evaluators, or obtaining their approval, so that the data we actually use in our applications may or may not be what the evaluators intended.

  3. Astronomy Outreach for Large and Unique Audiences

    Science.gov (United States)

    Lubowich, D.; Sparks, R. T.; Pompea, S. M.; Kendall, J. S.; Dugan, C.

    2013-04-01

    In this session, we discuss different approaches to reaching large audiences. In addition to star parties and astronomy events, the audiences for some of the events include music concerts or festivals, sick children and their families, minority communities, American Indian reservations, and tourist sites such as the National Mall. The goal is to bring science directly to the public—to people who attend astronomy events and to people who do not come to star parties, science museums, or science festivals. These programs allow the entire community to participate in astronomy activities to enhance the public appreciation of science. These programs attract large enthusiastic crowds often with young children participating in these family learning experiences. The public will become more informed, educated, and inspired about astronomy and will also be provided with information that will allow them to continue to learn after this outreach activity. Large and unique audiences often have common problems, and their solutions and the lessons learned will be presented. Interaction with the participants in this session will provide important community feedback used to improve astronomy outreach for large and unique audiences. New ways to expand astronomy outreach to new large audiences will be discussed.

  4. Beryllium - A Unique Material in Nuclear Applications

    Energy Technology Data Exchange (ETDEWEB)

    T., A. Tomberlin

    2004-11-01

    Beryllium, due to its unique combination of structural, chemical, atomic number, and neutron absorption cross section characteristics, has been used successfully as a neutron reflector for three generations of nuclear test reactors at the Idaho National Engineering and Environmental Laboratory (INEEL). The Advanced Test Reactor (ATR), the largest test reactor in the world, has utilized five successive beryllium neutron reflectors and is scheduled for continued operation with a sixth beryllium reflector. A high radiation environment in a test reactor produces radiation damage and other changes in beryllium. These changes necessitate safety analysis of the beryllium, methods to predict performance, and appropriate surveillances. Other nuclear applications also utilize beryllium. Beryllium, given its unique atomic, physical, and chemical characteristics, is widely used as a “window” for x-rays and gamma rays. Beryllium, intimately mixed with high-energy alpha radiation emitters has been successfully used to produce neutron sources. This paper addresses operational experience and methodologies associated with the use of beryllium in nuclear test reactors and in “windows” for x-rays and gamma rays. Other nuclear applications utilizing beryllium are also discussed.

  5. Targeting Transcription Factor Binding to DNA by Competing with DNA Binders as an Approach for Controlling Gene Expression.

    Science.gov (United States)

    Bouhlel, Mohamed Amine; Lambert, Melanie; David-Cordonnier, Marie-Helene

    2015-01-01

    Transcription factors are recognized as the master regulators of gene expression. Interestingly, about 10% of the transcription factors described in mammals are up to date directly implicated in a very large number of human diseases. With the exception of ligand-inducible nuclear receptors, transcription factors have longtime been considered as "undruggable" targets for therapeutics. However, the significant breakthroughs in their protein biochemistry and interactions with DNA at the structural level, together with increasing needs for new targeted-approaches particularly in cancers, has changed this postulate and opened the way for targeting transcription factors. Along with a better knowledge of their specific DNA binding sequences by genome wide and high throughput sequencing assay, these informations make possible the potent targeting of the transcription factors by three approaches dependently of their mechanism of action. In this review, we discuss the different physicochemical interactions between the transcription factors and the DNA helix, and the protein/protein interactions within a transcription factor complex and their impacts on the DNA structure. In order to impair transcription factor activities, small molecules compounds can either act by direct interaction on the transcription factor, or by blocking the protein/protein interactions in a transcription complex, or by competing with the transcription factor itself and specifically targeting its cognate binding sequence. For this latter mode of transcription targeting, we pay special attention to the DNA intercalating, alkylating or groove binders for transcription factor/DNA binding modulation.

  6. cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies

    Science.gov (United States)

    Chase, John H.; Bolyen, Evan; Rideout, Jai Ram

    2015-01-01

    ABSTRACT The number of samples in high-throughput comparative “omics” studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials, such as swabs or microcentrifuge tubes, however, so cual-id additionally generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project. By convention, we use “cual-id” to refer to the software, “CualID” to refer to the short, human-friendly identifiers, and “UUID” to refer to the globally unique identifiers. CualIDs are used by humans when they manually write or enter identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. Finally, cual-id optionally generates printable label sticker sheets containing Code 128 bar codes and CualIDs for labeling of sample collection and processing materials. IMPORTANCE The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more

  7. Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yingjie, E-mail: yzx@ansto.gov.au [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Bhadbhade, Mohan [Mark Wainwright Analytical Centre, University of New South Wales, Kensington, NSW 2052 (Australia); Karatchevtseva, Inna [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Price, Jason R. [Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168 (Australia); Liu, Hao [Centre for Clean Energy Technology, School of Chemistry and Forensic Science, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007 (Australia); Zhang, Zhaoming; Kong, Linggen [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Čejka, Jiří [Department of Mineralogy, National Museum, Václavské náměstí, 68, Prague 1, 115 79-CZ (Czech Republic); Lu, Kim; Lumpkin, Gregory R. [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia)

    2015-03-15

    Three new coordination polymers of uranium(VI) with pyromellitic acid (H{sub 4}btca) have been synthesized and structurally characterized. (ED)[(UO{sub 2})(btca)]·(DMSO)·3H{sub 2}O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH{sub 4}){sub 2}[(UO{sub 2}){sub 6}O{sub 2}(OH){sub 6}(btca)]·~6H{sub 2}O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO{sub 2}){sub 2}(H{sub 2}O)(btca)]·4H{sub 2}O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ{sub 5}-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5 Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H{sub 4}btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H{sub 4}btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ{sub 5}-(η{sub 1}:η{sub 2}:η{sub 1}:η{sub 2:}η{sub 1}) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported.

  8. Integration of transcriptional inputs at promoters of the arabinose catabolic pathway

    Directory of Open Access Journals (Sweden)

    Surette Michael G

    2010-06-01

    Full Text Available Abstract Background Most modelling efforts of transcriptional networks involve estimations of in vivo concentrations of components, binding affinities and reaction rates, derived from in vitro biochemical assays. These assays are difficult and in vitro measurements may not approximate actual in vivo conditions. Alternatively, changes in transcription factor activity can be estimated by using partially specified models which estimate the "hidden functions" of transcription factor concentration changes; however, non-unique solutions are a potential problem. We have applied a synthetic biology approach to develop reporters that are capable of measuring transcription factor activity in vivo in real time. These synthetic reporters are comprised of a constitutive promoter with an operator site for the specific transcription factor immediately downstream. Thus, increasing transcription factor activity is measured as repression of expression of the transcription factor reporter. Measuring repression instead of activation avoids the complications of non-linear interactions between the transcription factor and RNA polymerase which differs at each promoter. Results Using these reporters, we show that a simple model is capable of determining the rules of integration for multiple transcriptional inputs at the four promoters of the arabinose catabolic pathway. Furthermore, we show that despite the complex and non-linear changes in cAMP-CRP activity in vivo during diauxic shift, the synthetic transcription factor reporters are capable of measuring real-time changes in transcription factor activity, and the simple model is capable of predicting the dynamic behaviour of the catabolic promoters. Conclusions Using a synthetic biology approach we show that the in vivo activity of transcription factors can be quantified without the need for measuring intracellular concentrations, binding affinities and reaction rates. Using measured transcription factor activity we

  9. RNA-guided transcriptional regulation

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Mali, Prashant G.; Esvelt, Kevin M.

    2016-02-23

    Methods of modulating expression of a target nucleic acid in a cell are provided including introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to DNA, wherein the DNA includes the target nucleic acid, introducing into the cell a second foreign nucleic acid encoding a nuclease-null Cas9 protein that binds to the DNA and is guided by the one or more RNAs, introducing into the cell a third foreign nucleic acid encoding a transcriptional regulator protein or domain, wherein the one or more RNAs, the nuclease-null Cas9 protein, and the transcriptional regulator protein or domain are expressed, wherein the one or more RNAs, the nuclease-null Cas9 protein and the transcriptional regulator protein or domain co-localize to the DNA and wherein the transcriptional regulator protein or domain regulates expression of the target nucleic acid.

  10. Transcript Analysis of Stem Cells

    OpenAIRE

    Alison V. Nairn; Rosa, Mitche dela; Moremen, Kelley W.

    2010-01-01

    Quantitative real-time polymerase chain reaction (qRT-PCR) is a flexible and scalable method for analyzing transcript abundance that can be used at a single gene or high-throughput (>100 genes) level. Information obtained from this technique can be used as an indicator of potential regulation of glycosylation at the transcript level when combined with glycan structural or protein abundance data. This chapter describes detailed methods to design and perform qRT-PCR analyses and provides exampl...

  11. The core and unique proteins of haloarchaea

    Directory of Open Access Journals (Sweden)

    Capes Melinda D

    2012-01-01

    Full Text Available Abstract Background Since the first genome of a halophilic archaeon was sequenced in 2000, biologists have been advancing the understanding of genomic characteristics that allow for survival in the harsh natural environments of these organisms. An increase in protein acidity and GC-bias in the genome have been implicated as factors in tolerance to extreme salinity, desiccation, and high solar radiation. However, few previous attempts have been made to identify novel genes that would permit survival in such extreme conditions. Results With the recent release of several new complete haloarchaeal genome sequences, we have conducted a comprehensive comparative genomic analysis focusing on the identification of unique haloarchaeal conserved proteins that likely play key roles in environmental adaptation. Using bioinformatic methods, we have clustered 31,312 predicted proteins from nine haloarchaeal genomes into 4,455 haloarchaeal orthologous groups (HOGs. We assigned likely functions by association with established COG and KOG databases in NCBI. After identifying homologs in four additional haloarchaeal genomes, we determined that there were 784 core haloarchaeal protein clusters (cHOGs, of which 83 clusters were found primarily in haloarchaea. Further analysis found that 55 clusters were truly unique (tucHOGs to haloarchaea and qualify as signature proteins while 28 were nearly unique (nucHOGs, the vast majority of which were coded for on the haloarchaeal chromosomes. Of the signature proteins, only one example with any predicted function, Ral, involved in desiccation/radiation tolerance in Halobacterium sp. NRC-1, was identified. Among the core clusters, 33% was predicted to function in metabolism, 25% in information transfer and storage, 10% in cell processes and signaling, and 22% belong to poorly characterized or general function groups. Conclusion Our studies have established conserved groups of nearly 800 protein clusters present in all

  12. Unique expansions and intersections of Cantor sets

    Science.gov (United States)

    Baker, Simon; Kong, Derong

    2017-04-01

    To each α \\in (1/3,1/2) we associate the Cantor set Γα:={∑i=1∞ɛiαi:ɛi∈{0,1}, i⩾1}. In this paper we consider the intersection {{ Γ }α}{\\cap}≤ft({{ Γ }α}+t\\right) for any translation t\\in {R} . We pay special attention to those t with a unique {-1, 0, 1} α-expansion, and study the set Dα:={dimH(Γα∩(Γα+t)):t has a unique {-1,0,1} α-expansion}. We prove that there exists a transcendental number {αKL}≈ 0.394 33\\ldots such that: {{D}α} is finite for α \\in ≤ft({αKL},1/2\\right), {{D}{αKL}}} is infinitely countable, and {{D}α} contains an interval for α \\in ≤ft(1/3,{{αKL}\\right). We also prove that {{D}α} equals ≤ft[0,\\frac{log 2}{-log α}\\right] if and only if α \\in ≤ft(1/3,\\frac{3-\\sqrt{5}}{2}\\right] . As a consequence of our investigation we prove some results on the possible values of \\text{di}{{\\text{m}}H}≤ft({{ Γ }α}{\\cap}≤ft({{ Γ }α}+t\\right)\\right) when {{ Γ }α}{\\cap}≤ft({{ Γ }α}+t\\right) is a self-similar set. We also give examples of t with a continuum of {-1, 0, 1} α-expansions for which we can explicitly calculate \\text{di}{{\\text{m}}H}≤ft({{ Γ }α}{\\cap}≤ft({{ Γ }α}+t\\right)\\right), and for which {{ Γ }α}{\\cap}≤ft({{ Γ }α}+t\\right) is a self-similar set. We also construct α and t for which {{ Γ }α}{\\cap}≤ft({{ Γ }α}+t\\right) contains only transcendental numbers. Our approach makes use of digit frequency arguments and a lexicographic characterisation of those t with a unique {-1, 0, 1} α-expansion.

  13. Whispering Gallery Mode Thermometry.

    Science.gov (United States)

    Corbellini, Simone; Ramella, Chiara; Yu, Lili; Pirola, Marco; Fernicola, Vito

    2016-10-29

    This paper presents a state-of-the-art whispering gallery mode (WGM) thermometer system, which could replace platinum resistance thermometers currently used in many industrial applications, thus overcoming some of their well-known limitations and their potential for providing lower measurement uncertainty. The temperature-sensing element is a sapphire-crystal-based whispering gallery mode resonator with the main resonant modes between 10 GHz and 20 GHz. In particular, it was found that the WGM around 13.6 GHz maximizes measurement performance, affording sub-millikelvin resolution and temperature stability of better than 1 mK at 0 °C. The thermometer system was made portable and low-cost by developing an ad hoc interrogation system (hardware and software) able to achieve an accuracy in the order of a few parts in 10⁸ in the determination of resonance frequencies. Herein we report the experimental assessment of the measurement stability, repeatability and resolution, and the calibration of the thermometer in the temperature range from -74 °C to 85 °C. The combined standard uncertainty for a single temperature calibration point is found to be within 5 mK (i.e., comparable with state-of-the-art for industrial thermometry), and is mainly due to the employed calibration setup. The uncertainty contribution of the WGM thermometer alone is within a millikelvin.

  14. Whispering Gallery Mode Thermometry

    Directory of Open Access Journals (Sweden)

    Simone Corbellini

    2016-10-01

    Full Text Available This paper presents a state-of-the-art whispering gallery mode (WGM thermometer system, which could replace platinum resistance thermometers currently used in many industrial applications, thus overcoming some of their well-known limitations and their potential for providing lower measurement uncertainty. The temperature-sensing element is a sapphire-crystal-based whispering gallery mode resonator with the main resonant modes between 10 GHz and 20 GHz. In particular, it was found that the WGM around 13.6 GHz maximizes measurement performance, affording sub-millikelvin resolution and temperature stability of better than 1 mK at 0 °C. The thermometer system was made portable and low-cost by developing an ad hoc interrogation system (hardware and software able to achieve an accuracy in the order of a few parts in 109 in the determination of resonance frequencies. Herein we report the experimental assessment of the measurement stability, repeatability and resolution, and the calibration of the thermometer in the temperature range from −74 °C to 85 °C. The combined standard uncertainty for a single temperature calibration point is found to be within 5 mK (i.e., comparable with state-of-the-art for industrial thermometry, and is mainly due to the employed calibration setup. The uncertainty contribution of the WGM thermometer alone is within a millikelvin.

  15. Uniqueness and Tradition, according to Patek Philippe

    Directory of Open Access Journals (Sweden)

    Costin Popescu

    2014-11-01

    Full Text Available Products tend to become objects of psycho-affective investments, more than instruments with practical-functional duties. Watches form a product category where this evolution is manifest. The biggest watch manufacturers sell subjective time, meant to give (more spiritual consistency to those who buy and use them. The advertisements of a campaign carried out in the 1990s by Patek Philippe, producer of luxury watches, convey elitist values: uniqueness, tradition. The requirements for the integration of such values claim a high complexity of the advertisements; the headlines, for example, ask their addressees to redefine concepts (tradition; the body texts use argumentative layers; the images present characters whose hands form expressive configurations, etc. Such efforts to elaborate commercial messages prove the symbolic ambitions of advertising, one of the most prominent factors to mould meaning in the social life.

  16. Imaging concerns unique to twin pregnancy.

    Science.gov (United States)

    Mahalingam, Sowmya; Dighe, Manjiri

    2014-01-01

    The incidence of multiple gestations is increasing with rising maternal age and the utilization of artificial reproductive techniques. Twinning confers an increased risk to the pregnancy, with higher incidence of structural anomalies, preterm delivery, and perinatal morbidity and mortality. Certain conditions are unique to twin pregnancy, such as the twin-to-twin transfusion syndrome and the acardiac twin, secondary to vascular sharing between both the fetuses. Conjoined twinning is a phenomenon occurring because of late splitting of the zygote. Advances in imaging have increased our ability to manage multiple pregnancies with accurate prenatal diagnosis, better antenatal surveillance, and novel image-guided procedures. The purpose of this article is to provide an overview of the twinning process, including the pathophysiology, diagnostic pearls, and dilemmas and to briefly outline the outcomes and available treatment options to assist the radiologist in better management of multiple gestations. Copyright © 2014 Mosby, Inc. All rights reserved.

  17. Mushrooms—Biologically Distinct and Nutritionally Unique

    Science.gov (United States)

    Feeney, Mary Jo; Miller, Amy Myrdal; Roupas, Peter

    2014-01-01

    Mushrooms are fungi, biologically distinct from plant- and animal-derived foods (fruits, vegetables, grains, dairy, protein [meat, fish, poultry, legumes, nuts, and seeds]) that comprise the US Department of Agriculture food patterns operationalized by consumer-focused MyPlate messages. Although mushrooms provide nutrients found in these food groups, they also have a unique nutrient profile. Classified into food grouping systems by their use as a vegetable, mushrooms’ increasing use in main entrées in plant-based diets is growing, supporting consumers’ efforts to follow dietary guidance recommendations. Mushrooms’ nutrient and culinary characteristics suggest it may be time to reevaluate food groupings and health benefits in the context of 3 separate food kingdoms: plants/botany, animals/zoology, and fungi/mycology. PMID:25435595

  18. Evaluation of a unique cw laser in radial thermokeratoplasty

    Science.gov (United States)

    Smithpeter, Colin L.; Welch, Ashley J.; Rylander, Henry G., III

    1993-06-01

    A unique continuous wave (cw) holmium laser ((lambda) equals 2.09 micrometers , Rare Earth Medical) has been evaluated as a new heating modality for thermokeratoplasty. Thermokeratoplasty is a refractive surgical procedure for the correction of hyperopia which uses selective heating to reshape the cornea. The holmium laser is highly effective in this procedure due to the high absorption coefficient ((mu) a equals 27.55 cm-1) of the cornea at 2.09 micrometers . The depth of corneal photocoagulation has been evaluated with histological studies of enucleated porcine eyes that were irradiated with the cw Ho:YAG laser. Laser power and exposure time ranged from 300 mW to 800 mW and 100 ms to 800 ms, respectively. The laser was delivered to the eyes via a 600 micrometers low-OH optical fiber. Coagulation depth was determined by birefringence microscopy of the corneal sections. Our studies also compared the effects of contact and non-contact irradiation and found significant advantages with the contact mode. The optimal laser parameters determined from the histology studies were used for in vivo rabbit studies to quantify the refractive correction possible. One coagulation was placed on each of sixteen equiangular rays taken from a central, clear, optical zone in the cornea with a diameter of 7 mm. Refractive changes in the central cornea were quantified with a keratoscope. Initial procedures resulted in refractive changes up to five diopters. The keratoscope results showed a significant regression at three weeks post- operatively.

  19. Liver diseases in pregnancy: Diseases not unique to pregnancy

    Science.gov (United States)

    Almashhrawi, Ashraf A; Ahmed, Khulood T; Rahman, Rubayat N; Hammoud, Ghassan M; Ibdah, Jamal A

    2013-01-01

    Pregnancy is a special clinical state with several normal physiological changes that influence body organs including the liver. Liver disease can cause significant morbidity and mortality in both pregnant women and their infants. Few challenges arise in reaching an accurate diagnosis in light of such physiological changes. Laboratory test results should be carefully interpreted and the knowledge of what normal changes to expect is prudent to avoid clinical misjudgment. Other challenges entail the methods of treatment and their safety for both the mother and the baby. This review summarizes liver diseases that are not unique to pregnancy. We focus on viral hepatitis and its mode of transmission, diagnosis, effect on the pregnancy, the mother, the infant, treatment, and breast-feeding. Autoimmune hepatitis, primary biliary cirrhosis, primary sclerosing cholangitis, Wilson’s disease, Budd Chiari and portal vein thrombosis in pregnancy are also discussed. Pregnancy is rare in patients with cirrhosis because of the metabolic and hormonal changes associated with cirrhosis. Variceal bleeding can happen in up to 38% of cirrhotic pregnant women. Management of portal hypertension during pregnancy is discussed. Pregnancy increases the pathogenicity leading to an increase in the rate of gallstones. We discuss some of the interventions for gallstones in pregnancy if symptoms arise. Finally, we provide an overview of some of the options in managing hepatic adenomas and hepatocellular carcinoma during pregnancy. PMID:24282352

  20. Unique contributions of Keraleeya Ayurveda in pediatric health care.

    Science.gov (United States)

    Chandran, Seetha; Dinesh, K S; Patgiri, B J; Dharmarajan, Prasanth

    2018-02-19

    Childhood is considered as the most important phase in life, which determines the quality of health, well being, learning and behaviour across the lifespan. This may be the reason for giving the foremost position for Balacikitsa among Ashtangas (8 branches) of Ayurveda. The regional growth of indigenous medicine gave significant contribution for the development of primary health care. Kerala has major contribution of many authentic textbooks of Balacikitsa like Arogyakalpadruma, Vaidya Tarakam etc. These are more practically oriented and it can be considered as a physician's quick reference hand book. Many new diseases which are not mentioned in classical textbooks have found their place in these books. Medications like Praakaara yoga, Uramarunnuprayoga were administered in children as a mode of immunization, which helps in the maintenance of health and prevention of disease. Many diseases like Karappan (balavisarpa), Shakarogas etc. were common in Kerala and various indigenous treatment modalities were developed for such diseases. Single drug Prayogas with herbs like Mayaphal (galls), Tripadi (DesmodiumTriflorum L.), etc. and yogams like Nalikerakwatha (Putapakakalpana), Mukkuti (Takrakalpana) etc. were practiced commonly. Many effective therapies like Shashtikapindasweda, Thalapothichil (Sirolepa) etc. are an inevitable part of Balacikitsa. In this paper, an attempt is made to compile the theoretical concepts and unique practices of Balacikitsa in Kerala and to convey it's importance. The present article also addresses, how these vernacular books and traditional knowledge waned away from the Mainstream Ayurveda. Copyright © 2017 Transdisciplinary University, Bangalore and World Ayurveda Foundation. Published by Elsevier B.V. All rights reserved.

  1. MicroRNA-27a regulates basal transcription by targeting the p44 subunit of general transcription factor IIH.

    Science.gov (United States)

    Portal, Maximiliano M

    2011-05-24

    General transcription factor IIH (TFIIH) is a complex RNA polymerase II basal transcription factor comprising 10 different polypeptides that display activities involved in transcription and DNA repair processes. Although biochemical studies have uncovered TFIIH importance, little is known about how the mRNAs that code for TFIIH subunits are regulated. Here it is shown that mRNAs encoding seven of the TFIIH subunits (p34, p44, p52, p62, XPB, CDK7, and p8) are regulated at the posttranscriptional level in a Dicer-dependent manner. Indeed, abolition of the miRNA pathway induces abnormal accumulation, stabilization, and translational activation of these seven mRNAs. Herein, miR-27a was identified as a key regulator of p44 mRNA. Moreover, miR-27a was shown to destabilize the p44 subunit of the TFIIH complex during the G2-M phase, thereby modulating the transcriptional shutdown observed during this transition. This work is unique in providing a demonstration of global transcriptional regulation through the action of a single miRNA.

  2. The ets-related transcription factor GABP directs bidirectional transcription.

    Directory of Open Access Journals (Sweden)

    Patrick J Collins

    2007-11-01

    Full Text Available Approximately 10% of genes in the human genome are distributed such that their transcription start sites are located less than 1 kb apart on opposite strands. These divergent gene pairs have a single intergenic segment of DNA, which in some cases appears to share regulatory elements, but it is unclear whether these regions represent functional bidirectional promoters or two overlapping promoters. A recent study showed that divergent promoters are enriched for consensus binding sequences of a small group of transcription factors, including the ubiquitous ets-family transcription factor GA-binding protein (GABP. Here we show that GABP binds to more than 80% of divergent promoters in at least one cell type. Furthermore, we demonstrate that GABP binding is correlated and associated with bidirectional transcriptional activity in a luciferase transfection assay. In addition, we find that the addition of a strict consensus GABP site into a set of promoters that normally function in only one direction significantly increases activity in the opposite direction in 67% of cases. Our findings demonstrate that GABP regulates the majority of divergent promoters and suggest that bidirectional transcriptional activity is mediated through GABP binding and transactivation at both divergent and nondivergent promoters.

  3. Étude et développement d'un flash X rafale à foyer unique

    Science.gov (United States)

    Idrissi, M. M.; Viladrosa, R.; Robert, E.; Cachoncinlle, C.; Pouvesle, J. M.

    2003-06-01

    Nous présentons les premiers résultats de l'étude d'une nouvelle source, compacte, permettant de produire à partir d'un foyer unique des trains d'impulsions de photons X d'énergie allant de quelques keV à quelques centaines de keV. La source doit fonctionner à très haute fréquence, de quelques centaines de Hz en mode pulsé sur plusieurs secondes, à quelques kHz en mode rafale sur quelques coups (3 à 5impulsions par rafale). Au stade actuel de développement la source peut fonctionner jusqu'à 500 1-12 en mode pulsé et à plus de 2kHz en mode rafale sur des trains de 5impulsions. L'énergie des rayons X dans ces deux modes peut atteindre plusieurs centaines dekeV.

  4. Mode-to-mode energy transfers in convective patterns

    Indian Academy of Sciences (India)

    Abstract. We investigate the energy transfer between various Fourier modes in a low- dimensional model for thermal convection. We have used the formalism of mode-to-mode energy transfer rate in our calculation. The evolution equations derived using this scheme is the same as those derived using the hydrodynamical ...

  5. Emerging Roles of CREB-Regulated Transcription Coactivators in Brain Physiology and Pathology.

    OpenAIRE

    Saura, C.A.; Cardinaux, J R

    2017-01-01

    The brain has the ability to sense, coordinate, and respond to environmental changes through biological processes involving activity-dependent gene expression. cAMP-response element binding protein (CREB)-regulated transcription coactivators (CRTCs) have recently emerged as novel transcriptional regulators of essential biological functions, while their deregulation is linked to age-related human diseases. In the brain, CRTCs are unique signaling factors that act as sensors and integrators of ...

  6. Azimuthal decomposition of optical modes

    CSIR Research Space (South Africa)

    Dudley, Angela L

    2012-07-01

    Full Text Available This presentation analyses the azimuthal decomposition of optical modes. Decomposition of azimuthal modes need two steps, namely generation and decomposition. An azimuthally-varying phase (bounded by a ring-slit) placed in the spatial frequency...

  7. Free boundary ballooning mode representation

    Science.gov (United States)

    Zheng, L. J.

    2012-10-01

    A new type of ballooning mode invariance is found in this paper. Application of this invariance is shown to be able to reduce the two-dimensional problem of free boundary high n modes, such as the peeling-ballooning modes, to a one-dimensional problem. Here, n is toroidal mode number. In contrast to the conventional ballooning representation, which requires the translational invariance of the Fourier components of the perturbations, the new invariance reflects that the independent solutions of the high n mode equations are translationally invariant from one radial interval surrounding a single singular surface to the other intervals. The conventional ballooning mode invariance breaks down at the vicinity of plasma edge, since the Fourier components with rational surfaces in vacuum region are completely different from those with rational surfaces in plasma region. But, the new type of invariance remains valid. This overcomes the limitation of the conventional ballooning mode representation for studying free boundary modes.

  8. Aristotelian Syllogistic, Subalternate Modes, Theophrastus’ Modes and the Fourth Figure

    OpenAIRE

    СЛИНИН Я.А.

    2015-01-01

    In his treatise «New Essays Concerning Human Understanding» Leibniz gives some evidence which suggests that he believed that each of the four figures of Aristotle’s categorical syllogism has 6 correct modes. It is known that Aristotle stated and proved correct syllogisms modes in the three figures, with the fi rst of them having a number of the indirect modes. Why Aristotle did not explicitly introduced into his syllogistic subalternative modes and modes with conversed conclusion? In the pape...

  9. Damage mechanics - failure modes

    Energy Technology Data Exchange (ETDEWEB)

    Krajcinovic, D.; Vujosevic, M. [Arizona State Univ., Tempe, AZ (United States)

    1996-12-31

    The present study summarizes the results of the DOE sponsored research program focused on the brittle failure of solids with disordered microstructure. The failure is related to the stochastic processes on the microstructural scale; namely, the nucleation and growth of microcracks. The intrinsic failure modes, such as the percolation, localization and creep rupture, are studied by emphasizing the effect of the micro-structural disorder. A rich spectrum of physical phenomena and new concepts that emerges from this research demonstrates the reasons behind the limitations of traditional, deterministic, and local continuum models.

  10. Localized Acoustic Surface Modes

    KAUST Repository

    Farhat, Mohamed

    2015-08-04

    We introduce the concept of localized acoustic surface modes (ASMs). We demonstrate that they are induced on a two-dimensional cylindrical rigid surface with subwavelength corrugations under excitation by an incident acoustic plane wave. Our results show that the corrugated rigid surface is acoustically equivalent to a cylindrical scatterer with uniform mass density that can be represented using a Drude-like model. This, indeed, suggests that plasmonic-like acoustic materials can be engineered with potential applications in various areas including sensing, imaging, and cloaking.

  11. Phylogenetic and Transcription Analysis of Chrysanthemum WRKY Transcription Factors

    Science.gov (United States)

    Song, Aiping; Li, Peiling; Jiang, Jiafu; Chen, Sumei; Li, Huiyun; Zeng, Jun; Shao, Yafeng; Zhu, Lu; Zhang, Zhaohe; Chen, Fadi

    2014-01-01

    WRKY transcription factors are known to function in a number of plant processes. Here we have characterized 15 WRKY family genes of the important ornamental species chrysanthemum (Chrysanthemum morifolium). A total of 15 distinct sequences were isolated; initially internal fragments were amplified based on transcriptomic sequence, and then the full length cDNAs were obtained using RACE (rapid amplification of cDNA ends) PCR. The transcription of these 15 genes in response to a variety of phytohormone treatments and both biotic and abiotic stresses was characterized. Some of the genes behaved as would be predicted based on their homology with Arabidopsis thaliana WRKY genes, but others showed divergent behavior. PMID:25196345

  12. The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts

    NARCIS (Netherlands)

    Peviani, Alessia; Lastdrager, Jeroen; Hanson, Johannes; Snel, Berend

    2016-01-01

    Basic leucine zippers (bZIPs) form a large plant transcription factor family. C and S1 bZIP groups can heterodimerize, fulfilling crucial roles in seed development and stress response. S1 sequences also harbor a unique regulatory mechanism, termed Sucrose-Induced Repression of Translation (SIRT).

  13. A rational framework for selecting modes of ventilation.

    Science.gov (United States)

    Mireles-Cabodevila, Eduardo; Hatipoğlu, Umur; Chatburn, Robert L

    2013-02-01

    Mechanical ventilation is a life-saving intervention for respiratory failure and thus has become the cornerstone of the practice of critical care medicine. A mechanical ventilation mode describes the predetermined pattern of patient-ventilator interaction. In recent years there has been a dizzying proliferation of mechanical ventilation modes, driven by technological advances and market pressures, rather than clinical data. The comparison of these modes is hampered by the sheer number of combinations that need to be tested against one another, as well as the lack of a coherent, logical nomenclature that accurately describes a mode. In this paper we propose a logical nomenclature for mechanical ventilation modes, akin to biological taxonomy. Accordingly, the control variable, breath sequence, and targeting schemes for the primary and secondary breaths represent the order, family, genus, and species, respectively, for the described mode. To distinguish unique operational algorithms, a fifth level of distinction, termed variety, is utilized. We posit that such coherent ordering would facilitate comparison and understanding of modes. Next we suggest that the clinical goals of mechanical ventilation may be simplified into 3 broad categories: provision of safe gas exchange; provision of comfort; and promotion of liberation from mechanical ventilation. Safety is achieved via optimization of ventilation-perfusion matching and pressure-volume relationship of the lungs. Comfort is provided by fostering patient-ventilator synchrony. Liberation is promoted by optimization of the weaning experience. Then we follow a paradigm that matches the technological capacity of a particular mode to achieving a specific clinical goal. Finally, we provide the reader with a comparison of existing modes based on these principles. The status quo in mechanical ventilation mode nomenclature impedes communication and comparison of existing mechanical ventilation modes. The proposed model

  14. Independent tunability of the double-mode-locked cw dye laser.

    LENUS (Irish Health Repository)

    Bourkoff, E

    1979-06-01

    We report a new configuration that enables the double-mode-locked cw dye laser to be independently tunable. In addition, the output coupling at each of the two wavelengths can be independently specified. A series of oscillographs shows some interesting features unique to double mode locking and also shows the effects of varying the two cavity lengths with respect to each other.

  15. Unique type of isolated cardiac valvular amyloidosis

    Directory of Open Access Journals (Sweden)

    Reehana Salma

    2006-10-01

    Full Text Available Abstract Background Amyloid deposition in heart is a common occurrence in systemic amyloidosis. But localised valvular amyloid deposits are very uncommon. It was only in 1922 that the cases of valvular amyloidosis were reported. Then in 1980, Goffin et al reported another type of valvular amyloidosis, which he called the dystrophic valvular amyloidosis. We report a case of aortic valve amyloidosis which is different from the yet described valvular amyloidosis. Case presentation A 72 years old gentleman underwent urgent aortic valve replacement. Intraoperatively, a lesion was found attached to the inferior surface of his bicuspid aortic valve. Histopathology examination of the valve revealed that the lesion contained amyloid deposits, identified as AL amyloidosis. The serum amyloid A protein (SAP scan was normal and showed no evidence of systemic amyloidosis. The ECG and echocardiogram were not consistent with cardiac amyloidosis. Conclusion Two major types of cardiac amyloidosis have been described in literature: primary-myelomatous type (occurs with systemic amyolidosis, and senile type(s. Recently, a localised cardiac dystrophic valvular amyloidosis has been described. In all previously reported cases, there was a strong association of localised valvular amyloidosis with calcific deposits. Ours is a unique case which differs from the previously reported cases of localised valvular amyloidosis. In this case, the lesion was not associated with any scar tissue. Also there was no calcific deposit found. This may well be a yet unknown type of isolated valvular amyloidosis.

  16. Unique Ganglioside Recognition Strategies for Clostridial Neurotoxins

    Energy Technology Data Exchange (ETDEWEB)

    Benson, Marc A.; Fu, Zhuji; Kim, Jung-Ja P.; Baldwin, Michael R. (MCW); (UMC)

    2012-03-15

    Botulinum neurotoxins (BoNTs) and tetanus neurotoxin are the causative agents of the paralytic diseases botulism and tetanus, respectively. The potency of the clostridial neurotoxins (CNTs) relies primarily on their highly specific binding to nerve terminals and cleavage of SNARE proteins. Although individual CNTs utilize distinct proteins for entry, they share common ganglioside co-receptors. Here, we report the crystal structure of the BoNT/F receptor-binding domain in complex with the sugar moiety of ganglioside GD1a. GD1a binds in a shallow groove formed by the conserved peptide motif E ... H ... SXWY ... G, with additional stabilizing interactions provided by two arginine residues. Comparative analysis of BoNT/F with other CNTs revealed several differences in the interactions of each toxin with ganglioside. Notably, exchange of BoNT/F His-1241 with the corresponding lysine residue of BoNT/E resulted in increased affinity for GD1a and conferred the ability to bind ganglioside GM1a. Conversely, BoNT/E was not able to bind GM1a, demonstrating a discrete mechanism of ganglioside recognition. These findings provide a structural basis for ganglioside binding among the CNTs and show that individual toxins utilize unique ganglioside recognition strategies.

  17. Arachnoiditis ossificans and syringomyelia: A unique presentation

    Science.gov (United States)

    Opalak, Charles F.; Opalak, Michael E.

    2015-01-01

    Background: Arachnoiditis ossificans (AO) is a rare disorder that was differentiated from leptomeningeal calcification by Kaufman and Dunsmore in 1971. It generally presents with progressive lower extremity myelopathy. Though the underlying etiology has yet to be fully described, it has been associated with various predisposing factors including vascular malformations, previous intradural surgery, myelograms, and adhesive arachnoiditis. Associated conditions include syringomyelia and arachnoid cyst. The preferred diagnostic method is noncontrast computed tomography (CT). Surgical intervention is still controversial and can include decompression and duroplasty or durotomy. Case Description: The authors report the case of a 62-year-old male with a history of paraplegia who presented with a urinary tract infection and dysautonomia. His past surgical history was notable for a C4–C6 anterior fusion and an intrathecal phenol injection for spasticity. A magnetic resonance image (MR) also demonstrated a T6-conus syringx. At surgery, there was significant ossification of the arachnoid/dura, which was removed. After a drain was placed in the syrinx, there was a significant neurologic improvement. Conclusion: This case demonstrates a unique presentation of AO and highlights the need for CT imaging when a noncommunicating syringx is identified. In addition, surgical decompression can achieve good results when AO is associated with concurrent compressive lesions. PMID:26693389

  18. Biomechanics of the unique pterosaur pteroid.

    Science.gov (United States)

    Palmer, Colin; Dyke, Gareth J

    2010-04-07

    Pterosaurs, flying reptiles from the Mesozoic, had wing membranes that were supported by their arm bones and a super-elongate fourth finger. Associated with the wing, pterosaurs also possessed a unique wrist bone--the pteroid--that functioned to support the forward part of the membrane in front of the leading edge, the propatagium. Pteroid shape varies across pterosaurs and reconstructions of its orientation vary (projecting anteriorly to the wing leading edge or medially, lying alongside it) and imply differences in the way that pterosaurs controlled their wings. Here we show, using biomechanical analysis and considerations of aerodynamic efficiency of a representative ornithocheirid pterosaur, that an anteriorly orientated pteroid is highly unlikely. Unless these pterosaurs only flew steadily and had very low body masses, their pteroids would have been likely to break if orientated anteriorly; the degree of movement required for a forward orientation would have introduced extreme membrane strains and required impractical tensioning in the propatagium membrane. This result can be generalized for other pterodactyloid pterosaurs because the resultant geometry of an anteriorly orientated pteroid would have reduced the aerodynamic performance of all wings and required the same impractical properties in the propatagium membrane. We demonstrate quantitatively that the more traditional reconstruction of a medially orientated pteroid was much more stable both structurally and aerodynamically, reflecting likely life position.

  19. Detecting Beer Intake by Unique Metabolite Patterns.

    Science.gov (United States)

    Gürdeniz, Gözde; Jensen, Morten Georg; Meier, Sebastian; Bech, Lene; Lund, Erik; Dragsted, Lars Ove

    2016-12-02

    Evaluation of the health related effects of beer intake is hampered by the lack of accurate tools for assessing intakes (biomarkers). Therefore, we identified plasma and urine metabolites associated with recent beer intake by untargeted metabolomics and established a characteristic metabolite pattern representing raw materials and beer production as a qualitative biomarker of beer intake. In a randomized, crossover, single-blinded meal study (MSt1), 18 participants were given, one at a time, four different test beverages: strong, regular, and nonalcoholic beers and a soft drink. Four participants were assigned to have two additional beers (MSt2). In addition to plasma and urine samples, test beverages, wort, and hops extract were analyzed by UPLC-QTOF. A unique metabolite pattern reflecting beer metabolome, including metabolites derived from beer raw material (i.e., N-methyl tyramine sulfate and the sum of iso-α-acids and tricyclohumols) and the production process (i.e., pyro-glutamyl proline and 2-ethyl malate), was selected to establish a compliance biomarker model for detection of beer intake based on MSt1. The model predicted the MSt2 samples collected before and up to 12 h after beer intake correctly (AUC = 1). A biomarker model including four metabolites representing both beer raw materials and production steps provided a specific and accurate tool for measurement of beer consumption.

  20. A Unique Civil Engineering Capstone Design Course

    Directory of Open Access Journals (Sweden)

    G Padmanabhan

    2018-02-01

    Full Text Available The North Dakota State University, USA, capstone course was developed as a unique model in response to the effort of the Accreditation Board of Engineering and Technology, USA, to streamline and improve design instruction in the curriculum and has steadily evolved to keep pace with the ever-changing technology and the expectations of the profession and the society we serve. A capstone design course by definition should be a design experience for students in the final year before graduation integrating all major design concepts they have learned up until then in the program. Carefully chosen real world projects with design content in all sub-disciplines of civil engineering are assigned in this team-taught course. Faculty and practicing professionals make presentations on design process; project management; leadership in an engineering environment; and public policy; global perspectives in engineering; and professional career and licensure. Practicing professionals also critique the final student presentations. Students work in teams with number of faculty serving as technical consultants, and a faculty mentor for each team to provide non-technical guidance and direction. The course requires students to demonstrate mastery of the curriculum and to work with others in a team environment. Course assessment includes evaluation of the final design, presentations, written technical reports, project design schedule, a project design journal, and reaction papers.

  1. Phase Transition and Uniqueness of Levelset Percolation

    Science.gov (United States)

    Broman, Erik; Meester, Ronald

    2017-06-01

    The main purpose of this paper is to introduce and establish basic results of a natural extension of the classical Boolean percolation model (also known as the Gilbert disc model). We replace the balls of that model by a positive non-increasing attenuation function l:(0,\\infty ) → [0,\\infty ) to create the random field Ψ (y)=\\sum _{x\\in η }l(|x-y|), where η is a homogeneous Poisson process in {\\mathbb {R}}^d. The field Ψ is then a random potential field with infinite range dependencies whenever the support of the function l is unbounded. In particular, we study the level sets Ψ _{\\ge h}(y) containing the points y\\in {\\mathbb {R}}^d such that Ψ (y)\\ge h. In the case where l has unbounded support, we give, for any d\\ge 2, a necessary and sufficient condition on l for Ψ _{\\ge h}(y) to have a percolative phase transition as a function of h. We also prove that when l is continuous then so is Ψ almost surely. Moreover, in this case and for d=2, we prove uniqueness of the infinite component of Ψ _{\\ge h} when such exists, and we also show that the so-called percolation function is continuous below the critical value h_c.

  2. Unique biosynthesis of sesquarterpenes (C35 terpenes).

    Science.gov (United States)

    Sato, Tsutomu

    2013-01-01

    To the best of my knowledge, only 19 cyclic and 8 linear C35 terpenes have been identified to date, and no family name was assigned to this terpene class until recently. In 2011, it was proposed that these C35 terpenes should be called sesquarterpenes. This review highlights the biosynthesis of two kinds of sesquarterpenes (C35 terpenes) that are produced via cyclization of a linear C35 isoprenoid in Bacillus and Mycobacterium species. In Bacillus species, a new type of terpene cyclase that has no sequence homology with any known terpene synthases, as well as a bifunctional terpene cyclase that biosynthesizes two classes of cyclic terpenes with different numbers of carbons as natural products, have been identified. On the other hand, in Mycobacterium species, the first bifunctional Z-prenyltransferase has been found, but a novel terpene cyclase and a unique polyprenyl reductase remain unidentified. The identification of novel enzyme types should lead to the discovery of many homologous enzymes and their products including novel natural compounds. On the other hand, many enzymes responsible for the biosynthesis of natural products have low substrate specificities in vitro. Therefore, to find novel natural products present in organisms, the multifunctionality of enzymes in the biosynthetic pathway of natural products should be analyzed.

  3. The AD: The unique anti-accelerator

    CERN Multimedia

    Slide show by Maximilien Brice. Voice (French only): Jacques Fichet. Content: Paola Catapano, Django Manglunki, CERN Bulletin

    2011-01-01

    Unlike other machines whose performance is measured in terms of energy records, AD's uniqueness resides in the fact that it can very effectively decelerate beams. At the hearth of antimatter production at CERN, the AD is making headlines in the world's press. This provides an excellent opportunity for us to retrace its history in images.   var flash_video_player=get_video_player_path(); insert_player_for_external('Video/Public/Movies/2011/CERN-MOVIE-2011-083/CERN-MOVIE-2011-083-0753-kbps-480x360-25-fps-audio-64-kbps-44-kHz-stereo', 'mms://mediastream.cern.ch/MediaArchive/Video/Public/Movies/2011/CERN-MOVIE-2011-083/CERN-MOVIE-2011-083-0480-kbps-384x288-25-fps-audio-128-kbps-48-kHz-stereo.wmv', 'false', 480, 360, 'http://mediaarchive.cern.ch/MediaArchive/Video/Public/Movies/2011/CERN-MOVIE-2011-083/CERN-MOVIE-2011-083-posterframe-480x360-at-5-percent.jpg', '1357551', true, '');  

  4. Standardization of Keyword Search Mode

    Science.gov (United States)

    Su, Di

    2010-01-01

    In spite of its popularity, keyword search mode has not been standardized. Though information professionals are quick to adapt to various presentations of keyword search mode, novice end-users may find keyword search confusing. This article compares keyword search mode in some major reference databases and calls for standardization. (Contains 3…

  5. Raman amplification of OAM modes

    DEFF Research Database (Denmark)

    Ingerslev, Kasper; Gregg, Patrick; Galili, Michael

    2017-01-01

    The set of fibre modes carrying orbital angular momentum (OAM) is a possible basis for mode division multiplexing. In this regard, fibres supporting OAM modes have been fabricated [1], and optical communication using these fibres, has been demonstrated [2]. A vital part of any long range communic...

  6. Fluxon modes in superconducting multilayers

    DEFF Research Database (Denmark)

    Pedersen, Niels Falsig; Madsen, Søren Peder

    2004-01-01

    We show how to construct fluxon modes from plasma modes in the inductively coupled stacked Josephson junctions, and consider some special cases of these fluxon modes analytically. In some cases we can find exact analytical solutions when we choose the bias current in a special way. We also consid...

  7. Design of large mode area, mode selection fiber

    Science.gov (United States)

    Jin, Liang; Xu, Li; Zhang, He; Zou, Yonggang; Ding, Ye; Ma, Xiaohui

    2014-12-01

    The paper study on the effect of index distribution on the mode field and calculated the mode distribution in various index profiles. A single mode gaussian hybrid multicore fiber with 19 hexagonally arranged high index quartz rods is designed and investigated. Theoretical and simulative results are presented and compared to the conventional large mode area double clad fiber, the fundamental mode (FM) area can be reached 694.28 μm2, the confinement loss of FM and high order modes (HOMs) are 0.186 dB/m and 1.48 dB/m respectively with the bending radius of 20 cm at 1.064 μm wavelength, moreover, the index distribution can resistant the mode field distortion, which caused by fiber bending. So the FM delivery can be formed and the beam quality can be improved.

  8. 7 CFR 780.13 - Verbatim transcripts.

    Science.gov (United States)

    2010-01-01

    ... of the hearing. The party requesting a verbatim transcript shall pay for the transcription service... 7 Agriculture 7 2010-01-01 2010-01-01 false Verbatim transcripts. 780.13 Section 780.13... AGRICULTURE SPECIAL PROGRAMS APPEAL REGULATIONS § 780.13 Verbatim transcripts. (a) Appellants and their...

  9. A Comparative Study of RNA Polymerase II Transcription Machinery in Yeasts

    Science.gov (United States)

    Sharma, Nimisha; Mehta, Surbhi

    The control of gene expression, predominantly at the level of transcription, plays a fundamental role in biological processes determining the phenotypic changes in cells and organisms. The eukaryotes have evolved a complex and sophisticated transcription machinery to transcribe DNA into RNA. RNA polymerase II enzyme lies at the centre of the transcription apparatus that comprises nearly 60 polypeptides and is responsible for the expression and regulation of proteinencoding genes. Much of our present understanding and knowledge of the RNA polymerase II transcription apparatus in eukaryotes has been derived from studies in Saccharomyces cerevisiae. More recently, Schizosaccharomyces pombe has emerged as a better model system to study transcription because the transcription mechanism in this yeast is closer to that in higher eukaryotes. Also, studies on components of the basal transcription machinery have revealed a number of properties that are common with other eukaryotes, but have also highlighted some features unique to S. pombe. In fact, the fungal transcription associated protein families show greater species specificity and only 15% of these proteins contain homologues shared between both S. cerevisiae and S. pombe. In this chapter, we compare the RNA polymerase II transcription apparatus in different yeasts.

  10. Circadian Control of Global Transcription

    Science.gov (United States)

    Li, Shujing; Zhang, Luoying

    2015-01-01

    Circadian rhythms exist in most if not all organisms on the Earth and manifest in various aspects of physiology and behavior. These rhythmic processes are believed to be driven by endogenous molecular clocks that regulate rhythmic expression of clock-controlled genes (CCGs). CCGs consist of a significant portion of the genome and are involved in diverse biological pathways. The transcription of CCGs is tuned by rhythmic actions of transcription factors and circadian alterations in chromatin. Here, we review the circadian control of CCG transcription in five model organisms that are widely used, including cyanobacterium, fungus, plant, fruit fly, and mouse. Comparing the similarity and differences in the five organisms could help us better understand the function of the circadian clock, as well as its output mechanisms adapted to meet the demands of diverse environmental conditions. PMID:26682214

  11. Circadian Control of Global Transcription

    Directory of Open Access Journals (Sweden)

    Shujing Li

    2015-01-01

    Full Text Available Circadian rhythms exist in most if not all organisms on the Earth and manifest in various aspects of physiology and behavior. These rhythmic processes are believed to be driven by endogenous molecular clocks that regulate rhythmic expression of clock-controlled genes (CCGs. CCGs consist of a significant portion of the genome and are involved in diverse biological pathways. The transcription of CCGs is tuned by rhythmic actions of transcription factors and circadian alterations in chromatin. Here, we review the circadian control of CCG transcription in five model organisms that are widely used, including cyanobacterium, fungus, plant, fruit fly, and mouse. Comparing the similarity and differences in the five organisms could help us better understand the function of the circadian clock, as well as its output mechanisms adapted to meet the demands of diverse environmental conditions.

  12. Mitochondrial transcription in mammalian cells.

    Science.gov (United States)

    Shokolenko, Inna N; Alexeyev, Mikhail F

    2017-01-01

    As a consequence of recent discoveries of intimate involvement of mitochondria with key cellular processes, there has been a resurgence of interest in all aspects of mitochondrial biology, including the intricate mechanisms of mitochondrial DNA maintenance and expression. Despite four decades of research, there remains a lot to be learned about the processes that enable transcription of genetic information from mitochondrial DNA to RNA, as well as their regulation. These processes are vitally important, as evidenced by the lethality of inactivating the central components of mitochondrial transcription machinery. Here, we review the current understanding of mitochondrial transcription and its regulation in mammalian cells. We also discuss key theories in the field and highlight controversial subjects and future directions as we see them.

  13. Evolution of a Unique Systems Engineering Capability

    Energy Technology Data Exchange (ETDEWEB)

    Robert M. Caliva; James A. Murphy; Kyle B. Oswald

    2011-06-01

    The Idaho National Laboratory (INL) is a science-based, applied engineering laboratory dedicated to supporting U.S. Department of Energy missions in nuclear and energy research, science, and national security. The INL’s Systems Engineering organization supports all of the various programs under this wide array of missions. As with any multifaceted organization, strategic planning is essential to establishing a consistent culture and a value discipline throughout all levels of the enterprise. While an organization can pursue operational excellence, product leadership or customer intimacy, it is extremely difficult to excel or achieve best-in-class at all three. In fact, trying to do so has resulted in the demise of a number of organizations given the very intricate balancing act that is necessary. The INL’s Systems Engineering Department has chosen to focus on customer intimacy where the customer’s needs are first and foremost and a more total solution is the goal. Frequently a total solution requires the employment of specialized tools to manage system complexity. However, it is only after understanding customer needs that tool selection and use would be pursued. This results in using both commercial-off-the-shelf (COTS) tools and, in some cases, requires internal development of specialized tools. This paper describes how a unique systems engineering capability, through the development of customized tools, evolved as a result of this customer-focused culture. It also addresses the need for a common information model or analysis framework and presents an overview of the tools developed to manage and display relationships between entities, support trade studies through the application of utility theory, and facilitate the development of a technology roadmap to manage system risk and uncertainty.

  14. Chromatin and Transcription in Yeast

    Science.gov (United States)

    Rando, Oliver J.; Winston, Fred

    2012-01-01

    Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field. PMID:22345607

  15. The rbcL gene of Populus deltoides has multiple transcripts and is redox-regulated in vitro.

    Science.gov (United States)

    Mehrotra, Sandhya; Trivedi, Prabodh Kumar; Sethuraman, Ajay; Mehrotra, Rajesh

    2011-03-15

    We report the discovery of three types of transcripts for the gene encoding large subunit of Rubisco (rbcL) from chloroplast genome of Populus deltoides, an angiospermic tree. While the larger two transcripts are in confirmation with reported transcripts for other rbcL genes as far as the 5' ends are concerned, the third transcript is unique since it lacks the consensus ribosome-binding site. We also report the molecular weights of several proteins interacting with the 5' untranslated region of the same mRNA and that the RNA-protein interaction in vitro is influenced by redox reagents. Copyright © 2010 Elsevier GmbH. All rights reserved.

  16. Transcription-dependent association of HDAC2 with active chromatin.

    Science.gov (United States)

    Jahan, Sanzida; Sun, Jian-Min; He, Shihua; Davie, James R

    2018-02-01

    Histone deacetylase 2 (HDAC2) catalyzes deacetylation of histones at the promoter and coding regions of transcribed genes and regulates chromatin structure and transcription. To explore the role of HDAC2 and phosphorylated HDAC2 in gene regulation, we studied the location along transcribed genes, the mode of recruitment and the associated proteins with HDAC2 and HDAC2S394ph in chicken polychromatic erythrocytes. We show that HDAC2 and HDAC2S394ph are associated with transcriptionally active chromatin and located in the interchromatin channels. HDAC2S394ph was present primarly at the upstream promoter region of the transcribed CA2 and GAS41 genes, while total HDAC2 was also found within the coding region of the CA2 gene. Recruitment of HDAC2 to these genes was partially dependent upon on-going transcription. Unmodified HDAC2 was associated with RNA binding proteins and interacted with RNA bound to the initiating and elongating forms of RNA polymerase II. HDAC2S394ph was not associated with RNA polymerase II. These results highlight the differential properties of unmodified and phosphorylated HDAC2 and the organization of acetylated transcriptionally active chromatin in the chicken polychromatic erythrocyte. © 2017 Wiley Periodicals, Inc.

  17. Expression of alternatively spliced sodium channel alpha-subunit genes. Unique splicing patterns are observed in dorsal root ganglia.

    Science.gov (United States)

    Raymond, Christopher K; Castle, John; Garrett-Engele, Philip; Armour, Christopher D; Kan, Zhengyan; Tsinoremas, Nicholas; Johnson, Jason M

    2004-10-29

    Molecular medicine requires the precise definition of drug targets, and tools are now in place to provide genome-wide information on the expression and alternative splicing patterns of any known gene. DNA microarrays were used to monitor transcript levels of the nine well-characterized alpha-subunit sodium channel genes across a broad range of tissues from cynomolgus monkey, a non-human primate model. Alternative splicing of human transcripts for a subset of the genes that are expressed in dorsal root ganglia, SCN8A (Na(v)1.6), SCN9A (Na(v)1.7), and SCN11A (Na(v)1.9) was characterized in detail. Genomic sequence analysis among gene family paralogs and between cross-species orthologs suggested specific alternative splicing events within transcripts of these genes, all of which were experimentally confirmed in human tissues. Quantitative PCR revealed that certain alternative splice events are uniquely expressed in dorsal root ganglia. In addition to characterization of human transcripts, alternatively spliced sodium channel transcripts were monitored in a rat model for neuropathic pain. Consistent down-regulation of all transcripts was observed, as well as significant changes in the splicing patterns of SCN8A and SCN9A.

  18. FOXO Transcriptional Factors and Long-Term Living

    Directory of Open Access Journals (Sweden)

    Ghulam Murtaza

    2017-01-01

    Full Text Available Several pathologies such as neurodegeneration and cancer are associated with aging, which is affected by many genetic and environmental factors. Healthy aging conceives human longevity, possibly due to carrying the defensive genes. For instance, FOXO (forkhead box O genes determine human longevity. FOXO transcription factors are involved in the regulation of longevity phenomenon via insulin and insulin-like growth factor signaling. Only one FOXO gene (FOXO DAF-16 exists in invertebrates, while four FOXO genes, that is, FOXO1, FOXO3, FOXO4, and FOXO6 are found in mammals. These four transcription factors are involved in the multiple cellular pathways, which regulate growth, stress resistance, metabolism, cellular differentiation, and apoptosis in mammals. However, the accurate mode of longevity by FOXO factors is unclear until now. This article describes briefly the existing knowledge that is related to the role of FOXO factors in human longevity.

  19. Polarization Mode Dispersion

    CERN Document Server

    Galtarossa, Andrea

    2005-01-01

    This book contains a series of tutorial essays on polarization mode dispersion (PMD) by the leading experts in the field. It starts with an introductory review of the basic concepts and continues with more advanced topics, including a thorough review of PMD mitigation techniques. Topics covered include mathematical representation of PMD, how to properly model PMD in numerical simulations, how to accurately measure PMD and other related polarization effects, and how to infer fiber properties from polarization measurements. It includes discussions of other polarization effects such as polarization-dependent loss and the interaction of PMD with fiber nonlinearity. It additionally covers systems issues like the impact of PMD on wavelength division multiplexed systems. This book is intended for research scientists or engineers who wish to become familiar with PMD and its system impacts.

  20. Thiol dioxygenases: unique families of cupin proteins.

    Science.gov (United States)

    Stipanuk, Martha H; Simmons, Chad R; Karplus, P Andrew; Dominy, John E

    2011-06-01

    motif for ADOs, or DUF1637 family members, is proposed. In ADOs, the conserved glutamate residue in cupin motif 1 is replaced by either glycine or valine. Both ADOs and CDOs appear to represent unique clades within the cupin superfamily.

  1. Unitary Evolution as a Uniqueness Criterion

    Science.gov (United States)

    Cortez, J.; Mena Marugán, G. A.; Olmedo, J.; Velhinho, J. M.

    2015-01-01

    It is well known that the process of quantizing field theories is plagued with ambiguities. First, there is ambiguity in the choice of basic variables describing the system. Second, once a choice of field variables has been made, there is ambiguity concerning the selection of a quantum representation of the corresponding canonical commutation relations. The natural strategy to remove these ambiguities is to demand positivity of energy and to invoke symmetries, namely by requiring that classical symmetries become unitarily implemented in the quantum realm. The success of this strategy depends, however, on the existence of a sufficiently large group of symmetries, usually including time-translation invariance. These criteria are therefore generally insufficient in non-stationary situations, as is typical for free fields in curved spacetimes. Recently, the criterion of unitary implementation of the dynamics has been proposed in order to select a unique quantization in the context of manifestly non-stationary systems. Specifically, the unitarity criterion, together with the requirement of invariance under spatial symmetries, has been successfully employed to remove the ambiguities in the quantization of linearly polarized Gowdy models as well as in the quantization of a scalar field with time varying mass, propagating in a static background whose spatial topology is either of a d-sphere (with d = 1, 2, 3) or a three torus. Following Ref. 3, we will see here that the symmetry and unitarity criteria allows for a complete removal of the ambiguities in the quantization of scalar fields propagating in static spacetimes with compact spatial sections, obeying field equations with an explicitly time-dependent mass, of the form ddot φ - Δ φ + s(t)φ = 0 . These results apply in particular to free fields in spacetimes which, like e.g. in the closed FRW models, are conformal to a static spacetime, by means of an exclusively time-dependent conformal factor. In fact, in such

  2. Do pediatric hospitalizations have a unique geography?

    Directory of Open Access Journals (Sweden)

    Jablonski Kathleen A

    2004-01-01

    Full Text Available Abstract Background In the U.S. small-area health services research studies are often based on the hospital service areas (HSAs defined by the Dartmouth Atlas of Healthcare project. These areas are based on the geographic origins of Medicare Part A hospital patients, the great majority of whom are seniors. It is reasonable to question whether the geographic system so defined is appropriate for health services research for all ages, particularly for children, who have a very different system of healthcare financing and provision in the U.S. Methods This article assesses the need for a unique system of HSAs to support pediatric small-area analyses. It is a cross-sectional analysis of California hospital discharges for two age groups – non-newborns 0–17 years old, and seniors. The measure of interest was index of localization, which is the percentage of HSA residents hospitalized in their home HSA. Indices were computed separately for each age group, and index agreement was assessed for 219 of the state's HSAs. We examined the effect of local pediatric inpatient volume and pediatric inpatient resources on the divergence of the age group indices. We also created a new system of HSAs based solely on pediatric patient origins, and visually compared maps of the traditional and the new system. Results The mean localization index for pediatric discharges was 20 percentage points lower than for Medicare cases, indicating a poorer fit of the traditional geographic system for children. The volume of pediatric cases did not appear to be associated with the magnitude of index divergence between the two age groups. Pediatric medical and surgical case subgroups gave very similar results, and both groups differed substantially from seniors. Location of children's hospitals and local pediatric bed supply were associated with Medicare-pediatric divergence. There was little visual correspondence between the maps of traditional and pediatric-specific HSAs

  3. Onions: a source of unique dietary flavonoids.

    Science.gov (United States)

    Slimestad, Rune; Fossen, Torgils; Vågen, Ingunn Molund

    2007-12-12

    Onion bulbs (Allium cepa L.) are among the richest sources of dietary flavonoids and contribute to a large extent to the overall intake of flavonoids. This review includes a compilation of the existing qualitative and quantitative information about flavonoids reported to occur in onion bulbs, including NMR spectroscopic evidence used for structural characterization. In addition, a summary is given to index onion cultivars according to their content of flavonoids measured as quercetin. Only compounds belonging to the flavonols, the anthocyanins, and the dihydroflavonols have been reported to occur in onion bulbs. Yellow onions contain 270-1187 mg of flavonols per kilogram of fresh weight (FW), whereas red onions contain 415-1917 mg of flavonols per kilogram of FW. Flavonols are the predominant pigments of onions. At least 25 different flavonols have been characterized, and quercetin derivatives are the most important ones in all onion cultivars. Their glycosyl moieties are almost exclusively glucose, which is mainly attached to the 4', 3, and/or 7-positions of the aglycones. Quercetin 4'-glucoside and quercetin 3,4'-diglucoside are in most cases reported as the main flavonols in recent literature. Analogous derivatives of kaempferol and isorhamnetin have been identified as minor pigments. Recent reports indicate that the outer dry layers of onion bulbs contain oligomeric structures of quercetin in addition to condensation products of quercetin and protocatechuic acid. The anthocyanins of red onions are mainly cyanidin glucosides acylated with malonic acid or nonacylated. Some of these pigments facilitate unique structural features like 4'-glycosylation and unusual substitution patterns of sugar moieties. Altogether at least 25 different anthocyanins have been reported from red onions, including two novel 5-carboxypyranocyanidin-derivatives. The quantitative content of anthocyanins in some red onion cultivars has been reported to be approximately 10% of the total

  4. The impact of transcriptional tuning on in vitro integrated rRNA transcription and ribosome construction

    Science.gov (United States)

    Fritz, Brian R.; Jewett, Michael C.

    2014-01-01

    In vitro ribosome construction could enable studies of ribosome assembly and function, provide a route toward constructing minimal cells for synthetic biology, and permit the construction of ribosome variants with new functions. Toward these long-term goals, we recently reported on an integrated, one-pot ribosomal RNA synthesis (rRNA), ribosome assembly, and translation technology (termed iSAT) for the construction of Escherichia coli ribosomes in crude ribosome-free S150 extracts. Here, we aimed to improve the activity of iSAT through transcriptional tuning. Specifically, we increased transcriptional efficiency through 3′ modifications to the rRNA gene sequences, optimized plasmid and polymerase concentrations, and demonstrated the use of a T7-promoted rRNA operon for stoichiometrically balanced rRNA synthesis and native rRNA processing. Our modifications produced a 45-fold improvement in iSAT protein synthesis activity, enabling synthesis of 429 ± 15 nmol/l green fluorescent protein in 6 h batch reactions. Further, we show that the translational activity of ribosomes purified from iSAT reactions is about 20% the activity of native ribosomes purified directly from E. coli cells. Looking forward, we believe iSAT will enable unique studies to unravel the systems biology of ribosome biogenesis and open the way to new methods for making and studying ribosomal variants. PMID:24792158

  5. Transcriptional Silencing of Retroviral Vectors

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M.; Pedersen, F.S.

    1996-01-01

    Although retroviral vector systems have been found to efficiently transduce a variety of cell types in vitro, the use of vectors based on murine leukemia virus in preclinical models of somatic gene therapy has led to the identification of transcriptional silencing in vivo as an important problem...

  6. Transcription factors in alkaloid biosynthesis.

    Science.gov (United States)

    Yamada, Yasuyuki; Sato, Fumihiko

    2013-01-01

    Higher plants produce a large variety of low-molecular weight secondary compounds. Among them, nitrogen-containing alkaloids are the most biologically active and are often used pharmaceutically. Whereas alkaloid chemistry has been intensively investigated, alkaloid biosynthesis, including the relevant biosynthetic enzymes, genes and their regulation, and especially transcription factors, is largely unknown, as only a limited number of plant species produce certain types of alkaloids and they are difficult to study. Recently, however, several groups have succeeded in isolating the transcription factors that are involved in the biosynthesis of several types of alkaloids, including bHLH, ERF, and WRKY. Most of them show Jasmonate (JA) responsiveness, which suggests that the JA signaling cascade plays an important role in alkaloid biosynthesis. Here, we summarize the types and functions of transcription factors that have been isolated in alkaloid biosynthesis, and characterize their similarities and differences compared to those in other secondary metabolite pathways, such as phenylpropanoid and terpenoid biosyntheses. The evolution of this biosynthetic pathway and regulatory network, as well as the application of these transcription factors to metabolic engineering, is discussed. © 2013, Elsevier Inc. All Rights Reserved.

  7. Medical transcription outsourcing greased lightning?

    Science.gov (United States)

    Bikman, Jeremy; Whiting, Stacilee

    2007-06-01

    As medical transcription volume grows, providers need to decide whether to outsource the work, and if so, whether to retain offshore or onshore firms. There are benefits and drawbacks to both. To avoid problems, providers need to make sure the details are spelled out in the contract and that their expectations are understood and met by the outsource firm.

  8. Synthetic in vitro transcription circuits.

    Science.gov (United States)

    Weitz, Maximilian; Simmel, Friedrich C

    2012-01-01

    With the help of only two enzymes--an RNA polymerase and a ribonuclease--reduced versions of transcriptional regulatory circuits can be implemented in vitro. These circuits enable the emulation of naturally occurring biochemical networks, the exploration of biological circuit design principles and the biochemical implementation of powerful computational models.

  9. The Integrated Mode Management Interface

    Science.gov (United States)

    Hutchins, Edwin

    1996-01-01

    Mode management is the processes of understanding the character and consequences of autoflight modes, planning and selecting the engagement, disengagement and transitions between modes, and anticipating automatic mode transitions made by the autoflight system itself. The state of the art is represented by the latest designs produced by each of the major airframe manufacturers, the Boeing 747-400, the Boeing 777, the McDonnell Douglas MD-11, and the Airbus A320/A340 family of airplanes. In these airplanes autoflight modes are selected by manipulating switches on the control panel. The state of the autoflight system is displayed on the flight mode annunciators. The integrated mode management interface (IMMI) is a graphical interface to autoflight mode management systems for aircraft equipped with flight management computer systems (FMCS). The interface consists of a vertical mode manager and a lateral mode manager. Autoflight modes are depicted by icons on a graphical display. Mode selection is accomplished by touching (or mousing) the appropriate icon. The IMMI provides flight crews with an integrated interface to autoflight systems for aircraft equipped with flight management computer systems (FMCS). The current version is modeled on the Boeing glass-cockpit airplanes (747-400, 757/767). It runs on the SGI Indigo workstation. A working prototype of this graphics-based crew interface to the autoflight mode management tasks of glass cockpit airplanes has been installed in the Advanced Concepts Flight Simulator of the CSSRF of NASA Ames Research Center. This IMMI replaces the devices in FMCS equipped airplanes currently known as mode control panel (Boeing), flight guidance control panel (McDonnell Douglas), and flight control unit (Airbus). It also augments the functions of the flight mode annunciators. All glass cockpit airplanes are sufficiently similar that the IMMI could be tailored to the mode management system of any modern cockpit. The IMMI does not replace the

  10. Dual-mode acoustic wave biosensors microarrays

    Science.gov (United States)

    Auner, Gregory W.; Shreve, Gina; Ying, Hao; Newaz, Golam; Hughes, Chantelle; Xu, Jianzeng

    2003-04-01

    We have develop highly sensitive and selective acoustic wave biosensor arrays with signal analysis systems to provide a fingerprint for the real-time identification and quantification of a wide array of bacterial pathogens and environmental health hazards. We have developed an unique highly sensitive dual mode acoustic wave platform prototype that, when combined with phage based selective detection elements, form a durable bacteria sensor. Arrays of these new real-time biosensors are integrated to form a biosensor array on a chip. This research and development program optimizes advanced piezoelectric aluminum nitride wide bandgap semiconductors, novel micromachining processes, advanced device structures, selective phage displays development and immobilization techniques, and system integration and signal analysis technology to develop the biosensor arrays. The dual sensor platform can be programmed to sense in a gas, vapor or liquid environment by switching between acoustic wave resonate modes. Such a dual mode sensor has tremendous implications for applications involving monitoring of pathogenic microorganisms in the clinical setting due to their ability to detect airborne pathogens. This provides a number of applications including hospital settings such as intensive care or other in-patient wards for the reduction of nosocomial infections and maintenance of sterile environments in surgical suites. Monitoring for airborn pathogen transmission in public transportation areas such as airplanes may be useful for implementation of strategies for redution of airborn transmission routes. The ability to use the same sensor in the liquid sensing mode is important for tracing the source of airborn pathogens to local liquid sources. Sensing of pathogens in saliva will be useful for sensing oral pathogens and support of decision-making strategies regarding prevention of transmission and support of treatment strategies.

  11. 76 FR 39234 - Federal Acquisition Regulation; Unique Procurement Instrument Identifier

    Science.gov (United States)

    2011-07-05

    ... Federal Acquisition Regulation; Unique Procurement Instrument Identifier AGENCIES: Department of Defense... Regulation (FAR) to standardize use of unique Procurement Instrument Identifiers (PIID) throughout the..., including the Federal Government, contractors, and the public, to potential duplicate, overlapping, or...

  12. An Ikaros Promoter Element with Dual Epigenetic and Transcriptional Activities.

    Directory of Open Access Journals (Sweden)

    Elizabeth A Perotti

    Full Text Available Ikaros DNA binding factor plays critical roles in lymphocyte development. Changes in Ikaros expression levels during lymphopoiesis are controlled by redundant but also unique regulatory elements of its locus that are critical for this developmental process. We have recently shown that Ikaros binds its own locus in thymocytes in vivo. Here, we evaluated the role of an Ikaros binding site within its major lympho-myeloid promoter. We identified an Ikaros/Ets binding site within a promoter sub-region that was highly conserved in mouse and human. Deletion of this binding site increased the percentage of the reporter-expressing mouse lines, indicating that its loss provided a more permissive chromatin environment. However, once transcription was established, the lack of this site decreased transcriptional activity. These findings implicate a dual role for Ikaros/Ets1 binding on Ikzf1 expression that is exerted at least through its promoter.

  13. Characterization of beef transcripts correlated with tenderness and moisture.

    Science.gov (United States)

    Kee, Hyun-Jung; Park, Eung-Woo; Lee, Cheol-Koo

    2008-05-31

    To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r|>0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture.

  14. Modes of Action of Microbially-Produced Phytotoxins

    Directory of Open Access Journals (Sweden)

    Franck E. Dayan

    2011-08-01

    Full Text Available Some of the most potent phytotoxins are synthesized by microbes. A few of these share molecular target sites with some synthetic herbicides, but many microbial toxins have unique target sites with potential for exploitation by the herbicide industry. Compounds from both non-pathogenic and pathogenic microbes are discussed. Microbial phytotoxins with modes of action the same as those of commercial herbicides and those with novel modes of action of action are covered. Examples of the compounds discussed are tentoxin, AAL-toxin, auscaulitoxin aglycone, hydantocidin, thaxtomin, and tabtoxin.

  15. ROSAT Discovers Unique, Distant Cluster of Galaxies

    Science.gov (United States)

    1995-06-01

    Brightest X-ray Cluster Acts as Strong Gravitational Lens Based on exciting new data obtained with the ROSAT X-ray satellite and a ground-based telescope at the ESO La Silla Observatory, a team of European astronomers [2] has just discovered a very distant cluster of galaxies with unique properties. It emits the strongest X-ray emission of any cluster ever observed by ROSAT and is accompanied by two extraordinarily luminous arcs that represent the gravitationally deflected images of even more distant objects. The combination of these unusual characteristics makes this cluster, now known as RXJ1347.5-1145, a most interesting object for further cosmological studies. DISCOVERY AND FOLLOW-UP OBSERVATIONS This strange cluster of galaxies was discovered during the All Sky Survey with the ROSAT X-ray satellite as a moderately intense X-ray source in the constellation of Virgo. It could not be identified with any already known object and additional ground-based observations were therefore soon after performed with the Max-Planck-Society/ESO 2.2-metre telescope at the La Silla observatory in Chile. These observations took place within a large--scale redshift survey of X-ray clusters of galaxies detected by the ROSAT All Sky Survey, a so-called ``ESO Key Programme'' led by astronomers from the Max-Planck-Institut fur Extraterrestrische Physik and the Osservatorio Astronomico di Brera. The main aim of this programme is to identify cluster X-ray sources, to determine the distance to the X-ray emitting clusters and to investigate their overall properties. These observations permitted to measure the redshift of the RXJ1347.5-1145 cluster as z = 0.45, i.e. it moves away from us with a velocity (about 106,000 km/sec) equal to about one-third of the velocity of light. This is an effect of the general expansion of the universe and it allows to determine the distance as about 5,000 million light-years (assuming a Hubble constant of 75 km/sec/Mpc). In other words, we see these

  16. Sex-specific transcriptional regulation of the C. elegans sex-determining gene her-1.

    Science.gov (United States)

    Trent, C; Purnell, B; Gavinski, S; Hageman, J; Chamblin, C; Wood, W B

    1991-03-01

    Expression of the sex-determining gene her-1 is required in C. elegans for the normal male development of XO animals. Abnormal expression in XX animals, which normally develop as hermaphrodites, results in aberrant male development. We have isolated a molecular clone of the her-1 gene and have identified two transcripts that are present in XO animals at all stages of development: an abundant 0.8 kb transcript and a less abundant 1.2 kb transcript. In preparations of XX animals, the 0.8 kb transcript was observed only at very low levels in embryos or L1 larvae and the 1.2 kb transcript was not detected. Two gain-of-function her-1 mutations result in high levels of the 1.2 and 0.8 kb transcripts in XX animals. The levels of these transcripts are also elevated in XX animals carrying a loss-of-function mutation in either sdc-1 or sdc-2, consistent with the proposed roles of these genes as negative regulators of her-1. These results demonstrate that expression of the her-1 gene in males and hermaphrodites is controlled at the level of transcript synthesis or accumulation. This mode of regulation contrasts with that found for the Drosophila sex-determining genes, whose sex-specific expression is controlled by differential splicing in males and females.

  17. Protein-protein interactions in the regulation of WRKY transcription factors.

    Science.gov (United States)

    Chi, Yingjun; Yang, Yan; Zhou, Yuan; Zhou, Jie; Fan, Baofang; Yu, Jing-Quan; Chen, Zhixiang

    2013-03-01

    It has been almost 20 years since the first report of a WRKY transcription factor, SPF1, from sweet potato. Great progress has been made since then in establishing the diverse biological roles of WRKY transcription factors in plant growth, development, and responses to biotic and abiotic stress. Despite the functional diversity, almost all analyzed WRKY proteins recognize the TTGACC/T W-box sequences and, therefore, mechanisms other than mere recognition of the core W-box promoter elements are necessary to achieve the regulatory specificity of WRKY transcription factors. Research over the past several years has revealed that WRKY transcription factors physically interact with a wide range of proteins with roles in signaling, transcription, and chromatin remodeling. Studies of WRKY-interacting proteins have provided important insights into the regulation and mode of action of members of the important family of transcription factors. It has also emerged that the slightly varied WRKY domains and other protein motifs conserved within each of the seven WRKY subfamilies participate in protein-protein interactions and mediate complex functional interactions between WRKY proteins and between WRKY and other regulatory proteins in the modulation of important biological processes. In this review, we summarize studies of protein-protein interactions for WRKY transcription factors and discuss how the interacting partners contribute, at different levels, to the establishment of the complex regulatory and functional network of WRKY transcription factors.

  18. Phylogenetic and Transcription Analysis of Chrysanthemum WRKY Transcription Factors

    Directory of Open Access Journals (Sweden)

    Aiping Song

    2014-08-01

    Full Text Available WRKY transcription factors are known to function in a number of plant processes. Here we have characterized 15 WRKY family genes of the important ornamental species chrysanthemum (Chrysanthemum morifolium. A total of 15 distinct sequences were isolated; initially internal fragments were amplified based on transcriptomic sequence, and then the full length cDNAs were obtained using RACE (rapid amplification of cDNA ends PCR. The transcription of these 15 genes in response to a variety of phytohormone treatments and both biotic and abiotic stresses was characterized. Some of the genes behaved as would be predicted based on their homology with Arabidopsis thaliana WRKY genes, but others showed divergent behavior.

  19. Transcriptional Profiling of Whole Blood Identifies a Unique 5-Gene Signature for Myelofibrosis and Imminent Myelofibrosis Transformation

    DEFF Research Database (Denmark)

    Hasselbalch, Hans Carl; Skov, Vibe; Stauffer Larsen, Thomas

    2014-01-01

    selectively and highly deregulated in myelofibrosis patients. Gene expression microarray studies have been performed on whole blood from 69 patients with myeloproliferative neoplasms. Amongst the top-20 of the most upregulated genes in PMF compared to controls, we identified 5 genes (DEFA4, ELA2, OLFM4, CTSG...

  20. Plasmodium falciparum spermidine synthase inhibition results in unique perturbation-specific effects observed on transcript, protein and metabolite levels

    CSIR Research Space (South Africa)

    Becker, JVW

    2010-01-01

    Full Text Available This study details the malaria parasite's response to PfSpdSyn inhibition on the transcriptomic, proteomic and metabolic levels. The results corroborate and significantly expand previous functional genomics studies relating to polyamine depletion...

  1. Waveguides having patterned, flattened modes

    Energy Technology Data Exchange (ETDEWEB)

    Messerly, Michael J.; Pax, Paul H.; Dawson, Jay W.

    2015-10-27

    Field-flattening strands may be added to and arbitrarily positioned within a field-flattening shell to create a waveguide that supports a patterned, flattened mode. Patterning does not alter the effective index or flattened nature of the mode, but does alter the characteristics of other modes. Compared to a telecom fiber, a hexagonal pattern of strands allows for a three-fold increase in the flattened mode's area without reducing the separation between its effective index and that of its bend-coupled mode. Hexagonal strand and shell elements prove to be a reasonable approximation, and, thus, to be of practical benefit vis-a-vis fabrication, to those of circular cross section. Patterned flattened modes offer a new and valuable path to power scaling.

  2. Transcription Blockage Leads to New Beginnings

    Science.gov (United States)

    Andrade-Lima, Leonardo C.; Veloso, Artur; Ljungman, Mats

    2015-01-01

    Environmental agents are constantly challenging cells by damaging DNA, leading to the blockage of transcription elongation. How do cells deal with transcription-blockage and how is transcription restarted after the blocking lesions are removed? Here we review the processes responsible for the removal of transcription-blocking lesions, as well as mechanisms of transcription restart. We also discuss recent data suggesting that blocked RNA polymerases may not resume transcription from the site of the lesion following its removal but, rather, are forced to start over from the beginning of genes. PMID:26197343

  3. Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription

    OpenAIRE

    Dumay-Odelot, Hélène; Durrieu-Gaillard, Stéphanie; El Ayoubi, Leyla; Parrot, Camila; Teichmann, Martin

    2014-01-01

    Human RNA polymerase III transcribes small untranslated RNAs that contribute to the regulation of essential cellular processes, including transcription, RNA processing and translation. Analysis of this transcription system by in vitro transcription techniques has largely contributed to the discovery of its transcription factors and to the understanding of the regulation of human RNA polymerase III transcription. Here we review some of the key steps that led to the identification of transcript...

  4. Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures.

    Directory of Open Access Journals (Sweden)

    Moon Young Lee

    Full Text Available Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC, which serve as slow-wave electrical pacemakers for gastrointestinal (GI smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes. In analyzing the transcriptome, we identified a unique set of ICC-restricted markers including transcription factors, epigenetic enzymes/regulators, growth factors, receptors, protein kinases/phosphatases, and ion channels/transporters. This analysis provides new and unique insights into the cellular and biological functions of ICC in GI physiology. Additionally, we constructed an interactive ICC genome browser (http://med.unr.edu/physio/transcriptome based on the UCSC genome database. To our knowledge, this is the first online resource that provides a comprehensive library of all known genetic transcripts expressed in primary ICC. Our genome browser offers a new perspective into the alternative expression of genes in ICC and provides a valuable reference for future functional studies.

  5. Canadian Journal of Kidney Health and Disease: a unique launch of a unique journal.

    Science.gov (United States)

    Levin, Adeera; Clase, Catherine M; Sood, Manish M; Dicks, Elizabeth; Fortin, Marie-Chantal; Hartwig, Sunny; Holden, Rachel; Lafrance, Jean-Philippe; Molzahn, Anita; Rosenblum, Norman; Samuel, Susan; Soroka, Steven

    2014-01-01

    Usually inaugural editorials are written by the Editor-in-Chief to describe the scope and vision for the journal to potential authors and readers. This editorial is written by the Editor-in-Chief, the Deputy Editors and the Associate Editors collaboratively as a clear signal that this is a unique and different journal. We will build this journal on a set of principles which are fundamental to improving the outcomes of patients with kidney disease. To that end, we aim to be supportive, to collaborate, to integrate multiple perspectives and to be open to possibilities.

  6. Whispering gallery mode sensors.

    Science.gov (United States)

    Foreman, Matthew R; Swaim, Jon D; Vollmer, Frank

    2015-06-30

    We present a comprehensive overview of sensor technology exploiting optical whispering gallery mode (WGM) resonances. After a short introduction we begin by detailing the fundamental principles and theory of WGMs in optical microcavities and the transduction mechanisms frequently employed for sensing purposes. Key recent theoretical contributions to the modeling and analysis of WGM systems are highlighted. Subsequently we review the state of the art of WGM sensors by outlining efforts made to date to improve current detection limits. Proposals in this vein are numerous and range, for example, from plasmonic enhancements and active cavities to hybrid optomechanical sensors, which are already working in the shot noise limited regime. In parallel to furthering WGM sensitivity, efforts to improve the time resolution are beginning to emerge. We therefore summarize the techniques being pursued in this vein. Ultimately WGM sensors aim for real-world applications, such as measurements of force and temperature, or alternatively gas and biosensing. Each such application is thus reviewed in turn, and important achievements are discussed. Finally, we adopt a more forward-looking perspective and discuss the outlook of WGM sensors within both a physical and biological context and consider how they may yet push the detection envelope further.

  7. Elongation factor P mediates a novel post-transcriptional regulatory pathway critical for bacterial virulence

    DEFF Research Database (Denmark)

    Zou, S Betty; Roy, Hervé; Ibba, Michael

    2012-01-01

    of the pathogen to respond to external cues are typically attenuating. Here we discuss our recent discovery of a novel post-transcriptional regulatory pathway critical for Salmonella virulence and stress resistance. The enzymes PoxA and YjeK coordinately attach a unique beta-amino acid onto a highly conserved...

  8. Intrinsic localized modes and nonlinear impurity modes in curved ...

    Indian Academy of Sciences (India)

    We explore the nature of intrinsic localized modes (ILMs) in a curved Fermi–. Pasta–Ulam (FPU) chain ... We further demonstrate that a nonlinear impurity mode may be treated as a bound state of an ILM with the impurity .... length [14] and see that the particular choice of the chain geometry ensures the DB propagation with ...

  9. Target Choice and Unique Synergies in Global Mobile Telephony

    DEFF Research Database (Denmark)

    Claussen, Jörg; Köhler, Rebecca; Kretschmer, Tobias

    2017-01-01

    The success of acquisitions rests on detecting and realizing unique synergies between buyer and target through their dyadic relationships. We study the role of unique dyad-specific synergies in the selection of takeover targets in the global mobile telecommunications industry. Firms use their for......The success of acquisitions rests on detecting and realizing unique synergies between buyer and target through their dyadic relationships. We study the role of unique dyad-specific synergies in the selection of takeover targets in the global mobile telecommunications industry. Firms use...... industry. This helps us in identifying unique synergies as drivers of acquisition performance....

  10. Gene isoform specificity through enhancer-associated antisense transcription.

    Directory of Open Access Journals (Sweden)

    Courtney S Onodera

    Full Text Available Enhancers and antisense RNAs play key roles in transcriptional regulation through differing mechanisms. Recent studies have demonstrated that enhancers are often associated with non-coding RNAs (ncRNAs, yet the functional role of these enhancer:ncRNA associations is unclear. Using RNA-Sequencing to interrogate the transcriptomes of undifferentiated mouse embryonic stem cells (mESCs and their derived neural precursor cells (NPs, we identified two novel enhancer-associated antisense transcripts that appear to control isoform-specific expression of their overlapping protein-coding genes. In each case, an enhancer internal to a protein-coding gene drives an antisense RNA in mESCs but not in NPs. Expression of the antisense RNA is correlated with expression of a shorter isoform of the associated sense gene that is not present when the antisense RNA is not expressed. We demonstrate that expression of the antisense transcripts as well as expression of the short sense isoforms correlates with enhancer activity at these two loci. Further, overexpression and knockdown experiments suggest the antisense transcripts regulate expression of their associated sense genes via cis-acting mechanisms. Interestingly, the protein-coding genes involved in these two examples, Zmynd8 and Brd1, share many functional domains, yet their antisense ncRNAs show no homology to each other and are not present in non-murine mammalian lineages, such as the primate lineage. The lack of homology in the antisense ncRNAs indicates they have evolved independently of each other and suggests that this mode of lineage-specific transcriptional regulation may be more widespread in other cell types and organisms. Our findings present a new view of enhancer action wherein enhancers may direct isoform-specific expression of genes through ncRNA intermediates.

  11. Mode Launcher Design for the Multi-moded DLDS

    CERN Document Server

    Li, Z

    2003-01-01

    The DLDS (Delay Line Distribution System) power delivery system proposed by KEK combines several klystrons to obtain the high peak power required to drive a TeV scale linear collider. In this system the combined klystron output is subdivided into shorter pulses by proper phasing of the sources, and each subpulse is delivered to various accelerator sections via separate waveguides. A cost-saving improvement suggested by SLAC is to use a single multimoded waveguide to deliver the power of all the subpulses. This scheme requires a mode launcher that can deliver each subpulse by way of a different waveguide mode through selective phasing of the sources when combining their power. We present a compact design for such a mode launcher that converts the power from four rectangular waveguide feeds to separate modes in a multi-moded circular guide through coupling slots. Such a design has been simulated and found to satisfy the requirements for high efficiency and low surface fields.

  12. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

    DEFF Research Database (Denmark)

    Kröger, Carsten; Dillon, Shane C.; Cameron, Andrew D. S.

    2012-01-01

    for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing...... expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and...... identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two...

  13. Building a Synthetic Transcriptional Oscillator.

    Science.gov (United States)

    Schwarz-Schilling, Matthaeus; Kim, Jongmin; Cuba, Christian; Weitz, Maximilian; Franco, Elisa; Simmel, Friedrich C

    2016-01-01

    Reaction circuits mimicking genetic oscillators can be realized with synthetic, switchable DNA genes (so-called genelets), and two enzymes only, an RNA polymerase and a ribonuclease. The oscillatory behavior of the genelets is driven by the periodic production and degradation of RNA effector molecules. Here, we describe the preparation, assembly, and testing of a synthetic, transcriptional two-node negative-feedback oscillator, whose dynamics can be followed in real-time by fluorescence read-out.

  14. Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

    Energy Technology Data Exchange (ETDEWEB)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal; Thomsen, Bo; Larsen, Knud; Hedegaard, Jakob; Bendixen, Christian; Madsen, Lone Bruhn, E-mail: LoneB.Madsen@agrsci.dk

    2013-08-23

    Highlights: •Transcriptome sequencing yielded 223 mill porcine RNA-seq reads, and 59,000 transcribed locations. •Establishment of unique transcription profiles for ten porcine tissues including four brain tissues. •Comparison of transcription profiles at gene, isoform, promoter and transcription start site level. •Highlights a high level of regulation of neuro-related genes at both gene, isoform, and TSS level. •Our results emphasize the pig as a valuable animal model with respect to human biological issues. -- Abstract: The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable the differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i

  15. Aptasensors Based on Whispering Gallery Mode Resonators.

    Science.gov (United States)

    Nunzi Conti, Gualtiero; Berneschi, Simome; Soria, Silvia

    2016-07-16

    In this paper, we review the literature on optical evanescent field sensing in resonant cavities where aptamers are used as biochemical receptors. The combined advantages of highly sensitive whispering gallery mode resonator (WGMR)-based transducers, and of the unique properties of aptamers make this approach extremely interesting in the medical field, where there is a particularly high need for devices able to provide real time diagnosis for cancer, infectious diseases, or strokes. However, despite the superior performances of aptamers compared to antibodies and WGMR to other evanescent sensors, there is not much literature combining both types of receptors and transducers. Up to now, the WGMR that have been used are silica microspheres and silicon oxynitride (SiON) ring resonators.

  16. Aptasensors Based on Whispering Gallery Mode Resonators

    Directory of Open Access Journals (Sweden)

    Gualtiero Nunzi Conti

    2016-07-01

    Full Text Available In this paper, we review the literature on optical evanescent field sensing in resonant cavities where aptamers are used as biochemical receptors. The combined advantages of highly sensitive whispering gallery mode resonator (WGMR-based transducers, and of the unique properties of aptamers make this approach extremely interesting in the medical field, where there is a particularly high need for devices able to provide real time diagnosis for cancer, infectious diseases, or strokes. However, despite the superior performances of aptamers compared to antibodies and WGMR to other evanescent sensors, there is not much literature combining both types of receptors and transducers. Up to now, the WGMR that have been used are silica microspheres and silicon oxynitride (SiON ring resonators.

  17. Transcription Through Chromatin - Dynamic Organization of Genes

    Indian Academy of Sciences (India)

    Elongation. Residual Promoter Complex. Elongation complex. Figure 2. Assembly of Transcription initiation complex on a TATA containing promoter: The single line with boxes represent promoter DNA and the +1 indicates the transcription start ...

  18. Transcriptional control of t lymphocyte differentiation

    NARCIS (Netherlands)

    F.J.T. Staal (Frank); F. Weerkamp (Floor); A.W. Langerak (Anton); R.W. Hendriks (Rudi); H.C. Clevers (Hans)

    2001-01-01

    textabstractInitiation of gene transcription by transcription factors (TFs) is an important regulatory step in many developmental processes. The differentiation of T cell progenitors in the thymus is tightly controlled by signaling molecules, ultimately activating

  19. 16 CFR 1502.36 - Official transcript.

    Science.gov (United States)

    2010-01-01

    ... presiding officer will arrange for a verbatim stenographic transcript of oral testimony and for necessary.... Corrections are permitted only for transcription errors. The presiding officer shall promptly order justified...

  20. Functionality of intergenic transcription: an evolutionary comparison.

    Directory of Open Access Journals (Sweden)

    Philipp Khaitovich

    2006-10-01

    Full Text Available Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression patterns of known genes as well as intergenic transcripts within the ENCODE regions between humans and chimpanzees in brain, heart, testis, and lymphoblastoid cell lines. We find that intergenic transcripts show patterns of tissue-specific conservation of their expression, which are comparable to exonic transcripts of known genes. This suggests that intergenic transcripts are subject to functional constraints that restrict their rate of evolutionary change as well as putative positive selection to an extent comparable to that of classical protein-coding genes. In brain and testis, we find that part of this intergenic transcription is caused by widespread use of alternative promoters. Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts.

  1. Structural Fingerprints of Transcription Factor Binding Site Regions

    Directory of Open Access Journals (Sweden)

    Peter Willett

    2009-03-01

    Full Text Available Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data.

  2. A molecular link between gene-specific and chromosome-wide transcriptional repression.

    Science.gov (United States)

    Chu, Diana S; Dawes, Heather E; Lieb, Jason D; Chan, Raymond C; Kuo, Annie F; Meyer, Barbara J

    2002-04-01

    Gene-specific and chromosome-wide mechanisms of transcriptional regulation control development in multicellular organisms. SDC-2, the determinant of hermaphrodite fate in Caenorhabditis elegans, is a paradigm for both modes of regulation. SDC-2 represses transcription of X chromosomes to achieve dosage compensation, and it also represses the male sex-determination gene her-1 to elicit hermaphrodite differentiation. We show here that SDC-2 recruits the entire dosage compensation complex to her-1, directing this X-chromosome repression machinery to silence an individual, autosomal gene. Functional dissection of her-1 in vivo revealed DNA recognition elements required for SDC-2 binding, recruitment of the dosage compensation complex, and transcriptional repression. Elements within her-1 differed in location, sequence, and strength of repression, implying that the dosage compensation complex may regulate transcription along the X chromosome using diverse recognition elements that play distinct roles in repression.

  3. Theory of psychological adaptive modes.

    Science.gov (United States)

    Lehti, Juha

    2016-05-01

    When an individual is facing a stressor and normal stress-response mechanism cannot guarantee sufficient adaptation, special emotional states, adaptive modes, are activated (for example a depressive reaction). Adaptive modes are involuntary states of mind, they are of comprehensive nature, they interfere with normal functioning, and they cannot be repressed or controlled the same way as many emotions. Their transformational nature differentiates them from other emotional states. The object of the adaptive mode is to optimize the problem-solving abilities according to the situation that has provoked the mode. Cognitions and emotions during the adaptive mode are different than in a normal mental state. These altered cognitions and emotional reactions guide the individual to use the correct coping skills in order to deal with the stressor. Successful adaptation will cause the adaptive mode to fade off since the adaptive mode is no longer necessary, and the process as a whole will lead to raised well-being. However, if the adaptation process is inadequate, then the transformation period is prolonged, and the adaptive mode will turn into a dysfunctional state. Many psychiatric disorders are such maladaptive processes. The maladaptive processes can be turned into functional ones by using adaptive skills that are used in functional adaptive processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Transformation and Modes of Production

    DEFF Research Database (Denmark)

    Høst, Jeppe Engset

    2015-01-01

    modes of production and examine the ways of life that are enabled by the two modes of production. The central questions are around how market-based fisheries management transforms the principal preconditions for the self-employed fishers; and, in turn, why capitalist organized large-scale fisheries...

  5. Mutual interdependence of splicing and transcription elongation.

    Science.gov (United States)

    Brzyżek, Grzegorz; Świeżewski, Szymon

    2015-01-01

    Transcription and splicing are intrinsically linked, as splicing needs a pre-mRNA substrate to commence. The more nuanced view is that the rate of transcription contributes to splicing regulation. On the other hand there is accumulating evidence that splicing has an active role in controlling transcription elongation by DNA-dependent RNA polymerase II (RNAP II). We briefly review those mechanisms and propose a unifying model where splicing controls transcription elongation to provide an optimal timing for successive rounds of splicing.

  6. Production of the 2400 kb Duchenne muscular dystrophy (DMD) gene transcript; transcription time and cotranscriptional splicing

    Energy Technology Data Exchange (ETDEWEB)

    Tennyson, C.N.; Worton, R.G. [Univ. of Toronto and the Hospital for Sick Children, Ontario (Canada)

    1994-09-01

    The largest known gene in any organism is the human DMD gene which has 79 exons that span 2400 kb. The extreme nature of the DMD gene raises questions concerning the time required for transcription and whether splicing begins before transcription is complete. DMD gene transcription is induced as cultured human myoblasts differentiate to form multinucleated myotubes, providing a system for studying the kinetics of transcription and splicing. Using quantitative RT-PCR, transcript accumulation was monitored from four different regions within the gene following induction of expression. By comparing the accumulation of transcripts from the 5{prime} and 3{prime} ends of the gene we have shown that approximately 12 hours are required to transcribe 1770 kb of the gene, extrapolating to a time of 16 hours for the transcription unit expressed in muscle. Comparison of accumulation profiles for spliced and total transcript demonstrated that transcripts are spliced at the 5{prime} end before transcription is complete, providing strong evidence for cotranscriptional splicing of DMD gene transcripts. Finally, the rate of transcript accumulation was reduced at the 3{prime} end of the gene relative to the 5{prime} end, perhaps due to premature termination of transcription complexes as they traverse this enormous transcription unit. The lag between transcription initiation and the appearance of complete transcripts could be important in limiting transcript production in dividing cells and to the timing of mRNA appearance in differentiating muscle.

  7. Cluster secondary ion mass spectrometry microscope mode mass spectrometry imaging.

    Science.gov (United States)

    Kiss, András; Smith, Donald F; Jungmann, Julia H; Heeren, Ron M A

    2013-12-30

    Microscope mode imaging for secondary ion mass spectrometry is a technique with the promise of simultaneous high spatial resolution and high-speed imaging of biomolecules from complex surfaces. Technological developments such as new position-sensitive detectors, in combination with polyatomic primary ion sources, are required to exploit the full potential of microscope mode mass spectrometry imaging, i.e. to efficiently push the limits of ultra-high spatial resolution, sample throughput and sensitivity. In this work, a C60 primary source was combined with a commercial mass microscope for microscope mode secondary ion mass spectrometry imaging. The detector setup is a pixelated detector from the Medipix/Timepix family with high-voltage post-acceleration capabilities. The system's mass spectral and imaging performance is tested with various benchmark samples and thin tissue sections. The high secondary ion yield (with respect to 'traditional' monatomic primary ion sources) of the C60 primary ion source and the increased sensitivity of the high voltage detector setup improve microscope mode secondary ion mass spectrometry imaging. The analysis time and the signal-to-noise ratio are improved compared with other microscope mode imaging systems, all at high spatial resolution. We have demonstrated the unique capabilities of a C60 ion microscope with a Timepix detector for high spatial resolution microscope mode secondary ion mass spectrometry imaging. Copyright © 2013 John Wiley & Sons, Ltd.

  8. Ketamine and Imipramine Reverse Transcriptional Signatures of Susceptibility and Induce Resilience-Specific Gene Expression Profiles.

    Science.gov (United States)

    Bagot, Rosemary C; Cates, Hannah M; Purushothaman, Immanuel; Vialou, Vincent; Heller, Elizabeth A; Yieh, Lynn; LaBonté, Benoit; Peña, Catherine J; Shen, Li; Wittenberg, Gayle M; Nestler, Eric J

    2017-02-15

    Examining transcriptional regulation by antidepressants in key neural circuits implicated in depression and understanding the relation to transcriptional mechanisms of susceptibility and natural resilience may help in the search for new therapeutic agents. Given the heterogeneity of treatment response in human populations, examining both treatment response and nonresponse is critical. We compared the effects of a conventional monoamine-based tricyclic antidepressant, imipramine, and a rapidly acting, non-monoamine-based antidepressant, ketamine, in mice subjected to chronic social defeat stress, a validated depression model, and used RNA sequencing to analyze transcriptional profiles associated with susceptibility, resilience, and antidepressant response and nonresponse in the prefrontal cortex (PFC), nucleus accumbens, hippocampus, and amygdala. We identified similar numbers of responders and nonresponders after ketamine or imipramine treatment. Ketamine induced more expression changes in the hippocampus; imipramine induced more expression changes in the nucleus accumbens and amygdala. Transcriptional profiles in treatment responders were most similar in the PFC. Nonresponse reflected both the lack of response-associated gene expression changes and unique gene regulation. In responders, both drugs reversed susceptibility-associated transcriptional changes and induced resilience-associated transcription in the PFC. We generated a uniquely large resource of gene expression data in four interconnected limbic brain regions implicated in depression and its treatment with imipramine or ketamine. Our analyses highlight the PFC as a key site of common transcriptional regulation by antidepressant drugs and in both reversing susceptibility- and inducing resilience-associated molecular adaptations. In addition, we found region-specific effects of each drug, suggesting both common and unique effects of imipramine versus ketamine. Copyright © 2016 Society of Biological

  9. Mammalian transcription-coupled excision repair

    NARCIS (Netherlands)

    W. Vermeulen (Wim); M.I. Fousteri (Maria)

    2013-01-01

    textabstractTranscriptional arrest caused by DNA damage is detrimental for cells and organisms as it impinges on gene expression and thereby on cell growth and survival. To alleviate transcrip-tional arrest, cells trigger a transcription-dependent genome surveillance pathway, termed

  10. Hydra constitutively expresses transcripts involved in vertebrate ...

    Indian Academy of Sciences (India)

    Unknown

    conserved glycolytic pathway. Noggin is expressed in the Spemann organizer in the. Xenopus embryo and is required for neural induction. Figure 1. Noggin- and goosecoid-like transcripts in P. oligactis. (a) Noggin-like transcripts in the hypostomal region (hp) and basal disc (bp) in an adult hydra. (b) Noggin-like transcripts ...

  11. Mode coupling trigger of neoclassical magnetohydrodynamic tearing modes in tokamaks

    Energy Technology Data Exchange (ETDEWEB)

    Gianakon, T.A.; Hegna, C.C.; Callen, J.D.

    1997-05-01

    Numerical studies of the nonlinear evolution of coupled magnetohydrodynamic - type tearing modes in three-dimensional toroidal geometry with neoclassical effects are presented. The inclusion of neoclassical physics introduces an additional free-energy source for the nonlinear formation of magnetic islands through the effects of a bootstrap current in Ohm`s law. The neoclassical tearing mode is demonstrated to be destabilized in plasmas which are otherwise {Delta}{prime} stable, albeit once a threshold island width is exceeded. A possible mechanism for exceeding or eliminating this threshold condition is demonstrated based on mode coupling due to toroidicity with a pre-existing instability at the q = 1 surface.

  12. Mode-by-mode hydrodynamics: Ideas and concepts

    Energy Technology Data Exchange (ETDEWEB)

    Floerchinger, Stefan

    2014-06-15

    The main ideas, technical concepts and perspectives for a mode resolved description of the hydrodynamical regime of relativistic heavy ion collisions are discussed. A background-fluctuation splitting and a Bessel–Fourier expansion for the fluctuating part of the hydrodynamical fields allows for a complete characterization of initial conditions, the fluid dynamical propagation of single modes, the study of interaction effects between modes, the determination of the associated particle spectra and the generalization of the whole program to event-by-event correlations and probability distributions.

  13. Development of the Modes of Collaboration framework

    Directory of Open Access Journals (Sweden)

    Alanna Pawlak

    2018-01-01

    Full Text Available Group work is becoming increasingly common in introductory physics classrooms. Understanding how students engage in these group learning environments is important for designing and facilitating productive learning opportunities for students. We conducted a study in which we collected video of groups of students working on conceptual electricity and magnetism problems in an introductory physics course. In this setting, students needed to negotiate a common understanding and coordinate group decisions in order to complete the activity successfully. We observed students interacting in several distinct ways while solving these problems. Analysis of these observations focused on identifying the different ways students interacted and articulating what defines and distinguishes them, resulting in the development of the modes of collaboration framework. The modes of collaboration framework defines student interactions along three dimensions: social, discursive, and disciplinary content. This multidimensional approach offers a unique lens through which to consider group work and provides a flexibility that could allow the framework to be adapted for a variety of contexts. We present the framework and several examples of its application here.

  14. Development of the Modes of Collaboration framework

    Science.gov (United States)

    Pawlak, Alanna; Irving, Paul W.; Caballero, Marcos D.

    2018-01-01

    Group work is becoming increasingly common in introductory physics classrooms. Understanding how students engage in these group learning environments is important for designing and facilitating productive learning opportunities for students. We conducted a study in which we collected video of groups of students working on conceptual electricity and magnetism problems in an introductory physics course. In this setting, students needed to negotiate a common understanding and coordinate group decisions in order to complete the activity successfully. We observed students interacting in several distinct ways while solving these problems. Analysis of these observations focused on identifying the different ways students interacted and articulating what defines and distinguishes them, resulting in the development of the modes of collaboration framework. The modes of collaboration framework defines student interactions along three dimensions: social, discursive, and disciplinary content. This multidimensional approach offers a unique lens through which to consider group work and provides a flexibility that could allow the framework to be adapted for a variety of contexts. We present the framework and several examples of its application here.

  15. Anapole nanolasers for mode-locking and ultrafast pulse generation

    KAUST Repository

    Gongora, J. S. Totero

    2017-05-31

    Nanophotonics is a rapidly developing field of research with many suggestions for a design of nanoantennas, sensors and miniature metadevices. Despite many proposals for passive nanophotonic devices, the efficient coupling of light to nanoscale optical structures remains a major challenge. In this article, we propose a nanoscale laser based on a tightly confined anapole mode. By harnessing the non-radiating nature of the anapole state, we show how to engineer nanolasers based on InGaAs nanodisks as on-chip sources with unique optical properties. Leveraging on the near-field character of anapole modes, we demonstrate a spontaneously polarized nanolaser able to couple light into waveguide channels with four orders of magnitude intensity than classical nanolasers, as well as the generation of ultrafast (of 100 fs) pulses via spontaneous mode locking of several anapoles. Anapole nanolasers offer an attractive platform for monolithically integrated, silicon photonics sources for advanced and efficient nanoscale circuitry.

  16. Anapole nanolasers for mode-locking and ultrafast pulse generation

    Science.gov (United States)

    Totero Gongora, Juan S.; Miroshnichenko, Andrey E.; Kivshar, Yuri S.; Fratalocchi, Andrea

    2017-05-01

    Nanophotonics is a rapidly developing field of research with many suggestions for a design of nanoantennas, sensors and miniature metadevices. Despite many proposals for passive nanophotonic devices, the efficient coupling of light to nanoscale optical structures remains a major challenge. In this article, we propose a nanoscale laser based on a tightly confined anapole mode. By harnessing the non-radiating nature of the anapole state, we show how to engineer nanolasers based on InGaAs nanodisks as on-chip sources with unique optical properties. Leveraging on the near-field character of anapole modes, we demonstrate a spontaneously polarized nanolaser able to couple light into waveguide channels with four orders of magnitude intensity than classical nanolasers, as well as the generation of ultrafast (of 100 fs) pulses via spontaneous mode locking of several anapoles. Anapole nanolasers offer an attractive platform for monolithically integrated, silicon photonics sources for advanced and efficient nanoscale circuitry.

  17. Transcript-specific effects of adrenalectomy on seizure-induced BDNF expression in rat hippocampus

    DEFF Research Database (Denmark)

    Lauterborn, J C; Poulsen, F R; Stinis, C T

    1998-01-01

    Activity-induced brain-derived neurotrophic factor (BDNF) expression is negatively modulated by circulating adrenal steroids. The rat BDNF gene gives rise to four major transcript forms that each contain a unique 5' exon (I-IV) and a common 3' exon (V) that codes for BDNF protein. Exon......-specific in situ hybridization was used to determine if adrenalectomy has differential effects on basal and activity-induced BDNF transcript expression in hippocampus. Adrenalectomy alone had only modest effects on BDNF mRNA levels with slight increases in exon III-containing mRNA with 7-10-day survival...... no effect on exon IV-containing mRNA content. These results demonstrate that the negative effects of adrenal hormones on activity-induced BDNF expression are by far the greatest for transcripts containing exons I and II. Together with evidence for region-specific transcript expression, these results suggest...

  18. TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells

    Directory of Open Access Journals (Sweden)

    Liana Fasching

    2015-01-01

    Full Text Available TRIM28 is a corepressor that mediates transcriptional silencing by establishing local heterochromatin. Here, we show that deletion of TRIM28 in neural progenitor cells (NPCs results in high-level expression of two groups of endogenous retroviruses (ERVs: IAP1 and MMERVK10C. We find that NPCs use TRIM28-mediated histone modifications to dynamically regulate transcription and silencing of ERVs, which is in contrast to other somatic cell types using DNA methylation. We also show that derepression of ERVs influences transcriptional dynamics in NPCs through the activation of nearby genes and the expression of long noncoding RNAs. These findings demonstrate a unique dynamic transcriptional regulation of ERVs in NPCs. Our results warrant future studies on the role of ERVs in the healthy and diseased brain.

  19. Comprehensive Profiling of Amino Acid Response Uncovers Unique Methionine-Deprived Response Dependent on Intact Creatine Biosynthesis

    Science.gov (United States)

    Tang, Xiaohu; Keenan, Melissa M.; Wu, Jianli; Lin, Chih-An; Dubois, Laura; Thompson, J. Will; Freedland, Stephen J.; Murphy, Susan K.; Chi, Jen-Tsan

    2015-01-01

    Besides being building blocks for protein synthesis, amino acids serve a wide variety of cellular functions, including acting as metabolic intermediates for ATP generation and for redox homeostasis. Upon amino acid deprivation, free uncharged tRNAs trigger GCN2-ATF4 to mediate the well-characterized transcriptional amino acid response (AAR). However, it is not clear whether the deprivation of different individual amino acids triggers identical or distinct AARs. Here, we characterized the global transcriptional response upon deprivation of one amino acid at a time. With the exception of glycine, which was not required for the proliferation of MCF7 cells, we found that the deprivation of most amino acids triggered a shared transcriptional response that included the activation of ATF4, p53 and TXNIP. However, there was also significant heterogeneity among different individual AARs. The most dramatic transcriptional response was triggered by methionine deprivation, which activated an extensive and unique response in different cell types. We uncovered that the specific methionine-deprived transcriptional response required creatine biosynthesis. This dependency on creatine biosynthesis was caused by the consumption of S-Adenosyl-L-methionine (SAM) during creatine biosynthesis that helps to deplete SAM under methionine deprivation and reduces histone methylations. As such, the simultaneous deprivation of methionine and sources of creatine biosynthesis (either arginine or glycine) abolished the reduction of histone methylation and the methionine-specific transcriptional response. Arginine-derived ornithine was also required for the complete induction of the methionine-deprived specific gene response. Collectively, our data identify a previously unknown set of heterogeneous amino acid responses and reveal a distinct methionine-deprived transcriptional response that results from the crosstalk of arginine, glycine and methionine metabolism via arginine

  20. Cloning of the sea urchin mitochondrial RNA polymerase and reconstitution of the transcription termination system

    Science.gov (United States)

    Polosa, Paola Loguercio; Deceglie, Stefania; Falkenberg, Maria; Roberti, Marina; Di Ponzio, Barbara; Gadaleta, Maria Nicola; Cantatore, Palmiro

    2007-01-01

    Termination of transcription is a key process in the regulation of mitochondrial gene expression in animal cells. To investigate transcription termination in sea urchin mitochondria, we cloned the mitochondrial RNA polymerase (mtRNAP) of Paracentrotus lividus and used a recombinant form of the enzyme in a reconstituted transcription system, in the presence of the DNA-binding protein mtDBP. Cloning of mtRNAP was performed by a combination of PCR with degenerate primers and library screening. The enzyme contains 10 phage-like conserved motifs, two pentatricopeptide motifs and a serine-rich stretch. The protein expressed in insect cells supports transcription elongation in a promoter-independent assay. Addition of recombinant mtDBP caused arrest of the transcribing mtRNAP when the enzyme approached the mtDBP-binding site in the direction of transcription of mtDNA l-strand. When the polymerase encountered the protein-binding site in the opposite direction, termination occurred in a protein-independent manner, inside the mtDBP-binding site. Pulse-chase experiments show that mtDBP caused true transcription termination rather than pausing. These data indicate that mtDBP acts as polar termination factor and suggest that transcription termination in sea urchin mitochondria could take place by two alternative modes based on protein-mediated or sequence-dependent mechanisms. PMID:17392338

  1. Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription.

    Science.gov (United States)

    Dumay-Odelot, Hélène; Durrieu-Gaillard, Stéphanie; El Ayoubi, Leyla; Parrot, Camila; Teichmann, Martin

    2014-01-01

    Human RNA polymerase III transcribes small untranslated RNAs that contribute to the regulation of essential cellular processes, including transcription, RNA processing and translation. Analysis of this transcription system by in vitro transcription techniques has largely contributed to the discovery of its transcription factors and to the understanding of the regulation of human RNA polymerase III transcription. Here we review some of the key steps that led to the identification of transcription factors and to the definition of minimal promoter sequences for human RNA polymerase III transcription.

  2. Unique roles of the unfolded protein response pathway in fungal development and differentiation.

    Science.gov (United States)

    Jung, Kwang-Woo; So, Yee-Seul; Bahn, Yong-Sun

    2016-09-15

    Cryptococcus neoformans, a global fungal meningitis pathogen, employs the unfolded protein response pathway. This pathway, which consists of an evolutionarily conserved Ire1 kinase/endoribonuclease and a unique transcription factor (Hxl1), modulates the endoplasmic reticulum stress response and pathogenicity. Here, we report that the unfolded protein response pathway governs sexual and unisexual differentiation of C. neoformans in an Ire1-dependent but Hxl1-independent manner. The ire1∆ mutants showed defects in sexual mating, with reduced cell fusion and pheromone-mediated formation of the conjugation tube. Unexpectedly, these mating defects did not result from defective pheromone production because expression of the mating pheromone gene (MFα1) was strongly induced in the ire1∆ mutant. Ire1 controls sexual differentiation by modulating the function of the molecular chaperone Kar2 and by regulating mating-induced localisation of mating pheromone transporter (Ste6) and receptor (Ste3/Cprα). Deletion of IRE1, but not HXL1, also caused significant defects in unisexual differentiation in a Kar2-independent manner. Moreover, we showed that Rim101 is a novel downstream factor of Ire1 for production of the capsule, which is a unique structural determinant of C. neoformans virulence. Therefore, Ire1 uniquely regulates fungal development and differentiation in an Hxl1-independent manner.

  3. Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata.

    Science.gov (United States)

    Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

    2013-01-07

    Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem-loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping-pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration.

  4. SARS-unique fold in the Rousettus bat coronavirus HKU9.

    Science.gov (United States)

    Hammond, Robert G; Tan, Xuan; Johnson, Margaret A

    2017-09-01

    The coronavirus nonstructural protein 3 (nsp3) is a multifunctional protein that comprises multiple structural domains. This protein assists viral polyprotein cleavage, host immune interference, and may play other roles in genome replication or transcription. Here, we report the solution NMR structure of a protein from the "SARS-unique region" of the bat coronavirus HKU9. The protein contains a frataxin fold or double-wing motif, which is an α + β fold that is associated with protein/protein interactions, DNA binding, and metal ion binding. High structural similarity to the human severe acute respiratory syndrome (SARS) coronavirus nsp3 is present. A possible functional site that is conserved among some betacoronaviruses has been identified using bioinformatics and biochemical analyses. This structure provides strong experimental support for the recent proposal advanced by us and others that the "SARS-unique" region is not unique to the human SARS virus, but is conserved among several different phylogenetic groups of coronaviruses and provides essential functions. © 2017 The Protein Society.

  5. Exotic decay: Transition from cluster mode to fission mode

    Indian Academy of Sciences (India)

    ' reaction were studied taking interacting barrier consisting of Coulomb and proximity potential. Calculated half-life time shows that some modes of decay are well within the present upper limit for measurements (1/2 < 1030 s). Cluster ...

  6. Mode control and mode conversion in nonlinear aluminum nitride waveguides.

    Science.gov (United States)

    Stegmaier, Matthias; Pernice, Wolfram H P

    2013-11-04

    While single-mode waveguides are commonly used in integrated photonic circuits, emerging applications in nonlinear and quantum optics rely fundamentally on interactions between modes of different order. Here we propose several methods to evaluate the modal composition of both externally and device-internally excited guided waves and discuss a technique for efficient excitation of arbitrary modes. The applicability of these methods is verified in photonic circuits based on aluminum nitride. We control modal excitation through suitably engineered grating couplers and are able to perform a detailed study of waveguide-internal second harmonic generation. Efficient and broadband power conversion between orthogonal polarizations is realized within an asymmetric directional coupler to demonstrate selective excitation of arbitrary higher-order modes. Our approach holds promise for applications in nonlinear optics and frequency up/down-mixing in a chipscale framework.

  7. Genome wide transcriptional profile analysis of Vitis amurensis and Vitis vinifera in response to cold stress.

    Directory of Open Access Journals (Sweden)

    Haiping Xin

    Full Text Available Grape is one of the most important fruit crops worldwide. The suitable geographical locations and productivity of grapes are largely limited by temperature. Vitis amurensis is a wild grapevine species with remarkable cold-tolerance, exceeding that of Vitis vinifera, the dominant cultivated species of grapevine. However, the molecular mechanisms that contribute to the enhanced freezing tolerance of V. amurensis remain unknown. Here we used deep sequencing data from restriction endonuclease-generated cDNA fragments to evaluate the whole genome wide modification of transcriptome of V. amurensis under cold treatment. Vitis vinifera cv. Muscat of Hamburg was used as control to help investigate the distinctive features of V. amruensis in responding to cold stress. Approximately 9 million tags were sequenced from non-cold treatment (NCT and cold treatment (CT cDNA libraries in each species of grapevine sampled from shoot apices. Alignment of tags into V. vinifera cv. Pinot noir (PN40024 annotated genome identified over 15,000 transcripts in each library in V. amruensis and more than 16,000 in Muscat of Hamburg. Comparative analysis between NCT and CT libraries indicate that V. amurensis has fewer differential expressed genes (DEGs, 1314 transcripts than Muscat of Hamburg (2307 transcripts when exposed to cold stress. Common DEGs (408 transcripts suggest that some genes provide fundamental roles during cold stress in grapes. The most robust DEGs (more than 20-fold change also demonstrated significant differences between two kinds of grapevine, indicating that cold stress may trigger species specific pathways in V. amurensis. Functional categories of DEGs indicated that the proportion of up-regulated transcripts related to metabolism, transport, signal transduction and transcription were more abundant in V. amurensis. Several highly expressed transcripts that were found uniquely accumulated in V. amurensis are discussed in detail. This subset of unique

  8. Genome Wide Transcriptional Profile Analysis of Vitis amurensis and Vitis vinifera in Response to Cold Stress

    Science.gov (United States)

    Xin, Haiping; Zhu, Wei; Wang, Lina; Xiang, Yue; Fang, Linchuan; Li, Jitao; Sun, Xiaoming; Wang, Nian; Londo, Jason P.; Li, Shaohua

    2013-01-01

    Grape is one of the most important fruit crops worldwide. The suitable geographical locations and productivity of grapes are largely limited by temperature. Vitis amurensis is a wild grapevine species with remarkable cold-tolerance, exceeding that of Vitis vinifera, the dominant cultivated species of grapevine. However, the molecular mechanisms that contribute to the enhanced freezing tolerance of V. amurensis remain unknown. Here we used deep sequencing data from restriction endonuclease-generated cDNA fragments to evaluate the whole genome wide modification of transcriptome of V. amurensis under cold treatment. Vitis vinifera cv. Muscat of Hamburg was used as control to help investigate the distinctive features of V. amruensis in responding to cold stress. Approximately 9 million tags were sequenced from non-cold treatment (NCT) and cold treatment (CT) cDNA libraries in each species of grapevine sampled from shoot apices. Alignment of tags into V. vinifera cv. Pinot noir (PN40024) annotated genome identified over 15,000 transcripts in each library in V. amruensis and more than 16,000 in Muscat of Hamburg. Comparative analysis between NCT and CT libraries indicate that V. amurensis has fewer differential expressed genes (DEGs, 1314 transcripts) than Muscat of Hamburg (2307 transcripts) when exposed to cold stress. Common DEGs (408 transcripts) suggest that some genes provide fundamental roles during cold stress in grapes. The most robust DEGs (more than 20-fold change) also demonstrated significant differences between two kinds of grapevine, indicating that cold stress may trigger species specific pathways in V. amurensis. Functional categories of DEGs indicated that the proportion of up-regulated transcripts related to metabolism, transport, signal transduction and transcription were more abundant in V. amurensis. Several highly expressed transcripts that were found uniquely accumulated in V. amurensis are discussed in detail. This subset of unique candidate

  9. Historypin for Library Image Collections: New Modes of Access for Unique Materials at the University of Saskatchewan Library

    Directory of Open Access Journals (Sweden)

    Craig Harkema

    2012-11-01

    Full Text Available A combination of user needs and an evolving information landscape make it imperative for libraries to plan for and initiate digital projects with interface in mind. To meet the needs of a wide range of digital library users, supplementary interfaces should be considered from the beginning of a project rather than simply adding an out-of-the-box interface with basic search functionality. This paper discusses the theoretical and practical considerations of selecting or implementing interfaces for the exploration of library content. It uses the University Library, University of Saskatchewan as a case study, drawing on, in particular, the use of Historypin as a way to geolocate and interact with the Library's Postcard Collection.

  10. Thiodiacetate-manganese chemistry with N ligands: unique control of the supramolecular arrangement over the metal coordination mode.

    Science.gov (United States)

    Grirrane, Abdessamad; Pastor, Antonio; Galindo, Agustín; Alvarez, Eleuterio; Mealli, Carlo; Ienco, Andrea; Orlandini, Annabella; Rosa, Patrick; Caneschi, Andrea; Barra, Anne-Laure; Sanz, Javier Fernández

    2011-09-12

    Compounds based on the Mn-tda unit (tda=S(CH(2)COO)(2)(-2) ) and N co-ligands have been analyzed in terms of structural, spectroscopic, magnetic properties and DFT calculations. The precursors [Mn(tda)(H(2)O)](n) (1) and [Mn(tda)(H(2)O)(3)]·H(2)O (2) have been characterized by powder and X-ray diffraction, respectively. Their derivatives with bipyridyl-type ligands have formulas [Mn(tda)(bipy)](n) (3), [{Mn(N-N)}(2)(μ-H(2)O)(μ-tda)(2)](n) (N-N=4,4'-Me(2)bipy (4), 5,5'-Me(2)bipy, (5)) and [Mn(tda){(MeO)(2)bipy}·2H(2)O](n) (6). Depending on the presence/position of substituents at bipy, the supramolecular arrangement can affect the metal coordination type. While all the complexes consist of 1D coordination polymers, only 3 has a copper-acetate core with local trigonal prismatic metal coordination. The presence of substituents in 4-6, together with water co-ligands, reduces the supramolecular interactions and typical octahedral Mn(II) ions are observed. The unicity of 3 is also supported by magnetic studies and by DFT calculations, which confirm that the unusual Mn coordination is a consequence of extended noncovalent interactions (π-π stacking) between bipy ligands. Moreover, 3 is an example of broken paradigm for supramolecular chemistry. In fact, the desired stereochemical properties are achieved by using rigid metal building blocks, whereas in 3 the accumulation of weak noncovalent interactions controls the metal geometry. Other N co-ligands have also been reacted with 1 to give the compounds [Mn(tda)(phen)](2)·6H(2)O (7) (phen=1,10-phenanthroline), [Mn(tda)(terpy)](n) (8) (terpy=2,2':6,2''-terpyridine), [Mn(tda)(pyterpy)](n) (9) (pyterpy=4'-(4-pyridyl)-2,2':6,2''-terpyridine), [Mn(tda)(tpt)(H(2)O)]·2H(2)O (10) and [Mn(tda)(tpt)(H(2)O)](2)·2H(2)O (11) (tpt=2,4,6-tris(2-pyridyl)-1,3,5-triazine). Their identified mono-, bi- or polynuclear structures clearly indicate that hydrogen bonding is variously competitive with π-π stacking. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Characteristics of high-confinement modes in Alcator C Mod

    Energy Technology Data Exchange (ETDEWEB)

    Snipes, J.A.; Boivin, R.L.; Christensen, C.; Fiore, C.; Garnier, D.; Goetz, J.; Golovato, S.N.; Graf, M.; Granetz, R.S.; Greenwald, M.; Hubbard, A.; Hutchinson, I.H.; Irby, J.; LaBombard, B.; Marmar, E.S.; Niemczewski, A.; OShea, P.; Porkolab, M.; Stek, P.; Takase, Y.; Terry, J.L.; Umansky, M.; Wolfe, S.M. [Plasma Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    1996-05-01

    The regime of high particle and energy confinement known as the H mode [Phys. Rev. Lett. {bold 49}, 1408 (1982)] has been extended to a unique range of operation for divertor tokamaks up to toroidal fields of nearly 8 T, line-averaged electron densities of 3{times}10{sup 20} m{sup {minus}3}, and surface power densities of nearly 0.6 MW/m{sup 2} in the compact high-field tokamak Alcator C Mod [Phys. Plasmas {bold 1}, 1511 (1994)]. H modes are achieved in Alcator C Mod with Ion Cyclotron Resonant Frequency (ICRF) heating and with Ohmic heating alone without boronization of the all molybdenum tiled first wall. Large increases in charge exchange flux are observed during the H mode over the entire range of energies from 2 to 10 keV. There appears to be an upper limit to the midplane neutral pressure, of about 0.08 Pa above which no H modes have been observed. The plasmas with the best energy confinement have the lowest midplane neutral pressures, below 0.01 Pa. There is an edge electron temperature threshold such that {ital T}{sub {ital e}}{ge}280 eV {plus_minus}40 eV for sustaining the H mode, which is equal at L{endash}H and H{endash}L transitions. The hysteresis in the threshold power between L{endash}H and H{endash}L transitions is less than 25{percent} on average. Both core and edge particle confinement improve by a factor of 2{endash}4 from L mode to H mode. Energy confinement also improves by up to a factor of 2 over L mode. {copyright} {ital 1996 American Institute of Physics.}

  12. Principal Metabolic Flux Mode Analysis.

    Science.gov (United States)

    Bhadra, Sahely; Blomberg, Peter; Castillo, Sandra; Rousu, Juho; Wren, Jonathan

    2018-02-06

    In the analysis of metabolism, two distinct and complementary approaches are frequently used: Principal component analysis (PCA) and stoichiometric flux analysis. PCA is able to capture the main modes of variability in a set of experiments and does not make many prior assumptions about the data, but does not inherently take into account the flux mode structure of metabolism. Stoichiometric flux analysis methods, such as Flux Balance Analysis (FBA) and Elementary Mode Analysis, on the other hand, are able to capture the metabolic flux modes, however, they are primarily designed for the analysis of single samples at a time, and not best suited for exploratory analysis on a large sets of samples. We propose a new methodology for the analysis of metabolism, called Principal Metabolic Flux Mode Analysis (PMFA), which marries the PCA and stoichiometric flux analysis approaches in an elegant regularized optimization framework. In short, the method incorporates a variance maximization objective form PCA coupled with a stoichiometric regularizer, which penalizes projections that are far from any flux modes of the network. For interpretability, we also introduce a sparse variant of PMFA that favours flux modes that contain a small number of reactions. Our experiments demonstrate the versatility and capabilities of our methodology. The proposed method can be applied to genome-scale metabolic network in efficient way as PMFA does not enumerate elementary modes. In addition, the method is more robust on out-of-steady steady-state experimental data than competing flux mode analysis approaches. Matlab software for PMFA and SPMFA and data set used for experiments are available in https://github.com/aalto-ics-kepaco/PMFA. sahely@iitpkd.ac.in, juho.rousu@aalto.fi, Peter.Blomberg@vtt.fi, Sandra.Castillo@vtt.fi. Detailed results are in Supplementary files. Supplementary data are available at https://github.com/aalto-ics-kepaco/PMFA/blob/master/Results.zip.

  13. HAfTs are novel lncRNA transcripts from aflatoxin exposure.

    Directory of Open Access Journals (Sweden)

    B Alex Merrick

    Full Text Available The transcriptome can reveal insights into precancer biology. We recently conducted RNA-Seq analysis on liver RNA from male rats exposed to the carcinogen, aflatoxin B1 (AFB1, for 90 days prior to liver tumor onset. Among >1,000 differentially expressed transcripts, several novel, unannotated Cufflinks-assembled transcripts, or HAfTs (Hepatic Aflatoxin Transcripts were found. We hypothesized PCR-cloning and RACE (rapid amplification of cDNA ends could further HAfT identification. Sanger data was obtained for 6 transcripts by PCR and 16 transcripts by 5'- and 3'-RACE. BLAST alignments showed, with two exceptions, HAfT transcripts were lncRNAs, >200nt without apparent long open reading frames. Six rat HAfT transcripts were classified as 'novel' without RefSeq annotation. Sequence alignment and genomic synteny showed each rat lncRNA had a homologous locus in the mouse genome and over half had homologous loci in the human genome, including at least two loci (and possibly three others that were previously unannotated. While HAfT functions are not yet clear, coregulatory roles may be possible from their adjacent orientation to known coding genes with altered expression that include 8 HAfT-gene pairs. For example, a unique rat HAfT, homologous to Pvt1, was adjacent to known genes controlling cell proliferation. Additionally, PCR and RACE Sanger sequencing showed many alternative splice variants and refinements of exon sequences compared to Cufflinks assembled transcripts and gene prediction algorithms. Presence of multiple splice variants and short tandem repeats found in some HAfTs may be consequential for secondary structure, transcriptional regulation, and function. In summary, we report novel, differentially expressed lncRNAs after exposure to the genotoxicant, AFB1, prior to neoplastic lesions. Complete cloning and sequencing of such transcripts could pave the way for a new set of sensitive and early prediction markers for chemical

  14. 15 CFR 748.8 - Unique application and submission requirements.

    Science.gov (United States)

    2010-01-01

    ... devices, motion control boards, numerically controlled machine tools, dimensional inspection machines... APPLICATIONS (CLASSIFICATION, ADVISORY, AND LICENSE) AND DOCUMENTATION § 748.8 Unique application and...

  15. Mode synthesizing atomic force microscopy and mode-synthesizing sensing

    Science.gov (United States)

    Passian, Ali; Thundat, Thomas George; Tetard, Laurene

    2013-05-17

    A method of analyzing a sample that includes applying a first set of energies at a first set of frequencies to a sample and applying, simultaneously with the applying the first set of energies, a second set of energies at a second set of frequencies, wherein the first set of energies and the second set of energies form a multi-mode coupling. The method further includes detecting an effect of the multi-mode coupling.

  16. Distributed Mode Filtering Rod Fiber Amplifier With Improved Mode Stability

    DEFF Research Database (Denmark)

    Laurila, Marko; Alkeskjold, Thomas Tanggaard; Broeng, Jes

    2012-01-01

    We report 216W of average output power from a photonic crystal rod fiber amplifier. We demonstrate 44% power improvement before onset of the mode instability by operating the rod fiber in a leaky guiding regime.......We report 216W of average output power from a photonic crystal rod fiber amplifier. We demonstrate 44% power improvement before onset of the mode instability by operating the rod fiber in a leaky guiding regime....

  17. Mammalian Transcription-Coupled Excision Repair

    Science.gov (United States)

    Vermeulen, Wim; Fousteri, Maria

    2013-01-01

    Transcriptional arrest caused by DNA damage is detrimental for cells and organisms as it impinges on gene expression and thereby on cell growth and survival. To alleviate transcriptional arrest, cells trigger a transcription-dependent genome surveillance pathway, termed transcription-coupled nucleotide excision repair (TC-NER) that ensures rapid removal of such transcription-impeding DNA lesions and prevents persistent stalling of transcription. Defective TC-NER is causatively linked to Cockayne syndrome, a rare severe genetic disorder with multisystem abnormalities that results in patients’ death in early adulthood. Here we review recent data on how damage-arrested transcription is actively coupled to TC-NER in mammals and discuss new emerging models concerning the role of TC-NER-specific factors in this process. PMID:23906714

  18. The Journey of a Transcription Factor

    DEFF Research Database (Denmark)

    Pireyre, Marie

    Plants have developed astonishing networks regulating their metabolism to adapt to their environment. The complexity of these networks is illustrated by the expansion of families of regulators such as transcription factors in the plant kingdom. Transcription factors specifically impact...... transcriptional networks by integrating exogenous and endogenous stimuli and regulating gene expression accordingly. Regulation of transcription factors and their activation is thus highly important to modulate the transcriptional programs and increase fitness of the plant in a given environment. Plant metabolism....... The biosynthetic machinery of GLS is governed by interplay of six MYB and three bHLH transcription factors. MYB28, MYB29 and MYB76 regulate methionine-derived GLS, and MYB51, MYB34 and MYB122 regulate tryptophan-derived GLS. The three bHLH transcription factors MYC2, MYC3 and MYC4 physically interact with all six...

  19. Intelligence and musical mode preference

    DEFF Research Database (Denmark)

    Bonetti, Leonardo; Costa, Marco

    2016-01-01

    The relationship between fluid intelligence and preference for major–minor musical mode was investigated in a sample of 80 university students. Intelligence was assessed by the Raven’s Advanced Progressive Matrices. Musical mode preference was assessed by presenting 14 pairs of musical stimuli...... that varied only in mode. Mood and personality were assessed, respectively, by the Brief Mood Introspection Scale and the Big Five Questionnaire. Preference for minor stimuli was related positively and significantly to fluid intelligence and openness to experience. The results add evidence of individual...

  20. Few-mode fiber technology for mode division multiplexing

    Science.gov (United States)

    Mori, Takayoshi; Sakamoto, Taiji; Wada, Masaki; Yamamoto, Takashi; Nakajima, Kazuhide

    2017-02-01

    We review recent progress on few-mode fiber (FMF) technologies for mode-division multiplexing (MDM) transmission. First, we introduce fibers for use without and with multiple-input multiple-output (MIMO) digital signal processing (DSP) to compensate for modal crosstalk, and briefly report recent work on FMF for use without/with a MIMO DSP system. We next discuss in detail a fiber for MIMO transmission systems, and show numerically that a graded-index core can flexibly tune the differential mode group delay (DMD) and a cladding trench can flexibly control the guiding mode number. We optimized the spacing of the core and trench. Accordingly, we can achieve a 6 LP (10 spatial) mode operation and a low DMD while preventing the high index difference that leads to manufacturing difficulties and any loss increase. We finally describe our experimental results for a 6 LP (10 spatial) mode transmission line for use in a C + L band wavelength-division multiplexing (WDM) MDM transmission with MIMO DSP.

  1. Aire mediates thymic expression and tolerance of pancreatic antigens via an unconventional transcriptional mechanism.

    Science.gov (United States)

    Danso-Abeam, Dina; Staats, Kim A; Franckaert, Dean; Van Den Bosch, Ludo; Liston, Adrian; Gray, Daniel H D; Dooley, James

    2013-01-01

    The autoimmune regulator (Aire), mediates central tolerance of peripheral self. Its activity in thymic epithelial cells (TECs) directs the ectopic expression of thousands of tissue-restricted antigens (TRAs), causing the deletion of autoreactive thymocytes. The molecular mechanisms orchestrating the breadth of transcriptional regulation by Aire remain unknown. One prominent model capable of explaining both the uniquely high number of Aire-dependent targets and their specificity posits that tissue-specific transcription factors induced by Aire directly activate their canonical targets, exponentially adding to the total number of Aire-dependent TRAs. To test this "Hierarchical Transcription" model, we analysed mice deficient in the pancreatic master transcription factor pancreatic and duodenal homeobox 1 (Pdx1), specifically in TECs (Pdx1(ΔFoxn1) ), for the expression and tolerance of pancreatic TRAs. Surprisingly, we found that lack of Pdx1 in TECs did not reduce the transcription of insulin or somatostatin, or alter glucagon expression. Moreover, in a model of thymic deletion driven by a neo-TRA under the control of the insulin promoter, Pdx1 in TECs was not required to affect thymocyte deletion or the generation of regulatory T (Treg) cells. These findings suggest that the capacity of Aire to regulate expression of a huge array of TRAs relies solely on an unconventional transcriptional mechanism, without intermediary transcription factors. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. The transcriptional regulators, the immune system and the the circadian clock.

    Science.gov (United States)

    Vinciguerra, M; Borghesan, M; Pazienza, V; Piepoli, A; Palmieri, O; Tarquini, R; Tevy, M F; De Cata, A; Mazzoccoli, G

    2013-01-01

    The immune system function oscillates with a 24-hour period driving circadian rhythmicity of immune responses. A circadian timing system comprising central and peripheral oscillators entrains body rhythmicity of physiology and behavior to environmental cues by means of humoral signals and autonomic neural outputs. In every single cell an oscillator goes ticking through a molecular clock operated by transcriptional/translational feedback loops driven by the rhythmic expression of circadian genes. This clock gene machinery steers daily oscillations in the regulation of immune cell activity, driving the periodicity in immune system function. The transcriptional networks that regulate temporal variation in gene expression in immunocompetent cells and tissues respond to diverse physiological clues, addressing well-timed adjustments of transcription and translation processes. Nuclear receptors comprise a unique class of transcriptional regulators that are capable of gauging hormones, metabolites, endobiotics and xenobiotics, linking ligand sensing to transcriptional responses in various cell types through switching between coactivator and corepressor recruitment. The expression of coregulators is highly responsive to physiological signals, and plays an important role in the control of rhythmic patterns of gene expression, optimizing the switch between nycthemeral patterns, and synchronizing circadian rhythmicity with changing physiological demands across the light-dark cycle. The nuclear receptors and transcription factors expressed in the immune components contribute to the cross-talk between the circadian timing system, the clock gene machinery and the immune system, influencing transcriptional activities and directing cell-type specific gene expression programs linked to innate and adaptive immune responses.

  3. Identification of drought-induced transcription factors in peanut (Arachis hypogaea L.

    Directory of Open Access Journals (Sweden)

    Corley C Holbrook

    2012-10-01

    Full Text Available Transcription factors play key roles in the regulation of genes involved in normal development as well as tolerance to biotic and abiotic stresses. Specific transcription factors that are induced in peanut under drought conditions have not been identified.  The objectives of this study were to compare gene-expression patterns of various transcription factors of a drought tolerant versus a susceptible peanut genotype under drought conditions and to identify transcripts that were regulated in a drought dependent manner. Twelve putative transcription factors were identified and real-time PCR analysis was performed which resulted in the identification of three unique transcripts in which ahERF1 was highly induced in the recovery stage; ahERF7 and ahERF8 were also highly induced by drought and returned to nominal levels after recovery.  These sequences contain DNA binding domains that are present in the APETALA2/Ethelene Responsive Factors (AP2/ERF family of transcription factors which have been shown to be induced by stress.  Induction levels and patterns of gene-expression of ahERF1, ahERF7 and ahERF8 may be used to select plants that may have higher drought tolerance.

  4. The RNA polymerase II CTD coordinates transcription and RNA processing.

    Science.gov (United States)

    Hsin, Jing-Ping; Manley, James L

    2012-10-01

    The C-terminal domain (CTD) of the RNA polymerase II largest subunit consists of multiple heptad repeats (consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), varying in number from 26 in yeast to 52 in vertebrates. The CTD functions to help couple transcription and processing of the nascent RNA and also plays roles in transcription elongation and termination. The CTD is subject to extensive post-translational modification, most notably phosphorylation, during the transcription cycle, which modulates its activities in the above processes. Therefore, understanding the nature of CTD modifications, including how they function and how they are regulated, is essential to understanding the mechanisms that control gene expression. While the significance of phosphorylation of Ser2 and Ser5 residues has been studied and appreciated for some time, several additional modifications have more recently been added to the CTD repertoire, and insight into their function has begun to emerge. Here, we review findings regarding modification and function of the CTD, highlighting the important role this unique domain plays in coordinating gene activity.

  5. SVD identifies transcript length distribution functions from DNA microarray data and reveals evolutionary forces globally affecting GBM metabolism.

    Directory of Open Access Journals (Sweden)

    Nicolas M Bertagnolli

    Full Text Available To search for evolutionary forces that might act upon transcript length, we use the singular value decomposition (SVD to identify the length distribution functions of sets and subsets of human and yeast transcripts from profiles of mRNA abundance levels across gel electrophoresis migration distances that were previously measured by DNA microarrays. We show that the SVD identifies the transcript length distribution functions as "asymmetric generalized coherent states" from the DNA microarray data and with no a-priori assumptions. Comparing subsets of human and yeast transcripts of the same gene ontology annotations, we find that in both disparate eukaryotes, transcripts involved in protein synthesis or mitochondrial metabolism are significantly shorter than typical, and in particular, significantly shorter than those involved in glucose metabolism. Comparing the subsets of human transcripts that are overexpressed in glioblastoma multiforme (GBM or normal brain tissue samples from The Cancer Genome Atlas, we find that GBM maintains normal brain overexpression of significantly short transcripts, enriched in transcripts that are involved in protein synthesis or mitochondrial metabolism, but suppresses normal overexpression of significantly longer transcripts, enriched in transcripts that are involved in glucose metabolism and brain activity. These global relations among transcript length, cellular metabolism and tumor development suggest a previously unrecognized physical mode for tumor and normal cells to differentially regulate metabolism in a transcript length-dependent manner. The identified distribution functions support a previous hypothesis from mathematical modeling of evolutionary forces that act upon transcript length in the manner of the restoring force of the harmonic oscillator.

  6. Transcriptional control of steroid biosynthesis genes in the Drosophila prothoracic gland by Ventral veins lacking and Knirps

    DEFF Research Database (Denmark)

    Danielsen, Erik Thomas; Møller, Morten Erik; Dorry, Elad

    2014-01-01

    Specialized endocrine cells produce and release steroid hormones that govern development, metabolism and reproduction. In order to synthesize steroids, all the genes in the biosynthetic pathway must be coordinately turned on in steroidogenic cells. In Drosophila, the steroid producing endocrine...... cells are located in the prothoracic gland (PG) that releases the steroid hormone ecdysone. The transcriptional regulatory network that specifies the unique PG specific expression pattern of the ecdysone biosynthetic genes remains unknown. Here, we show that two transcription factors, the POU...

  7. Leaf carbohydrates influence transcriptional and post-transcriptional regulation of nocturnal carboxylation and starch degradation in the facultative CAM plant, Mesembryanthemum crystallinum.

    Science.gov (United States)

    Taybi, Tahar; Cushman, John C; Borland, Anne M

    2017-11-01

    Nocturnal degradation of transitory starch is a limiting factor for the optimal function of crassulacean acid metabolism and must be coordinated with phosphoenolypyruvate carboxylase (PEPC)-mediated CO2 uptake to optimise carbon gain over the diel cycle. The aim of this study was to test the hypothesis that nocturnal carboxylation is coordinated with starch degradation in CAM via a mechanism whereby the products of these pathways regulate diel transcript abundance and enzyme activities for both processes. To test this hypothesis, a starch and CAM-deficient mutant of Mesembryanthemum crystallinum was compared with wild type plants under well-watered and saline (CAM-inducing) conditions. Exposure to salinity increased the transcript abundance of genes required for nocturnal carboxylation, starch and sucrose degradation in both wild type and mutant, but the transcript abundance of several of these genes was not sustained over the dark period in the low-carbohydrate, CAM-deficient mutant. The diel pattern of transcript abundance for PEPC mirrored that of PEPC protein, as did the transcripts, protein, and activity of chloroplastic starch phosphorylase in both wild type and mutant, suggesting robust diel coordination of these metabolic processes. Activities of several amylase isoforms were low or lacking in the mutant, whilst the activity of a cytosolic isoform of starch phosphorylase was significantly elevated, indicating contrasting modes of metabolic regulation for the hydrolytic and phosphorylytic routes of starch degradation. Externally supplied sucrose resulted in an increase in nocturnal transcript abundance of genes required for nocturnal carboxylation and starch degradation. These results demonstrate that carbohydrates impact on transcriptional and post-transcriptional regulation of nocturnal carboxylation and starch degradation in CAM. Copyright © 2017 Elsevier GmbH. All rights reserved.

  8. Gene transcription and electromagnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, A.S.

    1992-01-01

    Our overall aim is to obtain sufficient information to allow us to ultimately determine whether ELF EM field exposure is an initiating factor in neoplastic transformation and/or if exposure can mimic characteristics of the second-step counterpart in neoplastic disease. This aim is based on our previous findings that levels of some transcripts are increased in cells exposed to EM fields. While the research is basic in nature, the ramifications have bearing on the general safety of exposure to EM fields in industrial and everyday life. A large array of diverse biological effects are reported to occur as the result of exposure to elf EM fields, suggesting that the cell response to EM fields is at a basic level, presumably initiated by molecular and/or biophysical events at the cell membrane. The hypothesized route is a signal transduction pathway involving membrane calcium fluxes. Information flow resulting from signal transduction can mediate the induction of regulatory factors in the cell, and directly affect how transcription is regulated.

  9. Fiber cavities with integrated mode matching optics.

    Science.gov (United States)

    Gulati, Gurpreet Kaur; Takahashi, Hiroki; Podoliak, Nina; Horak, Peter; Keller, Matthias

    2017-07-17

    In fiber based Fabry-Pérot Cavities (FFPCs), limited spatial mode matching between the cavity mode and input/output modes has been the main hindrance for many applications. We have demonstrated a versatile mode matching method for FFPCs. Our novel design employs an assembly of a graded-index and large core multimode fiber directly spliced to a single mode fiber. This all-fiber assembly transforms the propagating mode of the single mode fiber to match with the mode of a FFPC. As a result, we have measured a mode matching of 90% for a cavity length of ~400 μm. This is a significant improvement compared to conventional FFPCs coupled with just a single mode fiber, especially at long cavity lengths. Adjusting the parameters of the assembly, the fundamental cavity mode can be matched with the mode of almost any single mode fiber, making this approach highly versatile and integrable.

  10. Adaptive Structural Mode Control Project

    Data.gov (United States)

    National Aeronautics and Space Administration — M4 Engineering proposes the development of an adaptive structural mode control system. The adaptive control system will begin from a "baseline" dynamic model of the...

  11. Rotational Modes in Phononic Crystals

    Science.gov (United States)

    Wu, Ying; Peng, Pai; Mei, Jun

    2014-03-01

    We propose a lumped model for the rotational modes in two-dimensional phononic crystals comprised of square arrays of solid cylindrical scatterers in solid hosts. The model not only can reproduce the dispersion relations in a certain range with one fitted parameter, but also gives simple analytical expressions for the frequencies of the eigenmodes at the high symmetry points in the Brillouin zone. These expressions provide physical understandings of the rotational modes as well as certain translational and hybrid mode, and predict the presence of accidental degeneracy of the rotational and dipolar modes, which leads to a Dirac-like cone in the Brillouin zone center. Supported by KAUST Baseline Research Fund, National Natural Science Foundation of China (Grants No. 10804086 and No. 11274120), and the Fundamental Research Funds for the Central Universities (Grant No. 2012ZZ0077).

  12. Amplitude damping of vortex modes

    CSIR Research Space (South Africa)

    Dudley, Angela L

    2010-09-01

    Full Text Available An interferometer, mimicking an amplitude damping channel for vortex modes, is presented. Experimentally the action of the channel is in good agreement with that predicted theoretically. Since we can characterize the action of the channel on orbital...

  13. Novel Modes Workshop Summary Report

    Science.gov (United States)

    2015-12-01

    On December 2-3, 2014, the Federal Highway Administration's (FHWA's) Exploratory Advanced Research Program, with support from the John A. Volpe National Transportation Systems Center, convened the 2-day workshop "Novel Modes." It was held concurrentl...

  14. The Kuhnian mode of HPS

    DEFF Research Database (Denmark)

    Schindler, Samuel

    2013-01-01

    In this article I argue that a methodological challenge to an integrated history and philosophy of science approach put forth by Ronald Giere almost forty years ago can be met by what I call the Kuhnian mode of History and Philosophy of Science (HPS). Although in the Kuhnian mode of HPS norms about...... science are motivated by historical facts about scientific practice, the justifiers of the constructed norms are not historical facts. The Kuhnian mode of HPS therefore evades the naturalistic fallacy which Giere’s challenge is a version of. Against the backdrop of a discussion of Laudan’s normative...... naturalism I argue that the Kuhnian mode of HPS is a superior form of naturalism: it establishes contact to the practice of science without making itself dependent on its contingencies....

  15. A revisit of the mode of interaction of small transcription inhibitors ...

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... with genomic DNA. DIPAK DASGUPTA*, PARIJAT MAJUMDER and AMRITA BANERJEE. Biophysics Division, Saha Institute of Nuclear Physics, Bidhan Nagar, Kolkata ... Structural effects of the DNA-binding molecules upon chromatin in light ... features that may be exploited for the design of small mol-.

  16. Examination of the 'web mode effect'

    DEFF Research Database (Denmark)

    Clement, Sanne Lund; Shamshiri-Petersen, Ditte

    for different modes, and mode differences then are influenced by stratification differences. In both cases the real mode differences are nearly impossible to determine and remains rather speculative. The purpose of this contribution is to examine potential “web mode effects” in mixed-mode surveys. Compared...

  17. The Fifth Mode of Representation

    DEFF Research Database (Denmark)

    Hansen, Per Krogh; Behrendt, Poul Olaf

    2011-01-01

    “The fifth mode of representation: Ambiguous voices in unreliable third person narration”. Sammen med Poul Behrendt. In Per Krogh Hansen, Stefan Iversen, Henrik Skov Nielsen og Rolf Reitan (red.): Strange Voices. Walter de Gruyter, Berlin & New York......“The fifth mode of representation: Ambiguous voices in unreliable third person narration”. Sammen med Poul Behrendt. In Per Krogh Hansen, Stefan Iversen, Henrik Skov Nielsen og Rolf Reitan (red.): Strange Voices. Walter de Gruyter, Berlin & New York...

  18. An interdecadal American rainfall mode

    Science.gov (United States)

    Jury, Mark R.

    2009-04-01

    Low-frequency climate variability across the American continents and surrounding oceans is analyzed by application of singular value decomposition (SVD) to gauge-based rainfall and environmental anomaly fields in the period 1901-2002. A 5-year filter is used to maintain a focus on interdecadal cycles. The rainfall regime of particular interest (mode 1) is when West Africa and the Caribbean share positive loading and North and South America share negative loading. Wavelet cospectral energy is found at ˜8, 24, and 50 years for Caribbean/West African zones and 16 and 32 years for North/South America. West Africa and South America exhibit antiphase multidecadal variability, while North America and the Caribbean rainfall exhibit quasi-decadal cycles. The rainfall associations are nonstationary. In the early 1900s, Caribbean and South American rainfall were antiphase. Since 1930 low-frequency oscillations of North American (West African) rainfall have been positively (negatively) associated with South America. Low-frequency oscillations of North American rainfall have been consistently antiphase with respect to Caribbean rainfall; however, West Africa rainfall fluctuations have been in phase with the Caribbean more in the period 1920-1950 than at other times. Hemispheric-scale environmental SVD patterns and scores were compared with the leading rainfall modes. The north-south gradient modes in temperature are influential in respect of mode 1 rainfall, while east-west gradients relate to mode 2 (northern Brazil) rainfall. The ability of the GFDL2.1 coupled (ocean-atmosphere) general circulation model to represent interdecadal rainfall modes in the 20th century was evaluated. While mode 2 is reproduced, mode 1 remains elusive.

  19. Uniqueness of meromorphic functions sharing two finite sets

    Directory of Open Access Journals (Sweden)

    Chen Jun-Fan

    2017-10-01

    Full Text Available We prove uniqueness theorems of meromorphic functions, which show how two meromorphic functions are uniquely determined by their two finite shared sets. This answers a question posed by Gross. Moreover, some examples are provided to demonstrate that all the conditions are necessary.

  20. Unique Protein Signature of Circulating Microparticles in Systemic Lupus Erythematosus

    DEFF Research Database (Denmark)

    Østergaard, Ole; Nielsen, Christoffer; Iversen, Line V

    2013-01-01

    To characterize the unique qualities of proteins associated with circulating subcellular material in systemic lupus erythematosus (SLE) patients compared with healthy controls and patients with other chronic autoimmune diseases.......To characterize the unique qualities of proteins associated with circulating subcellular material in systemic lupus erythematosus (SLE) patients compared with healthy controls and patients with other chronic autoimmune diseases....

  1. 10 CFR 9.108 - Certification, transcripts, recordings and minutes.

    Science.gov (United States)

    2010-01-01

    ... transcription as provided in § 9.14. The Secretary shall maintain a complete verbatim copy of the transcript, a...). Copies of such transcript, or minutes, or a transcription of such recording disclosing the identity of...

  2. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences.

    Science.gov (United States)

    Bhatia, Shipra; Kleinjan, Dirk A

    2014-07-01

    The precise control of gene expression programs is crucial for the establishment of the diverse gene activity patterns required for the correct development, patterning and differentiation of the myriad of cell types within an organism. The crucial importance of non-coding regions of the genome in the control of gene regulation is well established and depends on a diverse group of sequence fragments called cis-regulatory elements that reside in these regions. Advances in novel genome-wide techniques have greatly increased the ability to identify potential regulatory elements. In contrast, their functional characterisation and the determination of their diverse modes of action remain a major bottleneck. Greater knowledge of gene expression control is of major importance for human health as disruption of gene regulation has become recognised as a significant cause of human disease. Appreciation of the role of cis-regulatory polymorphism in natural variation and susceptibility to common disease is also growing. While novel techniques such as GWAS and NGS provide the ability to collect large genomic datasets, the challenge for the twenty-first century will be to extract the relevant sequences and how to investigate the functional consequences of disease-associated changes. Here, we review how studies of transcriptional control at selected paradigm disease gene loci have revealed general principles of cis-regulatory logic and regulatory genome organisation, yet also demonstrate how the variety of mechanisms can combine to result in unique phenotypic outcomes. Integration of these principles with the emerging wealth of genome-wide data will provide enhanced insight into the workings of our regulatory genome.

  3. A novel pea mitochondrial in vitro transcription system recognizes homologous and heterologous mRNA and tRNA promoters.

    Science.gov (United States)

    Binder, S; Hatzack, F; Brennicke, A

    1995-09-22

    To elucidate the mechanism involved in the transcription initiation process in mitochondria of dicotyledonous plants, an in vitro transcription system was established for pea (Pisum sativum L.). The partially purified mitochondrial protein extract initiates transcription on homologous pea templates as well as on heterologous mitochondrial DNA from other dicot plant species. In vitro transcription begins within the nonanucleotide 5'-(-7)CRTAAGAGA(+2)-3' (transcription start site is underlined) conserved at most of the identified transcription initiation sites in dicot plant mitochondria. The in vitro initiation at promoters of protein as well as of tRNA coding genes indicates a common mode of transcription initiation for different types of RNA. The competent recognition of different heterologous templates supports a general functional role of the conserved nonanucleotide within mitochondrial promoters of dicotyledonous plants. Initial studies of the promoter structure by deletion analysis in the 5' region of the pea atp9 promoter show that in addition to the conserved nonanucleotide, which is essential for transcription initiation in vitro, sequences up to 25 nucleotides upstream of the transcription start site are necessary for an efficient initiation event.

  4. Salience of unique hues and implications for color theory.

    Science.gov (United States)

    Wool, Lauren E; Komban, Stanley J; Kremkow, Jens; Jansen, Michael; Li, Xiaobing; Alonso, Jose-Manuel; Zaidi, Qasim

    2015-02-06

    The unique hues--blue, green, yellow, red--form the fundamental dimensions of opponent-color theories, are considered universal across languages, and provide useful mental representations for structuring color percepts. However, there is no neural evidence for them from neurophysiology or low-level psychophysics. Tapping a higher prelinguistic perceptual level, we tested whether unique hues are particularly salient in search tasks. We found no advantage for unique hues over their nonunique complementary colors. However, yellowish targets were detected faster, more accurately, and with fewer saccades than their complementary bluish targets (including unique blue), while reddish-greenish pairs were not significantly different in salience. Similarly, local field potentials in primate V1 exhibited larger amplitudes and shorter latencies for yellowish versus bluish stimuli, whereas this effect was weaker for reddish versus greenish stimuli. Consequently, color salience is affected more by early neural response asymmetries than by any possible mental or neural representation of unique hues. © 2015 ARVO.

  5. Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis.

    Science.gov (United States)

    Liang, Kaiwei; Woodfin, Ashley R; Slaughter, Brian D; Unruh, Jay R; Box, Andrew C; Rickels, Ryan A; Gao, Xin; Haug, Jeffrey S; Jaspersen, Sue L; Shilatifard, Ali

    2015-11-05

    Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to activate and transcribe until the end of the gene to clear Pol II from mitotic chromatin, followed by global impairment of transcription reinitiation through MTI. Global nascent RNA sequencing and RNA fluorescence in situ hybridization demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Both genetic and chemical inhibition of P-TEFb in mitosis lead to delays in the progression of cell division. Together, our study reveals a mechanism for MTA and MTI whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Normal modes and mode transformation of pure electron vortex beams.

    Science.gov (United States)

    Thirunavukkarasu, G; Mousley, M; Babiker, M; Yuan, J

    2017-02-28

    Electron vortex beams constitute the first class of matter vortex beams which are currently routinely produced in the laboratory. Here, we briefly review the progress of this nascent field and put forward a natural quantum basis set which we show is suitable for the description of electron vortex beams. The normal modes are truncated Bessel beams (TBBs) defined in the aperture plane or the Fourier transform of the transverse structure of the TBBs (FT-TBBs) in the focal plane of a lens with the said aperture. As these modes are eigenfunctions of the axial orbital angular momentum operator, they can provide a complete description of the two-dimensional transverse distribution of the wave function of any electron vortex beam in such a system, in analogy with the prominent role Laguerre-Gaussian (LG) beams played in the description of optical vortex beams. The characteristics of the normal modes of TBBs and FT-TBBs are described, including the quantized orbital angular momentum (in terms of the winding number l) and the radial index p>0. We present the experimental realization of such beams using computer-generated holograms. The mode analysis can be carried out using astigmatic transformation optics, demonstrating close analogy with the astigmatic mode transformation between LG and Hermite-Gaussian beams.This article is part of the themed issue 'Optical orbital angular momentum'. © 2017 The Author(s).

  7. Investigating the Mode Structure of the Weakly Coherent Mode

    Science.gov (United States)

    Golfinopoulos, T.; Labombard, B.; Hubbard, A.; Hughes, J. W.; Whyte, D.; Granetz, R.; Davis, E. M.; Edlund, E.; Ennever, P.; Greenwald, M.; Marmar, E.; Porkolab, M.; Wolfe, S. M.; Wukitch, S. J.; Alcator C-Mod Team

    2017-10-01

    The Weakly Coherent Mode (WCM, 200-500 kHz, k⊥ρs < 0.1) is an edge phenomenon associated with I-mode, a steady state, ELM-free confinement regime that has been observed on the Alcator C-Mod, ASDEX-Upgrade, and DIII-D tokamaks. I-mode is characterized by high particle flux, creating a separation of transport channels that leads to the development of a temperature pedestal, but not a density pedestal. The WCM is thought to contribute to this increased particle flux, though its precise role in regulating edge transport is not well-understood. Here, we investigate the structure of the WCM, particularly regarding poloidal asymmetry, using data from poloidally- and toroidally-arrayed Mirnov coils, as well as phase contrast imaging, with radial profiles of Te, ne, and Φ in the scrape-off layer provided by the Mirror Langmuir Probe. The WCM phenomenology is then compared to that of the Quasi-Coherent Mode, the edge fluctuation responsible for exhausting impurities in the Enhanced Dα H-mode. This work is supported by USDoE award DE-FC02-99ER54512.

  8. Novel fusion genes and chimeric transcripts in ependymal tumors.

    Science.gov (United States)

    Olsen, Thale Kristin; Panagopoulos, Ioannis; Gorunova, Ludmila; Micci, Francesca; Andersen, Kristin; Kilen Andersen, Hege; Meling, Torstein R; Due-Tønnessen, Bernt; Scheie, David; Heim, Sverre; Brandal, Petter

    2016-12-01

    We have previously identified two ALK rearrangements in a subset of ependymal tumors using a combination of cytogenetic data and RNA sequencing. The aim of this study was to perform an unbiased search for fusion transcripts in our entire series of ependymal tumors. Fusion analysis was performed using the FusionCatcher algorithm on 12 RNA-sequenced ependymal tumors. Candidate transcripts were prioritized based on the software's filtering and manual visualization using the BLAST (Basic Local Alignment Search Tool) and BLAT (BLAST-like alignment tool) tools. Genomic and reverse transcriptase PCR with subsequent Sanger sequencing was used to validate the potential fusions. Fluorescent in situ hybridization (FISH) using locus-specific probes was also performed. A total of 841 candidate chimeric transcripts were identified in the 12 tumors, with an average of 49 unique candidate fusions per tumor. After algorithmic and manual filtering, the final list consisted of 24 potential fusion events. Raw RNA-seq read sequences and PCR validation supports two novel fusion genes: a reciprocal fusion gene involving UQCR10 and C1orf194 in an adult spinal ependymoma and a TSPAN4-CD151 fusion gene in a pediatric infratentorial anaplastic ependymoma. Our previously reported ALK rearrangements and the RELA and YAP1 fusions found in supratentorial ependymomas were until now the only known fusion genes present in ependymal tumors. The chimeric transcripts presented here are the first to be reported in infratentorial or spinal ependymomas. Further studies are required to characterize the genomic rearrangements causing these fusion genes, as well as the frequency and functional importance of the fusions. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  9. Transcriptional Characterization of Porcine Leptin and Leptin Receptor Genes.

    Science.gov (United States)

    Pérez-Montarelo, Dafne; Fernández, Almudena; Barragán, Carmen; Noguera, Jose L; Folch, Josep M; Rodríguez, M Carmen; Ovilo, Cristina; Silió, Luis; Fernández, Ana I

    2013-01-01

    The leptin (LEP) and its receptor (LEPR) regulate food intake and energy balance through hypothalamic signaling. However, the LEP-LEPR axis seems to be more complex and its expression regulation has not been well described. In pigs, LEP and LEPR genes have been widely studied due to their relevance. Previous studies reported significant effects of SNPs located in both genes on growth and fatness traits. The aim of this study was to determine the expression profiles of LEP and LEPR across hypothalamic, adipose, hepatic and muscle tissues in Iberian x Landrace backcrossed pigs and to analyze the effects of gene variants on transcript abundance. To our knowledge, non porcine LEPR isoforms have been described rather than LEPRb. A short porcine LEPR isoform (LEPRa), that encodes a protein lacking the intracellular residues responsible of signal transduction, has been identified for the first time. The LEPRb isoform was only quantifiable in hypothalamus while LEPRa appeared widely expressed across tissues, but at higher levels in liver, suggesting that both isoforms would develop different roles. The unique LEP transcript showed expression in backfat and muscle. The effects of gene variants on transcript expression revealed interesting results. The LEPRc.1987C>T polymorphism showed opposite effects on LEPRb and LEPRa hypothalamic expression. In addition, one out of the 16 polymorphisms identified in the LEPR promoter region revealed high differential expression in hepatic LEPRa. These results suggest a LEPR isoform-specific regulation at tissue level. Conversely, non-differential expression of LEP conditional on the analyzed polymorphisms could be detected, indicating that its regulation is likely affected by other mechanisms rather than gene sequence variants. The present study has allowed a transcriptional characterization of LEP and LEPR isoforms on a range of tissues. Their expression patterns seem to indicate that both molecules develop peripheral roles apart from

  10. Unitary evolution and uniqueness of the Fock representation of Dirac fields in cosmological spacetimes

    Science.gov (United States)

    Cortez, Jerónimo; Elizaga Navascués, Beatriz; Martín-Benito, Mercedes; Mena Marugán, Guillermo A.; Velhinho, José M.

    2015-11-01

    We present a privileged Fock quantization of a massive Dirac field in a closed Friedmann-Robertson-Walker cosmology, partially selected by the criteria of invariance of the vacuum under the symmetries of the field equations, and unitary implementation of the dynamics. When quantizing free scalar fields in homogeneous and isotropic spacetimes with compact spatial sections, these criteria have been shown to pick out a unique Fock representation (up to unitary equivalence). Here, we employ the same criteria for fermion fields and explore whether that uniqueness result can be extended to the case of the Fock quantization of fermions. For the massive Dirac field, we start by introducing a specific choice of the complex structure that determines the Fock representation. Such a structure is invariant under the symmetries of the equations of motion. We then prove that the corresponding representation of the canonical anticommutation relations admits a unitary implementation of the dynamics. Moreover, we construct a rather general class of representations that satisfy the above criteria, and we demonstrate that they are all unitarily equivalent to our previous choice. The complex structures in this class are restricted only by certain conditions on their asymptotic behavior for modes in the ultraviolet sector of the Dirac operator. We finally show that, if one assumes that these asymptotic conditions are in fact trivial once our criteria are fulfilled, then the time-dependent scaling in the definition of the fermionic annihilation and creationlike variables is essentially unique.

  11. Optically Mediated Hybridization Between Two Mechanical Modes

    CERN Document Server

    Shkarin, A B; Hoch, S W; Deutsch, C; Reichel, J; Harris, J G E

    2013-01-01

    In this paper we study a system consisting of two nearly degenerate mechanical modes that couple to a single mode of an optical cavity. We show that this coupling leads to nearly complete (99.5%) hybridization of the two mechanical modes into a bright mode that experiences strong optomechanical interactions and a dark mode that experiences almost no optomechanical interactions. We use this hybridization to transfer energy between the mechanical modes with 40% efficiency.

  12. Challenges in higher order mode Raman amplifiers

    DEFF Research Database (Denmark)

    Rottwitt, Karsten; Nielsen, Kristian; Friis, Søren Michael Mørk

    2015-01-01

    A higher order Raman amplifier model that take random mode coupling into account ispresented. Mode dependent gain and signal power fluctuations at the output of the higher order modeRaman amplifier are discussed......A higher order Raman amplifier model that take random mode coupling into account ispresented. Mode dependent gain and signal power fluctuations at the output of the higher order modeRaman amplifier are discussed...

  13. Transcriptional architecture of the mammalian circadian clock.

    Science.gov (United States)

    Takahashi, Joseph S

    2017-03-01

    Circadian clocks are endogenous oscillators that control 24-hour physiological and behavioural processes in organisms. These cell-autonomous clocks are composed of a transcription-translation-based autoregulatory feedback loop. With the development of next-generation sequencing approaches, biochemical and genomic insights into circadian function have recently come into focus. Genome-wide analyses of the clock transcriptional feedback loop have revealed a global circadian regulation of processes such as transcription factor occupancy, RNA polymerase II recruitment and initiation, nascent transcription, and chromatin remodelling. The genomic targets of circadian clocks are pervasive and are intimately linked to the regulation of metabolism, cell growth and physiology.

  14. A brain-specific transcription activator.

    Science.gov (United States)

    Korner, M; Rattner, A; Mauxion, F; Sen, R; Citri, Y

    1989-11-01

    We have identified a DNA binding protein, named BETA, that interacts with the same (B) transcriptional regulatory sequence as the known transcription factor NF-kappa B. BETA is found only in gray matter throughout the brain, and not in a variety of other rat tissues. Two binding sites for BETA are present adjacent to the promoter of the rat proenkephalin gene. Transfection of primary brain cultures that express BETA, with a reporter gene driven by the SV40 promoter linked to BETA DNA binding sites, results in transcriptional activation. We infer that BETA is a brain-specific transcription activator.

  15. Heritable change caused by transient transcription errors.

    Directory of Open Access Journals (Sweden)

    Alasdair J E Gordon

    2013-06-01

    Full Text Available Transmission of cellular identity relies on the faithful transfer of information from the mother to the daughter cell. This process includes accurate replication of the DNA, but also the correct propagation of regulatory programs responsible for cellular identity. Errors in DNA replication (mutations and protein conformation (prions can trigger stable phenotypic changes and cause human disease, yet the ability of transient transcriptional errors to produce heritable phenotypic change ('epimutations' remains an open question. Here, we demonstrate that transcriptional errors made specifically in the mRNA encoding a transcription factor can promote heritable phenotypic change by reprogramming a transcriptional network, without altering DNA. We have harnessed the classical bistable switch in the lac operon, a memory-module, to capture the consequences of transient transcription errors in living Escherichia coli cells. We engineered an error-prone transcription sequence (A9 run in the gene encoding the lac repressor and show that this 'slippery' sequence directly increases epigenetic switching, not mutation in the cell population. Therefore, one altered transcript within a multi-generational series of many error-free transcripts can cause long-term phenotypic consequences. Thus, like DNA mutations, transcriptional epimutations can instigate heritable changes that increase phenotypic diversity, which drives both evolution and disease.

  16. The Unique Destination Proposition of Eskisehir: Industrial Heritage

    Directory of Open Access Journals (Sweden)

    Hakan Yılmaz

    2014-12-01

    Full Text Available This paper examines the transformation of Unique Sales Proposition (USP concept which is one of the most important strategies of advertising history, to the Unique Destination Proposition (UDP for the case of Eskisehir. This study aims to propose industrial heritage as the UDP of Eskisehir by a descriptive approach. Industrial heritage helps Eskisehir destination brand to attain a meaningful, sustainable and distinctive dimension from its competitors. The current industrial heritage samples of Eskisehir were initially evaluated in this context. Subsequently, in the focus of the relation between industrial heritage and tourism, an excursion route and a tour program is suggested including the unique industrial heritage values of Eskisehir.

  17. Dissection of Ire1 functions reveals stress response mechanisms uniquely evolved in Candida glabrata.

    Directory of Open Access Journals (Sweden)

    Taiga Miyazaki

    2013-01-01

    Full Text Available Proper protein folding in the endoplasmic reticulum (ER is vital in all eukaryotes. When misfolded proteins accumulate in the ER lumen, the transmembrane kinase/endoribonuclease Ire1 initiates splicing of HAC1 mRNA to generate the bZIP transcription factor Hac1, which subsequently activates its target genes to increase the protein-folding capacity of the ER. This cellular machinery, called the unfolded protein response (UPR, is believed to be an evolutionarily conserved mechanism in eukaryotes. In this study, we comprehensively characterized mutant phenotypes of IRE1 and other related genes in the human fungal pathogen Candida glabrata. Unexpectedly, Ire1 was required for the ER stress response independently of Hac1 in this fungus. C. glabrata Ire1 did not cleave mRNAs encoding Hac1 and other bZIP transcription factors identified in the C. glabrata genome. Microarray analysis revealed that the transcriptional response to ER stress is not mediated by Ire1, but instead is dependent largely on calcineurin signaling and partially on the Slt2 MAPK pathway. The loss of Ire1 alone did not confer increased antifungal susceptibility in C. glabrata contrary to UPR-defective mutants in other fungi. Taken together, our results suggest that the canonical Ire1-Hac1 UPR is not conserved in C. glabrata. It is known in metazoans that active Ire1 nonspecifically cleaves and degrades a subset of ER-localized mRNAs to reduce the ER load. Intriguingly, this cellular response could occur in an Ire1 nuclease-dependent fashion in C. glabrata. We also uncovered the attenuated virulence of the C. glabrata Δire1 mutant in a mouse model of disseminated candidiasis. This study has unveiled the unique evolution of ER stress response mechanisms in C. glabrata.

  18. Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression.

    Science.gov (United States)

    Green, Benjamin B; Houseman, E Andres; Johnson, Kevin C; Guerin, Dylan J; Armstrong, David A; Christensen, Brock C; Marsit, Carmen J

    2016-08-01

    The conversion of cytosine to 5-methylcystosine (5mC) is an important regulator of gene expression. 5mC may be enzymatically converted to 5-hydroxymethylcytosine (5hmC), with a potentially distinct regulatory function. We sought to investigate these cytosine modifications and their effect on gene expression by parallel processing of genomic DNA using bisulfite and oxidative bisulfite conversion in conjunction with RNA sequencing. Although values of 5hmC across the placental genome were generally low, we identified ∼21,000 loci with consistently elevated levels of 5-hydroxymethycytosine. Absence of 5hmC was observed in CpG islands and, to a greater extent, in non-CpG island-associated regions. 5hmC was enriched within poised enhancers, and depleted within active enhancers, as defined by H3K27ac and H3K4me1 measurements. 5hmC and 5mC were significantly elevated in transcriptionally silent genes when compared with actively transcribed genes. 5hmC was positively associated with transcription in actively transcribed genes only. Our data suggest that dynamic cytosine regulation, associated with transcription, provides the most complete epigenomic landscape of the human placenta, and will be useful for future studies of the placental epigenome.-Green, B. B., Houseman, E. A., Johnson, K. C., Guerin, D. J., Armstrong, D. A., Christensen, B. C., Marsit, C. J. Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression. © FASEB.

  19. Separation of crack extension modes in composite delamination problems

    Science.gov (United States)

    Beuth, Jack L.

    1994-01-01

    This work concerns fracture mechanics modeling of composite delamination problems. In order to predict delamination resistance, an applied stress intensity factor, K, or energy release rate, G, must be compared to a mode-dependent critical value of K or G from experiment. In the interfacial fracture analysis of most applications and some tests, the mode of crack extension is not uniquely defined. It is instead a function of distance from the crack tip due to the oscillating singularity existing at the tip. In this work, a consistent method is presented of extracting crack extension modes in such cases. In particular, use of the virtual crack closure technique (VCCT) to extract modes of crack extension is studied for cases of a crack along the interface between two in-plane orthotropic materials. Modes of crack extension extracted from oscillatory analyses using VCCT are a function of the virtual crack extension length, delta. Most existing efforts to obtain delta-independent modes of crack extension involve changing the analysis in order to eliminate its oscillatory nature. One such method involves changing one or more properties of the layers to make the oscillatory exponent parameter, epsilon, equal zero. Standardized application of this method would require consistent criteria for identifying which properties can be altered without changing the physical aspects of the problem. Another method involves inserting a thin homogeneous layer (typically referred to as a resin interlayer) along the interface and placing the crack within it. The drawbacks of this method are that it requires increased modeling effort and introduces the thickness of the interlayer as an additional length parameter. The approach presented here does not attempt to alter the interfacial fracture analysis to eliminate its oscillatory behavior. Instead, the argument is made that the oscillatory behavior is non-physical and that if its effects were separated from VCCT quantities, then consistent

  20. Tapping mode microwave impedance microscopy

    KAUST Repository

    Lai, K.

    2009-01-01

    We report tapping mode microwave impedance imaging based on atomic force microscope platforms. The shielded cantilever probe is critical to localize the tip-sample interaction near the tip apex. The modulated tip-sample impedance can be accurately simulated by the finite-element analysis and the result agrees quantitatively to the experimental data on a series of thin-film dielectric samples. The tapping mode microwave imaging is also superior to the contact mode in that the thermal drift in a long time scale is totally eliminated and an absolute measurement on the dielectric properties is possible. We demonstrated tapping images on working nanodevices, and the data are consistent with the transport results. © 2009 American Institute of Physics.

  1. Macroscopic (and microscopic massless modes

    Directory of Open Access Journals (Sweden)

    Michael C. Abbott

    2015-05-01

    Full Text Available We study certain spinning strings exploring the flat directions of AdS3×S3×S3×S1, the massless sector cousins of su(2 and sl(2 sector spinning strings. We describe these, and their vibrational modes, using the D(2,1;α2 algebraic curve. By exploiting a discrete symmetry of this structure which reverses the direction of motion on the spheres, and alters the masses of the fermionic modes s→κ−s, we find out how to treat the massless fermions which were previously missing from this formalism. We show that folded strings behave as a special case of circular strings, in a sense which includes their mode frequencies, and we are able to recover this fact in the worldsheet formalism. We use these frequencies to calculate one-loop corrections to the energy, with a version of the Beisert–Tseytlin resummation.

  2. Quasiadiabatic modes from viscous inhomogeneities

    CERN Document Server

    Giovannini, Massimo

    2016-04-20

    The viscous inhomogeneities of a relativistic plasma determine a further class of entropic modes whose amplitude must be sufficiently small since curvature perturbations are observed to be predominantly adiabatic and Gaussian over large scales. When the viscous coefficients only depend on the energy density of the fluid the corresponding curvature fluctuations are shown to be almost adiabatic. After addressing the problem in a gauge-invariant perturbative expansion, the same analysis is repeated at a non-perturbative level by investigating the nonlinear curvature inhomogeneities induced by the spatial variation of the viscous coefficients. It is demonstrated that the quasiadiabatic modes are suppressed in comparison with a bona fide adiabatic solution. Because of its anomalously large tensor to scalar ratio the quasiadiabatic mode cannot be a substitute for the conventional adiabatic paradigm so that, ultimately, the present findings seems to exclude the possibility of a successful accelerated dynamics solely...

  3. Novel Manufacturing Process for Unique Mixed Carbide Refractory Composites Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This STTR Phase I project will establish the feasibility of an innovative manufacturing process to fabricate a range of unique hafnium/silicon based carbide...

  4. Unique morphology of dispersed clay particles in a polymer nanocomposite

    CSIR Research Space (South Africa)

    Malwela, T

    2011-02-01

    Full Text Available This communication reports a unique morphology of dispersed clay particles in a polymer nanocomposite. A nanocomposite of poly[butylene succinate)-co-adipate] (PBSA) with 3 wt% of organically modified montmorillonite was prepared by melt...

  5. Unique Role of Occupational Therapy in Rehabilitation of the Hand

    Science.gov (United States)

    Fact Sheet The Unique Role of Occupational Therapy in Rehabilitation of the Hand Hand therapy, a specialty practice area of occupational therapy, is typically concerned with treating orthopedic-based upper- ...

  6. Strict monotonicity and unique continuation of the biharmonic operator

    Directory of Open Access Journals (Sweden)

    Najib Tsouli

    2012-01-01

    Full Text Available In this paper, we will show that the strict monotonicity of the eigenvalues of the biharmonic operator holds if and only if some unique continuation property is satisfied by the corresponding eigenfunctions.

  7. Salience of unique hues and implications for color theory

    National Research Council Canada - National Science Library

    Wool, Lauren E; Komban, Stanley J; Kremkow, Jens; Jansen, Michael; Li, Xiaobing; Alonso, Jose-Manuel; Zaidi, Qasim

    2015-01-01

    The unique hues--blue, green, yellow, red--form the fundamental dimensions of opponent-color theories, are considered universal across languages, and provide useful mental representations for structuring color percepts...

  8. Soft mode and acoustic mode ferroelectric properties of deuterated ...

    Indian Academy of Sciences (India)

    SO4 crystal by a theoretical model which is extended with two sublattice pseudospin lattice coupled mode model by adding third, fourth and fifth order phonon anharmonic interaction terms as well as external electric field term in the crystal ...

  9. Practical relevance of pattern uniqueness in forensic science.

    Science.gov (United States)

    Jayaprakash, Paul T

    2013-09-10

    Uniqueness being unprovable, it has recently been argued that individualization in forensic science is irrelevant and, probability, as applied for DNA profiles, should be applied for all identifications. Critiques against uniqueness have omitted physical matching, a realistic and tangible individualization that supports uniqueness. Describing case examples illustrating pattern matches including physical matching, it is indicated that individualizations are practically relevant for forensic science as they establish facts on a definitive basis providing firm leads benefitting criminal investigation. As a tenet of forensic identification, uniqueness forms a fundamental paradigm relevant for individualization. Evidence on the indeterministic and stochastic causal pathways of characteristics in patterns available in the related fields of science sufficiently supports the proposition of uniqueness. Characteristics involved in physical matching and matching achieved in patterned evidence existing in the state of nature are not events amenable for counting; instead these are ensemble of visible units occupying the entire pattern area stretching the probability of re-occurrence of a verisimilitude pattern into infinity offering epistemic support to uniqueness. Observational methods are as respectable as instrumental or statistical methods since they are capable of generating results that are tangible and obviously valid as in physical matching. Applying the probabilistic interpretation used for DNA profiles to the other patterns would be unbefitting since these two are disparate, the causal pathways of the events, the loci, in the manipulated DNA profiles being determinable. While uniqueness enables individualizations, it does not vouch for eliminating errors. Instead of dismissing uniqueness and individualization, accepting errors as human or system failures and seeking remedial measures would benefit forensic science practice and criminal investigation. Copyright © 2013

  10. PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events.

    Science.gov (United States)

    Izuogu, Osagie G; Alhasan, Abd A; Alafghani, Hani M; Santibanez-Koref, Mauro; Elliott, David J; Elliot, David J; Jackson, Michael S

    2016-01-13

    Transcripts, which have been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with the underlying genomic sequence. These have been identified in a wide variety of tissues and cell types from many eukaryotes, and are now known to be mostly circular, cytoplasmic, and non-coding. Although there is no uniformly ascribed function, several have been shown to be involved in gene regulation. Accurate identification of these transcripts can, however, be difficult due to artefacts from a wide variety of sources. Here, we present a computational method, PTESFinder, to identify these transcripts from high throughput RNAseq data. Uniquely, it systematically excludes potential artefacts emanating from pseudogenes, segmental duplications, and template switching, and outputs both PTES and canonical exon junction counts to facilitate comparative analyses. In comparison with four existing methods, PTESFinder achieves highest specificity and comparable sensitivity at a variety of read depths. PTESFinder also identifies between 13 % and 41.6 % more structures, compared to publicly available methods recently used to identify human circular RNAs. With high sensitivity and specificity, user-adjustable filters that target known sources of false positives, and tailored output to facilitate comparison of transcript levels, PTESFinder will facilitate the discovery and analysis of these poorly understood transcripts.

  11. Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis.

    Science.gov (United States)

    Chow, Brenda Y; Sanchez, Sabrina E; Breton, Ghislain; Pruneda-Paz, Jose L; Krogan, Naden T; Kay, Steve A

    2014-07-07

    Circadian clocks allow organisms to anticipate daily changes in the environment to enhance overall fitness. Transcription factors (TFs) play a prominent role in the molecular mechanism but are incompletely described possibly due to functional redundancy, gene family proliferation, and/or lack of context-specific assays. To overcome these, we performed a high-throughput yeast one-hybrid screen using the LUX ARRYHTHMO (LUX) gene promoter as bait against an Arabidopsis TF library. LUX is a unique gene because its mutation causes severe clock defects and transcript maintains high-amplitude cycling in the cold. We report the well-characterized cold-inducible C-repeat (CRT)/drought-responsive element (DRE) binding factor CBF1/DREB1b is a transcriptional regulator of LUX. We show that CBF1 binds the CRT in the LUX promoter, and both genes overlap in temporal and spatial expression. CBF1 overexpression causes upregulation of LUX and also alters other clock gene transcripts. LUX promoter regions including the CRT and Evening Element (EE) are sufficient for high-amplitude transcriptional cycling in the cold, and cold-acclimated lux seedlings are sensitive to freezing stress. Our data show cold signaling is integrated into the clock by CBF-mediated regulation of LUX expression, thereby defining a new transcriptional mechanism for temperature input to the circadian clock. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. X-ray bounds on the r-mode amplitude in millisecond pulsars

    Science.gov (United States)

    Schwenzer, Kai; Boztepe, Tuğba; Güver, Tolga; Vurgun, Eda

    2017-04-01

    r-mode asteroseismology provides a unique way to study the internal composition of compact stars. Due to their precise timing, recycled millisecond radio pulsars present a particularly promising class of sources. Although their thermal properties are still poorly constrained, X-ray data is very useful for asteroseismology since r-modes could strongly heat a star. Using known and new upper bounds on the temperatures and luminosities of several non-accreting millisecond radio pulsars, we derive bounds on the r-mode amplitude as low as α ≲ 10-8 and discuss the impact on scenarios for their internal composition.

  13. Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination

    Directory of Open Access Journals (Sweden)

    Abreha Measho

    2006-12-01

    Full Text Available Abstract Background HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid virus production, strand transfers during reverse transcription, and then selection. In this study, recombination frequencies were measured in the C1-C4 regions of the envelope gene in the presence (using a multiple cycle infection system and absence (in vitro reverse transcription and single cycle infection systems of selection for replication-competent virus. Ugandan subtypes A and D HIV-1 env sequences (115-A, 120-A, 89-D, 122-D, 126-D were employed in all three assay systems. These subtypes co-circulate in East Africa and frequently recombine in this human population. Results Increased sequence identity between viruses or RNA templates resulted in increased recombination frequencies, with the exception of the 115-A virus or RNA template. Analyses of the recombination breakpoints and mechanistic studies revealed that the presence of a recombination hotspot in the C3/V4 env region, unique to 115-A as donor RNA, could account for the higher recombination frequencies with the 115-A virus/template. Single-cycle infections supported proportionally less recombination than the in vitro reverse transcription assay but both systems still had significantly higher recombination frequencies than observed in the multiple-cycle virus replication system. In the multiple cycle assay, increased replicative fitness of one HIV-1 over the other in a dual infection dramatically decreased recombination frequencies. Conclusion Sequence variation at specific sites between HIV-1 isolates can introduce unique recombination hotspots, which increase recombination frequencies and skew the general observation that decreased HIV-1 sequence identity reduces recombination rates. These findings also suggest that the majority of

  14. Theory on the mechanism of distal action of transcription factors: looping of DNA versus tracking along DNA

    Energy Technology Data Exchange (ETDEWEB)

    Murugan, R, E-mail: rmurugan@gmail.co [Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036 (India)

    2010-10-15

    In this paper, we develop a theory on the mechanism of distal action of the transcription factors, which are bound at their respective cis-regulatory enhancer modules on the promoter-RNA polymerase II (PR) complexes to initiate the transcription event in eukaryotes. We consider both the looping and tracking modes of their distal communication and calculate the mean first passage time that is required for the distal interactions of the complex of enhancer and transcription factor with the PR via both these modes. We further investigate how this mean first passage time is dependent on the length of the DNA segment (L, base-pairs) that connects the cis-regulatory binding site and the respective promoter. When the radius of curvature of this connecting segment of DNA is R that was induced upon binding of the transcription factor at the cis-acting element and RNAPII at the promoter in cis-positions, our calculations indicate that the looping mode of distal action will dominate when L is such that L > 2{pi}R and the tracking mode of distal action will be favored when L < 2{pi}R. The time required for the distal action will be minimum when L = 2{pi}R where the typical value of R for the binding of histones will be R {approx} 16 bps and L {approx} 10{sup 2} bps. It seems that the free energy associated with the binding of the transcription factor with its cis-acting element and the distance of this cis-acting element from the corresponding promoter of the gene of interest is negatively correlated. Our results suggest that the looping and tracking modes of distal action are concurrently operating on the transcription activation and the physics that determines the timescales associated with the looping/tracking in the mechanism of action of these transcription factors on the initiation of the transcription event must put a selection pressure on the distribution of the distances of cis-regulatory modules from their respective promoters of the genes. The computational analysis

  15. Transcriptional regulatory proteins as biosensing tools.

    Science.gov (United States)

    Turner, Kendrick; Joel, Smita; Feliciano, Jessika; Feltus, Agatha; Pasini, Patrizia; Wynn, Daniel; Dau, Peter; Dikici, Emre; Deo, Sapna K; Daunert, Sylvia

    2017-06-22

    We have developed sensing systems employing different classes of transcriptional regulatory proteins genetically and chemically modified to incorporate a fluorescent reporter molecule for detection of arsenic, hydroxylated polychlorinated biphenyls (OH-PCBs), and cyclic AMP (cAMP). These are the first examples of optical sensing systems based on transcriptional regulatory proteins.

  16. Transcriptional regulation of the cell cycle

    NARCIS (Netherlands)

    Stahl, M.

    2006-01-01

    Transcriptional regulators play an important role during cell cycle progression. A subset of these even seems to have a critical function in regulating cell cycle transitions. In this thesis, I have addressed the importance of transcriptional control in the regulation of cell cycle progression, in

  17. Overlapping transcription structure of human cytomegalovirus ...

    Indian Academy of Sciences (India)

    2013-01-21

    Jan 21, 2013 ... Transcription of human cytomegalovirus UL/b′ region has been studied extensively for some genes. In this study, transcripts of the UL140 and UL141, two of the UL/b′ genes, were identified in late RNAs of three HCMV isolates using Northern blot hybridization, cDNA library screening and RACE-PCR.

  18. Transcription of Byzantine Chant - Problems, Possibilities, Formats

    DEFF Research Database (Denmark)

    Troelsgård, Christian

    2007-01-01

    Discusses the problems and possibilities for transsription of Byzantine chant on the basis of medieval musical manuscripts. A relatively 'neutral' style of transcription is suggested for musicological purposes.......Discusses the problems and possibilities for transsription of Byzantine chant on the basis of medieval musical manuscripts. A relatively 'neutral' style of transcription is suggested for musicological purposes....

  19. Speech Transcript Evaluation for Information Retrieval

    NARCIS (Netherlands)

    van der Werff, Laurens Bastiaan; Kraaij, Wessel; de Jong, Franciska M.G.

    Speech recognition transcripts are being used in various fields of research and practical applications, putting various demands on their accuracy. Traditionally ASR research has used intrinsic evaluation measures such as word error rate to determine transcript quality. In non-dictation-type

  20. DNA dynamically directs its own transcription initiation

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, K. O. (Kim O.); Kalosakas, G. (George); Bishop, A. R. (Alan R.); Choi, C. H. (Chu H.); Usheva, A. (Anny)

    2004-01-01

    Initiation of DNA gene transcription requires a transient opening in the double helix at the transcriptional start site. It is generally assumed that the location of this 'transcriptional bubble' is determined by sequence-specific protein binding, and that the energy required for unwinding the double helix comes from torsional strain. Physical twisting should cause DNA to open consistently in weakly bonded A/T rich stretches, however, simple base-pairing energetics alone can not account for the variety of observed transcriptional start sites. Applying the Peyrard-Bishop nonlinear cooperativity model to DNA, we are able to predict that thermally-induced DNA bubbles, similar in size to transcription bubbles, form at specific locations on DNA promoters. These predicted openings agree remarkably well with experiment, and that they correlate exactly with known transcription start sites and important regulatory sites on three different promoters. We propose that the sequence-specific location of the transcriptional start site is predetermined by the inherent opening patterns of specific DNA sequences. As DNA bubble formation is independent of protein binding, it appears that DNA is not only a passive carrier of information, but its dynamics plays an important role in directing the transcription and regulation of the genes it contains.

  1. Overlapping transcription structure of human cytomegalovirus ...

    Indian Academy of Sciences (India)

    Transcription of human cytomegalovirus UL/b′ region has been studied extensively for some genes. In this study, transcripts of the UL140 and UL141, two of the UL/b′ genes, were identified in late RNAs of three HCMV isolates using Northern blot hybridization, cDNA library screening and RACE-PCR. At least three ...

  2. Unique spectral markers discern recurrent Glioblastoma cells from heterogeneous parent population

    Science.gov (United States)

    Kaur, Ekjot; Sahu, Aditi; Hole, Arti R.; Rajendra, Jacinth; Chaubal, Rohan; Gardi, Nilesh; Dutt, Amit; Moiyadi, Aliasgar; Krishna, C. Murali; Dutt, Shilpee

    2016-01-01

    An inability to discern resistant cells from bulk tumour cell population contributes to poor prognosis in Glioblastoma. Here, we compared parent and recurrent cells generated from patient derived primary cultures and cell lines to identify their unique molecular hallmarks. Although morphologically similar, parent and recurrent cells from different samples showed variable biological properties like proliferation and radiation resistance. However, total RNA-sequencing revealed transcriptional landscape unique to parent and recurrent populations. These data suggest that global molecular differences but not individual biological phenotype could differentiate parent and recurrent cells. We demonstrate that Raman Spectroscopy a label-free, non-invasive technique, yields global information about biochemical milieu of recurrent and parent cells thus, classifying them into distinct clusters based on Principal-Component-Analysis and Principal-Component-Linear-Discriminant-Analysis. Additionally, higher lipid related spectral peaks were observed in recurrent population. Importantly, Raman spectroscopic analysis could further classify an independent set of naïve primary glioblastoma tumour tissues into non-responder and responder groups. Interestingly, spectral features from the non-responder patient samples show a considerable overlap with the in-vitro generated recurrent cells suggesting their similar biological behaviour. This feasibility study necessitates analysis of a larger cohort of naïve primary glioblastoma samples to fully envisage clinical utility of Raman spectroscopy in predicting therapeutic response. PMID:27221528

  3. Whipworm kinomes reflect a unique biology and adaptation to the host animal.

    Science.gov (United States)

    Stroehlein, Andreas J; Young, Neil D; Korhonen, Pasi K; Chang, Bill C H; Nejsum, Peter; Pozio, Edoardo; La Rosa, Giuseppe; Sternberg, Paul W; Gasser, Robin B

    2017-11-01

    Roundworms belong to a diverse phylum (Nematoda) which is comprised of many parasitic species including whipworms (genus Trichuris). These worms have adapted to a biological niche within the host and exhibit unique morphological characteristics compared with other nematodes. Although these adaptations are known, the underlying molecular mechanisms remain elusive. The availability of genomes and transcriptomes of some whipworms now enables detailed studies of their molecular biology. Here, we defined and curated the full complement of an important class of enzymes, the protein kinases (kinomes) of two species of Trichuris, using an advanced and integrated bioinformatic pipeline. We investigated the transcription of Trichuris suis kinase genes across developmental stages, sexes and tissues, and reveal that selectively transcribed genes can be linked to central roles in developmental and reproductive processes. We also classified and functionally annotated the curated kinomes by integrating evidence from structural modelling and pathway analyses, and compared them with other curated kinomes of phylogenetically diverse nematode species. Our findings suggest unique adaptations in signalling processes governing worm morphology and biology, and provide an important resource that should facilitate experimental investigations of kinases and the biology of signalling pathways in nematodes. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

  4. Evolution of general transcription factors.

    Science.gov (United States)

    Gunbin, K V; Ruvinsky, A

    2013-02-01

    Three genes GTF2IRD1, GTF2I, and GTF2IRD2, which encode members of the GTF2I (or TFII-I) family of so-called general transcription factors, were discovered and studied during the last two decades. Chromosome location and similarity of exon-intron structures suggest that the family evolved by duplications. The initial duplication of ancestral proto-GTF2IRD1 gene likely occurred in early vertebrates prior to origin of cartilaginous fish and led to formation of GTF2I (>450 MYA), which was later lost in bony fish but successfully evolved in the land vertebrates. The second duplication event, which created GTF2IRD2, occurred prior to major radiation events of eutherian mammalian evolution (>100 MYA). During recent steps of primate evolution there was another duplication which led to formation of GTF2IRD2B (evolution of the genes. The atypical substitutions are often located on secondary structures joining α-helices and affect 3D arrangement of the protein globule. Such substitutions are commonly traced at the early stages of evolution in Tetrapoda, Amniota, and Mammalia.

  5. Transcription Factor Networks in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    David Y. Rhee

    2014-09-01

    Full Text Available Specific cellular fates and functions depend on differential gene expression, which occurs primarily at the transcriptional level and is controlled by complex regulatory networks of transcription factors (TFs. TFs act through combinatorial interactions with other TFs, cofactors, and chromatin-remodeling proteins. Here, we define protein-protein interactions using a coaffinity purification/mass spectrometry method and study 459 Drosophila melanogaster transcription-related factors, representing approximately half of the established catalog of TFs. We probe this network in vivo, demonstrating functional interactions for many interacting proteins, and test the predictive value of our data set. Building on these analyses, we combine regulatory network inference models with physical interactions to define an integrated network that connects combinatorial TF protein interactions to the transcriptional regulatory network of the cell. We use this integrated network as a tool to connect the functional network of genetic modifiers related to mastermind, a transcriptional cofactor of the Notch pathway.

  6. Histone variants in plant transcriptional regulation.

    Science.gov (United States)

    Jiang, Danhua; Berger, Frédéric

    2017-01-01

    Chromatin based organization of eukaryotic genome plays a profound role in regulating gene transcription. Nucleosomes form the basic subunits of chromatin by packaging DNA with histone proteins, impeding the access of DNA to transcription factors and RNA polymerases. Exchange of histone variants in nucleosomes alters the properties of nucleosomes and thus modulates DNA exposure during transcriptional regulation. Growing evidence indicates the important function of histone variants in programming transcription during developmental transitions and stress response. Here we review how histone variants and their deposition machineries regulate the nucleosome stability and dynamics, and discuss the link between histone variants and transcriptional regulation in plants. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Transcription Factor Pathways and Congenital Heart Disease

    Science.gov (United States)

    McCulley, David J.; Black, Brian L.

    2013-01-01

    Congenital heart disease is a major cause of morbidity and mortality throughout life. Mutations in numerous transcription factors have been identified in patients and families with some of the most common forms of cardiac malformations and arrhythmias. This review discusses factor pathways known to be important for normal heart development and how abnormalities in these pathways have been linked to morphological and functional forms of congenital heart defects. A comprehensive, current list of known transcription factor mutations associated with congenital heart disease is provided, but the review focuses primarily on three key transcription factors, Nkx2-5, GATA4, and Tbx5, and their known biochemical and genetic partners. By understanding the interaction partners, transcriptional targets, and upstream activators of these core cardiac transcription factors, additional information about normal heart formation and further insight into genes and pathways affected in congenital heart disease should result. PMID:22449847

  8. Chromosomal organization of transcription: in a nutshell.

    Science.gov (United States)

    Meyer, Sam; Reverchon, Sylvie; Nasser, William; Muskhelishvili, Georgi

    2017-11-28

    Early studies of transcriptional regulation focused on individual gene promoters defined specific transcription factors as central agents of genetic control. However, recent genome-wide data propelled a different view by linking spatially organized gene expression patterns to chromosomal dynamics. Therefore, the major problem in contemporary molecular genetics concerned with transcriptional gene regulation is to establish a unifying model that reconciles these two views. This problem, situated at the interface of polymer physics and network theory, requires development of an integrative methodology. In this review, we discuss recent achievements in classical model organism E. coli and provide some novel insights gained from studies of a bacterial plant pathogen, D. dadantii. We consider DNA topology and the basal transcription machinery as key actors of regulation, in which activation of functionally relevant genes is coupled to and coordinated with the establishment of extended chromosomal domains of coherent transcription. We argue that the spatial organization of genome plays a fundamental role in its own regulation.

  9. Photons uniques indiscernables à partir d'une boîte quantique unique dans un cristal photonique

    Science.gov (United States)

    Laurent, S.; Varoutsis, S.; Le Gratiet, L.; Lemaître, A.; Sagnes, I.; Raineri, F.; Levenson, A.; Robert-Philip, I.; Abram, I.

    2006-10-01

    Nous avons développé et caractérisé une source de photons uniques basée sur l'émission spontanée d'une boîte quantique unique insérée dans une cavité à bande interdite photonique bidimensionnelle. Ce système nous a d'abord permis de produire des photons uniques, puis des photons uniques indiscernables avec une indiscernabilité supérieure à 70%. L'observation de l'indiscernabilité des photons, impossible sans un raccourcissement important de la durée de vie, met en évidence un effet Purcell supérieur à 25 dans ce système.

  10. Dually-mode-locked ND: YAG laser

    Science.gov (United States)

    Osmundson, J.; Rowe, E.; Santarpia, D.

    1974-01-01

    Mode-locking is stabilized effectively by conventional loss-modulator and phase-modulator, mode-locking elements placed in laser cavity in optical series with one another. Resulting dually-mode-locked system provides pulses with constant phase relative to mode-lock drive signal without presence of relaxation oscillation noise.

  11. DNA recognition mechanism of the ONECUT homeodomain of transcription factor HNF-6.

    Science.gov (United States)

    Iyaguchi, Daisuke; Yao, Min; Watanabe, Nobuhisa; Nishihira, Jun; Tanaka, Isao

    2007-01-01

    Hepatocyte nuclear factor-6 (HNF-6), a liver-enriched transcription factor, controls the development of various tissues, such as the pancreas and liver, and regulates the expression of several hepatic genes. This protein belongs to the ONECUT class of homeodomain proteins and contains a bipartite DNA-binding domain composed of a single cut domain and a characteristic homeodomain. This transcription factor has two distinct modes of DNA binding and transcriptional activation that use different coactivators depending on the target gene. The crystal structure of the bipartite DNA-binding domain of HNF-6alpha complexed with the HNF-6-binding site of the TTR promoter revealed the DNA recognition mechanism of this protein. Comparing our structure with the DNA-free structure of HNF-6 or the structure of Oct-1, we discuss characteristic features associated with DNA binding and the structural basis for the dual mode of action of this protein, and we suggest a strategy for variability of transcriptional activation of the target gene.

  12. Rubble Mound Breakwater Failure Modes

    DEFF Research Database (Denmark)

    Burcharth, H. F.; Z., Liu

    1995-01-01

    The RMBFM-Project (Rubble Mound Breakwater Failure Modes) is sponsored by the Directorate General XII of the Commission of the European Communities under the Contract MAS-CT92- 0042, with the objective of contributing to the development of rational methods for the design of rubble mound breakwate...

  13. Mode structure of active resonators

    NARCIS (Netherlands)

    Ernst, G.J.; Witteman, W.J.

    1973-01-01

    An analysis is made of the mode structure of lasers when the interaction with the active medium is taken into account. We consider the combined effect of gain and refractive-index variations for arbitrary mirror configurations. Using a dimensionless round-trip matrix for a medium with a quadratic

  14. Single-mode optical fibres

    CERN Document Server

    Cancellieri, G

    1991-01-01

    This book describes signal propagation in single-mode optical fibres for telecommunication applications. Such description is based on the analysis of field propagation, considering waveguide properties and also some of the particular characteristics of the material fibre. The book covers such recent advances as, coherent transmissions; optical amplification; MIR fibres; polarization maintaining; polarization diversity and photon counting.

  15. Theory of Modes and Impulses

    Science.gov (United States)

    Apsche, Jack A.

    2005-01-01

    In his work on the Theory of Modes, Beck (1996) suggested that there were flaws with his cognitive theory. He suggested that though there are shortcomings to his cognitive theory, there were not similar shortcomings to the practice of Cognitive Therapy. The author suggests that if there are shortcomings to cognitive theory the same shortcomings…

  16. Planck intermediate results. XLI. A map of lensing-induced B-modes

    Science.gov (United States)

    Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartolo, N.; Basak, S.; Battaner, E.; Benabed, K.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bock, J. J.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Boulanger, F.; Burigana, C.; Butler, R. C.; Calabrese, E.; Cardoso, J.-F.; Catalano, A.; Chiang, H. C.; Christensen, P. R.; Clements, D. L.; Colombi, S.; Colombo, L. P. L.; Combet, C.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davis, R. J.; de Bernardis, P.; de Zotti, G.; Delabrouille, J.; Dickinson, C.; Diego, J. M.; Doré, O.; Ducout, A.; Dupac, X.; Elsner, F.; Enßlin, T. A.; Eriksen, H. K.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A. A.; Franceschi, E.; Galeotta, S.; Galli, S.; Ganga, K.; Ghosh, T.; Giard, M.; Giraud-Héraud, Y.; Gjerløw, E.; González-Nuevo, J.; Górski, K. M.; Gruppuso, A.; Gudmundsson, J. E.; Harrison, D. L.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hornstrup, A.; Hovest, W.; Hurier, G.; Jaffe, A. H.; Jones, W. C.; Keihänen, E.; Keskitalo, R.; Kisner, T. S.; Knoche, J.; Knox, L.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lähteenmäki, A.; Lamarre, J.-M.; Lasenby, A.; Lattanzi, M.; Leonardi, R.; Levrier, F.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maffei, B.; Maggio, G.; Maino, D.; Mandolesi, N.; Mangilli, A.; Maris, M.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; Meinhold, P. R.; Melchiorri, A.; Mennella, A.; Migliaccio, M.; Mitra, S.; Miville-Deschênes, M.-A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Novikov, D.; Novikov, I.; Pagano, L.; Pajot, F.; Paoletti, D.; Pasian, F.; Patanchon, G.; Perdereau, O.; Perotto, L.; Pettorino, V.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pointecouteau, E.; Polenta, G.; Pratt, G. W.; Rachen, J. P.; Reinecke, M.; Remazeilles, M.; Renault, C.; Renzi, A.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Rossetti, M.; Roudier, G.; Rubiño-Martín, J. A.; Rusholme, B.; Sandri, M.; Santos, D.; Savelainen, M.; Savini, G.; Scott, D.; Spencer, L. D.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sunyaev, R.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Wehus, I. K.; Yvon, D.; Zacchei, A.; Zonca, A.

    2016-12-01

    The secondary cosmic microwave background (CMB) B-modes stem from the post-decoupling distortion of the polarization E-modes due to the gravitational lensing effect of large-scale structures. These lensing-induced B-modes constitute both a valuable probe of the dark matter distribution and an important contaminant for the extraction of the primary CMB B-modes from inflation. Planck provides accurate nearly all-sky measurements of both the polarization E-modes and the integrated mass distribution via the reconstruction of the CMB lensing potential. By combining these two data products, we have produced an all-sky template map of the lensing-induced B-modes using a real-space algorithm that minimizes the impact of sky masks. The cross-correlation of this template with an observed (primordial and secondary) B-mode map can be used to measure the lensing B-mode power spectrum at multipoles up to 2000. In particular, when cross-correlating with the B-mode contribution directly derived from the Planck polarization maps, we obtain lensing-induced B-mode power spectrum measurement at a significance level of 12σ, which agrees with the theoretical expectation derived from the Planck best-fit Λ cold dark matter model. This unique nearly all-sky secondary B-mode template, which includes the lensing-induced information from intermediate to small (10 ≲ ℓ ≲ 1000) angular scales, is delivered as part of the Planck 2015 public data release. It will be particularly useful for experiments searching for primordial B-modes, such as BICEP2/Keck Array or LiteBIRD, since it will enable an estimate to be made of the lensing-induced contribution to the measured total CMB B-modes.

  17. Imaging modes of atomic force microscopy for application in molecular and cell biology

    Science.gov (United States)

    Dufrêne, Yves F.; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J.

    2017-04-01

    Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

  18. Imaging modes of atomic force microscopy for application in molecular and cell biology.

    Science.gov (United States)

    Dufrêne, Yves F; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J

    2017-04-06

    Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

  19. Leggett Modes and the Anderson-Higgs Mechanism in Superconductors without Inversion Symmetry.

    Science.gov (United States)

    Bittner, Nikolaj; Einzel, Dietrich; Klam, Ludwig; Manske, Dirk

    2015-11-27

    We develop a microscopic and gauge-invariant theory for collective modes resulting from the phase of the superconducting order parameter in noncentrosymmetric superconductors. Considering various crystal symmetries, we derive the corresponding gauge mode ω_{G}(q) and find, in particular, new Leggett modes ω_{L}(q) with characteristic properties that are unique to noncentrosymmetric superconductors. We calculate their mass and dispersion that reflect the underlying spin-orbit coupling and thus the balance between triplet and singlet superconductivity occurring simultaneously. Finally, we demonstrate the role of the Anderson-Higgs mechanism: while the long-range Coulomb interaction shifts ω_{G}(q) to the condensate plasma mode ω_{P}(q), it leaves the mass Λ_{0} of the new Leggett mode unaffected and only slightly modifies its dispersion.

  20. Two-mode Nonlinear Coherent States

    OpenAIRE

    Wang, Xiao-Guang

    2000-01-01

    Two-mode nonlinear coherent states are introduced in this paper. The pair coherent states and the two-mode Perelomov coherent states are special cases of the two-mode nonlinear coherent states. The exponential form of the two-mode nonlinear coherent states is given. The photon-added or photon-subtracted two-mode nonlinear coherent states are found to be two-mode nonlinear coherent states with different nonlinear functions. The parity coherent states are introduced as examples of two-mode nonl...

  1. Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells

    Directory of Open Access Journals (Sweden)

    Zhao Zhixin

    2011-05-01

    Full Text Available Abstract Background In the presence of drought and other desiccating stresses, plants synthesize and redistribute the phytohormone abscisic acid (ABA. ABA promotes plant water conservation by acting on specialized cells in the leaf epidermis, guard cells, which border and regulate the apertures of stomatal pores through which transpirational water loss occurs. Following ABA exposure, solute uptake into guard cells is rapidly inhibited and solute loss is promoted, resulting in inhibition of stomatal opening and promotion of stomatal closure, with consequent plant water conservation. There is a wealth of information on the guard cell signaling mechanisms underlying these rapid ABA responses. To investigate ABA regulation of gene expression in guard cells in a systematic genome-wide manner, we analyzed data from global transcriptomes of guard cells generated with Affymetrix ATH1 microarrays, and compared these results to ABA regulation of gene expression in leaves and other tissues. Results The 1173 ABA-regulated genes of guard cells identified by our study share significant overlap with ABA-regulated genes of other tissues, and are associated with well-defined ABA-related promoter motifs such as ABREs and DREs. However, we also computationally identified a unique cis-acting motif, GTCGG, associated with ABA-induction of gene expression specifically in guard cells. In addition, approximately 300 genes showing ABA-regulation unique to this cell type were newly uncovered by our study. Within the ABA-regulated gene set of guard cells, we found that many of the genes known to encode ion transporters associated with stomatal opening are down-regulated by ABA, providing one mechanism for long-term maintenance of stomatal closure during drought. We also found examples of both negative and positive feedback in the transcriptional regulation by ABA of known ABA-signaling genes, particularly with regard to the PYR/PYL/RCAR class of soluble ABA receptors and

  2. Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells

    Science.gov (United States)

    2011-01-01

    Background In the presence of drought and other desiccating stresses, plants synthesize and redistribute the phytohormone abscisic acid (ABA). ABA promotes plant water conservation by acting on specialized cells in the leaf epidermis, guard cells, which border and regulate the apertures of stomatal pores through which transpirational water loss occurs. Following ABA exposure, solute uptake into guard cells is rapidly inhibited and solute loss is promoted, resulting in inhibition of stomatal opening and promotion of stomatal closure, with consequent plant water conservation. There is a wealth of information on the guard cell signaling mechanisms underlying these rapid ABA responses. To investigate ABA regulation of gene expression in guard cells in a systematic genome-wide manner, we analyzed data from global transcriptomes of guard cells generated with Affymetrix ATH1 microarrays, and compared these results to ABA regulation of gene expression in leaves and other tissues. Results The 1173 ABA-regulated genes of guard cells identified by our study share significant overlap with ABA-regulated genes of other tissues, and are associated with well-defined ABA-related promoter motifs such as ABREs and DREs. However, we also computationally identified a unique cis-acting motif, GTCGG, associated with ABA-induction of gene expression specifically in guard cells. In addition, approximately 300 genes showing ABA-regulation unique to this cell type were newly uncovered by our study. Within the ABA-regulated gene set of guard cells, we found that many of the genes known to encode ion transporters associated with stomatal opening are down-regulated by ABA, providing one mechanism for long-term maintenance of stomatal closure during drought. We also found examples of both negative and positive feedback in the transcriptional regulation by ABA of known ABA-signaling genes, particularly with regard to the PYR/PYL/RCAR class of soluble ABA receptors and their downstream targets

  3. Modes of transmission of influenza B virus in households.

    Directory of Open Access Journals (Sweden)

    Benjamin J Cowling

    Full Text Available While influenza A and B viruses can be transmitted via respiratory droplets, the importance of small droplet nuclei "aerosols" in transmission is controversial.In Hong Kong and Bangkok, in 2008-11, subjects were recruited from outpatient clinics if they had recent onset of acute respiratory illness and none of their household contacts were ill. Following a positive rapid influenza diagnostic test result, subjects were randomly allocated to one of three household-based interventions: hand hygiene, hand hygiene plus face masks, and a control group. Index cases plus their household contacts were followed for 7-10 days to identify secondary infections by reverse transcription polymerase chain reaction (RT-PCR testing of respiratory specimens. Index cases with RT-PCR-confirmed influenza B were included in the present analyses. We used a mathematical model to make inferences on the modes of transmission, facilitated by apparent differences in clinical presentation of secondary infections resulting from aerosol transmission. We estimated that approximately 37% and 26% of influenza B virus transmission was via the aerosol mode in households in Hong Kong and Bangkok, respectively. In the fitted model, influenza B virus infections were associated with a 56%-72% risk of fever plus cough if infected via aerosol route, and a 23%-31% risk of fever plus cough if infected via the other two modes of transmission.Aerosol transmission may be an important mode of spread of influenza B virus. The point estimates of aerosol transmission were slightly lower for influenza B virus compared to previously published estimates for influenza A virus in both Hong Kong and Bangkok. Caution should be taken in interpreting these findings because of the multiple assumptions inherent in the model, including that there is limited biological evidence to date supporting a difference in the clinical features of influenza B virus infection by different modes.

  4. The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse.

    Directory of Open Access Journals (Sweden)

    Clement Y Chow

    2015-02-01

    Full Text Available Endoplasmic reticulum (ER stress occurs when misfolded proteins accumulate in the ER. The cellular response to ER stress involves complex transcriptional and translational changes, important to the survival of the cell. ER stress is a primary cause and a modifier of many human diseases. A first step to understanding how the ER stress response impacts human disease is to determine how the transcriptional response to ER stress varies among individuals. The genetic diversity of the eight mouse Collaborative Cross (CC founder strains allowed us to determine how genetic variation impacts the ER stress transcriptional response. We used tunicamycin, a drug commonly used to induce ER stress, to elicit an ER stress response in mouse embryonic fibroblasts (MEFs derived from the CC founder strains and measured their transcriptional responses. We identified hundreds of genes that differed in response to ER stress across these genetically diverse strains. Strikingly, inflammatory response genes differed most between strains; major canonical ER stress response genes showed relatively invariant responses across strains. To uncover the genetic architecture underlying these strain differences in ER stress response, we measured the transcriptional response to ER stress in MEFs derived from a subset of F1 crosses between the CC founder strains. We found a unique layer of regulatory variation that is only detectable under ER stress conditions. Over 80% of the regulatory variation under ER stress derives from cis-regulatory differences. This is the first study to characterize the genetic variation in ER stress transcriptional response in the laboratory mouse. Our findings indicate that the ER stress transcriptional response is highly variable among strains and arises from genetic variation in individual downstream response genes, rather than major signaling transcription factors. These results have important implications for understanding how genetic variation

  5. Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs.

    Science.gov (United States)

    Zhu, Hong; Xia, Rui; Zhao, Bingyu; An, Yong-qiang; Dardick, Chris D; Callahan, Ann M; Liu, Zongrang

    2012-08-21

    MicroRNAs (miRNAs) have recently emerged as important gene regulators in plants. MiRNAs and their targets have been extensively studied in Arabidopsis and rice. However, relatively little is known about the characterization of miRNAs and their target genes in peach (Prunus persica), which is a complex crop with unique developmental programs. We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in the regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.

  6. Unique expression, processing regulation, and regulatory network of peach (Prunus persica miRNAs

    Directory of Open Access Journals (Sweden)

    Zhu Hong

    2012-08-01

    Full Text Available Abstract Background MicroRNAs (miRNAs have recently emerged as important gene regulators in plants. MiRNAs and their targets have been extensively studied in Arabidopsis and rice. However, relatively little is known about the characterization of miRNAs and their target genes in peach (Prunus persica, which is a complex crop with unique developmental programs. Results We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in the regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Conclusions Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.

  7. Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition

    DEFF Research Database (Denmark)

    Liu, Tao; Li, Yingjun; Wang, Xiaodi

    2015-01-01

    Acquisition of de novo spacer sequences confers CRISPR-Cas with a memory to defend against invading genetic elements. However, the mechanism of regulation of CRISPR spacer acquisition remains unknown. Here we examine the transcriptional regulation of the conserved spacer acquisition genes in Type I......, it was demonstrated that the transcription level of csa1, cas1, cas2 and cas4 was significantly enhanced in a csa3a-overexpression strain and, moreover, the Csa1 and Cas1 protein levels were increased in this strain. Furthermore, we demonstrated the hyperactive uptake of unique spacers within both CRISPR loci...... in the presence of the csa3a overexpression vector. The spacer acquisition process is dependent on the CCN PAM sequence and protospacer selection is random and non-directional. These results suggested a regulation mechanism of CRISPR spacer acquisition where a single transcriptional regulator senses the presence...

  8. The proteomes of transcription factories containing RNA polymerases I, II or III.

    Science.gov (United States)

    Melnik, Svitlana; Deng, Binwei; Papantonis, Argyris; Baboo, Sabyasachi; Carr, Ian M; Cook, Peter R

    2011-09-25

    Human nuclei contain three RNA polymerases (I, II and III) that transcribe different groups of genes; the active forms of all three are difficult to isolate because they are bound to the substructure. Here we describe a purification approach for isolating active RNA polymerase complexes from mammalian cells. After isolation, we analyzed their protein content by mass spectrometry. Each complex represents part of the core of a transcription factory. For example, the RNA polymerase II complex contains subunits unique to RNA polymerase II plus various transcription factors but shares a number of ribonucleoproteins with the other polymerase complexes; it is also rich in polymerase II transcripts. We also describe a native chromosome conformation capture method to confirm that the complexes remain attached to the same pairs of DNA templates found in vivo.

  9. Small-Molecule Inhibitors of the SOX18 Transcription Factor.

    Science.gov (United States)

    Fontaine, Frank; Overman, Jeroen; Moustaqil, Mehdi; Mamidyala, Sreeman; Salim, Angela; Narasimhan, Kamesh; Prokoph, Nina; Robertson, Avril A B; Lua, Linda; Alexandrov, Kirill; Koopman, Peter; Capon, Robert J; Sierecki, Emma; Gambin, Yann; Jauch, Ralf; Cooper, Matthew A; Zuegg, Johannes; Francois, Mathias

    2017-03-16

    Pharmacological modulation of transcription factors (TFs) has only met little success over the past four decades. This is mostly due to standard drug discovery approaches centered on blocking protein/DNA binding or interfering with post-translational modifications. Recent advances in the field of TF biology have revealed a central role of protein-protein interaction in their mode of action. In an attempt to modulate the activity of SOX18 TF, a known regulator of vascular growth in development and disease, we screened a marine extract library for potential small-molecule inhibitors. We identified two compounds, which inspired a series of synthetic SOX18 inhibitors, able to interfere with the SOX18 HMG DNA-binding domain, and to disrupt HMG-dependent protein-protein interaction with RBPJ. These compounds also perturbed SOX18 transcriptional activity in a cell-based reporter gene system. This approach may prove useful in developing a new class of anti-angiogenic compounds based on the inhibition of TF activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Entreprenurial Modes of Teaching in Health Promoting Interventions

    DEFF Research Database (Denmark)

    Christensen, Marie Ernst; Thorø, Karsten

    2014-01-01

    a pratice-related teaching program focused on health promotion. The project creates a framework for the interaction of theory and practice. Moreover, this blend generates new modes of teaching due to the fact that the teaching is transferred from the usu-al environment to sites where the students experience...... the potential of engaging with real-time media, instead of just practising their professional skills amongst their fellow students. The emerging didactical graphics in the teaching of entrepreneurship are conceptualized as elements where the students take action and thereby develop an active approach...... to learning (Blenker et al 2004). In this entrepreneurial mode of teaching the students get a unique opportunity to enhance their competences in a relation with the participants from the organizations selected. This concept will reflect a close association with the students' professional practice in terms...

  11. Thermodynamic description of peptide adsorption on mixed-mode resins.

    Science.gov (United States)

    Chilamkurthi, Sreekanth; Sevillano, David Méndez; Albers, Leonoor H G; Sahoo, Manas Ranjan; Verheijen, Peter J T; van der Wielen, Luuk A M; den Hollander, Jeroen L; Ottens, Marcel

    2014-05-09

    In this work the adsorption of tri-peptides on a mixed-mode resin was studied using isocratic pulse response experiments. Various salt concentration, temperature and pH combinations were used to measure retention times of several tri-peptides. The experiments were evaluated according to an extension of the stoichiometric displacement model and the steric mass action model of protein-ligand binding. The application of this model in the understanding of mixed mode adsorption process is discussed. A unique set of meaningful thermodynamic parameters was obtained for each resin-peptide-temperature and resin-peptide-pH combination. Finally it was shown that these thermodynamic parameters can be used in defining quantitative relationships within the framework of extra thermodynamic relationships. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Transcriptional profiles of Treponema denticola in response to environmental conditions.

    Directory of Open Access Journals (Sweden)

    Ian McHardy

    Full Text Available The periodontal pathogen T. denticola resides in a stressful environment rife with challenges, the human oral cavity. Knowledge of the stress response capabilities of this invasive spirochete is currently very limited. Whole genome expression profiles in response to different suspected stresses including heat shock, osmotic downshift, oxygen and blood exposure were examined. Most of the genes predicted to encode conserved heat shock proteins (HSPs were found to be induced under heat and oxygen stress. Several of these HSPs also seem to be important for survival in hypotonic solutions and blood. In addition to HSPs, differential regulation of many genes encoding metabolic proteins, hypothetical proteins, transcriptional regulators and transporters was observed in patterns that could betoken functional associations. In summary, stress responses in T. denticola exhibit many similarities to the corresponding stress responses in other organisms but also employ unique components including the induction of hypothetical proteins.

  13. Social marketing and diffusion-based strategies for communicating with unique populations: HIV prevention in San Francisco.

    Science.gov (United States)

    Dearing, J W; Rogers, E M; Meyer, G; Casey, M K; Rao, N; Campo, S; Henderson, G M

    1996-01-01

    We conducted a 2-year investigation of the extent to which strategies based on social marketing and diffusion of innovations concepts are used in preventive health communication with unique (highly ostracized) populations. Of the 49 organizations in San Francisco that operate HIV prevention programs (N = 100), programs that most highly targeted unique populations were surveyed. Personal interviews were then conducted with 38 staff leaders who operated the most and least effective programs. Audiotapes and transcripts were content analyzed to identify the strategies used by program staff. Strategies based on social marketing concepts were more prevalent than strategies based on the diffusion of innovations: More effective programs were characterized by emphasis on homophily, audience segmentation, compatibility-based strategies, and interorganizational collaboration.

  14. Range imager performance comparison in homodyne and heterodyne operating modes

    Science.gov (United States)

    Conroy, Richard M.; Dorrington, Adrian A.; Künnemeyer, Rainer; Cree, Michael J.

    2009-01-01

    Range imaging cameras measure depth simultaneously for every pixel in a given field of view. In most implementations the basic operating principles are the same. A scene is illuminated with an intensity modulated light source and the reflected signal is sampled using a gain-modulated imager. Previously we presented a unique heterodyne range imaging system that employed a bulky and power hungry image intensifier as the high speed gain-modulation mechanism. In this paper we present a new range imager using an internally modulated image sensor that is designed to operate in heterodyne mode, but can also operate in homodyne mode. We discuss homodyne and heterodyne range imaging, and the merits of the various types of hardware used to implement these systems. Following this we describe in detail the hardware and firmware components of our new ranger. We experimentally compare the two operating modes and demonstrate that heterodyne operation is less sensitive to some of the limitations suffered in homodyne mode, resulting in better linearity and ranging precision characteristics. We conclude by showing various qualitative examples that demonstrate the system's three-dimensional measurement performance.

  15. Revealing a steroid receptor ligand as a unique PPAR[gamma] agonist

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Shengchen; Han, Ying; Shi, Yuzhe; Rong, Hui; Zheng, Songyang; Jin, Shikan; Lin, Shu-Yong; Lin, Sheng-Cai; Li, Yong (Pitt); (Xiamen)

    2012-06-28

    Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) regulates metabolic homeostasis and is a molecular target for anti-diabetic drugs. We report here the identification of a steroid receptor ligand, RU-486, as an unexpected PPAR{gamma} agonist, thereby uncovering a novel signaling route for this steroid drug. Similar to rosiglitazone, RU-486 modulates the expression of key PPAR{gamma} target genes and promotes adipocyte differentiation, but with a lower adipogenic activity. Structural and functional studies of receptor-ligand interactions reveal the molecular basis for a unique binding mode for RU-486 in the PPAR{gamma} ligand-binding pocket with distinctive properties and epitopes, providing the molecular mechanisms for the discrimination of RU-486 from thiazolidinediones (TZDs) drugs. Our findings together indicate that steroid compounds may represent an alternative approach for designing non-TZD PPAR{gamma} ligands in the treatment of insulin resistance.

  16. Classical many-particle systems with unique disordered ground states.

    Science.gov (United States)

    Zhang, G; Stillinger, F H; Torquato, S

    2017-10-01

    Classical ground states (global energy-minimizing configurations) of many-particle systems are typically unique crystalline structures, implying zero enumeration entropy of distinct patterns (aside from trivial symmetry operations). By contrast, the few previously known disordered classical ground states of many-particle systems are all high-entropy (highly degenerate) states. Here we show computationally that our recently proposed "perfect-glass" many-particle model [Sci. Rep. 6, 36963 (2016)10.1038/srep36963] possesses disordered classical ground states with a zero entropy: a highly counterintuitive situation . For all of the system sizes, parameters, and space dimensions that we have numerically investigated, the disordered ground states are unique such that they can always be superposed onto each other or their mirror image. At low energies, the density of states obtained from simulations matches those calculated from the harmonic approximation near a single ground state, further confirming ground-state uniqueness. Our discovery provides singular examples in which entropy and disorder are at odds with one another. The zero-entropy ground states provide a unique perspective on the celebrated Kauzmann-entropy crisis in which the extrapolated entropy of a supercooled liquid drops below that of the crystal. We expect that our disordered unique patterns to be of value in fields beyond glass physics, including applications in cryptography as pseudorandom functions with tunable computational complexity.

  17. Transcription-dependent degradation controls the stability of the SREBP family of transcription factors.

    Science.gov (United States)

    Sundqvist, Anders; Ericsson, Johan

    2003-11-25

    Cholesterol metabolism is tightly controlled by members of the sterol regulatory element-binding protein (SREBP) family of transcription factors. Here we demonstrate that the ubiquitination and degradation of SREBPs depend on their transcriptional activity. Mutations in the transactivation or DNA-binding domains of SREBPs inhibit their transcriptional activity and stabilize the proteins. The transcriptional activity and degradation of these mutants are restored when fused to heterologous transactivation or DNA-binding domains. When SREBP1a was fused to the DBD of Gal4, the ubiquitination and degradation of the fusion protein depended on coexpression of a promoter-reporter gene containing Gal4-binding sites. In addition, disruption of the interaction between WT SREBP and endogenous p300/CBP resulted in inhibition of SREBP-dependent transcription and stabilization of SREBP. Chemical inhibitors of transcription reduced the degradation of transcriptionally active SREBP1a, whereas they had no effect on the stability of transcriptionally inactive mutants, demonstrating that transcriptional activation plays an important role in the degradation of SREBPs. Thus, transcription-dependent degradation of SREBP constitutes a feedback mechanism to regulate the expression of genes involved in cholesterol metabolism and may represent a general mechanism to regulate the duration of transcriptional responses.

  18. Suppression of high order modes employing active self-imaging mode filter in large mode area strongly pumped fiber amplifier

    Science.gov (United States)

    Zhao, Xiang; Bai, Gang; Zheng, Ye; Chen, Xiaolong; Yang, Yifeng; Qi, Yunfeng; He, Bing; Zhou, Jun

    2017-10-01

    To suppress high order modes and improve the beam quality, an active self-imaging mode filter based on multimode interference and self-imaging effect is proposed in large mode area (LMA) fiber amplifier. With this filter structure, transverse mode competition and individual transverse mode power distributions in strongly pumped fiber amplifiers are theoretically demonstrated. Employing this mode selection technique in 30/400 LMA strongly pumped fiber amplifier, the percentage of the fundamental mode rises from 27.8% (without filter) to 96.3%. By the modal power decomposition, the M2 parameter of beam quality decrease dramatically from 2.24 to 1.11 (0 relative phase) and from 3.01 to 1.24 (π/2 relative phase). This study provides a new method to achieve single mode in LMA fiber amplifier and this filter would be extended to larger mode area fiber amplifier to improve the beam quality.

  19. Transcriptional Responses Associated with Virulence and Defence in the Interaction between Heterobasidion annosum s.s. and Norway Spruce

    Science.gov (United States)

    Lundén, Karl; Danielsson, Marie; Durling, Mikael Brandström; Ihrmark, Katarina; Gorriz, Miguel Nemesio; Stenlid, Jan; Asiegbu, Frederick O.; Elfstrand, Malin

    2015-01-01

    Heterobasidion annosum sensu lato is a serious pathogen causing root and stem rot to conifers in the northern hemisphere and rendering the timber defective for sawing and pulping. In this study we applied next-generation sequencing to i) identify transcriptional responses unique to Heterobasidion-inoculated Norway spruce and ii) investigate the H. annosum transcripts to identify putative virulence factors. To address these objectives we wounded or inoculated 30-year-old Norway spruce clones with H. annosum and 454-sequenced the transcriptome of the interaction at 0, 5 and 15 days post inoculation. The 491860 high-quality reads were de novo assembled and the relative expression was analysed. Overall, very few H. annosum transcripts were represented in our dataset. Three delta-12 fatty acid desaturase transcripts and one Clavaminate synthase-like transcript, both associated with virulence in other pathosystems, were found among the significantly induced transcripts. The analysis of the Norway spruce transcriptional responses produced a handful of differentially expressed transcripts. Most of these transcripts originated from genes known to respond to H. annosum. However, three genes that had not previously been reported to respond to H. annosum showed specific induction to inoculation: an oxophytodienoic acid–reductase (OPR), a beta–glucosidase and a germin-like protein (GLP2) gene. Even in a small data set like ours, five novel highly expressed Norway spruce transcripts without significant alignment to any previously annotated protein in Genbank but present in the P. abies (v1.0) gene catalogue were identified. Their expression pattern suggests a role in defence. Therefore a more complete survey of the transcriptional responses in the interactions between Norway spruce and its major pathogen H. annosum would probably provide a better understanding of gymnosperm defence than accumulated until now. PMID:26151363

  20. Transcriptional Responses Associated with Virulence and Defence in the Interaction between Heterobasidion annosum s.s. and Norway Spruce.

    Directory of Open Access Journals (Sweden)

    Karl Lundén

    Full Text Available Heterobasidion annosum sensu lato is a serious pathogen causing root and stem rot to conifers in the northern hemisphere and rendering the timber defective for sawing and pulping. In this study we applied next-generation sequencing to i identify transcriptional responses unique to Heterobasidion-inoculated Norway spruce and ii investigate the H. annosum transcripts to identify putative virulence factors. To address these objectives we wounded or inoculated 30-year-old Norway spruce clones with H. annosum and 454-sequenced the transcriptome of the interaction at 0, 5 and 15 days post inoculation. The 491,860 high-quality reads were de novo assembled and the relative expression was analysed. Overall, very few H. annosum transcripts were represented in our dataset. Three delta-12 fatty acid desaturase transcripts and one Clavaminate synthase-like transcript, both associated with virulence in other pathosystems, were found among the significantly induced transcripts. The analysis of the Norway spruce transcriptional responses produced a handful of differentially expressed transcripts. Most of these transcripts originated from genes known to respond to H. annosum. However, three genes that had not previously been reported to respond to H. annosum showed specific induction to inoculation: an oxophytodienoic acid-reductase (OPR, a beta-glucosidase and a germin-like protein (GLP2 gene. Even in a small data set like ours, five novel highly expressed Norway spruce transcripts without significant alignment to any previously annotated protein in Genbank but present in the P. abies (v1.0 gene catalogue were identified. Their expression pattern suggests a role in defence. Therefore a more complete survey of the transcriptional responses in the interactions between Norway spruce and its major pathogen H. annosum would probably provide a better understanding of gymnosperm defence than accumulated until now.

  1. Asymmetric excitation of surface plasmons by dark mode coupling

    KAUST Repository

    Zhang, X.

    2016-02-19

    Control over surface plasmons (SPs) is essential in a variety of cutting-edge applications, such as highly integrated photonic signal processing systems, deep-subwavelength lasing, high-resolution imaging, and ultrasensitive biomedical detection. Recently, asymmetric excitation of SPs has attracted enormous interest. In free space, the analog of electromagnetically induced transparency (EIT) in metamaterials has been widely investigated to uniquely manipulate the electromagnetic waves. In the near field, we show that the dark mode coupling mechanism of the classical EIT effect enables an exotic and straightforward excitation of SPs in a metasurface system. This leads to not only resonant excitation of asymmetric SPs but also controllable exotic SP focusing by the use of the Huygens-Fresnel principle. Our experimental findings manifest the potential of developing plasmonic metadevices with unique functionalities.

  2. Fourier-mode dynamics for the nonlinear Schrödinger equation in one-dimensional bounded domains.

    Science.gov (United States)

    Caputo, J G; Efremidis, N K; Hang, Chao

    2011-09-01

    We analyze the 1D focusing nonlinear Schrödinger equation in a finite interval with homogeneous Dirichlet or Neumann boundary conditions. There are two main dynamics, the collapse which is very fast and a slow cascade of Fourier modes. For the cubic nonlinearity the calculations show no long-term energy exchange between Fourier modes as opposed to higher nonlinearities. This slow dynamics is explained by fairly simple amplitude equations for the resonant Fourier modes. Their solutions are well behaved so filtering high frequencies prevents collapse. Finally, these equations elucidate the unique role of the zero mode for the Neumann boundary conditions.

  3. Scaling Fiber Lasers to Large Mode Area: An Investigation of Passive Mode-Locking Using a Multi-Mode Fiber

    Science.gov (United States)

    Ding, Edwin; Lefrancois, Simon; Kutz, Jose Nathan; Wise, Frank W.

    2011-01-01

    The mode-locking of dissipative soliton fiber lasers using large mode area fiber supporting multiple transverse modes is studied experimentally and theoretically. The averaged mode-locking dynamics in a multi-mode fiber are studied using a distributed model. The co-propagation of multiple transverse modes is governed by a system of coupled Ginzburg–Landau equations. Simulations show that stable and robust mode-locked pulses can be produced. However, the mode-locking can be destabilized by excessive higher-order mode content. Experiments using large core step-index fiber, photonic crystal fiber, and chirally-coupled core fiber show that mode-locking can be significantly disturbed in the presence of higher-order modes, resulting in lower maximum single-pulse energies. In practice, spatial mode content must be carefully controlled to achieve full pulse energy scaling. This paper demonstrates that mode-locking performance is very sensitive to the presence of multiple waveguide modes when compared to systems such as amplifiers and continuous-wave lasers. PMID:21731106

  4. 5 CFR 1632.10 - Transcripts, recordings, and minutes.

    Science.gov (United States)

    2010-01-01

    ... actual cost of duplication or transcription. (d) A complete verbatim copy of the transcript, a complete copy of the minutes, or a complete electronic recording or verbatim copy of a transcription thereof of... maintain a complete transcript or electronic recording or transcription thereof adequate to record fully...

  5. Nuclear Actin in Development and Transcriptional Reprogramming.

    Science.gov (United States)

    Misu, Shinji; Takebayashi, Marina; Miyamoto, Kei

    2017-01-01

    Actin is a highly abundant protein in eukaryotic cells and dynamically changes its polymerized states with the help of actin-binding proteins. Its critical function as a constituent of cytoskeleton has been well-documented. Growing evidence demonstrates that actin is also present in nuclei, referred to as nuclear actin, and is involved in a number of nuclear processes, including transcriptional regulation and chromatin remodeling. The contribution of nuclear actin to transcriptional regulation can be explained by its direct interaction with transcription machineries and chromatin remodeling factors and by controlling the activities of transcription factors. In both cases, polymerized states of nuclear actin affect the transcriptional outcome. Nuclear actin also plays an important role in activating strongly silenced genes in somatic cells for transcriptional reprogramming. When these nuclear functions of actin are considered, it is plausible to speculate that nuclear actin is also implicated in embryonic development, in which numerous genes need to be activated in a well-coordinated manner. In this review, we especially focus on nuclear actin's roles in transcriptional activation, reprogramming and development, including stem cell differentiation and we discuss how nuclear actin can be an important player in development and cell differentiation.

  6. Structural characterization of mammalian bHLH-PAS transcription factors.

    Science.gov (United States)

    Wu, Dalei; Rastinejad, Fraydoon

    2017-04-01

    The mammalian basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factors share common architectural features that include a bHLH DNA-binding domain and tandemly positioned PAS domains. The sixteen members of this family include the hypoxia-inducible factors (HIF-1α and HIF-2α), ARNT (also known as HIF-1β), CLOCK and BMAL1. Most bHLH-PAS proteins have been genetically linked to variety of diseases in humans, including cancers, metabolic syndromes and psychiatric conditions. To function as transcription factors, the bHLH-PAS proteins must form heterodimeric complexes. Recent crystallographic studies of HIF-α-ARNT and CLOCK-BMAL1 complexes have unveiled the organization of their multi-domain bHLH-PAS-A-PAS-B segments, revealing how these architectures can give rise to unique patterns of heterodimerization. As our structural understanding becomes better integrated with ligand-discovery and target gene identification, a more comprehensive picture of their architectural and functional properties will emerge. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Transcriptional dysregulation in NIPBL and cohesin mutant human cells.

    Directory of Open Access Journals (Sweden)

    Jinglan Liu

    2009-05-01

    Full Text Available Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozygous mutations in the cohesin regulator NIPBL or cohesin structural components SMC1A and SMC3 result in the multisystem developmental disorder Cornelia de Lange Syndrome (CdLS. Genome-wide assessment of transcription in 16 mutant cell lines from severely affected CdLS probands has identified a unique profile of dysregulated gene expression that was validated in an additional 101 samples and correlates with phenotypic severity. This profile could serve as a diagnostic and classification tool. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of a boundary/insulator interacting protein. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS proband, indicating an alternative role of cohesin as a transcription factor.

  8. Human-specific transcriptional networks in the brain

    Science.gov (United States)

    Konopka, Genevieve; Friedrich, Tara; Davis-Turak, Jeremy; Winden, Kellen; Oldham, Michael C.; Gao, Fuying; Chen, Leslie; Wang, Guang-Zhong; Luo, Rui; Preuss, Todd M.; Geschwind, Daniel H.

    2013-01-01

    Summary Understanding human-specific patterns of brain gene expression and regulation can provide key insights into human brain evolution and speciation. Here, we use next generation sequencing, and Illumina and Affymetrix microarray platforms, to compare the transcriptome of human, chimpanzee, and macaque telencephalon. Our analysis reveals a predominance of genes differentially expressed within human frontal lobe and a striking increase in transcriptional complexity specific to the human lineage in the frontal lobe. In contrast, caudate nucleus gene expression is highly conserved. We also identify gene co-expression signatures related to either neuronal processes or neuropsychiatric diseases, including a human-specific module with CLOCK as its hub gene and another module enriched for neuronal morphological processes and genes co-expressed with FOXP2, a gene important for language evolution. These data demonstrate that transcriptional networks have undergone evolutionary remodeling even within a given brain region, providing a new window through which to view the foundation of uniquely human cognitive capacities. PMID:22920253

  9. A microarray for assessing transcription from pelagic marine microbial taxa.

    Science.gov (United States)

    Shilova, Irina N; Robidart, Julie C; James Tripp, H; Turk-Kubo, Kendra; Wawrik, Boris; Post, Anton F; Thompson, Anne W; Ward, Bess; Hollibaugh, James T; Millard, Andy; Ostrowski, Martin; Scanlan, David J; Paerl, Ryan W; Stuart, Rhona; Zehr, Jonathan P

    2014-07-01

    Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.

  10. All-fiber 6-mode multiplexers based on fiber mode selective couplers.

    Science.gov (United States)

    Chang, Sun Hyok; Moon, Sang-Rok; Chen, Haoshuo; Ryf, Roland; Fontaine, Nicolas K; Park, Kyung Jun; Kim, Kwangjoon; Lee, Joon Ki

    2017-03-06

    All-fiber 6-mode multiplexer composed of two consecutive LP11-mode selective couplers (MSC), two LP21-MSCs and an LP02-MSC is fully characterized by wavelength-swept interferometer technique. The MSCs are fabricated by polished-type fiber couplers coupling LP01 mode of a single mode fiber into a higher-order mode of a few mode fiber. A pair of the mode multiplexers has minimum mode dependent loss of 4 dB and high mode group selectivity of over 15 dB. Mode division multiplexed transmission enabled by the all-fiber mode multiplexers is demonstrated over fiber spans of 117 km employing an in-line multi-mode optical amplifier. 6 modes of 120 Gb/s dual polarization quadrature phase shift keying signals combined with 30 wavelength channels are successfully transmitted.

  11. Early transcriptional response of soybean contrasting accessions to root dehydration.

    Directory of Open Access Journals (Sweden)

    José Ribamar Costa Ferreira Neto

    Full Text Available Drought is a significant constraint to yield increase in soybean. The early perception of water deprivation is critical for recruitment of genes that promote plant tolerance. DeepSuperSAGE libraries, including one control and a bulk of six stress times imposed (from 25 to 150 min of root dehydration for drought-tolerant and sensitive soybean accessions, allowed to identify new molecular targets for drought tolerance. The survey uncovered 120,770 unique transcripts expressed by the contrasting accessions. Of these, 57,610 aligned with known cDNA sequences, allowing the annotation of 32,373 unitags. A total of 1,127 unitags were up-regulated only in the tolerant accession, whereas 1,557 were up-regulated in both as compared to their controls. An expression profile concerning the most representative Gene Ontology (GO categories for the tolerant accession revealed the expression "protein binding" as the most represented for "Molecular Function", whereas CDPK and CBL were the most up-regulated protein families in this category. Furthermore, particular genes expressed different isoforms according to the accession, showing the potential to operate in the distinction of physiological behaviors. Besides, heat maps comprising GO categories related to abiotic stress response and the unitags regulation observed in the expression contrasts covering tolerant and sensitive accessions, revealed the unitags potential for plant breeding. Candidate genes related to "hormone response" (LOX, ERF1b, XET, "water response" (PUB, BMY, "salt stress response" (WRKY, MYB and "oxidative stress response" (PER figured among the most promising molecular targets. Additionally, nine transcripts (HMGR, XET, WRKY20, RAP2-4, EREBP, NAC3, PER, GPX5 and BMY validated by RT-qPCR (four different time points confirmed their differential expression and pointed that already after 25 minutes a transcriptional reorganization started in response to the new condition, with important

  12. Word from the CSO - CERN’s unique scientific breadth

    CERN Multimedia

    2008-01-01

    Whilst we are all clearly focused on completion of the LHC and the detectors around it and look forward to a successful start of operations later this year, we should not forget that CERN has yet more to offer in addition to this highest priority programme ‘at the energy frontier’. Indeed, CERN also attracts a large scientific community seizing the opportunities offered by its other facilities. Sometimes I wonder whether we are not too modest and should not emphasize more CERN’s unique scientific breadth. ISOLDE, at the PS Booster, relies on innovative techniques to produce results at the forefront of nuclear physics very cost-effectively. nTOF has provided unique measurements of interest to nuclear technology, nuclear astrophysics and basic nuclear physics, and still has an ambitious programme ahead of it after refurbishment of the target. Another unique facility is the Antiproton Decelerator, at which the study of antimatter is being pursued with ingenious experiment...

  13. New Method of Vapour Discrimination Using the Thickness Shear Mode (TSM Resonator

    Directory of Open Access Journals (Sweden)

    J. Siddiqi

    2003-06-01

    Full Text Available The Impedance analysis technique complimented with curve fitting software was used to monitor changes in film properties of Thickness Shear Mode (TSM resonator on vapour exposure. The approach demonstrates how sensor selectivity can be achieved through unique changes in film viscosity caused by organic vapour adsorption.

  14. Three-Mode Factor Analysis by Means of Candecomp/Parafac

    NARCIS (Netherlands)

    Stegeman, Alwin; Lam, Tam T T

    A three-mode covariance matrix contains covariances of N observations (e.g., subject scores) on J variables for K different occasions or conditions. We model such an JK×JK covariance matrix as the sum of a (common) covariance matrix having Candecomp/Parafac form, and a diagonal matrix of unique

  15. Modes of an endlessly single-mode photonic crystal fiber: a finite element investigation

    NARCIS (Netherlands)

    Uranus, H.P.; Hoekstra, Hugo; van Groesen, Embrecht W.C.

    2004-01-01

    Using a finite-element mode solver, the modes of a commercial endlessly single-mode photonic crystal fiber (ESM-PCF) were investigated. Based on the loss discrimination between the dominant and the nearest higher order mode, we set-up a criterion for the single-modeness. Using that measure, we

  16. A note on unique solvability of the absolute value equation

    Directory of Open Access Journals (Sweden)

    Taher Lotfi

    2014-05-01

    Full Text Available It is proved that applying sufficient regularity conditions to the interval matrix $[A-|B|,A+|B|]$‎, ‎we can create a new unique solvability condition for the absolute value equation $Ax+B|x|=b$‎, ‎since regularity of interval matrices implies unique solvability of their corresponding absolute value equation‎. ‎This condition is formulated in terms of positive definiteness of a certain point matrix‎. ‎Special case $B=-I$ is verified too as an application.

  17. Uniqueness for a boundary identification problem in thermal imaging

    Directory of Open Access Journals (Sweden)

    Kurt Bryan

    1998-11-01

    Full Text Available An inverse problem for an initial-boundary value problem is considered. The goal is to determine an unknown portion of the boundary of a region in ${mathbb R}^n$ from measurements of Cauchy data on a known portion of the boundary. The dynamics in the interior of the region are governed by a differential operator of parabolic type. Utilizing a unique continuation result for evolution operators, along with the method of eigenfunction expansions, it is shown that uniqueness holds for a large and physically reasonable class of Cauchy data pairs.

  18. Optogenetic control of transcription in zebrafish.

    Directory of Open Access Journals (Sweden)

    Hongtao Liu

    Full Text Available Light inducible protein-protein interactions are powerful tools to manipulate biological processes. Genetically encoded light-gated proteins for controlling precise cellular behavior are a new and promising technology, called optogenetics. Here we exploited the blue light-induced transcription system in yeast and zebrafish, based on the blue light dependent interaction between two plant proteins, blue light photoreceptor Cryptochrome 2 (CRY2 and the bHLH transcription factor CIB1 (CRY-interacting bHLH 1. We demonstrate the utility of this system by inducing rapid transcription suppression and activation in zebrafish.

  19. Vainshtein solutions without superluminal modes

    Science.gov (United States)

    Gabadadze, Gregory; Kimura, Rampei; Pirtskhalava, David

    2015-06-01

    The Vainshtein mechanism suppresses the fifth force at astrophysical distances, while enabling it to compete with gravity at cosmological scales. Typically, Vainshtein solutions exhibit superluminal perturbations. However, a restricted class of solutions with special boundary conditions was shown to be devoid of the faster-than-light modes. Here we extend this class by finding solutions in a theory of quasidilaton, amended by derivative terms consistent with its symmetries. Solutions with Minkowski asymptotics are not stable, while the ones that exhibit the Vainshtein mechanism by transitioning to cosmological backgrounds are free of ghosts, tachyons, gradient instability, and superluminality, for all propagating modes present in the theory. These solutions require a special choice of the strength and signs of nonlinear terms, as well as a choice of asymptotic cosmological boundary conditions.

  20. Hypersonic modes in nanophononic semiconductors.

    Science.gov (United States)

    Hepplestone, S P; Srivastava, G P

    2008-09-05

    Frequency gaps and negative group velocities of hypersonic phonon modes in periodically arranged composite semiconductors are presented. Trends and criteria for phononic gaps are discussed using a variety of atomic-level theoretical approaches. From our calculations, the possibility of achieving semiconductor-based one-dimensional phononic structures is established. We present results of the location and size of gaps, as well as negative group velocities of phonon modes in such structures. In addition to reproducing the results of recent measurements of the locations of the band gaps in the nanosized Si/Si{0.4}Ge{0.6} superlattice, we show that such a system is a true one-dimensional hypersonic phononic crystal.

  1. What's Unique about Unique Entities? An fMRI Investigation of the Semantics of Famous Faces and Landmarks

    Science.gov (United States)

    Olson, Ingrid R.

    2012-01-01

    Famous people and artifacts are referred to as “unique entities” (UEs) due to the unique nature of the knowledge we have about them. Past imaging and lesion experiments have indicated that the anterior temporal lobes (ATLs) as having a special role in the processing of UEs. It has remained unclear which attributes of UEs were responsible for the observed effects in imaging experiments. In this study, we investigated what factors of UEs influence brain activity. In a training paradigm, we systematically varied the uniqueness of semantic associations, the presence/absence of a proper name, and the number of semantic associations to determine factors modulating activity in regions subserving the processing of UEs. We found that a conjunction of unique semantic information and proper names modulated activity within a section of the left ATL. Overall, the processing of UEs involved a wider left-hemispheric cortical network. Within these regions, brain activity was significantly affected by the unique semantic attributes especially in the presence of a proper name, but we could not find evidence for an effect of the number of semantic associations. Findings are discussed in regard to current models of ATL function, the neurophysiology of semantics, and social cognitive processing. PMID:22021913

  2. Evaluation of Advanced Bionics high resolution mode.

    Science.gov (United States)

    Buechner, Andreas; Frohne-Buechner, Carolin; Gaertner, Lutz; Lesinski-Schiedat, Anke; Battmer, Rolf-Dieter; Lenarz, Thomas

    2006-07-01

    The objective of this paper is to evaluate the advantages of the Advanced Bionic high resolution mode for speech perception, through a retrospective analysis. Forty-five adult subjects were selected who had a minimum experience of three months' standard mode (mean of 10 months) before switching to high resolution mode. Speech perception was tested in standard mode immediately before fitting with high resolution mode, and again after a maximum of six months high resolution mode usage (mean of two months). A significant improvement was found, between 11 and 17%, depending on the test material. The standard mode preference does not give any indication about the improvement when switching to high resolution. Users who are converted within any study achieve a higher performance improvement than those converted in the clinical routine. This analysis proves the significant benefits of high resolution mode for users, and also indicates the need for guidelines for individual optimization of parameter settings in a high resolution mode program.

  3. Comparative Analysis of 35 Basidiomycete Genomes Reveals Diversity and Uniqueness of the Phylum

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Otillar, Robert; Fagnan, Kirsten; Boussau, Bastien; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Held, Benjamin; Nagy, Laszlo; Floudas, Dimitris; Morin, Emmanuelle; Manning, Gerard; Baker, Scott; Martin, Francis; Blanchette, Robert; Hibbett, David; Grigoriev, Igor V.

    2013-03-11

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCA analysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth assays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.

  4. Dual Mode Slotted Monopole Antenna

    Science.gov (United States)

    2017-01-05

    of 15 DUAL MODE SLOTTED MONOPOLE ANTENNA STATEMENT OF GOVERNMENT INTEREST [0001] The invention described herein may be manufactured and used by...REFERENCE TO OTHER PATENT APPLICATIONS [0002] None. BACKGROUND OF THE INVENTION (1) Field of the Invention [0003] The present invention is directed...such as this that is capable of radiating at a different frequency below this cutoff. The present invention provides a means by which the overall

  5. Substructuring and Component Mode Synthesis

    Directory of Open Access Journals (Sweden)

    P. Seshu

    1997-01-01

    Full Text Available Substructuring and component mode synthesis (CMS, is a very popular method of model reduction for large structural dynamics problems. Starting from the pioneering works on this technique in the early 1960s, many researchers have studied and used this technique in a variety of applications. Besides model reduction, CMS offers several other crucial advantages. The present work aims to provide a review of the available literature on this important technique.

  6. The Ku-Mar zinc finger: A segment-swapped zinc ribbon in MarR-like transcription regulators related to the Ku bridge.

    Science.gov (United States)

    Kaur, Gurmeet; Subramanian, Srikrishna

    2015-09-01

    Two putative oxidative-stress sensor proteins from Pseudomonas aeruginosa, PA1607 and PA1374, belong to the MarR family of transcription regulators and possess a unique mode of dimerization. In these proteins, in addition to the α-helices involved in dimerization, inter-subunit contacts are strengthened by additional C-terminal β-strands. Using sequence and structure analysis we show that these β-strands constitute a novel segment-swapped zinc ribbon domain. We detect the presence of the zinc ribbon domain in MarR proteins from many bacterial homologs. While the metal-chelating residues of the zinc ribbons are absent in most members of this family, we could however identify several species of Proteobacteria, Actinobacteria and Firmicutes that possess intact zinc-chelating sites. Conservation pattern of metal-chelating residues together with the extensive structural resemblance to zinc ribbons, in particular to the bridge-region of the dsDNA break repair protein Ku, suggests that the C-terminal β-rich region of these proteins is a zinc ribbon. Sequence analysis also supports a distant evolutionary connection between the zinc ribbons of the MarR and Ku families. However, unlike Ku where the segment-swapped zinc ribbons play a role in DNA-binding and obligate dimerization, their primary role in MarR appears to be in dimerization and strengthening of inter-subunit contacts. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Mode pumping experiments on biomolecules

    Energy Technology Data Exchange (ETDEWEB)

    Austin, R.H.; Erramilli, S. [Princeton Univ., NJ (United States); Xie, A.; Schramm, A.

    1995-12-31

    We will explore several aspects of protein dynamics and energy transfer that can be explored by using the intense, picosecond, tunable mid-IR output of the FEL. In order of appearance they are: (1) Saturation recovery and inter-level coupling of the low temperature amide-I band in acetanilide. This is a continuation of earlier experiments to test soliton models in crystalline hydrogen bonded solids. In this experiment we utilize the sub-picosecond time resolution and low repetition rate of the Stanford SCLA FEL to do both T{sub 1} and T{sub 2} relaxation measurements at 1650 cm{sup -1}. (2) Probing the influence of collective dynamics in sensory rhodopsin. In this experiment we use the FIR output of the Stanford FIREFLY FEL to determine the lifetime of collective modes in the photo-active protein sensory rhodopsin, and begin experiments on the influence of collective modes on retinal reaction dynamics. (3) Probing the transition states of enzymes. This experiment, in the initial stages, attempts to use the intense IR output of the FEL to probe and influence the reaction path of a transition state analog for the protein nucleoside hydrolase. The transition state of the inosine substrate is believed to have critical modes softened by the protein so that bond-breaking paths show absorption at approximately 800 cm{sup -1}. A form of action spectrum using FEL excitation will be used to probe this state.

  8. A History of Emerging Modes?

    Directory of Open Access Journals (Sweden)

    Schmitz Michael

    2016-03-01

    Full Text Available In this paper I first introduce Tomasello’s notion of thought and his account of its emergence and development through differentiation, arguing that it calls into question the theory bias of the philosophical tradition on thought as well as its frequent atomism. I then raise some worries that he may be overextending the concept of thought, arguing that we should recognize an area of intentionality intermediate between action and perception on the one hand and thought on the other. After that I argue that the co-operative nature of humans is reflected in the very structure of their intentionality and thought: in co-operative modes such as the mode of joint attention and action and the we-mode, they experience and represent others as co-subjects of joint relations to situations in the world rather than as mere objects. In conclusion, I briefly comment on what Tomasello refers to as one of two big open questions in the theory of collective intentionality, namely that of the irreducibility of jointness.

  9. Protected Edge Modes without Symmetry

    Directory of Open Access Journals (Sweden)

    Michael Levin

    2013-05-01

    Full Text Available We discuss the question of when a gapped two-dimensional electron system without any symmetry has a protected gapless edge mode. While it is well known that systems with a nonzero thermal Hall conductance, K_{H}≠0, support such modes, here we show that robust modes can also occur when K_{H}=0—if the system has quasiparticles with fractional statistics. We show that some types of fractional statistics are compatible with a gapped edge, while others are fundamentally incompatible. More generally, we give a criterion for when an electron system with Abelian statistics and K_{H}=0 can support a gapped edge: We show that a gapped edge is possible if and only if there exists a subset of quasiparticle types M such that (1 all the quasiparticles in M have trivial mutual statistics, and (2 every quasiparticle that is not in M has nontrivial mutual statistics with at least one quasiparticle in M. We derive this criterion using three different approaches: a microscopic analysis of the edge, a general argument based on braiding statistics, and finally a conformal field theory approach that uses constraints from modular invariance. We also discuss the analogous result for two-dimensional boson systems.

  10. Multiple MAPK cascades regulate the transcription of IME1, the master transcriptional activator of meiosis in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Smadar Kahana-Edwin

    Full Text Available The choice between alternative developmental pathways is primarily controlled at the level of transcription. Induction of meiosis in budding yeasts in response to nutrient levels provides a system to investigate the molecular basis of cellular decision-making. In Saccharomyces cerevisiae, entry into meiosis depends on multiple signals converging upon IME1, the master transcriptional activator of meiosis. Here we studied the regulation of the cis-acting regulatory element Upstream Activation Signal (UASru, which resides within the IME1 promoter. Guided by our previous data acquired using a powerful high-throughput screening system, here we provide evidence that UASru is regulated by multiple stimuli that trigger distinct signal transduction pathways as follows: (i The glucose signal inhibited UASru activity through the cyclic AMP (cAMP/protein kinase A (PKA pathway, targeting the transcription factors (TFs, Com2 and Sko1; (ii high osmolarity activated UASru through the Hog1/mitogen-activated protein kinase (MAPK pathway and its corresponding TF Sko1; (iii elevated temperature increased the activity of UASru through the cell wall integrity pathway and the TFs Swi4/Mpk1 and Swi4/Mlp1; (iv the nitrogen source repressed UASru activity through Sum1; and (v the absence of a nitrogen source was detected and transmitted to UASru by the Kss1 and Fus3 MAPK pathways through their respective downstream TFs, Ste12/Tec1 and Ste12/Ste12 as well as by their regulators Dig1/2. These signaling events were specific to UASru; they did not affect the mating and filamentation response elements that are regulated by MAPK pathways. The complex regulation of UASru through all the known vegetative MAPK pathways is unique to S. cerevisiae and is specific for IME1, likely because it is the master regulator of gametogenesis.

  11. Mixed-Mode-Bending Delamination Apparatus

    Science.gov (United States)

    Crews, John H., Jr.; Reeder, James R.

    1991-01-01

    Mixed-mode-bending delamination apparatus generates two types of delamination stress simultaneously in specimen from single externally applied point load. In technique, indivial mode I and mode II contributions to delamination in specimen analyzed by use of simple beam-theory equations, eliminating need for time-consuming, difficult numerical analysis. Allows wider range of mode I/mode II ratios than possible with many other methods. Mixed-mode delamination testing of interest in all fields utilizing composite materials, used mostly in aerospace field, but also used in automobiles, lightweight armored military vehicles, boats, and sporting equipment. Useful in general lumber, plywood, and adhesive industries, as well.

  12. Digital holograms for laser mode multiplexing

    CSIR Research Space (South Africa)

    Mhlanga, T

    2014-10-02

    Full Text Available the sensitivity of the setup to misalignment, that leads to mode-coupling. It is also important that the injected modes ha a uniform power spectrum so that are weighted equally. The size of the multi-modes is highly dependent on the resolution of the SLM. Keywords...: spatial modes, multiplex, mode coupling 1. INTRODUCTION Optical networks form a foundation of modern communications networks since the replacement of copper wires with optical fibres in the 1980’s. This fibre technology has been based on single mode fibres...

  13. Predicting the Diversity of Foreign Entry Modes

    DEFF Research Database (Denmark)

    Hashai, Niron; Geisler Asmussen, Christian; Benito, Gabriel

    2007-01-01

    This paper expands entry mode literature by referring to multiple modes exerted in different value chain activities within and across host markets, rather than to a single entry mode at the host market level. Scale of operations and knowledge intensity are argued to affect firms' entry mode...... diversity across value chain activities and host markets. Analyzing a sample of Israeli based firms we show that larger firms exhibit a higher degree of entry mode diversity both across value chain activities and across host markets. Higher levels of knowledge intensity are also associated with more...... diversity in firms' entry modes across both dimensions....

  14. Mixed-Mode Crack Growth in Wood

    Directory of Open Access Journals (Sweden)

    Octavian POP

    2012-09-01

    Full Text Available In timber elements the mixed mode dependsessentially of wood anatomy and load configuration.In these conditions, in order to evaluate the materialbehavior and the fracture process, it’s necessary toseparate the part of each mode. The mixed modeseparation allows evaluating the amplitude offracture mode. In the present paper, using a mixedmodecrack growth specimen made in Douglas fir,the mixed mode crack growth process is studythanks to marks tracking method. Using the markstracking method the characteristic displacementsassociated to opening and shear mode aremeasured. From the experimental measurements,the energy release rate associated to opening andshear modes is calculated into to account the crackadvancement during the test.

  15. 22 CFR 1500.9 - Transcripts, recording of closed meetings.

    Science.gov (United States)

    2010-04-01

    ... cost of duplication or transcription. The Foundation shall maintain a complete verbatim copy of the... contain information which may be withheld under § 1500.5. Copies of such transcript, or a transcription of...

  16. In silico and wet lab approaches to study transcriptional regulation

    NARCIS (Netherlands)

    Hestand, Matthew Scott

    2010-01-01

    Gene expression is a complicated process with multiple types of regulation, including binding of proteins termed transcription factors. This thesis looks at transcription factors and transcription factor binding site discovery through computational predictions and wet lab work to better elucidate

  17. A chromatin-based mechanism for limiting divergent noncoding transcription

    DEFF Research Database (Denmark)

    Marquardt, Sebastian; Escalante-Chong, Renan; Pho, Nam

    2014-01-01

    In addition to their annotated transcript, many eukaryotic mRNA promoters produce divergent noncoding transcripts. To define determinants of divergent promoter directionality, we used genomic replacement experiments. Sequences within noncoding transcripts specified their degradation pathways, and...

  18. CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences.

    Directory of Open Access Journals (Sweden)

    Sergey V Prykhozhij

    Full Text Available Genome engineering has been revolutionized by the discovery of clustered regularly interspaced palindromic repeats (CRISPR and CRISPR-associated system genes (Cas in bacteria. The type IIB Streptococcus pyogenes CRISPR/Cas9 system functions in many species and additional types of CRISPR/Cas systems are under development. In the type II system, expression of CRISPR single guide RNA (sgRNA targeting a defined sequence and Cas9 generates a sequence-specific nuclease inducing small deletions or insertions. Moreover, knock-in of large DNA inserts has been shown at the sites targeted by sgRNAs and Cas9. Several tools are available for designing sgRNAs that target unique locations in the genome. However, the ability to find sgRNA targets common to several similar sequences or, by contrast, unique to each of these sequences, would also be advantageous. To provide such a tool for several types of CRISPR/Cas system and many species, we developed the CRISPR MultiTargeter software. Similar DNA sequences in question are duplicated genes and sets of exons of different transcripts of a gene. Thus, we implemented a basic sgRNA target search of input sequences for single-sgRNA and two-sgRNA/Cas9 nickase targeting, as well as common and unique sgRNA target searches in 1 a set of input sequences; 2 a set of similar genes or transcripts; or 3 transcripts a single gene. We demonstrate potential uses of the program by identifying unique isoform-specific sgRNA sites in 71% of zebrafish alternative transcripts and common sgRNA target sites in approximately 40% of zebrafish duplicated gene pairs. The design of unique targets in alternative exons is helpful because it will facilitate functional genomic studies of transcript isoforms. Similarly, its application to duplicated genes may simplify multi-gene mutational targeting experiments. Overall, this program provides a unique interface that will enhance use of CRISPR/Cas technology.

  19. Three Unique Implementations of Processes for PyCSP

    DEFF Research Database (Denmark)

    Friborg, Rune Møllegaard; Bjørndalen, John Markus; Vinter, Brian

    2009-01-01

    In this work we motivate and describe three unique implementations of processes for PyCSP: process, thread and greenlet based. The overall purpose is to demonstrate the feasibility of Communicating Sequential Processes as a framework for different application types and target platforms. The resul...

  20. Determining hydraulic parameters of a karst aquifer using unique ...

    African Journals Online (AJOL)

    2014-07-15

    Jul 15, 2014 ... of local karst hydrology the present study also aimed at retrieving and preserving valuable and unique historical datasets that otherwise would have been lost for scientific evaluation and the proactive preparation for mine closure. Keywords: karst, dewatering, deep level mining, porous medium analytical ...